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NUP155 is reported to be correlated with tumor development. However, the role of NUP155 in tumor physiology and the tumor immune microenvironment (TIME) has not been previously examined. This study comprehensively investigated the expression, immunological function, and prognostic significance of NUP155 in different cancer types. Bioinformatics analysis revealed that NUP155 was upregulated in 26 types of cancer. Additionally, NUP155 upregulation was strongly correlated with advanced pathological or clinical stages and poor prognosis in several cancers. Furthermore, NUP155 was significantly and positively correlated with DNA methylation, tumor mutational burden, microsatellite instability, and stemness score in most cancers. Additionally, NUP155 was also found to be involved in TIME and closely associated with tumor infiltrating immune cells and immunoregulation-related genes. Functional enrichment analysis revealed a strong correlation between NUP155 and immunomodulatory pathways, especially antigen processing and presentation. The role of NUP155 in breast cancer has not been examined. This study, for the first time, demonstrated that NUP155 was upregulated in breast invasive carcinoma (BRCA) cells and revealed its oncogenic role in BRCA using molecular biology experiments. Thus, our study highlights the potential value of NUP155 as a biomarker in the assessment of prognostic prediction, tumor microenvironment and immunotherapeutic response in pan-cancer. [ABSTRACT FROM AUTHOR]

After decades of research and development, synthetic nucleic acids are beginning to enjoy significant success in the clinic. Approved drugs have increased interest in the field, and many basic research studies have focused on synthetic nucleic acids to control the action of messenger RNA and noncoding RNAs. Unfortunately, experimental designs are often inadequate, resulting in misleading interpretation of data and unconvincing work that wastes resources and does little to advance the field. The goal of this commentary is to outline the problems facing many researchers, especially those new to the use of synthetic oligonucleotides. We describe the minimum control experiments necessary to build a strong case for real effects that are likely due to interactions at the intended molecular target. A common set of standards for preparing and judging experiments should facilitate better interpretation of data and publications that contribute positively to using synthetic nucleic acids as tools and drugs. [ABSTRACT FROM AUTHOR]

In recent years, we have studied the teaching reform of microbiology experiment course in depth. The experimental teaching system which is suitable for the cultivation of innovative talents has been explored in many ways, such as helping students to construct a reasonable knowledge structure, guiding the students to pay attention to the latest progress in related field and social life, so that the students’ ability of independent thinking can be cultivated, their imagination and creative thinking can be enriched, the inherent sense of talent can be stimulated. The method cultivates the students’ ability of obtaining knowledge autonomously and optimistic personality, maintains their lifelong learning, advocates autonomous and cooperative learning. Through the microbiology experimental teaching reform, we can effectively cultivate the innovative ability of college students, improve their scientific research level, enhance their social service capabilities, and improve the quality of microbiology experimental teaching comprehensively. [ABSTRACT FROM AUTHOR]

The aim of the present study was to establish the effect of salt-free - salt diet (SFSD) on the size of antral follicles during salt consumption, the duration of controlled breeding campaign and the fertilities of ewes from the Ile de France breed. The experiment was carried out with 57 ewes, which were divided into 3 groups (19 ewes in each) depending on whether they were subjected to SFSD and their contacts with rams during the first 8 days of the beginning of breeding: Group I - SFSD + ram contact; Group II - only SFSD; Group III - no SFSD, only ram contacts. The first day of the salt diet coincided with the first day of ram contacts. Transrectal ultrasound examinations of the ovaries were done on days 1, 2, 3, 5, 6 and 7. The time of manifestation of estrus (in days), pregnancy rate and fecundity were studied. A significant effect of time (P<0.05) and diet (P<0.01) on the size of follicles was established. The onset of the first estrus, the shortest terms of breeding campaign, the fertility and the fecundity results gave us reason to favour the scheme applied to Group II. A stimulatory effect of the diet in that study was demonstrated, but the pattern was different from our previous studies. [ABSTRACT FROM AUTHOR]

The article offers information on scientific experiment on the screening and identification method for regulated veterinary drug residues in food. Topics discussed include standards for method performance requirements; use of Liquid chromatography-tandem mass spectrometry (LC-MS/MS); and information on routine surveillance for genetically modified product compliance.

Consistent and accurate manipulation of liquids is essential for many biology experiments. Teaching these skills is challenging in the laboratory. I have developed Training Tips, a homemade teaching tool to train students to use micropipettes in the classroom and laboratory. Training Tips provide obvious visual targets that enable inexperienced students to know immediately if they are pipetting accurately. [ABSTRACT FROM AUTHOR]

The centrifuge is an important piece of equipment for any biology lab, necessary for a wide variety of experiments. Cost, however, often prevents the use of centrifuges in many teaching labs, greatly limiting educational experiences for students. As a result, we describe how to construct a "homemade" single-speed mini-centrifuge using inexpensive parts easily acquired online or at hardware or other stores (e.g., a 4.7-quart plastic bowl and lid, standard computer cooling fan, AC/DC adapter, electrical wire, etc.). We further used this design and a commercial mini-centrifuge to pellet 1-mL samples of Tetrahymena thermophila, and we found that the two performed comparably. Finally, because our plans and the materials needed to build this device are all open source, we call our design the OPN Minifuge, and we hope that it will help to expand the scope of experiments that students can run in introductory and upper-level biology teaching labs. [ABSTRACT FROM AUTHOR]

The article offers information on a study which deals with BioBits Explorer kit which enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms. It mentions that the next-generation synthetic biology educational kit described here addresses the need for easy-to-implement, hands-on biology demonstrations in STEM education.

Digital microfluidic is an emerging technology to reduce the cost and time of experiments and improve the flexibility, automate‐ability and correctness of biochemical assays. In many of applications such as drug discovery and DNA profiling, a large number of bio‐operations (e.g. the chemical operations used in biology applications) must be done. In these applications, parallelising the operations will be critical in accuracy and cost of the process and digital microfluidic biochips can be considered as a reasonable platform. In this study, a new microfluidic architecture and the corresponding CAD flow is introduced to parallelise the assays on this platform. The authors implemented the proposed architecture and evaluated it using the large real bioassays. The authors' simulations show that the degree‐of‐parallelism and speed of bioassays are increased more than 4× and the improvements will be better for larger assays. This contribution can open new horizons in drug testing, biology experiments and medical diagnosis operations that contain iterative, time‐consuming and labour experiments. [ABSTRACT FROM AUTHOR]

The aim of the present article is to show the relevance of «Experimental Methods in Microbiology and Virology» subject in the Professional Education Process. To this aim, we will analyze its contribution in program «D» to the comprehensive education of the microbiologist. Different Methodological Strategies were designed and executed which covered from subjects groups to methodological workshops, as well as compilation and analysis of the results of surveys made to students. All these elements allowed perceiving a greater comprehensive education of the students, particularly their acquisition of more abilities through the integration of theoretical knowledge with the practical one, together with the strengthening of human values. All this promotes the formation of professionals in the fields of services, production and scientific research according to the priorities of the country. [ABSTRACT FROM AUTHOR]

Despite numerous calls for science education to be driven by authentic investigation, many laboratory experiences continue to consist of disconnected weekly units during which students carry out instructions that lead to some predetermined finding. This study developed and evaluated a pedagogical design for introductory biology labs where students designed, carried out, analyzed, and presented their own experiments. Each lab module was 3 weeks long, allowing students to complete the entire experimental process four times over the course of the semester. Assessment of the pedagogy included pre- and postsurveys, video analysis of group work, exit interviews, analysis of changes in lab reports across the semester, and instructor observations. Students rated their lab experiences highly, became more confident in using scientific process, and improved in terms of scientific process and scientific reasoning. Students also learned science content, though the content varied from student to student. The pedagogical design presented here is relatively time efficient to implement and maintain, and with subtle adjustments could be transferred to other courses and disciplines. [ABSTRACT FROM AUTHOR]

Exemplary for social insects,Temnothoraxants allow for various hands-on investigations in biology classes. The aim of this study was to provide a quantitative and qualitative analysis of secondary school students’ learning achievement after teaching units with ants lasting between one and six weeks. The questionnaires included transfer and factual knowledge tasks divided into eight fields of knowledge. Students (N  =  459) from 22 classes participated in the study and received different treatments: The experimental group (n  =  366) started their investigations by initial observation using stereo microscopes, while the control group (n  =  93) conducted ant research without this introductory teaching unit. We investigated the influence of class level, gender and time period of participation on knowledge acquisition. Independent of class level, factual learning achievement was observed for all fields of knowledge except ecology. We did not find a positive correlation between time period of participation and basic ant knowledge acquisition. The findings suggest that ant research may be implemented within the framework of a progressive curriculum for all secondary school students. However, attentive and detailed observation of ant colonies with stereo microscopes and continuous repetition of technical terms seem to be inevitable preconditions for learning achievement. [ABSTRACT FROM AUTHOR]

Background: Although multidrug-resistant (MDR) gram-negative bacteremia (GNB) has been recognized as an important cause of morbidity and mortality among abdominal solid organ transplant (ASOT) recipients, there are no data on its prognostic factors after an interim standard definition of MDR was proposed in 2012. The objective of this study was to describe the epidemiology, microbiology, and predictors of infection-related 30-day mortality in ASOT recipients with MDR GNB.Methods: We performed a retrospective, double-center analysis of ASOT patients with MDR GNB over a 13-year study period. Univariate and multivariate analyses were performed to identify the risk factors for mortality.Results: During the observational period, 2169 subjects underwent ASOT. Ninety-nine episodes of MDR GNB were diagnosed in 91 (4.6%) ASOT recipients, with a predominance of E.coli (29 isolates, 29.3%) and A.baumanii (24 isolates, 24.2%). The median age of these 91 recipients was 45 years (interquartile range 35-54). Mortality after the first episode of MDR GNB was 39.6% (36 deaths). The univariate analysis identified the following variables as predictors of MDR GNB-related mortality: lung focus (P = 0.001),nosocomial origin (P = 0.002), graft from donation after cardiac death or deceased donors (P = 0.023), presence of other concomitant bloodstream infection (P < 0.001), temperature of 40 °C or greater at the onset of MDR GNB (P = 0.039), creatinine > 1.5 mg/dl (P = 0.006), albumin < 30 g/L (P = 0.009), platelet count < 50,000/mm3 (P < 0.001), and septic shock (P < 0.001). In the multivariate logistic regression analysis, septic shock (odds ratio (OR) = 160.463, 95% confidence interval (CI) = 19.377-1328.832, P < .001), as well as creatinine > 1.5 mg/dl (OR = 24.498, 95% CI = 3.449-173.998, P = 0.001), nosocomial origin (OR = 23.963, 95% CI = 1.285-46.991, P = 0.033), and presence of other concomitant bloodstream infections (OR = 27.074, 95% CI = 3.937-186.210, P = 0.001) were the variables associated with MDR GNB-related 30-day mortality.Conclusions: MDR GNB was associated with high morbidity and mortality in ASOT recipients, with a predominant causative organisms being E.coli and A.baumanii. Nosocomial origin, as well as presence of other concomitant bloodstream infections, increased creatinine level and septic shock were the main predictors of MDR GNB-related 30-day mortality. [ABSTRACT FROM AUTHOR]

Background: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. Results: This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. Conclusions: An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments. [ABSTRACT FROM AUTHOR]

In this inquiry activity, community-level physiological profiling (CLPP) with EcoPlates is described to quantitatively depict the community of microorganisms situated in a natural environment. Students can develop their own hypotheses and carry out experimentation about the makeup of microbial communities using EcoPlates. There are many independent variables that can be assessed or changed to determine how environmental differences can play important roles in the types of microorganisms that are found in an environment. [ABSTRACT FROM AUTHOR]

Human-assisted, trans-generational exposure to ocean warming and acidification has been proposed as a conservation and/or restoration tool to produce resilient offspring. To improve our understanding of the need for and the efficacy of this approach, we characterized life-history and physiological responses in offspring of the marine polychaete Ophryotrocha labronica exposed to predicted ocean warming ( OW: + 3°C), ocean acidification ( OA: pH −0.5) and their combination ( OWA: + 3°C, pH −0.5), following the exposure of their parents to either control conditions ( within-generational exposure) or the same conditions ( trans-generational exposure). Trans-generational exposure to OW fully alleviated the negative effects of within-generational exposure to OW on fecundity and egg volume and was accompanied by increased metabolic activity. While within-generational exposure to OA reduced juvenile growth rates and egg volume, trans-generational exposure alleviated the former but could not restore the latter. Surprisingly, exposure to OWA had no negative impacts within- or trans-generationally. Our results highlight the potential for trans-generational laboratory experiments in producing offspring that are resilient to OW and OA. However, trans-generational exposure does not always appear to improve traits and therefore may not be a universally useful tool for all species in the face of global change. [ABSTRACT FROM AUTHOR]

T4 is the Acanthamoeba genotype most related to cases of granulomatous amoebic encephalitis (GAE) in immunocompromised patients and of keratitis in contact lens wearers. The determination of the pathogenic potential of Acanthamoeba clinical and environmental isolates using experimental models is extremely important to elucidate the capacity of free-living organisms to establish and cause disease in hosts. The aim of this study was to compare and evaluate the histopathology and culture between two different routes of experimental infection of T4 Acanthamoeba isolated from environmental and clinical source in mice (intracranial and intraperitoneal). Swiss isogenic healthy mice were inoculated with 10 trophozoites by intracranial (IC) and intraperitoneal (IP) routes and observed during 21 days. The brains from animals inoculated by the IC route were collected and from the animals of the IP inoculation group, the brains, livers, kidneys, spleens, and lungs were removed. The organs were prepared and appropriately divided to be evaluated with histopathology and culture. There was no significant difference between the inoculation routes in terms of isolates recovery (χ = 0.09; p = 0.76). In the IC group, isolate recovery rate was significantly higher in histopathology than the one achieved by culture (χ = 6.45; p < 0.01). Experimental infection revealed that all isolates inoculated could be considered invasive because it was possible to recover evolutive forms of Acanthamoeba in both routes. This work represents the first in vivo pathogenicity assay of primary isolation source in Central region of Brazil showing in vivo pathogenicity and hematogenous spread capacity of these protozoa, improving the knowledge on free-living amoebae isolates. [ABSTRACT FROM AUTHOR]

Various types of restraint collars have been used for research animals, and the Elizabethan collar (E-collar) is the most commonly used. However, animals can be choked by the E-collar or they tend to remove it; furthermore, repeated rubbing and scratching of the collar may chafe the neck. We developed a new restraint collar with a vest to overcome these limitations. The vest-collar (V-collar) can be worn similarly to a vest, in contrast to the E-collar, which is fixed around the neck. A cone-shaped collar is attached to the vest in the V-collar and is made of Eva foam to surround the chest softly, accompanied by a transparent polyvinyl chloride (PVC) film for visibility. To evaluate the performance of the V-collar, we conducted experiments with mice wearing the V-collar and the E-collar. Both groups showed normal weight gain and food intake. Glucose and stress hormone levels showed no significant differences, and no stress-associated leukocyte profiles were observed during the experiments. However, despite the short experimental duration, more than half of the mice in the E-collar group showed injury to the skin on the neck, with increased thickness of the epidermal and keratin layers. Moreover, inflammatory cell counts were higher in the E-collar group than in the V-collar group. In conclusion, the V-collar, in contrast to the E-collar, does not cause skin injuries in animals and is thus beneficial for animals and investigators. Investigators can effectively use the V-collar to enhance laboratory animal welfare. [ABSTRACT FROM AUTHOR]

The paper presents an analysis of problems associated with the area and power reduction of readout circuits used in multichannel neurobiology experiments, in relation to noise minimization. The noise limits of a single channel considered as a function of the silicon occupation and power consumption are analyzed for an amplifier working with capacitive feedback. The paper also presents an efficient method of noise minimization in multichannel recording systems used in neurobiology experiments, when the power budget and silicon area per single recording channel are strictly limited. The proposed idea was verified in an eight-channel prototype integrated circuit fabricated in CMOS 180 nm process. The prototype IC measurements show that with the use of the proposed method, one can decrease the recording channels’ noise two times with the existing dedicated power and area budget. [ABSTRACT FROM AUTHOR]

Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems biology. In particular, examples reviewed in this paper suggest that rigorous mathematical expressions of design principles, imported primarily from engineering, could produce experimentally confirmable predictions of the regulatory properties of small biological networks. But this is not enough for contemporary systems biologists who adopt the holistic aspirations of early systemologists, seeking high-level organizing principles that could provide insights into problems of biological complexity at the whole-system level. While the presented evidence is not conclusive about whether this strategy could lead to the realization of the lofty goal of a comprehensive explanatory integration, it suggests that the ongoing quest for organizing principles is pragmatically advantageous for systems biologists. The formalisms postulated in the course of this process can serve as bridges between system-theoretic concepts and the results of molecular experimentation: they constitute theoretical tools for generalizing molecular data, thus producing increasingly accurate explanations of system-wide phenomena. [ABSTRACT FROM AUTHOR]

The aim of the study was to evaluate the biogenic amine (BA) content of Ciauscolo salami made with and without the use of a selected started culture. Two batches of salami were made following the guidelines of the Protected Geographical Indications: with and without adding a commercial starter culture made of Lactobacillus plantarum and Staphylococcus xylosus. Six samples of salami per batch were collected at different ripening times (0, 15, 30, 45 and 60 days) for physical, chemical and microbiological analyses and for the determination of BA content. No differences were recorded for physical, chemical and microbiological analyses except for Staphylococcus spp. count at the time of casing (T0) and total volatile basic nitrogen (TVBN) from 30 days (T2) to the end of the ripening time (60 days, T4). After 60 days of ripening, the use of selected starter culture significantly affected the amount of putrescine (195.15 vs 164.43 mg/100 g in salami without and with starters, respectively), cadaverine (96.95 vs 104.40 mg/100 g in salami without and with starters, respectively), histamine (81.94 vs 69.89 mg/100 g in salami without and with starters, respectively), and spermine (36.88 vs 33.57 mg/100 g in salami without and with starters, respectively). Despite significantly higher values of TVBN, the use of selected starter culture determined no significant effects on the BA content of the products. [ABSTRACT FROM AUTHOR]

Central to the attempt to develop a biosemiotics has been the discussion of what it means to be scientific. In Marcello Barbieri's latest argument for leaving Peircean biosemiotics and creating an alternative code-biology the definition of what it means to be scientific plays a major role. For Barbieri “scientific knowledge is obtained by building machine-like models of what we observe in nature”. Barbieri interestingly claims that – in combination with the empirical and experimental basis – mechanism is virtually equivalent to the scientific method. The consequences of this statement seem to be that the optimal type of knowledge science can produce about living system is to model them as machines. But the explicit goal of a Peircean semiotically based biosemiotics is (also) to model living systems as cognitive and communicative systems working on the basis of meaning and signification. These two concepts are not part of the mechanistic models of natural science today, not even of cognitive science. Barbieri tries to solve this problem by introducing a new concept of biological meaning that is separate from the Peircean biosemiotics and then add Peirce's semiotics on top. This article argues why this view is inconsistent on the grounds that Peirce's semiotic paradigm only gives meaning in its pragmaticist conception of a fallibilist view of science, which again is intrinsic connected to its non-mechanistic metaphysics of Tychism, Synechism and Agapism. The core of the biosemiotic enterprise is to establish another type of trans- and interdisciplinary wissenschaft than the received view of “science”. [ABSTRACT FROM AUTHOR]

Summary We recently published genetic lineage-tracing experiments using the Fezf2 and Cux2 loci. These experiments demonstrated that at both the clonal and population levels Fezf2 + RGCs are multipotent and that at the population level Cux2 + RGCs are multipotent. Here, we extend our work on the lineages of Fezf2 + and Cux2 + RGCs. Clonal analysis of E10.5 neocortical progenitors suggests that most, if not all, Cux2 + and Fezf2 + RGCs generate diverse projection neuron subtypes located throughout layers 2–6. These results support our previous conclusion that both Fezf2 + and Cux2 + RGCs are multipotent neocortical progenitors. This Matters Arising Response paper addresses the Gil-Sanz et al. (2015) Matters Arising paper, published concurrently in Neuron . [ABSTRACT FROM AUTHOR]

Sperm competition ( SC) occurs when the sperm of two or more males compete for the same set of ova. Theoretical models and experimental observations indicate that the presence of rival males causes focal males to adjust sperm allocation in a given copulation. Males allocate more sperm when they perceive the presence of one rival male ( SC risk), either before or during mating, or when they perceive the presence of multiple rival males before mating (previous SC intensity). Conversely, males are expected to allocate fewer sperm when they perceive the presence of rival males during mating (current SC intensity). Here, we varied male perception of SC by manipulating the number of rival males, both before mating (from emergence to mating) and during mating (at the time of mating) to examine their effects on mating latency, copulation duration, and sperm allocation in the South American fruit fly Anastrepha fraterculus. We showed that exposure to rival males at the time of mating decreased mating latency. However, in contrast to the theory, exposure to multiple rivals at the time of mating increased sperm allocation. Female and male size were significant predictors of mating latency, copulation duration, and sperm allocation. Our results showed that there is a plastic response of males to the level of perceived SC through the number of rival males. Current levels of SC intensity are important in shaping male responses to SC, although the patterns in this species are opposite to predictions from the existing theory. We propose that female preference for males forming leks could explain lower sperm counts when encountering only one or two males. [ABSTRACT FROM AUTHOR]

Leeches are fascinating creatures: they have simple modular nervous circuitry yet exhibit a rich spectrum of behavioural modes. Leeches could be ideal blue-prints for designing flexible soft robots which are modular, multi-functional, fault-tolerant, easy to control, capable for navigating using optical, mechanical and chemical sensorial inputs, have autonomous inter-segmental coordination and adaptive decision-making. With future designs of leech-robots in mind we study how leeches behave in geometrically constrained spaces. Core results of the paper deal with leeches exploring a row of rooms arranged along a narrow corridor. In laboratory experiments we find that rooms closer to ends of the corridor are explored by leeches more often than rooms in the middle of the corridor. Also, in series of scoping experiments, we evaluate leeches capabilities to navigating in mazes towards sources of vibration and chemo-attraction. We believe our results lay foundation for future developments of robots mimicking behaviour of leeches. [ABSTRACT FROM AUTHOR]

Soluble expression of de novo-designed proteins in Escherichia coli ( E. coli ) remains empirical. For given experimental conditions expression success is determined in part by protein primary sequence. This has been previously explored with varying success using a variety of statistical solubility prediction tools though without taking fold stability into account. In the present study, the three-dimensional structure of proteins in molecular dynamics (MD) simulations is used to predict expression as a new approach with a set of four-helix bundles. Stability-related parameters for ten structures were determined in a thermal unfolding MD simulation and used to build statistical models with a support vector machine (SVM) classifier. The most accurate models were identified by their performance on five independent four-helix bundle sequences. The final model provided accurate classification prediction for this test set and was successfully applied in a model challenge with two newly designed sequences. The combination of simulation-derived parameters and an SVM classifier has potential to predict recombinant expression outcome for this set of four-helix bundles. With further development, this approach of utilizing higher-dimensional protein structural information to predict expression may have potential to advance recombinant biotechnology through modern computational and statistical science. [ABSTRACT FROM AUTHOR]

A cost-effective and resource-efficient hands-on educational module that uses an interdisciplinary approach to characterize antimicrobial compounds, combining microbiology experiments and a physics-based analytical model. [ABSTRACT FROM AUTHOR]

In this essay I explore how Soviet policymakers, biologists, and writers negotiated the borderline dividing the human and animal domains and conceptualized the animal world for ideological purposes. I link the classic Soviet clash between stikhiinost' (spontaneity) and soznatel'nost' (consciousness) with biological experiments of the 1920s that were set to deconstruct the human-animal hierarchy and to create a vision of "classless" biology. I show why Dzhan, one of Andrei Platonov's first earnest attempts to evolve into a socialist realist writer glorifying the Soviet state's firm strides toward the communist future, fails to achieve the semantic certitude of the Stalinist text. Various recurrent and profoundly unconventional themes, often connected with animality and corporeality, drastically muddle the ideological coordinates of the text and preclude the possibility of a clear passage from stikhiinost' to soznatel'nost'. The (a)political status of the Dzhan people as a newly formed Soviet collective body manifests itself in the complex interplay between two rather commonplace categories: body and soul. The body acquires abstract political qualities by becoming collective, while the soul, as a designator for the Dzhan people and as a category, gains flesh. The novella reveals the "Turkmen" nation as a site of bare life itself in its indestructible corporeal glory. [ABSTRACT FROM AUTHOR]

This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments. [ABSTRACT FROM AUTHOR]

The in-chlorophyll centre waveband (ICCW) (640–680 nm) is the specific chlorophyll (Chl) absorption band, but the reflectance in this band has not been used as an optimal index for non-destructive determination of plant Chl content in recent decades. This study develops a new spectral index based solely on the ICCW for robust retrieval of leaf Chl content for the first time. A glasshouse experiment for solution-culture of one chlorophyll-deficient rice mutant and six wild types of rice genotypes was conducted, and the leaf reflectance (400–900 nm) was measured with a high spectral resolution (1 nm) spectrophotometer and the contents of chlorophyll a (Chla), chlorophyll b (Chlb) and chlorophyll a+b (Chlt) of the rice leaves were determined. It was found that the reflectance curves from 640 nm to 674 nm and from 675 nm to 680 nm of the low-chlorophyll mutant leaf were drastically steeper than that of the wild types in the ICCW. The new index based on the reflectance variation within ICCW, the difference of the first derivative sum within the ICCW (DFDS_ICCW), was highly sensitive (r = −0.77, n = 93, P<0.01) to Chlt while the mean reflectance (R_ICCW) in the ICCW became insensitive (r = −0.12, n = 93, P>0.05) to Chlt when the leaf Chlt was higher than 200 mg/m2. The best equations of R-ICCW and DFDS_ICCW yielded an RMSE of 78.7, 32.9 and 107.3 mg/m2, and an RMSE of 37.4, 16.0 and 45.3 mg/m−2, respectively, for predicting Chla, Chlb and Chlt. The new index could rank in the top 10 for prediction of Chla and Chlt as compared with the 55 existing indices. Additionally, most of the 55 existing Chl-related VIs performed robustly or strongly in simultaneous prediction of leaf Chla, Chlb and Chlt. [ABSTRACT FROM AUTHOR]

As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard designs for ChIP-seq experiments employ a paired control per ChIP-seq sample. Genomic coverage for control experiments is often sacrificed to increase the resources for ChIP samples. However, the quality of ChIP-enriched regions identifiable from a ChIP-seq experiment depends on the quality and the coverage of the control experiments. Insufficient coverage leads to loss of power in detecting enrichment. We investigate the effect of in silico pooling of control samples within multiple biological replicates, multiple treatment conditions, and multiple cell lines and tissues across multiple datasets with varying levels of genomic coverage. Our computational studies suggest guidelines for performing in silico pooling of control experiments. Using vast amounts of ENCODE data, we show that pairwise correlations between control samples originating from multiple biological replicates, treatments, and cell lines/tissues can be grouped into two classes representing whether or not in silico pooling leads to power gain in detecting enrichment between the ChIP and the control samples. Our findings have important implications for multiplexing samples. [ABSTRACT FROM AUTHOR]

Hiring committees address the glut of highly qualified applicants for faculty positions by experimenting with new evaluation methods and adapting their expectations for today’s increasingly competitive academic environment. [ABSTRACT FROM AUTHOR]

Many biogenic minerals are composed of aggregated particles at the nanoscale. These minerals usually form through the transformation of amorphous precursors into single crystals inside a privileged space controlled by the organism. Here, in vitro experiments aimed at understanding the factors responsible for producing such single crystals with aggregated particle texture are presented. Crystallization is achieved by a two-step reaction in which amorphous calcium carbonate (ACC) is first precipitated and then transformed into calcite in small volumes of water and in the presence of additives. The additives used are gel-forming molecules, phosphate ions, and the organic extract from sea urchin embryonic spicules - all are present in various biogenic crystals that grow via the transformation of ACC. Remarkably, this procedure yields faceted single-crystals of calcite that maintain the nanoparticle texture. The crystals grow predominantly by the accretion of ACC nanoparticles, which subsequently crystallize. Gels and phosphate ions stabilize ACC via a different mechanism than sea urchin spicule macromolecules. It is concluded that the unique nanoparticle texture of biogenic minerals results from formation pathways that may differ from one another, but given the appropriate precursor and micro-environment, share a common particle accretion mechanism. [ABSTRACT FROM AUTHOR]

It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems. [ABSTRACT FROM AUTHOR]

We outline a set of experiments that engage students in testing the effects of readily available household chemicals on maize seed germination and shoot growth, with three alcohols as examples. Proposing possible experimental outcomes, exposure to quantitative approaches, data recording, and the statistical analysis of data provide students with an experience that reflects the nature of modern scientific investigation. [ABSTRACT FROM AUTHOR]

The article lists the members of the periodical's advisory and editorial board including editor-in-chief Mike Tipton, deputy editor-in-chief Michael White and senior editor Greti Aguilera, along with information on the periodical's disclaimer, copyright and copying, and ethics of experimentation.

Abstract: Human Epithelial type 2 (HEp-2) cells play an important role in the diagnosis of autoimmune disorder. Traditional approach relies on specialists to observe HEp-2 slides via the fluorescence microscope, which suffers from a number of shortcomings like being subjective and labor intensive. Pattern recognition techniques have been recently introduced to this research issue to make the process automatic. However, performances of current systems available in literature are not satisfying. We propose in this paper a framework using intensity order pooling based gradient feature and bag of words for HEp-2 classification. By pooling the gradient features based on the intensity orders of local grid points, the pooled feature is rotationally invariant without requirement of orientation estimation. The proposed approach was fully tested using publicly available ICPR dataset and our own SZU dataset. Experimental results show that the propose method significantly outperformed widely used SIFT feature and the winner of ICPR contest 2012. Encouraging 100% image level accuracy was achieved on the SZU dataset. [Copyright &y& Elsevier]

Vinegar is a traditional fermented condiment, and the microbial diversity of DaQu makes the quality of vinegar products. Recently, turbidity spoilage of vinegar sharply tampered with the quality of vinegar. In this study, the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar was analyzed by plating technique, PCR-denaturing gradient gel electrophoresis (DGGE), and high-performance liquid chromatography (HPLC). The 16S rRNA sequencing and DGGE analysis indicated that Bacillus ( Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus thuringiensis) and Lactobacillus (including Lactobacillus acidipiscis and Lactobacillus pobuzihii) species were the dominant contaminants in vinegar products. Meanwhile, DGGE analysis showed that the dominant bacteria in DaQu belonged to genera Bacillus, Lactobacillus, Pseudomonas, Weissella, Saccharopolyspora, Enterobacter, and Pantoea. However, only two yeast species ( Pichia kudriavzevii and Saccharomycopsis fibuligera) and seven mold species including Aspergillus oryzae, Aspergillus niger, Aspergillus candidus, Rhizopus microspores, Eurotium herbariorum, Absidia corymbifera, and Eupenicillium javanicum were detected in the DaQu. The population level of fungi was below 5 log CFU/g in DaQu. The chemical and physical properties of vinegar and sediments were also determined. On the basis of a combined microbial diversity-chemical analysis, we demonstrated that turbidity spoilage of vinegar was a result of cooperation among the low population level and abundance of fungal species in DaQu, the suitable climate conditions, and the contaminants in vinegar. This is the first report to analyze the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar. [ABSTRACT FROM AUTHOR]

To make the teaching mode practical and operable, the paper explored new mode of microbiology experiment teaching in higher vocational education. Taking the job requirements as a key point, the paper proposed to create project teaching carrier. According to working process, a teaching method based on the task-driven approach was put forward to focus on ability cultivation. A multi-dimensional experimental evaluation system is established. After three years of research and practice, a microbiological experiment teaching mode based on working process had been established in authors' college and started to yield results. The teaching mode based on project teaching method of working process conforms to the new requirements of microbiological training in higher vocational education, it worth promoting. [ABSTRACT FROM AUTHOR]

Highlights: [•] Tissue specificity of DNA repair is not well understood and is understudied. [•] TNR instability is ideal to study DNA repair in different tissues. [•] Chromatin, repair rates, and protein levels may account for this tissue specificity. [•] System-level experiments will improve understanding of tissue-specific DNA repair. [Copyright &y& Elsevier]

Highlights: [•] G-CSF can modestly alleviate experimental NIHL in guinea pigs. [•] G-CSF can protect hair cells in experimental NIHL model. [•] G-CSF can reduce the rate of missing hair cells in experimental NIHL model. [ABSTRACT FROM AUTHOR]

Abstract: Mathematical descriptions of birth–death–movement processes are often calibrated to measurements from cell biology experiments to quantify tissue growth rates. Here we describe and analyze a discrete model of a birth–death–movement process applied to a typical two-dimensional cell biology experiment. We present three different descriptions of the system: (i) a standard mean-field description which neglects correlation effects and clustering; (ii) a moment dynamics description which approximately incorporates correlation and clustering effects; and (iii) averaged data from repeated discrete simulations which directly incorporates correlation and clustering effects. Comparing these three descriptions indicates that the mean-field and moment dynamics approaches are valid only for certain parameter regimes, and that both these descriptions fail to make accurate predictions of the system for sufficiently fast birth and death rates where the effects of spatial correlations and clustering are sufficiently strong. Without any method to distinguish between the parameter regimes where these three descriptions are valid, it is possible that either the mean-field or moment dynamics model could be calibrated to experimental data under inappropriate conditions, leading to errors in parameter estimation. In this work we demonstrate that a simple measurement of agent clustering and correlation, based on coordination number data, provides an indirect measure of agent correlation and clustering effects, and can therefore be used to make a distinction between the validity of the different descriptions of the birth–death–movement process. [Copyright &y& Elsevier]

Abstract: Information about the roles of both sexes in pair formation is required to better understand the mechanisms involved in sexual selection. Mate choice could depend on the courtship behavior, involving chemical, tactile and visual signals. We determined if Neohelice granulata mate choice is based on female or male choice, considering visual and chemical with contact and without contact signals between partners and different categories of individuals: receptive and unreceptive females; and large, small, mated or unmated males. Experiments showed that mate selection was based on receptive female's choice using chemical signals, but not visual ones. Since copulation occurs during high and low tides, water-borne chemical signals would be preferentially used during high tide, while contact ones during low tide. Females preferred large and unmated males, while males did not seem to recognize receptive females using chemical neither visual signals. Females were capable of detecting the presence of the chemical signals released by large and unmated males, but not its amount. It is proposed that small and mated males are probably releasing different types of chemical signals, not attractive to females, or that they are not emitting any signal. [Copyright &y& Elsevier]

Highlights: [•] A theoretical model based on shear forces from ultrasound cavities is proposed. [•] Two microbes with different sizes were treated by high-power low frequency ultrasound. [•] The log microbial reduction increased linearly with increasing treat time or power. [•] The rate of inactivation increased as the decreasing initial cell number. [•] The fits from the model are in very good agreement with the experimental data. [ABSTRACT FROM AUTHOR]

Highlights: [•] Establish a transferring efficiency model. [•] The model gave the relationship between transfer efficiency and ultrasound conditions. [•] The numerical results were fit well to the cell experimental results in several literatures. [•] Bring forward the ultrasound technology for drug/gene transferring into cells. [ABSTRACT FROM AUTHOR]

Aim The challenge for phylogeography, like other observational sciences, is to extract general relationships representing causes and effects from complex natural data. I describe comparisons of synchronously diverging co-distributed ( SDC) taxa, including sympatric sister species, to help meet this challenge. Location Global. Methods As an example, using narrative and best evidence synthesis, I re-evaluate ad hoc aggregate analyses relating population genetic structure ( FST) to dispersal potential. I deconstruct an aggregate global analysis to generate a regional subset of data which I compare with datasets describing co-distributed taxa, SDC species and sympatric sister species. Results A weak negative relationship between FST and dispersal potential is implied by aggregate global analysis (0.1 ≤ R2 ≤ 0.29). In contrast, regional datasets of co-distributed species show strong correlation between FST and dispersal potential (0.78 ≤ R2 ≤ 0.85). Comparisons between SDC and sympatric sister species consistently evince higher gene flow in species with higher dispersal potential. Main conclusions Ad hoc aggregate analyses can be compromised by multiple sources of error. Comparisons of SDC taxa, including sympatric sister species, adapt the experimental scientific method to natural situations, providing robust and repeatable tests of phylogeographic hypotheses and accurate estimates of effect sizes. To make strong inferences about phylogeography we should seek out the hidden wealth of natural experiments that provide particularly clear opportunities to study the factors that influence patterns of biodiversity. The SDC framework enables independent tests of existing hypotheses, integration of independent studies in meta-analyses across taxa and regions, and identification of general trends versus location- or taxon-specific phenomena. Coupled with advances in statistical phylogeography, species distribution modelling and palaeoecology, the SDC framework bridges the long-standing gap between observational and experimental sciences. [ABSTRACT FROM AUTHOR]