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Abstract Background and purpose The number of older people in prisons is increasing across the globe. Many have poor physical and mental health, higher prevalence of head injury, cognitive impairment and dementia than found in community populations. Meeting the complex needs of this vulnerable group has become an increasing concern for prison and prison healthcare services. The aim of this multi method qualitative study was to investigate how men with diagnosed or suspected dementia were identified, assessed, and cared for in Scottish prisons. It also explored the lived experience of individuals being assessed for or diagnosed with dementia within four prisons. The data from twenty nine interviews was thematically analysed and used to collaboratively propose principles for dementia care in prison and present the resultant co-designed care pathway. Results At the time of data collection almost all the men known to have a dementia diagnosis or suspected dementia had complex health and social care needs, and some were living with advanced dementia. Prison healthcare staff reported taking a ‘case by case’ approach to their pre- and post-diagnostic care. Meeting these prisoner’s needs was complicated by the absence of organisational leads for care of older adults or people with dementia and there was no pathway or model in place to guide staff. Prison healthcare teams often had difficulty accessing specialist community services to support diagnosis. There was a lack of dementia education and knowledge about how to provide pre and post diagnostic dementia care in this setting amongst staff. The findings arising from this research have informed the co-production of two important evidence informed innovations namely a Model of Care and a pre- and post-diagnostic Care Pathway. Conclusion This research adds insights critical to understanding the adequacy of current approaches to meeting dementia related needs within the prison setting. To our knowledge this paper offers the first co-produced evidence informed pre- and post- diagnostic dementia care pathway and model of care for use in prisons. These could serve as tools for change that could enable prison healthcare staff to deliver the right care, at the right time, by the right people, and provide an opportunity to assess risk and plan care for the future.

Abstract In China, the exigency for precise wheat grain protein content (GPC) data rises with growing food consumption demands and global market competition. However, due to the lack of extensive, prolonged high-resolution benchmark data, previous GPC studies have primarily focused on experimental fields, small geographic units, and limited temporal scopes. Additionally, the diverse geographical terrain in China exacerbates the challenges of large-scale GPC estimation. To address this challenge and the data gap, the first 500-meter spatial resolution, long-term winter wheat dataset covering major planting regions in China (CNWheatGPC-500) was created by integrating multi-source data from ERA5 and MODIS. The results demonstrate that the GPC estimation model based on hierarchical linear model significantly outperformed other conventional models. The validation dataset exhibited an R2 of 0.45 and an RMSE of 0.96%. In cross-validation, the RMSE values ranged from 0.90% in Gansu to 1.32% in Anhui. For leave-one-year-out cross-validation, the RMSE values ranged from 0.77% to 1.11%. CNWheatGPC-500 offers valuable insights for enhancing wheat production, quality control, and agricultural decision-making.

ABSTRACT: An economic simulation was carried out over 183 milk-producing countries to estimate the global economic impacts of 12 dairy cattle diseases and health conditions: mastitis (subclinical and clinical), lameness, paratuberculosis (Johne's disease), displaced abomasum, dystocia, metritis, milk fever, ovarian cysts, retained placenta, and ketosis (subclinical and clinical). Estimates of disease impacts on milk yield, fertility, and culling were collected from the literature, standardized, meta-analyzed using a variety of methods ranging from simple averaging to random-effects models, and adjusted for comorbidities to prevent overestimation. These comorbidity-adjusted disease impacts were then combined with a set of country-level estimates for lactational incidence or prevalence or both, herd characteristics, and price estimates within a series of Monte Carlo simulations that estimated and valued the economic losses due to these diseases. It was estimated that total annual global losses are US$65 billion (B). Subclinical ketosis, clinical mastitis, and subclinical mastitis were the costliest diseases modeled, resulting in mean annual global losses of approximately US$18B, US$13B, and US$9B, respectively. Estimated global annual losses due to clinical ketosis, displaced abomasum, dystocia, lameness, metritis, milk fever, ovarian cysts, paratuberculosis, and retained placenta were estimated to be US$0.2B, US$0.6B, US$0.6B, US$6B, US$5B, US$0.6B, US$4B, US$4B, and US$3B, respectively. Without adjustment for comorbidities, when statistical associations between diseases were disregarded, mean aggregate global losses would have been overestimated by 45%. Although annual losses were greatest in India (US$12B), the United States (US$8B), and China (US$5B), depending on the measure of losses used (losses as a percentage of gross domestic product, losses per capita, losses as a percentage of gross milk revenue), the relative economic burden of these dairy cattle diseases across countries varied markedly.

ABSTRACT: A 35-d study investigated the impact of dietary supplementation with Arginine (Arg) or branched-chain amino acids (BCAA) of broilers receiving low-protein diets whilst infected with mixed Eimeria species. All birds were given the same starter (d0–10) and finisher (d28–35) diets. The 4 grower diets used were a positive control (PC) with adequate protein (18.5%), a low protein diet (NC;16.5% CP), or the NC supplemented with Arg or BCAA. Supplemental AA was added at 50% above the recommended levels. The treatments were in a 4 × 2 factorial arrangement, with 4 diets, with or without Eimeria inoculation on d14. Birds and feed were weighed after inoculation in phases: prepatent (d14–17), acute (d18–21), recovery (d22–28), and compensatory (d29–35). Ileal digesta, jejunum, and breast tissue were collected on d21, 28, and 35. There was no diet × Eimeria inoculation on growth performance at any phase. Infected birds weighed less and consumed less feed (P < 0.05) in all phases. In the prepatent and acute phases, birds on the Arg diets had higher weight gain (P < 0.05) and lower FCR, similar to PC, when compared to NC and BCAA-fed ones. Infection reduced AA digestibility on d21 and 28 (Met and Cys). However, birds that received supplemental AA had higher digestibility (P < 0.05) of their respective supplemented AA on d 21 only. Infected birds had lower (P < 0.05) BO + AT and higher PEPT1 expression on d21. There was a diet × Eimeria interaction (P = 0.004) on gene expression at d28; 4EBP1 genes were significantly downwardly expressed (P < 0.05) in birds fed Arg diet, irrespective of infection. Infected birds exhibited an upward expression (P < 0.05) of Eef2 on d21 and d28 but experienced a downward expression on d35. Supplemental Arg and BCAA had variable effects on growth performance, apparent ileal AA digestibility, and genes of protein synthesis and degradation, but the effect of Arg on promoting weight gain, irrespective of the Eimeria challenge, was more consistent.

Cereal is an essential source of calories and protein for the global population. Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers, grading harvest and categorised storage for enterprises, future trading prices, and policy planning. The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits. Many studies have also proposed models and methods for predicting such traits based on multi-platform remote sensing data. In this paper, the key quality traits that are of interest to producers and consumers are introduced. The literature related to grain quality prediction was analyzed in detail, and a review was conducted on remote sensing platforms, commonly used methods, potential gaps, and future trends in crop quality prediction. This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.

ABSTRACT: We investigated the effects of supplementing low protein diets with methionine (Met) or threonine (Thr) during a mixed Eimeria (consisting of E. acervulina, E. maxima and E. tenella) challenge in broilers. All birds were fed the same starter diet (d1–9) and finisher diet (d28–35) which met Cobb 500 nutrient specifications. Birds were allocated to 1 of 4 dietary treatments from d9 to 28: a standard protein diet (19% CP); a low protein diet (16% CP); or the low protein diet supplemented with Met or Thr at 50% above recommendations. On d14, half of the birds were challenged, and half of the birds were unchallenged. From d14 to 28, feed intake was recorded daily and BW every 3 or 4 d. Oocyst excretion was measured daily from d18 to 27. On d21 and 28, 3 birds per pen were euthanized to assess nutrient digestibility, cytokine expression and intestinal histology. During the acute stage of the challenge, challenged birds reduced ADFI and ADG (P < 0.05). In the pre-patent and recovery stages, birds given the 16% CP diets increased ADFI (P < 0.05), meanwhile there were no differences in ADG in these stages (P > 0.05). Nutrient digestibility was reduced in challenged birds in the acute stage (P < 0.05) but tended to be greater than in unchallenged birds during the recovery stage. There was no significant effect of diet on oocyst excretion or intestinal histology (P > 0.05). Interactions were observed between diet and challenge on IL-10 and IL-21 expression in the cecal tonsils during the acute stage of the challenge (P < 0.05), due to reduced IL-10 expression in challenged Thr birds and greater IL-21 expression in challenged Met birds. Supplementation with Thr or Met had limited effects on the outcomes of a mixed Eimeria challenge but provides benefits to the host by enhancing their immune response.

Soil-borne Trichoderma spp. have been extensively studied for their biocontrol activities against pathogens and growth promotion ability in plants. However, the beneficial effect of Trichoderma on inducing resistance against insect herbivores has been underexplored. Among diverse Trichoderma species, consistent with previous reports, we showed that root colonization by T. virens triggered induced systemic resistance (ISR) to the leaf-infecting hemibiotrophic fungal pathogens Colletotrichum graminicola. Whether T. virens induces ISR to insect pests has not been tested before. In this study, we investigated whether T. virens affects jasmonic acid (JA) biosynthesis and defense against fall armyworm (FAW) and western corn rootworm (WCR). Unexpectedly, the results showed that T. virens colonization of maize seedlings grown in autoclaved soil suppressed wound-induced production of JA, resulting in reduced resistance to FAW. Similarly, the bacterial endophyte Pseudomonas chlororaphis 30-84 was found to suppress systemic resistance to FAW due to reduced JA. Further comparative analyses of the systemic effects of these endophytes when applied in sterile or non-sterile field soil showed that both T. virens and P. chlororaphis 30-84 triggered ISR against C. graminicola in both soil conditions, but only suppressed JA production and resistance to FAW in sterile soil, while no significant impact was observed when applied in non-sterile soil. In contrast to the effect on FAW defense, T. virens colonization of maize roots suppressed WCR larvae survival and weight gain. This is the first report suggesting the potential role of T. virens as a biocontrol agent against WCR.

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species’ co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.

This commentary offers the reader an alternative to mentoring through the use of PODCASTS. By providing the listener with an understanding of the challenges and opportunities for self-reflection and sharing of experiences by the interviewees, we are impacting the listener attitudes and future goals through lessons learned.

Background: The indigenous Tharu ethnic group inhabiting the Terai (lowland) region of Nepal has been shown to have a high prevalence of sickle cell disease (SCD); specifically, previous studies have found a prevalence of 9.3% for sickle cell trait in this group. The lack of knowledge about SCD in this population is suspected to be a major barrier in preventing early intervention. This qualitative study aimed to conduct a needs assessment and identify themes relating to the local Tharu population's perceptions of SCD and its related care. Methods: Using snowball sampling for recruitment, 133 Tharu community members in the rural district of Dang met inclusion criteria. Researchers conducted 22 focus group discussions (FGDs) using semi-structured interviews in the local Tharu dialect, Nepali, Hindi, or English until topic saturation. A constant comparison analysis based off grounded theory was used for thematic analysis (NVivo 11™). Results: Three major themes emerged that explored the Tharu community's views of SCD: the social implications of SCD, the importance of SCD education, and the role of positive interventions. Inequity and lack of access to healthcare services were also thought to contribute to the lack of SCD-specific care. Conclusion: Using participatory action-based research to empower underserved communities, we have identified major themes surrounding the lack of understanding and wish for enhanced SCD awareness and education within the Tharu community. Our research explores fundamental barriers that must be addressed to develop a sustainable, accessible, and comprehensive SCD care plan in the region.

ABSTRACT: We investigated the effects of supplementing arginine (Arg) and branched-chain amino acids (BCAA) in broilers fed reduced-protein diets and challenged with Eimeria spp. All birds were fed the same starter diet meeting Cobb 500 nutrient specifications from d 1 to 9. Four grower diets: positive control (PC) with 20.0% crude protein (CP); reduced-protein negative control (NC) with 17.5% CP; or NC supplemented with Arg or BCAA at 50% above recommendations (ARG or BCAA) were fed to the birds from d 9 to 28. Birds were allocated in a 2 × 4 factorial arrangement (4 diets, each with or without challenge), with 8 replicates per treatment. On d 14, the challenge groups were orally gavaged with mixed Eimeria spp. Intestinal permeability was higher (P < 0.05) in NC than PC, whereas the permeability of ARG and BCAA groups did not differ significantly from PC. On d 28, a significant interaction (P < 0.01) was observed in CD8+: CD4+ ratios in cecal tonsils (CT), Eimeria challenge increased the ratios in all groups except for the ARG group. On d 21, a significant interaction was found for CD4+CD25+ percentages in CT (P < 0.01) that Eimeria challenge increased the percentages only in PC and NC groups. On d 21 and 28, significant interactions (P < 0.01) were found for macrophage nitric oxide (NO) production. In nonchallenged birds, NO was higher in the ARG group than other groups, but in challenged birds, NO was higher in both ARG and BCAA groups. On d 21, a significant interaction was found for bile anticoccidial IgA concentrations (P < 0.05) that Eimeria challenge increased IgA only in NC and ARG groups. The results suggest that a reduced-protein diet exacerbates the impact of the Eimeria challenge on intestinal integrity, but this could be mitigated by Arg and BCAA supplementations. Arginine and BCAA supplementations in reduced-protein diets could be beneficial for broilers against Eimeria infection by enhancing the immune responses. The beneficial effects of Arg supplementation tended to be more pronounced compared to BCAA supplementation.

Cannabis sativa is a global multi-billion-dollar cash crop with numerous industrial uses, including in medicine and recreation where its value is largely owed to the production of pharmacological and psychoactive metabolites known as cannabinoids. Often underappreciated in this role, the lipoxygenase (LOX)-derived green leaf volatiles (GLVs), also known as the scent of cut grass, are the hypothetical origin of hexanoic acid, the initial substrate for cannabinoid biosynthesis. The LOX pathway is best known as the primary source of plant oxylipins, molecules analogous to the eicosanoids from mammalian systems. These molecules are a group of chemically and functionally diverse fatty acid-derived signals that govern nearly all biological processes including plant defense and development. The interaction between oxylipin and cannabinoid biosynthetic pathways remains to be explored. Despite their unique importance in this crop, there has not been a comprehensive investigation focusing on the genes responsible for oxylipin biosynthesis in any Cannabis species. This study documents the first genome-wide catalogue of the Cannabis sativa oxylipin biosynthetic genes and identified 21 LOX, five allene oxide synthases (AOS), three allene oxide cyclases (AOC), one hydroperoxide lyase (HPL), and five 12-oxo-phytodienoic acid reductases (OPR). Gene collinearity analysis found chromosomal regions containing several isoforms maintained across Cannabis, Arabidopsis, and tomato. Promoter, expression, weighted co-expression genetic network, and functional enrichment analysis provide evidence of tissue- and cultivar-specific transcription and roles for distinct isoforms in oxylipin and cannabinoid biosynthesis. This knowledge facilitates future targeted approaches towards Cannabis crop improvement and for the manipulation of cannabinoid metabolism.

Understanding the distribution of intercepted spray deposits is important for the study of the dose-response relationship of spraying a targeted pathogen and for the optimisation of the spraying process. However, carrying out exhaustive measurements of canopy spray deposits is difficult, particularly in production situations. This new experimental method for use in commercial vineyards was based on the installation of artificial targets (PVC collectors) within the canopy. To evaluate the quality of this experimental method for estimating the statistical distribution of deposition it was compared to an intensive manual method of foliar deposition measurements on real leaves. Intercepted deposition data on the real leaves and artificial targets were collected in a regular grid pattern within 12 non-contiguous vegetation sections. The results showed that although the means were similar, the variance in deposition appeared to differ between the distributions on artificial targets and real foliage, with CV values of between 37.4-52.7 % and 69.4-80.5 % respectively. Therefore, any central statistics must be supplemented with a statistical distribution analysis to account for the dispersion of deposition values within the vegetation. The results from comparisons between the cumulative distributions of intercepted deposition on the real leaves and on the PVC collector sections showed that the deposition estimates averaged over three-vine sections gave relevant, repeatable estimates for both approaches. The results also showed that for low deposition values, the experimental method led to a correct estimation of deposition on real leaves. However, above 230 ng dm² per 1 g/ha, the experimental method underestimated the deposition on real leaves by 13.6 %. Using these methodological results, it may be possible to develop models capable of predicting the distribution of deposition within the plant canopy. It would thereby be possible to develop an approach for variable-rate sprayer control that takes into account the phytosanitary risk and the site-specific variable structure of the vegetation during the season.

Like many of our neighbors, on April 27th of 2011 we sat in our living room watching on live television as menacing tornados destroyed several communities across Alabama. On that April night, the city of Gadsden appeared to have made it through the storm with minimal damage. Therefore, we spent the majority of our evening contacting our peers and colleagues who might have been initially impacted by the Tuscaloosa tornadoes. We spent the morning after the tornadoes discussing several approaches to usefully assist our community in assessing the relief needs in Tuscaloosa.

Background: Social determinants of health directly affect cancer survival. Driven by advances in technology and recent demands due to COVID-19, telemedicine has the ability to improve patient access to care, lower health care costs, and increase workflow efficiency. The role of telemedicine in radiation oncology is not established. Materials and Methods: We conducted an IRB-approved pilot trial using a telehealth platform for the first post-radiation visit in patients with any cancer diagnosis. The primary endpoint was feasibility of using telehealth defined by completion of five telehealth visits per month in a single department. Secondary endpoints included the ability to assess patients appropriately, patient and physician satisfaction. Physicians were surveyed again during the pandemic to determine whether viewpoints changed. Results: Between May 27, 2016 and August 1, 2018, 37 patients were enrolled in the Telehealth in Post-operative Radiation Therapy (TelePORT) trial, with 24 evaluable patients who completed their scheduled telehealth visit. On average, 1.4 patients were accrued per month. All patients were satisfied with their care, had enough time with their physician and 85.7% believed the telehealth communication was excellent. All physicians were able to accurately assess the patient's symptoms via telehealth, whereas 82.3% felt they could accurately assess treatment-related toxicity. Physicians assessing skin toxicity from breast radiation were those who did not feel they were able to assess toxicity. Discussion and Conclusions: Both health care providers and patients have identified telemedicine as a suitable platform for radiation oncology visits. Although there are limitations, telemedicine has significant potential for increasing access of cancer care delivery in radiation oncology.

Deep-sea benthic fauna is vital for a well-functioning marine ecosystem but is increasingly under threat from a changing environment. To monitor and conserve this fauna, an understanding of their large-scale spatial and bathymetric distribution and their environmental drivers is necessary. In this study, we conduct a multivariate analysis on abundance benthic fauna data collected at the phylum and multitaxon levels using an epibenthic sledge (EBS) across the Atlantic, and identify the environmental factors that affect such data. Our findings show a decrease in abundance with depth in most of the Atlantic but find relatively heterogeneous abundances with depth within the Southern Ocean. Principal component analyses indicate differences in environmental conditions south of the Antarctic Polar Front (~52° S), outlining contrasts in the quantities of macronutrients and physical factors. Despite this, community composition seemed markedly similar throughout the Atlantic with the Antarctic Circumpolar Current seemingly not affecting benthic community composition for higher taxonomic levels. Those differences that did occur were largely caused by benthic chlorophyll, benthic iron, and surface silicate through a Bio-ENV. Overall, we argue that further large-scale spatial and bathymetric distribution studies are important amid environmental changes that are driving shifts in benthic community abundance and composition.

Climate influence on grapevine physiology is prevalent and this influence is expected to increase with climate change. Climate influence on grapevine physiology can vary depending on the terroir. A better understanding of these local terroir variations is likely to be achieved with analyses that use local data; i.e., farm/vineyard data. Thus, the challenge lies in exploiting farm data to enable grape growers to understand their own terroir and consequently adapt their practices to the local conditions. In such a context, this article proposes an analytical process to site-specifically study climate influence on grapevine physiology by focusing on time series of the weather data often contained in farm data sets. This article focuses on temperature and precipitation influence on yield in the form of a case study. The analytical process includes the Extended Growing Degree Days (eGDD) and the Bayesian functional Linear regression with Sparse Steps functions (BLiSS) methods in order to detect site-specific periods of strong climate influence on grapevine yield. It uses data from three commercial vineyards situated in the Bordeaux region (France), California (USA) and Israel. In general, the periods of climate influence on grapevine yield detected for the three vineyards identified the same stages of yield development, which have already been studied in the scientific literature. However, some vineyard differences were observed, including: i) different periods of influence associated with a given stage of yield development between the vineyards, ii) different influential weather variables between the three vineyards for a given period, and iii) differing duration of the period of influence associated with a given stage of yield development between the vineyards. These results show the potential of the proposed analytical process for analysing the time series of farm weather data in order to extract site-specific climate indicators of grapevine yield.

The Ægir Ridge System (ARS) is an ancient extinct spreading axis in the Nordic seas extending from the upper slope east of Iceland (∼550 m depth), as part of its Exclusive Economic Zone (EEZ), to a depth of ∼3,800 m in the Norwegian basin. Geomorphologically a rift valley, the ARS has a canyon-like structure that may promote increased diversity and faunal density. The main objective of this study was to characterize benthic habitats and related macro- and megabenthic communities along the ARS, and the influence of water mass variables and depth on them. During the IceAGE3 expedition (Icelandic marine Animals: Genetics and Ecology) on RV Sonne in June 2020, benthic communities of the ARS were surveyed by means of a remotely-operated vehicle (ROV) and epibenthic sledge (EBS). For this purpose, two working areas were selected, including abyssal stations in the northeast and bathyal stations in the southwest of the ARS. Video and still images of the seabed were usedtoqualitatively describebenthic habitats based on the presence of habitat-forming taxa and the physical environment. Patterns of diversity and community composition of the soft-sediment macrofauna, retrieved from the EBS, were analyzed in a semiquantitative manner. These biological data were complemented by producing high-resolution bathymetric maps using the vessel’s multi-beam echosounder system. As suspected, we were able to identify differences in species composition and number of macro- and megafaunal communities associated with a depth gradient. A biological canyon effect became evident in dense aggregates of megafaunal filter feeders and elevated macrofaunal densities. Analysis of videos and still images from the ROV transects also led to the discovery of a number ofVulnerable Marine Ecosystems (VMEs) dominated by sponges and soft corals characteristic of the Arctic region. Directions for future research encompass a more detailed, quantitative study of the megafauna and more coherent sampling over the entire depth range in order to fully capture the diversity of the habitats and biota of the region. The presence of sensitive biogenic habitats, alongside seemingly high biodiversity and naturalness are supportive of ongoing considerations of designating part of the ARS as an “Ecologically and Biologically Significant Area” (EBSA).

ABSTRACT: A systematic review and meta-analysis was conducted to investigate the role of Eimeria species, dose and inoculation time, on performance and infection outcomes of different broiler strains infected for different study durations. The meta-analysis addressed E. acervulina, E. maxima, E. tenella, and mixed species infections, and involved data from 72 peer-reviewed articles, corresponding to 521 treatments performed on 20,756 broilers. A secondary objective was to investigate the effects of synthetic anticoccidials, ionophores, and vaccination against Eimeria on the above outcomes. Performance during infection was scaled (%) to that of the uninfected birds. Infection reduced scaled ADFI and ADG (P < 0.001) and increased feed conversion ratio (FCR; P < 0.05); there was a significant interaction between dose and species on scaled ADFI and ADG, suggesting that different species affected these variables to different extents (P < 0.001). There was a tendency for an interaction between dose and broiler strain on scaled ADFI (P = 0.079), and a significant interaction between these variables on scaled ADG (P < 0.01). A tendency for an interaction between oocyst dose and Eimeria species (P = 0.067) on maximum number of oocysts excreted was observed. Lesion scores were significantly affected by dose, species, and their interaction (P < 0.05), the latter caused by an increase in the lesion scores during E. maxima and E. tenella infections. Control methods significantly affected scaled ADG and FCR (P < 0.05) and there was an interaction between dose and control methods on ADFI (P < 0.001). Synthetic anticoccidial use improved scaled ADG (P < 0.01), whereas ionophores improved FCR compared with untreated birds (P < 0.01). An interaction between dose and control method on scaled ADFI was caused by the higher ADFI of vaccinated compared to untreated birds, as dose increased. There was a significant effect of control methods on lesion scores (P < 0.01). All findings advance our understanding of the factors that influence the impact of coccidiosis and its controls in broilers.

We are presenting this document to medical providers as a systematic approach to improve outcomes of patients with COVID-19. The following variables are considered: Autonomic nervous system viewed from the perspective of the Polyvagal Theory; Timing of interventions in terms of phase of the body’s defense (Fight, Flight, Freeze, Faint); The nervous system considered the context of a “One System” perspective; Protein/Enzyme function; Immune system; Cytokine load - activity, inflammation and metabolic response; Viral load; Angiotensin 2 load. The ARDS and multi-system organ failure of the COVID-19 is a complex problem. This approach acknowledges the complexity and presents a structure where the variables are systematically addressed. 1. The common risk factors for death are associated with baseline elevations of pro-inflammatory cytokines. Measures can be taken to lower them before being exposed to the virus–Plan A. 2. Strategies to optimize the body’s defenses should be assessed and optimized. These include nutrition, vitamins, and trace elements, sleep, exercise, and minimizing threat. 3. The body’s own resources are utilized through recruiting the autonomic nervous system to counteract elevated pro-inflammatory cytokines. The interventions are implemented in the context of what stage of defense the body is in–fight, flight, freeze, or faint. 4. Progressive pharmacological interventions are considered with the early interventions being those with minimal risk. We are asking the following: • This approach is viewed as the foundation for clinical interventions. They should be implemented in a systematic and stepwise manner. • Most of the treatments are already medically proven with minimal or no risk. • All basic treatments are in place before more aggressive interventions are implemented. • That this process be considered a framework to test clinical protocols and novel therapies. Much work needs to be done regarding dosing and timing. • We are particularly interested in the potential of the following interventions, which do need to be looked at in a protocol.• o Allowing ketosis in the Mid and Late Phases of the illness. • o Considering the use of ketone bodies instead of glucose for fuel in Mid and Late Phases of illness. • o Eliminating glucocorticosteroids in the Early and Mid-Phases the use of steroids. • o Utilizing the anti-inflammatory cholinergic nervous system (vagal stimulation, nicotine patches, etc.). • o Closer monitoring of IL-6 to in real time deliver the most appropriate interventions. Doi: 10.28991/SciMedJ-2020-02-SI-2 Full Text: PDF

Resumen: Introducción y objetivos: Nuestro estudio pretende comparar los resultados a corto y medio plazo de la cirugía asistida con circulación extracorpórea sin pinzamiento aórtico frente a la cirugía coronaria convencional con parada cardíaca en pacientes con disfunción ventricular severa. Métodos: Desde enero de 2012 hasta enero de 2019 se analiza un grupo de 64 pacientes con fracción de eyección disminuida (

ABSTRACT: In 2 experiments, we investigated whether diet composition plays a role in pathogen-induced anorexia, the voluntary reduction in ADFI during infection in broilers. We hypothesized that either energy or CP dietary content could influence the extent of anorexia in Ross 308 broilers and infection outcomes with Eimeria maxima. From d 13 of age, half of the birds were infected, and half were uninfected. ADFI was measured daily, and BW every 3 d until d 29. Oocyst excretion was measured daily from d 17 to 23. The impact of parasitism on the small intestine was assessed on d 19 and 25. In Experiment 1, 336 birds were offered diets progressively diluted with lignocellulose, starting from a diet with 3,105 (kcal ME/kg) and 20% CP. There was a significant interaction between infection and diet on ADFI during the acute stage of infection (d 17 to 21): for control birds diet dilution decreased ADFI and consequently reduced energy and CP intake. For infected birds, diet dilution increased ADFI, leading to the same energy and CP intake across diets. Oocyst excretion and villi length to crypt depth ratio (VCR) were constant across infected treatments. In Experiment 2, 432 birds were offered diets with constant ME (3,105 kcal/kg), but different CP contents (24, 20, 26, and 12%). Infection significantly reduced ADFI. Although there was no interaction between infection and diet on ADFI, there was an interaction on CP intake during the acute stage of infection. Infected birds on the 20% CP diet achieved the same CP intake as uninfected birds. There were no differences in the VCR and ADG of the infected birds on 24, 20 and 16% CP treatments, but birds on 12% had the lowest ADG and excreted more oocysts. We suggest that during infection, birds target a nutrient resource intake, which appears to be beneficial for infection outcomes, while at the same time they avoid excess protein intake. We conclude that different mechanisms regulate ADFI in infected and uninfected birds.

This paper considers the political, geo-philosophical musings of Deleuze and Guattari on spatialisation, place and movement in relation to the religious nomad (wandering ascetics and reclusive forest monks) inhabiting the borderlands of Thailand. A nomadic science involves improvised ascetic practices between the molar lines striated by modern state apparatuses. The wandering ascetics, inhabiting a frontier political ecology, stand in contrast to the appropriating, sedentary metaphysics and sanctifying arborescence of statism and its corollary place-making, embedded in rootedness and territorialisation. It is argued that the religious nomads, residing on the endo-exteriorities of the state, came to represent a rhizomatic and politico-ontological threat to centre-nation and its apparatus of capture. The paper also theorises transitions and movement at the borderlands in the context of the state’s monastic reforms. These reforms, and its pervasive royal science, problematised the interstitial zones of the early ascetic wanderers in their radical cross-cutting networks and lines, moving within and across demarcated frontiers. Indeed, the ascetic wanderers and their allegorical war machine were seen as a source of wild, free-floating charisma and mystical power, eventually appropriated by the centre-nation in it’s becoming unitary and fixed.

ABSTRACT: The use of alternative, often bulky ingredients is becoming widespread in poultry diets as the industry seeks to reduce its economic and environmental costs. Consequently, there is an increased need to accurately predict the performance of birds given such diets and identify their maximum capacity for bulk. We offered diets diluted with a range of bulky ingredients to male Ross 308 broilers to assess their capacity for bulk and identify a bulk characteristic responsible for limiting intake. Four hundred ninety-five day-old broilers allocated into 45 pens, were offered a common starter diet until day (d) 7, and 1 of 9 grower diets from d 8 to 29 (Period 1). Each of the grower diets was diluted with either 30 or 60% of oat hulls (OH), wheat bran (WB), or grass meal (GM), or a mixture of 2 bulky ingredients at an inclusion level of 30% each (OHWB, OHGM, WBGM). From d 29 to 43 (Period 2), all birds were offered the bulkiest diet (GM60). A number of bulk characteristics were measured on the diets. Feed intake was measured daily, and birds were dissected on d 29 and 43 for organ and carcass measurements. During d 8 to 14 diet water-holding capacity (WHC) was more consistent in predicting feed intake when scaled per unit of body weight than any other bulk characteristic. However, this was no longer the case during d 15 to 28. In Period 2, the response and adaptation to the bulkiest diet was determined by previous experience to bulk. Birds offered a bulkier diet during Period 1, were better able to adapt the size of their digestive organs and increase scaled feed intake, such that there were no differences between these birds and those offered the GM60; the converse was the case for birds on the least bulky diets. We conclude that WHC is able to predict maximum intake on bulky diets in unadapted birds. Adaptation to bulky diets can be very fast, so that their high bulk content no longer limits feed intake and performance.

During RV MS Merian expedition MSM75, an international, multidisciplinary team explored the Reykjanes Ridge from June to August 2018. The first area of study, Steinahóll (150–350 m depth), was chosen based on previous seismic data indicating hydrothermal activity. The sampling strategy included ship- and AUV-mounted multibeam surveys, Remotely Operated Vehicle (ROV), Epibenthic Sledge (EBS), and van Veen grab (vV) deployments. Upon returning to Steinahóll during the final days of MSM75, hydrothermal vent sites were discovered using the ROV Phoca (Kiel, GEOMAR). Here we describe and name three new, distinct hydrothermal vent site vulnerable marine ecosystems (VMEs); Hafgufa, Stökkull, Lyngbakr. The hydrothermal vent sites consisted of multiple anhydrite chimneys with large quantities of bacterial mats visible. The largest of the three sites (Hafgufa) was mapped, and reconstructed in 3D. In total 23,310 individual biological specimens were sampled comprising 41 higher taxa. Unique fauna located in the hydrothermally venting areas included two putative new species of harpacticoid copepod (Tisbe sp. nov. and Amphiascus sp. nov.), as well as the sponge Lycopodina cupressiformis (Carter, 1874). Capitellidae Grube, 1862 and Dorvilleidae Chamberlin, 1919 families dominated hydrothermally influenced samples for polychaetes. Around the hydrothermally influenced sites we observed a notable lack of megafauna, with only a few species being present. While we observed hydrothermal associations, the overall species composition is very similar to that seen at other shallow water vent sites in the north of Iceland, such as the Mohns Ridge vent fields, particularly with peracarid crustaceans. We therefore conclude the community overall reflects the usual “background” fauna of Iceland rather than consisting of “vent endemic” communities as is observed in deeper vent systems, with a few opportunistic species capable of utilizing this specialist environment.

This presentations examines a group of five mummies that were not prepared for the journey to the afterlife but rather preserved and exhibited for commercial enterprise, the sideshow. The study originally comprised five episodes of a forty episode series, «The Mummy Road Show» broadcast on the National Geographic Channel in the United States and internationally. A brief history of the sideshow will be presented to demonstrate the mummies’ roles in the development of that unique segment of the entertainment industry. The method of embalming will be discussed from both its historical context and ability to preserve internal organs. The use of conventional radiography, computed tomography and videoendoscopy to examine the skeletons and well preserved internal organs will be considered in an attempt to substantiate or refute the stories associated with each mummy. In addition, an autopsy conducted on one of the mummies will be correlated to the imaging studies.

Monitoring wine-growing regions and maximising the value of production based on their region/local specificities requires accurate spatial and temporal monitoring. The increasing amount and variability of information from remote sensing data is a potential tool to assess this challenge for the grape and wine industry. This article provides a first insight into the capacity of a multiway analysis method applied to Sentinel-2 time series to assess the value of simultaneously considering spectral and temporal information to highlight site-specific canopy evolution in relation to environmental factors and management practices, which present a large diversity at this regional scale. Parallel Factor Analysis (PARAFAC) was used as an unsupervised technique to recover pure spectra and temporal signatures from multi-way spectral imagery of vineyards in the Languedoc-Roussillon region in the south of France. The model was developed using a time series of Sentinel-2 satellite imagery collected over 4978 vineyard blocks between May 2019 and August 2020. From the Sentinel-2 (spectral and temporal) signal, the PARAFAC analysis allowed the identification of spectral and temporal profiles in the form of pure components, which corresponded to vegetation and soil. The PARAFAC analysis also identified that two of the pure spectra were strongly related to characteristics and dynamics of vineyard cultivation at a regional scale. A conceptual framework was proposed in order to simultaneously consider both vegetation and soil profiles and to summarise the mass of data accordingly. This methodology allowed the computation of a concentration index that characterised how close a field was to a vegetation or a soil profile over the season. The concentration indices were validated for the vegetation and the soil over two growing seasons (2019 and 2020) with geostatistical analysis. A non-random distribution of the concentration index at the regional scale was assumed to highlight a strongly spatially organised phenomenon related to spatially organised environmental factors (soil, climate, training system, etc.). In a second step, spatial patterns of indices were subjected to the expertise of a panel of advisors of the wine industry in order to validate them in relation to vine-growing conditions. Results showed that the introduction of the PARAFAC method opened up the possibility to identify relevant spectro-temporal profiles for vine monitoring purposes.

Abstract For the past two decades, precipitation radars (PR) onboard low‐orbiting satellites such as Tropical Rainfall Measuring Mission (TRMM) have provided invaluable insight into global precipitation variability and led to advancements in numerical weather prediction through data assimilation. Building upon this success, planning has begun on the next generation of satellite‐based PR instruments, with the consideration for a future geostationary‐based PR (GPR), bringing the advantage of higher observation frequency over previous and current PR satellites. Following the successful demonstration by a recent study to test the feasibility of a GPR to obtain three‐dimensional precipitation data, this study takes the first step to investigate the potential usefulness of GPR observations for numerical weather prediction by performing a perfect model observing system simulation experiment (OSSE) for a West Pacific tropical cyclone (TC). Data assimilation experiments are performed assimilating reflectivity observations obtained for a range of beam sampling spans, following a previous finding that oversampling improves observation quality. Results showed observations obtained with finer sampling spans of 5 km and 10 km were able to better capture key tropical cyclone features in analyses, including the eye, heavy rainfall associated with the eyewall, and outer convective rainbands. Results also showed that through increased moistening and upward velocity within the inner storm environment, assimilation of observations drove an intensification of the secondary circulation and deepening of the storm, leading to an improvement in TC intensity error. Intensity forecasts were found improved for assimilation of observations obtained with increasingly finer beam sampling span, suggesting an important benefit of oversampling.

Abstract Background Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Results Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments. Conclusions In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.

The view that genetic selection for carcass yield has limited the size of the gastrointestinal tract (GIT) of modern broilers has sparked concerns that their capacity to cope with energy dilution or bulk is also limited. We investigated the capacity of male Ross 308 broilers to deal with increasing levels of bulk and aimed to identify a feed bulk dimension responsible for limiting feed intake (FI). About 528 day-old broilers were allocated to 48 pens and offered a common starter feed until day 8, and 1 of 7 feeds from day 8 to 36 of age: a basal control (B), which was diluted to 3 levels (15, 30, or 45%) with either oat hulls (OH) or sugar beet pulp (SBP). Feed intake was measured daily and birds were dissected for GIT measurements at day 15, 22, and 36. Feed intake increased in birds offered OH15 (135 g/d), OH30 (140 g/d), and SBP15 (138 g/d) compared with birds offered the B feed (106 g/d; SEM 2.4). By increasing FI, birds were able to compensate for the lower energy content of their feeds. The greatest increase in FI was seen on OH30: its energy content (2,273 kcal/kg) was 26% lower than the B feed (3,081 kcal/kg). There was evidence of adaptation on the bulky feeds, as during the last week only birds on SBP45 were limited in FI and performance. The relative weights of the GIT were greater in the SBP than OH series, suggesting that the former needed to accommodate a higher bulk intake. For the OH series the increase in the relative GIT weights was confined to the gizzard and small intestine; whereas for the SBP series, the increase was extended to proventriculus and large intestine. Because only SBP45 was limiting FI, we were unable to identify a bulk dimension to be used to predict FI. Our data reject the suggestion that modern broilers have a reduced ability to cope with reductions in feed energy content.

BackgroundSickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized deoxygenated hemoglobin, rigid sickle red blood cells and vaso-occlusive crises (VOC). Recurrent hypoxia-reperfusion injury in the gut of SCD patients could increase tissue injury, permeability, and bacterial translocation. In this context, the gut microbiome, a major player in health and disease, might have significant impact. This study sought to characterize the gut microbiome in SCD.MethodsStool and saliva samples were collected from healthy controls (n = 14) and SCD subjects (n = 14). Stool samples were also collected from humanized SCD murine models including Berk, Townes and corresponding control mice. Amplified 16S rDNA was used for bacterial composition analysis using Next Generation Sequencing (NGS). Pairwise group analyses established differential bacterial groups at many taxonomy levels. Bacterial group abundance and differentials were established using DeSeq software.ResultsA major dysbiosis was observed in SCD patients. The Firmicutes/Bacteroidetes ratio was lower in these patients. The following bacterial families were more abundant in SCD patients: Acetobacteraceae, Acidaminococcaceae, Candidatus Saccharibacteria, Peptostreptococcaceae, Bifidobacteriaceae, Veillonellaceae, Actinomycetaceae, Clostridiales, Bacteroidacbactereae and Fusobacteriaceae. This dysbiosis translated into 420 different operational taxonomic units (OTUs). Townes SCD mice also displayed gut microbiome dysbiosis as seen in human SCD.ConclusionA major dysbiosis was observed in SCD patients for bacteria that are known strong pro-inflammatory triggers. The Townes mouse showed dysbiosis as well and might serve as a good model to study gut microbiome modulation and its impact on SCD pathophysiology.

In this study we focus on the ophiuroid species associated with cold-water corals south of Iceland. The specimens were sampled with the ROV Phoca (GEOMAR) in three different areas, during the recent expedition MSM75 connected to the IceAGE_RR (Icelandic marine Animals: Genetics and Ecology_Reykjanes Ridge hydrothermal vent activity) project. In each area, several corals were sampled and the ophiuroid specimens identified to the species level. The integrative taxonomic approach, based on morphological characters and DNA barcoding with COI of the collected ophiuroids, revealed five species that live on corals: Ophiomitrella clavigera (Ljungman, 1865); Ophiomyxa serpentaria (Lyman, 1883); Ophiacantha cuspidata (Lyman, 1879); Ophiactis abyssicola (M. Sars, 1861); and Ophiolebes bacata Koehler, 1921. Some of the sampled deep-sea corals exclusively host the species O.clavigera. The collected species are therefore associated with different corals but do not demonstrate a species-specific distribution. The video data support the integrative taxonomy and confirm the ecological evidence.

Spatial heterogeneity in microbial communities is observed in all natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non-desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.

Aim: The recent availability of Sentinel-2 satellites has led to an increasing interest in their use in viticulture. The aim of this short communication is to determine performance and limitation of a Sentinel-2 vegetation index in precision viticulture applications, in terms of correlation and variability assessment, compared to the same vegetation index derived from an unmanned aerial vehicle (UAV). Normalised difference vegetation index (NDVI) was used as reference vegetation index. Methods and Results: UAV and Sentinel-2 vegetation indices were acquired for 30 vineyard blocks located in the south of France without inter-row grass. From the UAV imagery, the vegetation index was calculated using both a mixed pixels approach (both vine and inter-row) and from pure vine-only pixels. In addition, the vine projected area data were extracted using a support vector machine algorithm for vineyard segmentation. The vegetation index was obtained from Sentinel-2 imagery obtained at approximately the same time as the UAV imagery. The Sentinel-2 images used a mixed pixel approach as pixel size is greater than the row width. The correlation between these three layers and the Sentinel-2 derived vegetation indices were calculated, considering spatial autocorrelation correction for the significance test. The Gini coefficient was used to estimate variability detected by each sensor at the within-field scale. The effects of block border and dimension on correlations were estimated. Conclusions: The comparison between Sentinel-2 and UAV vegetation index showed an increase in correlation when border pixels were removed. Block dimensions did not affect the significance of correlation unless blocks were < 0.5 ha. Below this threshold, the correlation was non-significant in most cases. Sentinel-2 acquired data were strongly correlated with UAV-acquired data at both the field (R2 = 0.87) and sub-field scale (R2 = 0.84). In terms of variability detected, Sentinel-2 proved to be able to detect the same amount of variability as the UAV mixed pixel vegetation index. Significance and impact of the study: This study showed at which field conditions the Sentinel-2 vegetation index can be used instead of UAV-acquired images when high spatial resolution (vine-specific) management is not needed and the vineyard is characterised by no inter-row grass. This type of information may help growers to choose the most appropriate information sources to detect variability according to their vineyard characteristics.

Aim: The objective of this short communication is to study the opportunity of using a smartphone application for leaf area index (LAI) observations within vineyards in southern France in a farmsourcing context, i.e. when several operators make parallel acquisitions over the same area. In this context, several sources of variability are likely to affect measurement quality, such as the smartphone model or the operator. Understanding these sources of variability will enhance the ability to properly interpret LAI observations to produce relevant information for decision-making. Methods and material: A study was specifically designed to evaluate the ability of a smartphone application to differentiate sites with different LAI and to determine the origin and the relative importance of different sources of variation in a context of farmsourcing data collection. This focused on the VitiCanopy application, which has been developed specifically for viticulture LAI measurements. Measurements were performed by 18 operators with 11 different smartphone models, on three different vines presenting controlled canopy size to evaluate the ability of the smartphone application to differentiate sites under varying acquisition conditions. Controlled repetitions over seven vines by seven operators with seven smartphone models were performed to further determine the sources of variation and their relative importance. Results: LAI estimations made with VitiCanopy were consistent with the different levels of controlled vine size in the experiment. The operator and the smartphone model had a significant effect on the variance of the estimated LAI. The variance caused by the observation protocol was relatively low compared to the variability between plants within the observation site (seven vines). Conclusions: This study showed that the VitiCanopy application was relevant for ordering or classifying vines according to LAI. In an operational context, the results of this study support the use of this smartphone application for relative measurements. However, the best results were achieved when smartphone model differences were minimised or avoided and with homogeneous acquisition conditions between operators. This last condition will require the organisation of group training sessions to minimise an observed operator effect on measurement variability. Significance and impact of the study: This short communication demonstrated the potential of LAI observations collected with smartphones by several operators for decision-making in a context of farmsourcing. The results showed that this new source of observations, which is inexpensive to collect, made it possible to characterise vine size (LAI) differences in vineyards of southern France. This shows the potential of this app for large production areas such as cooperatives. Further investigations are needed to understand how different training systems may affect the measurement. This source of observations could be complementary to other information sources that are more precise or more accurate, but also more expensive (i.e. destructive methods).

School attendance is important for student long-term academic and career success. However, in the U.S., our current practice often disenfranchises more at-risk students than it helps. Students slated for suspension and expulsion are often recipients of these practices. This manuscript offers a recommended change in how we frame student absenteeism and attendance using attendance markers and conceptual information by identifying the discrepancies, proposing options, and recommending a new way to actively leverage attendance data (not absenteeism data) for proactive student support. Particular attention is paid to how excused and unexcused absences and in-school suspensions are treated. An emerging pivot program, the Evaluation and Support Program, engages students while they receive school services, community support, and complete consequences is discussed as a possible, promising intervention.

Recent literature reflects the substantial progress in combining spatial, temporal and spectral capacities for remote sensing applications. As a result, new issues are arising, such as the need for methodologies that can process simultaneously the different dimensions of satellite information. This paper presents PLS regression extended to three-way data in order to integrate multiwavelengths as variables measured at several dates (time-series) and locations with Sentinel-2 at a regional scale. Considering that the multi-collinearity problem is present in remote sensing time-series to estimate one response variable and that the dataset is multidimensional, a multiway partial least squares (N-PLS) regression approach may be relevant to relate image information to ground variables of interest. N-PLS is an extension of the ordinary PLS regression algorithm where the bilinear model of predictors is replaced by a multilinear model. This paper presents a case study within the context of agriculture, conducted on a time-series of Sentinel-2 images covering regional scale scenes of southern France impacted by the heat wave episode that occurred on 28 June 2019. The model has been developed based on available heat wave impact data for 107 vineyard blocks in the Languedoc-Roussillon region and multispectral time-series predictor data for the period May to August 2019. The results validated the effectiveness of the proposed N-PLS method in estimating yield loss from spectral and temporal attributes. The performance of the model was evaluated by the R2 obtained on the prediction set (0.661), and the root mean square of error (RMSE), which was 10.7%. Limitations of the approach when dealing with time-series of large-scale images which represent a source of challenges are discussed; however, the N–PLS regression seems to be a suitable choice for analysing complex multispectral imagery data with different spectral domains and with a clear temporal evolution, such as an extreme weather event.

Abstract Background The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. Results To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP’s hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. Conclusions MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP.

Few studies have explored the effect of a changing environment on artificial chemical evolution. Here, the authors develop an evolutionary platform that alters the physical environment of droplet protocells, showing that a population of simple chemical species can adapt to its surroundings, in analogy to natural evolution.

The mammalian sperm genome is thought to lack substantial information for the regulation of future expression after fertilization. Here, we show that most promoters in mouse sperm are flanked by well-positioned nucleosomes marked by active histone modifications. Analysis of these modifications suggests that many enhancers and super-enhancers functional in embryonic and adult tissues are already specified in sperm. The sperm genome is bound by CTCF and cohesin at sites that are also present in round spermatids and embryonic stem cells (ESCs). These sites mediate interactions that organize the sperm genome into domains and compartments that overlap extensively with those found in mESCs. These results suggest that sperm carry a rich source of regulatory information, encoded in part by its three-dimensional folding specified by CTCF and cohesin. This information may contribute to future expression during embryonic and adult life, suggesting mechanisms by which environmental effects on the paternal germline are transmitted transgenerationally.

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.

Summary: Altered excitatory/inhibitory (E/I) balance is implicated in neuropsychiatric and neurodevelopmental disorders, but the underlying genetic etiology remains poorly understood. Copy number variations in CYFIP1 are associated with autism, schizophrenia, and intellectual disability, but its role in regulating synaptic inhibition or E/I balance remains unclear. We show that CYFIP1, and the paralog CYFIP2, are enriched at inhibitory postsynaptic sites. While CYFIP1 or CYFIP2 upregulation increases excitatory synapse number and the frequency of miniature excitatory postsynaptic currents (mEPSCs), it has the opposite effect at inhibitory synapses, decreasing their size and the amplitude of miniature inhibitory postsynaptic currents (mIPSCs). Contrary to CYFIP1 upregulation, its loss in vivo, upon conditional knockout in neocortical principal cells, increases expression of postsynaptic GABAA receptor β2/3-subunits and neuroligin 3, enhancing synaptic inhibition. Thus, CYFIP1 dosage can bi-directionally impact inhibitory synaptic structure and function, potentially leading to altered E/I balance and circuit dysfunction in CYFIP1-associated neurological disorders. : Copy number variations (CNVs) in CYFIP1 are associated with neuropsychiatric disorders. Davenport et al. uncover an essential role for CYFIP1 in regulating synaptic inhibition and in maintaining the excitatory/inhibitory balance. By altering CYFIP1 gene dosage, to model CNV, they reveal important bi-directional effects on inhibitory transmission in hippocampal neurons. Keywords: excitatory/inhibitory, CNV, ASD, GABA, dendritic spine, gephyrin, epilepsy, 15q11.2, microduplication, microdeletion

This article considers the role of digital recording methods and visualisation tools in the primary recording of archaeology at the Neolithic tell site of Çatalhöyük, Turkey. Operating within and building on Çatalhöyük Research Project's understanding of reflexive methods (Hodder 2000b, 2003; Berggren and Nilson 2014; Berggren et al. 2015) we incorporate elements of science and technology studies (Pickering 1995) in order to create a framework for documenting the complete process of devising, implementing, and assessing digitised and tablet-based workflows. These harness the project's existing SQL database and intra-site GIS, as well as the increasingly user-friendly suite of 3D recording technologies which are now available to archaeologists. The Çatalhöyük Research Project's longstanding engagement with digital methods in archaeology means that such a study is well placed to provide insights into wider disciplinary trends that might be described as a 'Digital Turn'. By offering a review of tablet recording and exploring the effects of its introduction upon the archaeologists' relationship with the archaeological remains, we investigate the applied integration of digital recording technologies and their role in facilitating a deeper reflexivity in the interpretation of the archaeology on the site.

Each individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. In the fly eye, the random mosaic of color-detecting R7 photoreceptor subtypes is determined by stochastic on/off expression of the transcription factor Spineless (Ss). In a genome-wide association study, we identified a naturally occurring insertion in a regulatory DNA element in ss that lowers the ratio of SsON to SsOFF cells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulates ss expression. Klu is expressed at intermediate levels to determine the normal ratio of SsON to SsOFF cells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic expression, setting the ratio of alternative fates and ultimately determining color preference.

James Taylor Carson reviews Gregory D. Smithers's The Cherokee Diaspora: An Indigenous History of Migration, Resettlement, and Identity (New Haven: Yale University Press, 2015).

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites). The subsequent exploratory stage is much more ad hoc and requires the development of custom scripts and pipelines, making it problematic for biomedical researchers. Here, we describe a hybrid platform combining common analysis pathways with the ability to explore data interactively. It aims to fully encompass and simplify the "raw data-to-publication" pathway and make it reproducible.