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The stratosphere can be a source of predictability for surface weather on timescales of several weeks to months. However, the potential predictive skill gained from stratospheric variability can be limited by biases in the representation of stratospheric processes and the coupling of the stratosphere with surface climate in forecast systems. This study provides a first systematic identification of model biases in the stratosphere across a wide range of subseasonal forecast systems. It is found that many of the forecast systems considered exhibit warm global-mean temperature biases from the lower to middle stratosphere, too strong/cold wintertime polar vortices, and too cold extratropical upper-troposphere/lower-stratosphere regions. Furthermore, tropical stratospheric anomalies associated with the Quasi-Biennial Oscillation tend to decay toward each system's climatology with lead time. In the Northern Hemisphere (NH), most systems do not capture the seasonal cycle of extreme-vortex-event probabilities, with an underestimation of sudden stratospheric warming events and an overestimation of strong vortex events in January. In the Southern Hemisphere (SH), springtime interannual variability in the polar vortex is generally underestimated, but the timing of the final breakdown of the polar vortex often happens too early in many of the prediction systems. These stratospheric biases tend to be considerably worse in systems with lower model lid heights. In both hemispheres, most systems with low-top atmospheric models also consistently underestimate the upward wave driving that affects the strength of the stratospheric polar vortex. We expect that the biases identified here will help guide model development for subseasonal-to-seasonal forecast systems and further our understanding of the role of the stratosphere in predictive skill in the troposphere.

The simulated Northern Hemisphere winter stationary wave (SW) field is investigated in 11 Subseasonal-to-Seasonal (S2S) prediction project models. It is shown that while most models considered can well simulate the stationary wavenumbers 1 and 2 during the first 2 weeks of integration, they diverge from observations following week 3. Those models with a poor resolution in the stratosphere struggle to simulate the waves, in both the troposphere and the stratosphere, even during the first 2 weeks. Focusing on the tropospheric regions where SWs peak in amplitude reveals that the models generally do a better job in simulating the northwestern Pacific stationary trough, while certain models struggle to simulate the stationary ridges in both western North America and the North Atlantic. In addition, a strong relationship is found between regional biases in the stationary height field and model errors in simulated upward propagation of planetary waves into the stratosphere. In the stratosphere, biases are mostly in wave 2 in those models with high stratospheric resolution, whereas in those models with low resolution in the stratosphere, a wave 1 bias is evident, which leads to a strong bias in the stratospheric mean zonal circulation due to the predominance of wave 1 there. Finally, biases in both amplitude and location of mean tropical convection and the subsequent subtropical downwelling are identified as possible contributors to biases in the regional SW field in the troposphere.

Abstract The human skin can be affected by a multitude of diseases including inflammatory conditions such as atopic dermatitis and psoriasis. Here, we describe how skin barrier integrity and immunity become dysregulated during these two most common inflammatory skin conditions. We summarise recent advances made in the field of the skin innate immune system and its interaction with adaptive immunity. We review gene variants associated with atopic dermatitis and psoriasis that affect innate immune mechanisms and skin barrier integrity. Finally, we discuss how current and future therapies may affect innate immune responses and skin barrier integrity in a generalized or more targeted approach in order to ameliorate disease in patients.

The implementation of antiretroviral therapy (ART) has effectively restricted the transmission of Human Immunodeficiency Virus (HIV) and improved overall clinical outcomes. However, a complete cure for HIV remains out of reach, as the virus persists in a stable pool of infected cell reservoir that is resistant to therapy and thus a main barrier towards complete elimination of viral infection. While the mechanisms by which host proteins govern viral gene expression and latency are well-studied, the emerging regulatory functions of non-coding RNAs (ncRNA) in the context of T cell activation, HIV gene expression and viral latency have not yet been thoroughly explored. Here, we report the identification of the Cytoskeleton Regulator (CYTOR) long non-coding RNA (lncRNA) as an activator of HIV gene expression that is upregulated following T cell stimulation. Functional studies show that CYTOR suppresses viral latency by directly binding to the HIV promoter and associating with the cellular positive transcription elongation factor (P-TEFb) to activate viral gene expression. CYTOR also plays a global role in regulating cellular gene expression, including those involved in controlling actin dynamics. Depletion of CYTOR expression reduces cytoplasmic actin polymerization in response to T cell activation. In addition, treating HIV-infected cells with pharmacological inhibitors of actin polymerization reduces HIV gene expression. We conclude that both direct and indirect effects of CYTOR regulate HIV gene expression.

The Ogallala aquifer, underlying eight states from South Dakota to Texas, is practically non-recharging south of Nebraska, and groundwater withdrawals for irrigation have lowered the aquifer in western Kansas. Subsequent well-yield declines encourage deficit irrigation, greater reliance on precipitation, and producing profitable drought-tolerant crops like upland cotton (Gossypium hirsutum (L.)). Our objective was to evaluate deficit irrigated cotton growth, yield, and water productivity (CWP) in northwest, west-central, and southwest Kansas in relation to El Niño southern oscillation (ENSO) phase effects on precipitation and growing season cumulative thermal energy (CGDD). Using the GOSSYM crop growth simulator with actual 1961–2000 location weather records partitioned by the ENSO phase, we modeled crop growth, yield, and evapotranspiration (ET) for irrigation capacities of 2.5, 3.75, and 5.0 mmd−1 and periods of 4, 6, and 8 weeks. Regardless of location, the ENSO phase did not influence CGDD, but precipitation and lint yield decreased significantly in southwest Kansas during La Niña compared with the Neutral and El Niño phases. Simulated lint yields, ET, CWP, and leaf area index (LAI) increased with increasing irrigation capacity despite application duration. Southwestern Kansas producers may use ENSO phase information with deficit irrigation to reduce groundwater withdrawals while preserving desirable cotton yields.

Cattle possess three IgG subclasses. However, the key immune functions, including complement and NK cell activation, and enhancement of phagocytosis, are not fully described for bovine IgG1, 2 and 3. We produced chimeric monoclonal antibodies (mAbs) consisting of a defined variable region linked to the constant regions of bovine IgG1, 2 and 3, and expressed His-tagged soluble recombinant bovine Fc gamma receptors (FcγRs) IA (CD64), IIA (CD32A), III (CD16) and Fcγ2R. Functional assays using bovinized mAbs were developed. IgG1 and IgG3, but not IgG2, activated complement-dependent cytotoxicity. Only IgG1 could activate cattle NK cells to mobilize CD107a after antigen crosslinking, a surrogate assay for antibody-dependent cell cytotoxicity. Both IgG1 and IgG2 could trigger monocyte-derived macrophages to phagocytose fluorescently labelled antigen-expressing target cells. IgG3 induced only weak antibody-dependent cellular phagocytosis (ADCP). By contrast, monocytes only exhibited strong ADCP when triggered by IgG2. IgG1 bound most strongly to recombinant FcγRs IA, IIA and III, with weaker binding by IgG3 and none by IgG2, which bound exclusively to Fcγ2R. Immune complexes containing IgG1, 2 and 3 bound differentially to leukocyte subsets, with IgG2 binding strongly to neutrophils and monocytes and all subclasses binding platelets. Differential expression of the FcγRs on leukocyte subsets was demonstrated by surface staining and/or RT-qPCR of sorted cells, e.g., Fcγ2R mRNA was expressed in monocytes/macrophages, neutrophils, and platelets, potentially explaining their strong interactions with IgG2, and FcγRIII was expressed on NK cells, presumably mediating IgG1-dependent NK cell activation. These data reveal differences in bovine IgG subclass functionality, which do not correspond to those described in humans, mice or pigs, which is relevant to the study of these IgG subclasses in vaccine and therapeutic antibody development.

Background : Changes in left ventricular (LV) systolic function have not been well described in premature neonates after transcatheter patent ductus arteriosus (PDA) closure. Methods and Results : We retrospectively identified all premature neonates < 3 kg who underwent a transcatheter PDA closure at our center between January 1 2015 and January 31, 2021. LV indices before and after closure were extracted and an analysis was performed. Overall, 23 neonates were included with a mean procedural weight of 1894 ± 622 g. At 24 h after closure, the median left ventricular ejection fraction (LVEF) (66% interquartile range [IQR] 12% vs. 61% IQR 12, P< 0.001) and median LV end-diastolic dimension z-score (3.3 IQR 1.8 vs. 1.4 IQR 2.6, P < 0.001) both decreased and 5 (22%) neonates had an LVEF

The impact of a dilated left ventricular (LV) on right ventricular (RV) diastolic function has not been investigated. We hypothesized that in patients with a patent ductus arteriosus (PDA), LV dilation causes elevation of the RV end-diastolic pressure (RVEDP) through ventricular-ventricular interaction. We identified patients' ages 6 months to 18 years who underwent transcatheter PDA closure at our center from 2010 to 2019. One hundred and thirteen patients were included with a median age of 3 years (0.5–18). The median LV end-diastolic dimension (LVEDD) Z-score was 1.6 (−1.4–6.3). RVEDP was positively associated with RV systolic pressure (0.38, P < 0.01), ratio of pulmonary artery/aortic systolic pressure (0.4, P < 0.01), and pulmonary capillary wedge pressure (0.71, P < 0.01). RVEDP was not associated with LVEDD Z-score (0.03, P = 0.74). In children with a PDA, RVEDP was not associated with LV dilation, but was positively associated with RV systolic pressure.

We report the case of a 20-year-old male who developed severe HO of the left hip secondary to a prolonged course of COVID-19 pneumonia. Upon extubation, he was found to have debilitating left hip pain and significant functional deficits with regard to his range of motion and functional status. There are numerous known causes of heterotopic ossification (HO), including trauma, surgery, and traumatic brain or spinal cord injuries. An increased incidence of HO has also been reported in patients who undergo prolonged intubation. While the COVID-19 virus has many known respiratory and medical complications, it has also resulted in unforeseen complications that present long-term challenges for patients. When treating patients with coronavirus, physicians should be aware of HO as a possible complication and consider it as a cause of musculoskeletal pain.

While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance accessibility and comparison, we have developed a BAC restriction map database. Using information from the National Center for Biotechnology Information’s cloneDB FTP site, we constructed a database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of the available restriction enzymes. Along with the database, we generated a set of Python functions to reconstruct the database and more easily access the information within. This data is valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy–light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy–light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.

This secondary analysis sought to determine if plasma menthol glucuronide (MG) concentrations predict changes in three outcomes, subjective drug effects, urges to smoke, and heart rate, following concurrent inhaled menthol and intravenous nicotine. A total of 45 menthol and non-menthol cigarettes smokers (36 male, nine female, 20 Black, and 23 White) were included in this double-blind, placebo-controlled study. Across three test sessions, participants were assigned to a different flavor condition for each session: 0% (no menthol), 0.5%, or 3.2% menthol. In each test session, participants received in a random order one intravenous delivery of saline and two intravenous deliveries of nicotine (0.25 mg/70 kg and 0.5 mg/70 kg), each 1 h apart, concurrent with menthol delivery by e-cigarettes. The main outcomes were subjective drug effects, urges to smoke, and heart rate. The results showed that following e-cigarette inhalation, changes in plasma MG concentrations or “menthol boost” increased proportionally to the menthol concentration in the e-liquids. While changes in plasma MG concentrations were not predictive of increases in heart rate or subjective drug effects that are reflective of acute effects from nicotine (i.e., feel good effects, stimulated, aversive effects), they were predictive of cooling effect, a typical effect of menthol, but only in menthol smokers in the absence of concurrent active nicotine infusion. These findings demonstrate the utility of plasma MG as a biomarker both for acute menthol exposure by e-cigarette inhalation and for the examination of the concentration-dependent behavioral and physiological effects of menthol in humans.

Despite the value of family-centered care (FCC) in intensive care units (ICUs), this approach is rarely a reality in this context. This article aims to increase the likelihood that ICU-based care incorporates best practices for FCC. Consistent with this goal, this article begins by overviewing FCC and its merits and challenges in ICUs. It then offers a systemic framework for conceptualizing FCC in this challenging environment, as such a model can help guide the implementation of this invaluable approach. This systemic framework combined with previous guidelines for FCC in the ICU are used to inform the series of recommended best practices for FCC in the ICU that balance the needs and realities of patients, families, and the interprofessional healthcare team. These best practices reflect an integration of the existing literature and previously published guidelines as well as our experiences as healthcare providers, family members, and patients. We encourage healthcare leaders and interprofessional ICU healthcare teams to adopt these best practices and modify them for the specific healthcare needs of the patients they serve and their families.

Objective: C-reactive protein (CRP), a marker of systemic inflammation, has been associated with psychiatric disorders including major depressive disorder (MDD) and post-traumatic stress disorder (PTSD). Some research suggests that exposure to trauma can trigger increased activity in the inflammatory system. Dissociation is associated with chronic trauma exposure and may be an important factor in understanding the risk for psychiatric outcomes associated with inflammation. The main objective of the current study was to understand how CRP was related to trauma, dissociation, PTSD and MDD in a sample of 55 traumatized African American women with type 2 diabetes mellitus recruited from an urban hospital. Method: High sensitivity CRP (hsCRP) was assayed through blood samples; psychiatric disorders were assessed with structured clinical interviews, dissociation was assessed with the Multiscale Dissociation Inventory, and exposure to trauma in childhood and adulthood was assessed with the Childhood Trauma Questionnaire and the Traumatic Events Inventory, respectively. Results: Correlational results showed a significant association between higher concentrations of hsCRP and child abuse (p

Abstract Background The human immunodeficiency virus (HIV) cell reservoir is currently a main obstacle towards complete eradication of the virus. This infected pool is refractory to anti-viral therapy and harbors integrated proviruses that are transcriptionally repressed but replication competent. As transcription silencing is key for establishing the HIV reservoir, significant efforts have been made to understand the mechanism that regulate HIV gene transcription, and the role of the elongation machinery in promoting this step. However, while the role of the super elongation complex (SEC) in enhancing transcription activation of HIV is well established, the function of SEC in modulating viral latency is less defined and its cell partners are yet to be identified. Results In this study we identify fused in sarcoma (FUS) as a partner of AFF4 in cells. FUS inhibits the activation of HIV transcription by AFF4 and ELL2, and silences overall HIV gene transcription. Concordantly, depletion of FUS elevates the occupancy of AFF4 and Cdk9 on the viral promoter and activates HIV gene transcription. Live cell imaging demonstrates that FUS co-localizes with AFF4 within nuclear punctuated condensates, which are disrupted upon treating cells with aliphatic alcohol. In HIV infected cells, knockout of FUS delays the gradual entry of HIV into latency, and similarly promotes viral activation in a T cell latency model that is treated with JQ1. Finally, effects of FUS on HIV gene transcription are also exhibited genome wide, where FUS mainly occupies gene promoters at transcription starting sites, while its knockdown leads to an increase in AFF4 and Cdk9 occupancy on gene promoters of FUS affected genes. Conclusions Towards eliminating the HIV infected reservoir, understanding the mechanisms by which the virus persists in the face of therapy is important. Our observations show that FUS regulates both HIV and global gene transcription and modulates viral latency, thus can potentially serve as a target for future therapy that sets to reactivate HIV from its latent state.

Traumatic brain injury (TBI) is a predisposing factor for many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson’s disease (PD), and chronic traumatic encephalopathy (CTE). Although defects in nucleocytoplasmic transport (NCT) is reported ALS and other neurodegenerative diseases, whether defects in NCT occur in TBI remains unknown. We performed proteomic analysis on Drosophila exposed to repeated TBI and identified resultant alterations in several novel molecular pathways. TBI upregulated nuclear pore complex (NPC) and nucleocytoplasmic transport (NCT) proteins as well as alter nucleoporin stability. Traumatic injury disrupted RanGAP1 and NPC protein distribution in flies and a rat model and led to coaggregation of NPC components and TDP-43. In addition, trauma-mediated NCT defects and lethality are rescued by nuclear export inhibitors. Importantly, genetic upregulation of nucleoporins in vivo and in vitro triggered TDP-43 cytoplasmic mislocalization, aggregation, and altered solubility and reduced motor function and lifespan of animals. We also found NUP62 pathology and elevated NUP62 concentrations in postmortem brain tissues of patients with mild or severe CTE as well as co-localization of NUP62 and TDP-43 in CTE. These findings indicate that TBI leads to NCT defects, which potentially mediate the TDP-43 pathology in CTE.

Parkinson disease (PD) is a progressive, neurodegenerative disorder affecting over 6.1 million people worldwide. Although the cause of PD remains unclear, studies of highly penetrant mutations identified in early-onset familial parkinsonism have contributed to our understanding of the molecular mechanisms underlying disease pathology. Dopamine (DA) transporter (DAT) deficiency syndrome (DTDS) is a distinct type of infantile parkinsonism-dystonia that shares key clinical features with PD, including motor deficits (progressive bradykinesia, tremor, hypomimia) and altered DA neurotransmission. Here, we define structural, functional, and behavioral consequences of a Cys substitution at R445 in human DAT (hDAT R445C), identified in a patient with DTDS. We found that this R445 substitution disrupts a phylogenetically conserved intracellular (IC) network of interactions that compromise the hDAT IC gate. This is demonstrated by both Rosetta molecular modeling and fine-grained simulations using hDAT R445C, as well as EPR analysis and X-ray crystallography of the bacterial homolog leucine transporter. Notably, the disruption of this IC network of interactions supported a channel-like intermediate of hDAT and compromised hDAT function. We demonstrate that Drosophila melanogaster expressing hDAT R445C show impaired hDAT activity, which is associated with DA dysfunction in isolated brains and with abnormal behaviors monitored at high-speed time resolution. We show that hDAT R445C Drosophila exhibit motor deficits, lack of motor coordination (i.e. flight coordination) and phenotypic heterogeneity in these behaviors that is typically associated with DTDS and PD. These behaviors are linked with altered dopaminergic signaling stemming from loss of DA neurons and decreased DA availability. We rescued flight coordination with chloroquine, a lysosomal inhibitor that enhanced DAT expression in a heterologous expression system. Together, these studies shed some light on how a DTDS-linked DAT mutation underlies DA dysfunction and, possibly, clinical phenotypes shared by DTDS and PD.

Continued pumping for irrigation from the non-recharging Ogallala aquifer in Kansas and Texas is unsustainable. Reducing risks for dryland wheat (Triticum aestivum L) and sorghum [Sorghum bicolor (L.) Moench] production, which depends exclusively on precipitation to meet water demand is critical for future adoption. Stormwater runoff reduces the amount of precipitation available to crops, but management practices to minimize runoff concomitantly increase the opportunity time for infiltration and improve precipitation storage as soil water for crop use. Our objectives in this study were to evaluate tillage, slope and the effects of contour or with-slope farming on runoff, soil water at planting, and the growth and yield of wheat and sorghum grown in the 3 years wheat-sorghum-fallow (WSF) rotation. Long-term, 1983 to present, runoff was measured from gauged terraced and contour farmed fields managed in the WSF rotation with no-tillage (NT) or stubble-mulch (SM) tillage. We found significantly greater mean cumulative runoff during fallow for NT than for SM but only for the 1.8% terrace slopes., The corresponding soil water with NT increased by a significant ~27 mm over SM due to reduced evaporation but generally did not differ due to slope. Wheat yield decreased significantly as slope decreased from 1.8 to 1.2% but exhibited no yield response tillage. In contrast, grain sorghum yields were greater with NT than SM tillage residue management. Farming along the contour or slope manifested no differences in soil water, crop grain yield, or water use; however, they did increased significantly with no tillage for sorghum but not wheat. We conclude that management of tillage was more effective than slope effects in increasing water availability to crops because of evaporation reduction with crop residue.

Despite the importance of tropical forests to global carbon balance, our understanding of how tropical plant physiology will respond to climate warming is limited. In addition, the contribution of tropical forest understories to global carbon cycling is predicted to increase with rising temperatures, however, in situ warming studies of tropical forest plants to date focus only on upper canopies. We present results of an in situ field-scale +4°C understory infrared warming experiment in Puerto Rico (Tropical Responses to Altered Climate Experiment; TRACE). We investigated gas exchange responses of two common understory shrubs, Psychotria brachiata and Piper glabrescens, after exposure to 4 and 8 months warming. We assessed physiological acclimation in two ways: (1) by comparing plot-level physiological responses in heated versus control treatments before and after warming, and (2) by examining physiological responses of individual plants to variation in environmental drivers across all plots, seasons, and treatments. P. brachiata has the capacity to up-regulate (i.e., acclimate) photosynthesis through broadened thermal niche and up-regulation of photosynthetic temperature optimum (Topt) with warmer temperatures. P. glabrescens, however, did not upregulate any photosynthetic parameter, but rather experienced declines in the rate of photosynthesis at the optimum temperature (Aopt), corresponding with lower stomatal conductance under warmer daily temperatures. Contrary to expectation, neither species showed strong evidence for respiratory acclimation. P. brachiata down-regulated basal respiration with warmer daily temperatures during the drier winter months only. P. glabrescens showed no evidence of respiratory acclimation. Unexpectedly, soil moisture, was the strongest environmental driver of daily physiological temperature responses, not vegetation temperature. Topt increased, while photosynthesis and basal respiration declined as soils dried, suggesting that drier conditions negatively affected carbon uptake for both species. Overall, P. brachiata, an early successional shrub, showed higher acclimation potential to daily temperature variations, potentially mitigating negative effects of chronic warming. The negative photosynthetic response to warming experienced by P. glabrescens, a mid-successional shrub, suggests that this species may not be able to as successfully tolerate future, warmer temperatures. These results highlight the importance of considering species when assessing climate change and relay the importance of soil moisture on plant function in large-scale warming experiments.

Abstract Objective The purpose of the study was to assess demographic features, rates of trauma exposure, prevalence of post‐traumatic stress and depressive symptoms in a group of urban, low‐income, African‐American women with type 1 or type 2 diabetes mellitus. Research Design and Methods We conducted a survey of (n = 290) low‐income, African‐American women seeking care in the diabetes clinic of an urban hospital and collected data on the demographic characteristics, childhood and nonchildhood abuse trauma exposure, and the severity of post‐traumatic stress and depressive symptoms using the Post‐traumatic Stress Disorder (PTSD) Symptom Scale (PSS) and the Beck Depression Inventory (BDI). In a subset of women with type 2 diabetes (n = 96), we assessed haemoglobin A1c to examine the relationship between psychopathology and glycaemic control. Results Of the overall sample, 61.7% reported exposure to trauma in their lifetime, and 30.4% and 29.3% had current PTSD and MDD, respectively. Exposure to both childhood and nonchildhood abuse trauma was associated with an increased PTSD and depressive symptom severity (P's

Background: Bleeding is the major risk of aspirin treatment, especially in the elderly. A consensus definition for clinically significant bleeding (CSB) in aspirin primary prevention trials is lacking in the literature. Methods: This paper details the development, modification, application, and quality control of a definition for clinically significant bleeding in the ASPirin in Reducing Events in the Elderly (ASPREE) trial, a primary prevention trial of aspirin in 19,114 community-dwelling elderly men and women. In ASPREE a confirmed bleeding event needed to meet criteria both for substantiated bleeding and clinical significance. Substantiated bleeding was defined as: 1) observed bleeding, 2) a reasonable report of symptoms of bleeding, 3) medical, nursing or paramedical report, or 4) imaging evidence. Bleeding was defined as clinically significant if it: 1) required transfusion of red blood cells, 2) required admission to the hospital for >24 h, or prolonged a hospitalization, with bleeding as the principal reason, 3) required surgery to stop the bleeding, or 4) resulted in death. Bleeding sites were subclassified as upper gastrointestinal, lower gastrointestinal, intracranial (hemorrhagic stroke, subarachnoid hemorrhage, subdural hematoma, extradural hematoma, or other), or other sites. Potential events were retrieved from medical records, self-report or notification from treating doctors. Two reviewers adjudicated each event using electronic adjudication software, and discordant cases were reviewed by a third reviewer. Adjudication rules evolved to become more strictly defined as the trial progressed and decision rules were added to assist with frequent scenarios such as post-operative bleeding. Conclusions: This paper provides a detailed methodologic description of the development of a standardized definition for clinically significant bleeding and provides a benchmark for development of a consensus definition for future aspirin primary prevention trials. Trial registration: ASPREE is registered on the International Standard Randomized Controlled Trial Number Register (ISRCTN83772183) and on clinicaltrials.gov (NCT01038583). Keywords: Aspirin, Primary prevention, Methods, Hemorrhage, Bleeding

Increased proliferation and breast cancer risk has been observed in postmenopausal women receiving estrogen (E) + progestin hormone replacement therapy (HRT). Progestin action is mediated through two progesterone receptor (PR) isoforms, PRA and PRB, with unique transcriptional activity and function. The current study examines hormonal regulation of PR isoforms in the normal postmenopausal human breast and the mechanism by which progestins increase proliferation and breast cancer risk. Archival benign breast biopsies from postmenopausal and premenopausal women, and luminal breast tumor biopsies from postmenopausal women, were analyzed for regulation of PRA and PRB expression by E and E+medroxyprogesterone acetate (MPA). In the postmenopausal breast without HRT, PRA and PRB expression was decreased compared to the premenopausal breast. Both E (n = 12) and E+MPA (n = 13) HRT in the postmenopausal breast were associated with increased PRA and PRB expression, increased nuclear cyclin E expression, and decreased nuclear p27 expression compared to no HRT (n = 16). With E+MPA HRT, there was a further decrease in nuclear p27 and increased Receptor Activator of NF-kappa B Ligand (RANKL) expression compared to E-alone HRT. In luminal breast cancers, E+MPA HRT (n = 6) was also associated with decreased nuclear expression of the cell cycle inhibitor p27 compared to E HRT (n = 6), but was not associated with increased proliferation. These results suggest that p27 mediates progestin-induced proliferation in the normal human breast and that regulation of this proliferative response by E+MPA is lost in breast tumors.

Premenopausal breast cancer is associated with increased animal fat consumption among normal-weight but not overweight women. Our previous findings in obesity-resistant BALB/c mice showed that a diet high in saturated animal fat (HFD) promotes mammary tumorigenesis in both DMBA carcinogenesis and Trp53-null transplant models. Having made these observations in BALB/c mice, which have very modest HFD weight gain, we determined the effects of HFD in FVB mice, which gain significant weight on HFD. Three-week-old FVB mice fed a low-fat diet or HFD were subjected to 7,12-dimethylbenz[a]anthracene-induced carcinogenesis. Like BALB/c mice, HFD promoted mammary tumorigenesis. Development of tumors largely occurred prior to mice becoming obese, indicating the role of animal-derived HFD rather than resulting obesity in tumor promotion. Also similar to BALB/c mice, early-occurring adenosquamous mammary tumors were abundant among HFD-fed FVB mice. Tumors from HFD mice also had increased intra-tumor M2 macrophages. Prior to tumor development, HFD accelerated normal mammary gland development and increased mammary M2 macrophages, similarly to BALB/c mice. The promotional effects of puberty-initiated HFD on carcinogen-induced mammary cancer are thus largely weight gain-independent. Like BALB/c mice, HFD promoted adenosquamous tumors, suggesting a role for early age HFD in promoting this subtype of triple negative mammary cancer. M2 macrophage recruitment was common to both mouse strains. We speculate that a similar effect of HFD on immune function may contribute to epidemiological findings of increased breast cancer risk in young, premenopausal, normal-weight women who consume a diet high in saturated animal fat.

Amyotrophic lateral sclerosis (ALS) is a synaptopathy accompanied by the presence of cytoplasmic aggregates containing TDP-43, an RNA-binding protein linked to ∼97% of ALS cases. Using a Drosophila model of ALS, we show that TDP-43 overexpression (OE) in motor neurons results in decreased expression of the Hsc70-4 chaperone at the neuromuscular junction (NMJ). Mechanistically, mutant TDP-43 sequesters hsc70-4 mRNA and impairs its translation. Expression of the Hsc70-4 ortholog, HSPA8, is also reduced in primary motor neurons and NMJs of mice expressing mutant TDP-43. Electrophysiology, imaging, and genetic interaction experiments reveal TDP-43-dependent defects in synaptic vesicle endocytosis. These deficits can be partially restored by OE of Hsc70-4, cysteine-string protein (Csp), or dynamin. This suggests that TDP-43 toxicity results in part from impaired activity of the synaptic CSP/Hsc70 chaperone complex impacting dynamin function. Finally, Hsc70-4/HSPA8 expression is also post-transcriptionally reduced in fly and human induced pluripotent stem cell (iPSC) C9orf72 models, suggesting a common disease pathomechanism.

This paper addresses two straightforward questions. First, how similar are the statistics of cirrus particle size distribution (PSD) datasets collected using the Two-Dimensional Stereo (2D-S) probe to cirrus PSD datasets collected using older Particle Measuring Systems (PMS) 2-D Cloud (2DC) and 2-D Precipitation (2DP) probes? Second, how similar are the datasets when shatter-correcting post-processing is applied to the 2DC datasets? To answer these questions, a database of measured and parameterized cirrus PSDs – constructed from measurements taken during the Small Particles in Cirrus (SPARTICUS); Mid-latitude Airborne Cirrus Properties Experiment (MACPEX); and Tropical Composition, Cloud, and Climate Coupling (TC4) flight campaigns – is used.Bulk cloud quantities are computed from the 2D-S database in three ways: first, directly from the 2D-S data; second, by applying the 2D-S data to ice PSD parameterizations developed using sets of cirrus measurements collected using the older PMS probes; and third, by applying the 2D-S data to a similar parameterization developed using the 2D-S data themselves. This is done so that measurements of the same cloud volumes by parameterized versions of the 2DC and 2D-S can be compared with one another. It is thereby seen – given the same cloud field and given the same assumptions concerning ice crystal cross-sectional area, density, and radar cross section – that the parameterized 2D-S and the parameterized 2DC predict similar distributions of inferred shortwave extinction coefficient, ice water content, and 94 GHz radar reflectivity. However, the parameterization of the 2DC based on uncorrected data predicts a statistically significantly higher number of total ice crystals and a larger ratio of small ice crystals to large ice crystals than does the parameterized 2D-S. The 2DC parameterization based on shatter-corrected data also predicts statistically different numbers of ice crystals than does the parameterized 2D-S, but the comparison between the two is nevertheless more favorable. It is concluded that the older datasets continue to be useful for scientific purposes, with certain caveats, and that continuing field investigations of cirrus with more modern probes is desirable.

Abstract Background The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Results Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. Conclusion The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.

The leukocyte receptor complex (LRC) encodes a large number of immunoglobulin (Ig)-like receptors involved in the immune response, particularly in modulating natural killer (NK) cell function. The killer cell Ig-like receptors (KIR), the leukocyte Ig-like receptors (LILR), and a recently described novel Ig-like receptor family are highly variable between species, which is consistent with rapid evolution driven by selection pressure from pathogens. Among the species studied to date, only simians (such as humans) and bovids (such as cattle and goats) have an expanded complement of KIR genes and represent an interesting model to study KIR evolution. Using recently improved genome assemblies and an assembly of bacterial artificial chromosomes, we describe the structure of the LRC, and the KIR region in particular, in goats and compare this to sheep as the assemblies allow. These species diverged from a common ancestor ~10 million years ago and from cattle ~25 million years ago. We identified conserved KIR genes common to both goats and sheep and confirm a partial sheep haplotype shared between the Rambouillet and Texel breeds. Goats and sheep have independently expanded two novel KIR subgroups, and unlike cattle or any other mammal, they do not appear to possess a functional 3DL-lineage KIR gene. Investigation of LRC gene expression using available transcriptomic data for various sheep and goat tissues largely confirmed putative gene annotation and revealed that a relatively conserved caprinae-specific KIR subgroup is expressed in macrophages. The LILR and novel Ig-like receptors were also highly expressed across a diverse range of tissues. This further step toward our understanding of the LRC receptor repertoire will help inform future studies investigating immune response variation in these species.