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Many journals in ecology and evolutionary biology encourage or require authors to make their data and code available alongside articles. In this study we investigated how often this data and code could be used together, when both were available, to computationally reproduce results published in articles. We surveyed the data and code sharing practices of 177 meta-analyses published in ecology and evolutionary biology journals published between 2015–17: 60% of articles shared data only, 1% shared code only, and 15% shared both data and code. In each of the articles which had shared both (n = 26), we selected a target result and attempted to reproduce it. Using the shared data and code files, we successfully reproduced the targeted results in 27–73% of the 26 articles, depending on the stringency of the criteria applied for a successful reproduction. The results from this sample of meta-analyses in the 2015–17 literature can provide a benchmark for future meta-research studies gauging the computational reproducibility of published research in ecology and evolutionary biology. [ABSTRACT FROM AUTHOR]

To increase the effectiveness of education is appropriate to incorporate varied teaching methods with multisensory stimulation and with an emphasis on personal and emotional experiences. This study aims to compare the knowledge of biology subject matter acquired by second and fourth-grade primary students. The lesson occurred at a farm in the experimental group and at school in the control group. Students' knowledge levels were assessed before the lesson, after the lesson, after 14 days, after a month, and after six months. When the levels of knowledge after the lesson were compared between the groups, significantly better results (p = 0.001) were recorded in students in the control group. Another 14 days after the lesson, there was no significant difference in knowledge between the groups (p = 0.848). The same results were obtained after a month (p = 0.760) and after six months (p = 0.649). In the experimental group, the intra-group analysis did not show any significant difference in the levels of knowledge before and after the lesson; it was recorded only after 14 days. In contrast, the control group showed a significant improvement in knowledge right after the lesson, which was not observed later on. Most often, this phenomenon was observed in second-grade students. The presence of animals in an educational setting can add many benefits, such as mental well-being, an increase in empathy, or support for socio-emotional development. Since the levels of subject matter knowledge acquired at a farm and at school were similar, it seems that farm lessons should not negatively impact education, and it offers many related positive effects. [ABSTRACT FROM AUTHOR]

Cinnamomum verum Blume (syn Cinnamomum zeylanicum) commonly known as Ceylon cinnamon, has gained worldwide attention due to its health benefits and its unique quality. Therefore, maintaining the yield quality and quantity is essential, especially for high-end value-added products. Knowledge on floral behaviour and reproductive biology is essential for breeding superior varieties and is critical for commercial cultivation efforts. However, limited literature is available on the floral biology of C. verum. Here in this study, we assessed the seasonal flowering, floral development and pollination of two cultivars of C. verum. Both macroscopic and microscopic data were collected on floral biology, pollination, and male and female floral organs before and after pollination. Cinnamomum verum is morpho-anatomically, structurally, and physiologically adapted for cross-pollination, possible between the two cultivars; type A (Sri Gemunu) and type B (Sri Wijaya) flowers; naturally evolved with Protogynous Dichogamy. However, due to changes in environmental conditions, female and male stages in the same tree overlap for about 45–60 min suggesting possible close-pollination within the same plant. During this event some of the pollens were observed hydrated even during self-pollination. In mean time, 4–8% of the flowers formed fruits after natural close and hand pollination which is between male and female phases of the same tree. Although C. verum is adapted for cross-pollination, natural close-pollination is also possible. The data suggest the complex nature of the sexual reproduction of C. verum. Well-managed breeding attempts with controlled factors like temperature and humidity will help to develop superior C. verum varieties. [ABSTRACT FROM AUTHOR]

The baculum of mammals offers the opportunity to study the reproductive biology of extinct species given that it is a fossilizable part of the male genitalia and that its size and shape correlate with several aspects of the reproductive biology of extant mammals. Fossil bacula, however, are rare. Currently, bacula have been described from only two extinct species of canids, one from the subfamily Caninae and the other from the extinct subfamily Hesperocyoninae. Here, I describe the bacula of five extinct species of Borophaginae, each of which was found with other skeletal elements that have enabled identification to the species level. Two specimens (Aelurodon ferox and Aelurodon stirtoni) are largely complete, while the baculum from Carpocyon compressus is complete but still embedded in matrix that obscures some of its features. The bacula of Paratomarctus euthos and Desmocyon thomsoni are incomplete, but they provide useful information nonetheless. These borophagine bacula are similar to extant canines in being robust, having a urethral groove, and a simple distal end. These features suggest that the Borophaginae had long-lasting copulation and possibly spontaneous ovulation, similar to the extant canines. However, unlike the straight baculum of extant canines, borophagine bacula are ventrally curved (arched), which is also observed in the hesperocyonine baculum. The implication of this curvature for the reproductive biology of these animals remains unknown. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic has led to a reimagining of many aspects of higher education, including how instructors interact with their students and how they encourage student participation. Text-based chatting during synchronous remote instruction is a simple form of student-student and student-instructor interaction. The importance of student participation has been documented, as have clear disparities in participation between those well-represented and those under-represented in science disciplines. Thus, we conducted an investigation into who is texting, what students are texting, and how these texts align with course content. We focused on two sections of a large-enrollment, introductory biology class offered remotely during Fall 2020. Using an analysis of in-class chatting, in combination with student survey responses, we find that text-based chatting suggests not only a high level of student engagement, but a type of participation that is disproportionately favored by women. Given the multiple lines of evidence indicating that women typically under-participate in their science courses, any vehicle that counters this trend merits further exploration. We conclude with suggestions for further research, and ideas for carrying forward text-based chatting in the post-COVID-19, in-person classroom. [ABSTRACT FROM AUTHOR]

Although closed-note exams have traditionally been used to evaluate students in undergraduate biology classes, open-note exams are becoming increasingly common, though little is known about how students prepare for these types of exams. We investigated student perceptions of and their preparation habits for online open-note exams in an undergraduate biology class, as compared to their previous experiences with closed-note exams in other classes. Specifically, we explored the following research questions: (1a) How do students perceive open-note exams impact their exam scores, their anxiety, the amount they studied, and the amount their peers studied? (1b) How do these perceptions impact performance outcomes? (2a) How do students prepare for open-note exams? (2b) How do these preparation methods impact performance outcomes? Results demonstrate students perceived increased exam scores, decreased exam-anxiety, decreased study time spent personally, and decreased study time spent by their peers for open-note exams, as compared to past experiences with closed-note exams. Open-ended survey responses analyzed through first- and second-cycle analyses showed students adapted their study habits by focusing on note preparation and broad conceptual understanding rather than rote memorization. Using linear mixed effects models to assess student performance, we found students who focused on understanding, note preparation and using external resources outperformed students who did not report those study habits. As institutions shift towards flexible and scalable assessments that can be used in face-to-face or online environments, the use of open-note exams can promote effective study habits and reward higher-order thinking with intentional guidance from the instructor. [ABSTRACT FROM AUTHOR]

Recently reported specimens of the enigmatic Ediacaran fossil Dickinsonia from Russia show damage and repair that provides evidence of how they grew, and of their biological affinities. Marginal and terminal areas of wilting deformation are necrotic zones separating regenerated growth, sometimes on two divergent axes, rather than a single axis. Necrotic zones of damage to Dickinsonia are not a thick scar or callus, like a wound or amputation. Nor are they smooth transitions to a regenerated tail or arm. The wilted necrotic zone is most like damage by freezing, salt, or sunburn of leaves and lichens, compatible with evidence of terrestrial habitat from associated frigid and gypsic paleosols. Dickinsonia did not regrow by postembryonic addition of modules from a subterminal or patterned growth zone as in earthworms, myriapods, trilobites, crustaceans, and lizards. Rather Dickinsonia postembryonic regrowth from sublethal damage was from microscopic apical and lateral meristems, as in plants and lichens. Considered as fungal, Dickinsonia, and perhaps others of Class Vendobionta, were more likely Glomeromycota or Mucoromycotina, rather than Ascomycota or Basidiomycota. [ABSTRACT FROM AUTHOR]

Seabirds play a vital role in marine ecosystems and the long-term study of their responses to environmental variations can be used to monitor the effects of climate change on marine fauna. However, slight differences in similar seabird species result in a range of responses which complicates our understanding of the effects of environmental changes to marine ecosystems. The present study investigated inter-annual differences in the breeding biology (breeding phenology, chick growth rates and breeding success) and environmental conditions (seasonal sea surface temperatures) of important foraging areas in two sympatric small Procellariiform species, the fairy prion (Pachyptila turtur) and the common diving petrel (Pelecanoides urinatrix), over four reproductive seasons (2017–2020) in Bass Strait, south-eastern Australia. Marine heatwaves occurred during the years of 2018/19 and 2019/20 and coincided with years of delayed laying dates, slower chick growth and reduced breeding success, in both species. While fairy prions maintained a relatively high breeding success and broadly constant breeding phenology, common diving petrels delayed the start of the breeding season by up to 50 days and experienced dramatic collapses in breeding success in years of high marine heat wave occurrence. The difference in foraging ecology and physiological capacity (largely in the production of stomach oils and fasting abilities of adults and chicks) between both species are likely to influence the variability and phenology in the observed breeding seasons. [ABSTRACT FROM AUTHOR]

Except cells circulating in the bloodstream, most cells in vertebrates are adherent. Studying the repercussions of adherence per se in cell physiology is thus very difficult to carry out, although it plays an important role in cancer biology, e.g. in the metastasis process. In order to study how adherence impacts major cell functions, we used a murine macrophage cell line. Opposite to the monocyte/macrophage system, where adherence is associated with the acquisition of differentiated functions, these cells can be grown in both adherent or suspension conditions without altering their differentiated functions (phagocytosis and inflammation signaling). We used a proteomic approach to cover a large panel of proteins potentially modified by the adherence status. Targeted experiments were carried out to validate the proteomic results, e.g. on metabolic enzymes, mitochondrial and cytoskeletal proteins. The mitochondrial activity was increased in non-adherent cells compared with adherent cells, without differences in glucose consumption. Concerning the cytoskeleton, a rearrangement of the actin organization (filopodia vs sub-cortical network) and of the microtubule network were observed between adherent and non-adherent cells. Taken together, these data show the mechanisms at play for the modification of the cytoskeleton and also modifications of the metabolic activity between adherent and non-adherent cells. [ABSTRACT FROM AUTHOR]

This study examined the effect of collaborative learning (CL) versus traditional lecture-based learning (TL) pedagogies and gender group composition in effecting positive or negative attitudes of biology major and nonmajor men and women students. The experimental research method was administered in experimental and control groups to test the hypotheses. Students' attitudes refer to their positive or negative feelings and inclinations to learn biology. A nine-factor attitude scale was administered in (1) single-gender nonmajor biology, (2) mixed-gender nonmajor biology, (3) single-gender major biology, and (4) mixed-gender biology major groups. Men (221) and women (219) were randomly assigned into single and mixed-gender classes without groups and single-gender groups (4M) or (4W) and mix-gender (2M+2W) groups. In CL nonmajor and major single-gender groups, women demonstrated significantly higher positive attitudes than men. In contrast, men's attitudes were significantly improved in mixed-gender CL groups for major and nonmajor sections, and the effect size was larger in mix-gender classes. Women feel less anxious in single-gender groups but more anxious in mixed-gender groups. In mixed-gender groups, men's self-efficacy, general interest, and motivation enhanced significantly; overall, men experienced greater satisfaction and triggered their desire to collaborate better, affecting all nine attitudinal factors. There was an interaction effect demonstrating the teaching pedagogy's impact on improving students' attitudes toward biology; students' gender and gender-specific group composition have been the most influential factor for nonmajor students. These findings suggest that there is a need for developing gender-specific and context-specific learning pedagogies, and instructors carefully select gender grouping in teaching undergraduate science subjects. [ABSTRACT FROM AUTHOR]

Introduction: Stroke is a common complication in children with tuberculous meningitis (TBM). Host proteins may give us insight into the mechanisms of stroke in TBM and serve as biomarkers for detection of stroke, however, they have not been widely explored. In this study, we compared the concentrations of cerebrospinal fluid (CSF) and serum proteins between children who had TBM-related stroke and children with TBM without stroke. Methods: We collected CSF and serum from 47 children consecutively admitted to the Tygerberg Academic Hospital in Cape Town, South Africa between November 2016, and November 2017, on suspicion of having TBM. A multiplex platform was used to measure the concentrations of 69 host proteins in CSF and serum from all study participants. Results: After classification of study participants, 23 (48.9%) out of the 47 study participants were diagnosed with TBM, of which 14 (60.9%) demonstrated radiological arterial ischemic infarction. The levels of lipocalin-2, sRAGE, IP-10/ CXCL10, sVCAM-1, MMP-1, and PDGF-AA in CSF samples and the levels of D-dimer, ADAMTS13, SAA, ferritin, MCP-1/ CCL2, GDF-15 and IL-13 in serum samples were statistically different between children who had TBM-related stroke and children with TBM without stroke. After correcting for multiple testing, only the levels of sVCAM-1, MMP-1, sRAGE, and IP-10/ CXCL10 in CSF were statistically different between the two groups. CSF and serum protein biosignatures indicated stroke in children diagnosed with TBM with up to 100% sensitivity and 88.9% specificity. Conclusion: Serum and CSF proteins may serve as biomarkers for identifying individuals with stroke amongst children diagnosed with TBM at admission and may guide us to understand the biology of stroke in TBM. This was a pilot study, and thus further investigations in larger studies are needed. [ABSTRACT FROM AUTHOR]

Assessment has long played an important role as a measurement tool of student mastery over course content. However, testing has also been shown to be an effective learning tool. Cumulative testing, in which all material from the entire learning period is covered, has been assumed to be effective, yet few studies have explicitly tested its effectiveness compared to non-cumulative testing. Studies in psychology and mathematics courses suggest that cumulative final exams increase long-term retention of information, and cumulative testing during the semester can increase cumulative final exam performance and long-term retention. Because frequent testing has also been shown to increase student learning, the purpose of this quasi-experimental study is to investigate the effects of cumulative versus non-cumulative midterms on student learning in a course that uses frequent assessment. In this study, one section of an introductory biology course for non-majors was given seven cumulative midterms, with about half of the questions drawn from previous units and the rest covering the current unit. The other section was given seven non-cumulative midterms that focused on current material while other course characteristics were held constant. Student performance on a common, cumulative final exam and a retention exam five months later were compared. Midterm format had no effect on final exam performance, contradicting the few studies done in psychology and mathematics courses. Thus, there may be no additional benefit of cumulative testing if exams are given frequently. Cumulative midterms appeared to increase retention after five months, but only for students who entered the course with low reasoning skills. Interestingly, students with high reasoning skills appeared to retain more from the course if they were given non-cumulative midterms. Possible explanations and ideas for future research are discussed. [ABSTRACT FROM AUTHOR]

Cannabis sativa has been cultivated since antiquity as a source of fibre, food and medicine. The recent resurgence of C. sativa as a cash crop is mainly driven by the medicinal and therapeutic properties of its resin, which contains compounds that interact with the human endocannabinoid system. Compared to other medicinal crops of similar value, however, little is known about the biology of C. sativa. Glandular trichomes are small hair-like projections made up of stalk and head tissue and are responsible for the production of the resin in C. sativa. Trichome productivity, as determined by C. sativa resin yield and composition, is only beginning to be understood at the molecular level. In this study the proteomes of glandular trichome stalks and heads, were investigated and compared to the proteome of the whole flower tissue, to help further elucidate C. sativa glandular trichome biochemistry. The data suggested that the floral tissue acts as a major source of carbon and energy to the glandular trichome head sink tissue, supplying sugars which drive secondary metabolite biosynthesis. The trichome stalk seems to play only a limited role in secondary metabolism and acts as both source and sink. [ABSTRACT FROM AUTHOR]

To study the dysregulated host immune response to infection in sepsis, gene expression profiles from the Gene Expression Omnibus (GEO) datasets GSE54514, GSE57065, GSE64456, GSE95233, GSE66099 and GSE72829 were selected. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) immune system pathways, 998 unique genes were selected, and genes were classified as follows based on gene annotation from KEGG, Gene Ontology, and Reactome: adaptive immunity, antigen presentation, cytokines and chemokines, complement, hematopoiesis, innate immunity, leukocyte migration, NK cell activity, platelet activity, and signaling. After correlation matrix formation, correlation coefficient of 0.8 was selected for network generation and network analysis. Total transcriptome was analyzed for differentially expressed genes (DEG), followed by gene set enrichment analysis. The network topological structure revealed that adaptive immunity tended to form a prominent and isolated cluster in sepsis. Common genes within the cluster from the 6 datasets included CD247, CD8A, ITK, LAT, and LCK. The clustering coefficient and modularity parameters were increased in 5/6 and 4/6 datasets in the sepsis group that seemed to be associated with functional aspect of the network. GSE95233 revealed that the nonsurvivor group showed a prominent and isolated adaptive immunity cluster, whereas the survivor group had isolated complement-coagulation and platelet-related clusters. T cell receptor signaling (TCR) pathway and antigen processing and presentation pathway were down-regulated in 5/6 and 4/6 datasets, respectively. Complement and coagulation, Fc gamma, epsilon related signaling pathways were up-regulated in 5/6 datasets. Altogether, network and gene set enrichment analysis showed that adaptive-immunity-related genes along with TCR pathway were down-regulated and isolated from immune the network that seemed to be associated with unfavorable prognosis. Prominence of platelet and complement-coagulation-related genes in the immune network was associated with survival in sepsis. Complement-coagulation pathway was up-regulated in the sepsis group that was associated with favorable prognosis. Network and gene set enrichment analysis supported elucidation of sepsis pathogenesis. [ABSTRACT FROM AUTHOR]

Background: Monitoring and treating metastatic progression remains a formidable task due, in part, to an inability to monitor specific differential molecular adaptations that allow the cancer to thrive within different tissue types. Hence, to develop optimal treatment strategies for metastatic disease, an important consideration is the divergence of the metastatic cancer growing in visceral organs from the primary tumor. We had previously reported the establishment of isogenic human metastatic breast cancer cell lines that are representative of the common metastatic sites observed in breast cancer patients. Methods: Here we have used proteomic, RNAseq, and metabolomic analyses of these isogenic cell lines to systematically identify differences and commonalities in pathway networks and examine the effect on the sensitivity to breast cancer therapeutic agents. Results: Proteomic analyses indicated that dissemination of cells from the primary tumor sites to visceral organs resulted in cell lines that adapted to growth at each new site by, in part, acquiring protein pathways characteristic of the organ of growth. RNAseq and metabolomics analyses further confirmed the divergences, which resulted in differential efficacies to commonly used FDA approved chemotherapeutic drugs. This model system has provided data that indicates that organ-specific growth of malignant lesions is a selective adaptation and growth process. Conclusions: The insights provided by these analyses indicate that the rationale of targeted treatment of metastatic disease may benefit from a consideration that the biology of metastases has diverged from the primary tumor biology and using primary tumor traits as the basis for treatment may not be ideal to design treatment strategies. [ABSTRACT FROM AUTHOR]

Dietary restriction (DR) increases life span and improves health in most model systems tested, including non-human primates. In C. elegans, as in other models, DR leads to reprogramming of metabolism, improvements in mitochondrial health, large changes in expression of cytoprotective genes and better proteostasis. Understandably, multiple global transcriptional regulators like transcription factors FOXO/DAF-16, FOXA/PHA-4, HSF1/HSF-1 and NRF2/SKN-1 are important for DR longevity. Considering the wide-ranging effects of p53 on organismal biology, we asked whether the C. elegans ortholog, CEP-1 is required for DR-mediated longevity assurance. We employed the widely-used TJ1 strain of cep-1(gk138). We show that cep-1(gk138) suppresses the life span extension of two genetic paradigms of DR, but two non-genetic modes of DR remain unaffected in this strain. We find that two aspects of DR, increased autophagy and up-regulation of the expression of cytoprotective xenobiotic detoxification program (cXDP) genes, are dampened in cep-1(gk138). Importantly, we find that background mutation(s) in the strain may be the actual cause for the phenotypic differences that we observed and cep-1 may not be directly involved in genetic DR-mediated longevity assurance in worms. Identifying these mutation(s) may reveal a novel regulator of longevity required specifically by genetic modes of DR. [ABSTRACT FROM AUTHOR]

Xanthium strumarium L. (Common cocklebur) is a noxious weed prevailing in different ecosystems around the world. It incurs significant yield and economic losses in different cropping systems globally. Successful management of any weed species depends on sound knowledge of seed germination biology. However, detailed knowledge on seed germination biology of the species is missing. Therefore, we investigated the impact of different environmental factors on seed germination and seed burial depths on seedling emergence of two X. strumarium populations. The impact of different sorghum mulch doses (0–10 t ha-1) on seedling emergence of the tested populations was also explored. Seed germination was evaluated under different photoperiods (0, 12 and 24), constant temperatures (0–50°C with 5°C stepwise rise), and different levels of pH (3–12), salinity (0–600 mM) and osmotic potential (0 to -1.6 MPa). Seedling emergence was observed for seeds buried at different depths (0–15 cm). Seeds of both populations proved non-photoblastic; however, higher germination was recorded under 12-hour photoperiod. The seeds germinated under a wide range of constant temperatures (10–45°C), pH (4–10), osmotic potentials (0 to -0.8 MPa) and salinity levels (0–400 mM NaCl). However, the highest germination was observed under 30–31°C temperature and neutral pH (7.51–7.52). Seeds were able to withstand 400 mM salinity and -1.00 MPa osmotic potential. Seedling emergence was initially improved with increasing burial depth and then a sharp decline was noted for the seeds buried >3 cm depth. Most of the seeds of both populations did not emerge from >8 cm depth. Different sorghum mulch doses linearly suppressed seedling emergence of tested populations, and 5.83–5.89 t ha-1 mulch application suppressed 50% of seedling emergence. Seedling emergence was completely retarded with 8 t ha-1 sorghum mulch. The tested populations germinated under diverse environmental circumstances indicating that the species can become troublesome in marginal habitats and cropped lands. Deep burial of seeds and application of sorghum mulches suppressed seedling emergence. Thus, deep burial followed by shallow tillage and application of sorghum mulches could be used as a successful strategy to manage the species in agricultural fields. Nonetheless, management strategies must be developed to control the species in other habitats. [ABSTRACT FROM AUTHOR]

The Greenland shark (Somniosus microcephalus, Squaliformes: Somniosidae) is a long-lived Arctic top predator, which in combination with the high historical and modern fishing pressures, has made it subject to increased scientific focus in recent years. Key aspects of reproduction are not well known as exemplified by sparse and contradictory information e.g. on birth size and number of pups per pregnancy. This study represents the first comprehensive work on Greenland shark reproductive biology based on data from 312 specimens collected over the past 60 years. We provide guidelines quantifying reproductive parameters to assess specific maturation stages, as well as calculate body length-at-maturity (TL50) which was 2.84±0.06 m for males and 4.19±0.04 m for females. From the available information on the ovarian fecundity of Greenland sharks as well as a meta-analysis of Squaliform reproductive parameters, we estimate up to 200–324 pups per pregnancy (depending on maternal size) with a body length-at-birth of 35–45 cm. These estimates remain to be verified by future observations from gravid Greenland sharks. [ABSTRACT FROM AUTHOR]

Background: Different perspectives exist regarding the clinicopathologic characteristics, biology and management of gallbladder polyps. Size is often used as the surrogate evidence of polyp behavior and size of ≥1cm is widely used as cholecystectomy indication. Most studies on this issue are based on the pathologic correlation of polyps clinically selected for resection, whereas, the data regarding the nature of polypoid lesions from pathology perspective -regardless of the cholecystectomy indication- is highly limited. Methods: In this study, 4231 gallbladders -606 of which had gallbladder carcinoma- were reviewed carefully pathologically by the authors for polyps (defined as ≥2 mm). Separately, the cases that were diagnosed as "gallbladder polyps" in the surgical pathology databases were retrieved. Results: 643 polyps identified accordingly were re-evaluated histopathologically. Mean age of all patients was 55 years (range: 20–94); mean polyp size was 9 mm. Among these 643 polyps, 223 (34.6%) were neoplastic: I. Non-neoplastic polyps (n = 420; 65.4%) were smaller (mean: 4.1 mm), occurred in younger patients (mean: 52 years). This group consisted of fibromyoglandular polyps (n = 196) per the updated classification, cholesterol polyps (n = 166), polypoid pyloric gland metaplasia (n = 41) and inflammatory polyps (n = 17). II. Neoplastic polyps were larger (mean: 21 mm), detected in older patients (mean: 61 years) and consisted of intra-cholecystic neoplasms (WHO's "adenomas" and "intracholecystic papillary neoplasms", ≥1 cm; n = 120), their "incipient" version (<1 cm) (n = 44), polypoid invasive carcinomas (n = 26) and non-neoplastic polyps with incidental dysplastic changes (n = 33). In terms of size cut-off correlations, overall, only 27% of polyps were ≥1 cm, 90% of which were neoplastic. All (except for one) ≥2 cm were neoplastic. However, 14% of polyps <1 cm were also neoplastic. Positive predictive value of ≥1 cm cut-off -which is widely used for cholecystectomy indication-, was 94.3% and negative predictive value was 85%. Conclusions: Approximately a third of polypoid lesions in the cholecystectomies (regardless of the indication) prove to be neoplastic. The vast majority of (90%) of polyps ≥1 cm and virtually all of those ≥2 cm are neoplastic confirming the current impression that polyps ≥1 cm ought to be removed. However, this study also illustrates that 30% of the neoplastic polyps are <1 cm and therefore small polyps should also be closely watched, especially in older patients. [ABSTRACT FROM AUTHOR]

Active learning pedagogies decrease failure rates in undergraduate introductory biology courses, but these practices also cause anxiety for some students. Classroom anxiety can impact student learning and has been associated with decreased student retention in the major, but little is known about how students cope with anxiety caused by active learning practices. In this study, we investigated student coping strategies for various types of active learning (clickers, volunteering to answer a question, cold calling, and group work) that were used in 13 introductory Biology courses at a large public university in 2016–2017. A survey asked students to rate their anxiety regarding the four active learning practices and over half of the students explained the coping strategies they used to manage their active learning anxieties. Coping responses from 880 students were sorted into pre-defined categories of coping strategies: problem solving, information seeking, self-reliance, support seeking, accommodation, helplessness, escape, delegation, and isolation. We found that a different category of coping was dominant for each type of active learning. The dominant coping strategies for anxiety associated with clickers, cold calling, and group work were adaptive coping strategies of information seeking, self-reliance, and support-seeking, respectively. The dominant coping strategy for volunteering to answer a question was escape, which is a maladaptive strategy. This study provides a detailed exploration of student self-reported coping in response to active learning practices and suggests several areas that could be foci for future psychosocial interventions to bolster student regulation of their emotions in response to these new classroom practices. [ABSTRACT FROM AUTHOR]

Obesity is a multifactorial disease caused by complex interactions between genes and dietary factors. Salt-rich diet is related to the development and progression of several chronic diseases including obesity. However, the molecular basis of how salt sensitivity genes (SSG) contribute to adiposity in obesity patients remains unexplored. In this study, we used the microarray expression data of visceral adipose tissue samples and constructed a complex protein-interaction network of salt sensitivity genes and their co-expressed genes to trace the molecular pathways connected to obesity. The Salt Sensitivity Protein Interaction Network (SSPIN) of 2691 differentially expressed genes and their 15474 interactions has shown that adipose tissues are enriched with the expression of 23 SSGs, 16 hubs and 84 bottlenecks (p = 2.52 x 10–16) involved in diverse molecular pathways connected to adiposity. Fifteen of these 23 SSGs along with 8 other SSGs showed a co-expression with enriched obesity-related genes (r ≥ 0.8). These SSGs and their co-expression partners are involved in diverse metabolic pathways including adipogenesis, adipocytokine signaling pathway, renin-angiotensin system, etc. This study concludes that SSGs could act as molecular signatures for tracing the basis of adipogenesis among obese patients. Integrated network centered methods may accelerate the identification of new molecular targets from the complex obesity genomics data. [ABSTRACT FROM AUTHOR]

This study aims to analyze the thermal biology and climatic vulnerability of two closely related lizard species (Stenocercus festae and S. guentheri) inhabiting the Ecuadorian Andes at high altitudes. Four physiological parameters—body temperature (Tb), preferred temperature (Tpref), critical thermal maximum (CTmax), and critical thermal minimum (CTmin)—were evaluated to analyze the variation of thermophysiological traits among these populations that inhabit different environmental and altitudinal conditions. We also evaluate the availability of operative temperatures, warming tolerance, and thermal safety margin of each population to estimate their possible risks in the face of future raising temperatures. Similar to previous studies, our results suggest that some physiological traits (CTmax and Tb) are influenced by environmental heterogeneity, which brings changes on the thermoregulatory behavior. Other parameters (Tpref and CTmin), may be also influenced by phylogenetic constraints. Moreover, the fluctuating air temperature (Tair) as well as the operative temperatures (Te) showed that these lizards exploit a variety of thermal microenvironments, which may facilitate behavioral thermoregulation. Warming tolerance and thermal safety margin analyses suggest that both species find thermal refugia and remain active without reducing their performance or undergoing thermal stress within their habitats. We suggest that studies on the thermal biology of tropical Andean lizards living at high altitudes are extremely important as these environments exhibit a unique diversity of microclimates, which consequently result on particular thermophysiological adaptations. [ABSTRACT FROM AUTHOR]

Objective: Amniotic fluid cytokines have been implicated in the mechanisms of preterm labor and birth. Cytokines can be packaged within or on the surface of extracellular vesicles. The main aim of this study was to test whether the protein abundance internal to and on the surface of extracellular vesicles changes in the presence of sterile intra-amniotic inflammation and proven intra-amniotic infection in women with preterm labor as compared to the women with preterm labor without either intra-amniotic inflammation or proven intra-amniotic infection. Study design: Women who had an episode of preterm labor and underwent an amniocentesis for the diagnosis of intra-amniotic infection or intra-amniotic inflammation were classified into three groups: 1) preterm labor without either intra-amniotic inflammation or proven intra-amniotic infection, 2) preterm labor with sterile intra-amniotic inflammation, and 3) preterm labor with intra-amniotic infection. The concentrations of 38 proteins were determined on the extracellular vesicle surface, within the vesicles, and in the soluble fraction of amniotic fluid. Results: 1) Intra-amniotic inflammation, regardless of detected microbes, was associated with an increased abundance of amniotic fluid cytokines on the extracellular vesicle surface, within vesicles, and in the soluble fraction. These changes were most prominent in women with proven intra-amniotic infection. 2) Cytokine changes on the surface of extracellular vesicles were correlated with those determined in the soluble fraction; yet the magnitude of the increase was significantly different between these compartments. 3) The performance of prediction models of early preterm delivery based on measurements on the extracellular vesicle surface was equivalent to those based on the soluble fraction. Conclusions: Differential packaging of amniotic fluid cytokines in extracellular vesicles during preterm labor with sterile intra-amniotic inflammation or proven intra-amniotic infection is reported herein for the first time. The current study provides insights into the biology of the intra-amniotic fluid ad may aid in the development of biomarkers for obstetrical disease. [ABSTRACT FROM AUTHOR]

Interleukin (IL)-38 is a member of the IL-1 family of cytokines, which was proposed to exert anti-inflammatory effects. IL-38 is constitutively expressed in the skin, where keratinocytes are the main producing cells. Little information is currently available concerning IL-38 biology. Here, we investigated the subcellular localization and interaction partners of the IL-38 protein in human keratinocytes. IL-38 expression was reduced in primary keratinocytes grown in monolayer (2D) cultures. We thus used IL-38 overexpressing immortalized normal human keratinocytes (NHK/38) to study this cytokine in cell monolayers. In parallel, differentiation of primary human keratinocytes in an in vitro reconstructed human epidermis (RHE) 3D model allowed us to restore endogenous IL-38 expression. In NHK/38 cells and in RHE, IL-38 was mainly cell-associated, rather than released into culture supernatants. Intracellular IL-38 was preferentially, although not exclusively, cytoplasmic. Similarly, in normal human skin sections, IL-38 was predominantly cytoplasmic in the epidermis and essentially excluded from keratinocyte nuclei. A yeast two-hybrid screen identified destrin/actin-depolymerizing factor (DSTN) as a potential IL-38-interacting molecule. Co-immunoprecipitation and proximity ligation assay confirmed this interaction. We further observed partial co-localization of IL-38 and DSTN in NHK/38 cells. Endogenous IL-38 and DSTN were also co-expressed in all epidermal layers in RHE and in normal human skin. Finally, IL-38 partially co-localized with F-actin in NHK/38 cells, in particular along the cortical actin network and in filopodia. In conclusion, IL-38 is found predominantly in the cytoplasm of human keratinocytes, where it interacts with DSTN. The functional relevance of this interaction remains to be investigated. [ABSTRACT FROM AUTHOR]

Background: The survival rates from breast cancer in Africa are poor and yet the incidence rates are on the rise. In this study, we hypothesized that, in Africa, a continent with great disparities in socio-economic status, race, tumor biology, and cultural characteristics, the survival rates from breast cancer vary greatly based on region, tumor biology (hormone receptor), gender, and race. We aimed to conduct the first comprehensive systematic review and meta-analysis on region, gender, tumor-biology and race-specific 5-year breast cancer survival rates in Africa and compared them to 20-year survival trends in the United States. Methods: We searched MEDLINE, EMBASE, and Cochrane Library to identify studies on breast cancer survival in African published before October 17, 2018. Pooled 5-year survival rates of breast cancer were estimated by random-effects models. We explored sources of heterogeneity through subgroup meta-analyses and meta-regression. Results were reported as absolute difference (AD) in percentages. We compared the survival rates of breast cancer in Africa and the United States. Findings: There were 54 studies included, consisting of 18,970 breast cancer cases. There was substantial heterogeneity in the survival rates (mean 52.9%, range 7–91%, I2 = 99.1%; p for heterogeneity <0.0001). Meta-regression analyses suggested that age and gender-adjusted 5-year survival rates were lower in sub-Saharan Africa compared to north Africa (AD: –25.4%; 95% CI: –34.9 - –15.82%), and in predominantly black populations compared to predominantly non-black populations (AD: –25.9%; 95% CI: 35.40 - –16.43%). Survival rates were 10 percentage points higher in the female population compared to male, but the difference was not significant. Progesterone and estrogen receptor-positive breast cancer subtypes were positively associated with survival (r = 0.39, p = 0.08 and r = 0.24, p = 0.29 respectively), but triple-negative breast cancer was negatively associated with survival. Survival rates are increasing over time more in non-black Africans (55% in 2000 versus 65% in 2018) compared to black Africans (33% in 2000 versus 40% in 2018); but, the survival rates for Africans are still significantly lower when compared to black (76% in 2015) and white (90% in 2015) populations in the United States. Conclusion: Regional, sub-regional, gender, and racial disparities exist, influencing the survival rates of breast cancer in Africa. Therefore, region and race-specific public health interventions coupled with prospective genetic studies are urgently needed to improve breast cancer survival in this region. [ABSTRACT FROM AUTHOR]

A growing body of evidence has shown that active learning has a considerable advantage over traditional lecture for student learning in undergraduate STEM classes, but there have been few large-scale studies to identify the specific types of activities that have the greatest impact on learning. We therefore undertook a large-scale, curriculum-wide study to investigate the effects of time spent on a variety of classroom activities on learning gains. We quantified classroom practices and related these to student learning, assessed using diagnostic tests written by over 3700 students, across 31 undergraduate biology classes at a research-intensive university in the Pacific Northwest. The most significant positive predictor of learning gains was the use of group work, supporting the findings of previous studies. Strikingly, we found that the addition of worksheets as an active learning tool for in-class group activities had the strongest impact on diagnostic test scores. This particular low-tech activity promotes student collaboration, develops problem solving skills, and can be used to inform the instructor about what students are struggling with, thus providing opportunities for valuable and timely feedback. Overall, our results indicate that group activities with low barriers to entry, such as worksheets, can result in significant learning gains in undergraduate science. [ABSTRACT FROM AUTHOR]

Polymorphonuclear neutrophils (PMNs) are the first line of defense against pathogens and their activation needs to be tightly regulated in order to limit deleterious effects. Nrf2 (Nuclear factor (erythroïd-derived 2)-like 2) transcription factor regulates oxidative stress and/or represses inflammation in various cells such as dendritic cells or macrophages. However, its involvement in PMN biology is still unclear. Using Nrf2 KO mice, we thus aimed to investigate the protective role of Nrf2 in various PMN functions such as oxidative burst, netosis, migration, cytokine production and phagocytosis, mainly in response to zymosan. We found that zymosan induced Nrf2 accumulation in PMNs leading to the upregulation of some target genes including Hmox-1, Nqo1 and Cat. Nrf2 was able to decrease zymosan-induced PMN oxidative burst; sulforaphane-induced Nrf2 hyperexpression confirmed its implication. Tnfα, Ccl3 and Cxcl2 gene transcription was decreased in zymosan-stimulated Nrf2 KO PMNs, suggesting a role for Nrf2 in the regulation of proinflammatory cytokine production. However, Nrf2 was not involved in phagocytosis. Finally, spontaneous migration of Nrf2 KO PMNs was lower than that of WT PMNs. Moreover, in response to low concentrations of CXCL2 or CXCL12, Nrf2 KO PMN migration was decreased despite similar CXCR2 and CXCR4 expression and ATP levels in PMNs from both genotypes. Nrf2 thus seems to be required for an optimal migration. Altogether these results suggest that Nrf2 has a protective role in several PMN functions. In particular, it downregulates their activation in response to zymosan and is required for an adequate migration. [ABSTRACT FROM AUTHOR]

Group A rotaviruses (RVA) are one of the major causes of acute gastroenteritis (AGE) in young children worldwide. Owing to lack of proper surveillance programs and health facilities, developing countries of Asia and Africa carry a disproportionately heavy share of the RVA disease burden. The aim of this hospital-based study was to investigate the circulation of RVA genotypes in Rawalpindi and Islamabad, Pakistan in 2015 and 2016, prior to the implementation of RVA vaccine. 639 faecal samples collected from children under 10 years of age hospitalized with AGE were tested for RVA antigen by ELISA. Among 171 ELISA positive samples, 143 were successfully screened for RT-PCR and sequencing. The prevalence of RVA was found to be 26.8% with the highest frequency (34.9%) found among children of age group 6–11 months. The most predominant circulating genotypes were G3P[8] (22.4%) followed by G12P[6] (20.3%), G2P[4] (12.6%), G1P[8] (11.9%), G9P[6] (11.9%), G3P[4] (9.1%), G1P[6] (4.2%), G9P[8] (4.2%), and G3P[6] (0.7%). A single mixed genotype G1G3P[8] was also detected. The findings of this study provide baseline data, that will help to assess if future vaccination campaigns using currently available RVA vaccine will reduce RVA disease burden and instigate evolutionary changes in the overall RVA biology. The high prevalence of RVA infections in Pakistan require to improve and strengthen the surveillance and monitoring system for RVA. This will provide useful information for health authorities in planning public health care strategies to mitigate the disease burden caused by RVA. [ABSTRACT FROM AUTHOR]

Background: More than 230,000 veterans—about 1/3 of US personnel deployed in the 1990–1991 Persian Gulf War—developed chronic, multi-symptom health problems now called “Gulf War illness” (GWI), for which mechanisms and objective diagnostic signatures continue to be sought. Methods: Targeted, broad-spectrum serum metabolomics was used to gain insights into the biology of GWI. 40 male participants, included 20 veterans who met both Kansas and CDC diagnostic criteria for GWI and 20 nonveteran controls without similar symptoms that were 1:1 matched to GWI cases by age, sex, and ethnicity. Serum samples were collected and archived at -80° C prior to testing. 358 metabolites from 46 biochemical pathways were measured by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Results: Veterans with GWI, compared to healthy controls, had abnormalities in 8 of 46 biochemical pathways interrogated. Lipid abnormalities accounted for 78% of the metabolic impact. Fifteen ceramides and sphingomyelins, and four phosphatidylcholine lipids were increased. Five of the 8 pathways were shared with the previously reported metabolic phenotype of males with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). However, 4 of the 5 shared pathways were regulated in opposite directions; key pathways that were up-regulated in GWI were down-regulated in ME/CFS. The single pathway regulated in the same direction was purines, which were decreased. Conclusions: Our data show that despite heterogeneous exposure histories, a metabolic phenotype of GWI was clearly distinguished from controls. Metabolomic differences between GWI and ME/CFS show that common clinical symptoms like fatigue can have different chemical mechanisms and different diagnostic implications. Larger studies will be needed to validate these findings. [ABSTRACT FROM AUTHOR]

Among calyptraeid gastropods, males become females as they get older, and egg capsules containing developing embryos are maintained beneath the mother’s shell until the encapsulated embryos hatch. Crepipatella dilatata is an interesting biological model considering that is an estuarine species and thus periodically exposed to elevated environment-physiological pressures. Presently, there is not much information about the reproductive biology and brooding parameters of this gastropod. This paper describes field and laboratory observations monitoring sex changes, brooding frequencies, sizes of brooding females, egg mass characteristics, and embryonic hatching conditions. Our findings indicate that C. dilatata is a direct-developing protandric hermaphrodite, changing from male to female when individuals were between 18 and 20 mm in shell length. At our study site in Quempillén estuary, females were found to be brooding almost continuously throughout the year, having an average maximum of 85% of simultaneous brooding, with a short rest from April through June. No relationship was found between the number of capsules per egg mass and the size of the brooding female. However, capsule size and the number of embryos and nurse eggs were strongly related to female size. The offspring hatched with an average shell length > 1 mm. About 25% of the hatched capsules were found to contain both metamorphosed (juveniles) and non-metamorphosed (veliger) individuals. The sizes of the latter were < 1000 μm. The length of hatching juveniles was inversely related to the number of individuals per capsule, which seems related to differences in the availability of nurse eggs per embryo. Although fecundity per reproductive event of this species is relatively low (maximum approx. 800 offspring per egg mass) compared with those of calyptraeid species showing mixed development, the overall reproductive potential of C. dilatata seems to be high considering that females can reproduce up to 5 times per year, protecting their encapsulated embryos from physical stresses until well-developed juveniles are released into the population, avoiding a dangerous pelagic period prior to metamorphosis. [ABSTRACT FROM AUTHOR]

Pachycrepoideus vindemmiae is a wasp that parasitizes and host-feeds on pupae of the invasive spotted-wing drosophila (SWD, Drosophila suzukii). Few studies have addressed interactions between these two species and little is known about the potential of this parasitoid as a biocontrol agent of SWD and the different variables that may affect it. Here, we investigated the impact of extrinsic and intrinsic factors on life-history traits of P. vindemmiae. Both constant (entire adulthood) and limited (30 minutes) supplies of water + honey, honey, or host increased parasitoid survival compared to controls (water or fasting). Water + honey caused the highest parasitoid survivals (35–60 days), independent of supply period, sex, and host availability. Females were intrinsically more resistant to water- and honey-deprivation than males, and host-feeding elevated such resistance even higher. Constant honey supply (either with or without water) supported the highest host-killing capacities (= capacity to kill hosts) (ca. 600 SWD pupae/wasp). However, in young females (4–9 days old), the impact of honey availability (with or without water) was insignificant while water deprivation (either with or without honey) caused the highest host-killing potential. This indicates that although sugar becomes a critical nutritional resource as females age, young females depend more on water than sugar to reproduce. Neither water nor honey affected the sex ratio of young females, but when we considered the entire adulthood, the availability of honey caused the lowest proportion of females (0.50), independent of water availability. Neither water nor honey affected parasitoid emergence rate (0.97), independent of female age. Based on survival and host-killing capacity, we conclude that P. vindemmiae has a tremendous biocontrol potential against SWD. Both limited and constant supply of water, sugar, and host increase parasitoid survival, while constant supply of water and/or honey enhance its host-killing potential and decrease sex ratio depending on maternal age. [ABSTRACT FROM AUTHOR]

Tauopathies are neurodegenerative diseases that affect millions of people worldwide including those with Alzheimer’s disease. While many efforts have focused on understanding the role of tau protein in neurodegeneration, there has been little done to systematically analyze and study the structures within tau’s encoding RNA and their connection to disease pathology. Knowledge of RNA structure can provide insights into disease mechanisms and how to affect protein production for therapeutic benefit. Using computational methods based on thermodynamic stability and evolutionary conservation, we identified structures throughout the tau pre-mRNA, especially at exon-intron junctions and within the 5′ and 3′ untranslated regions (UTRs). In particular, structures were identified at twenty exon-intron junctions. The 5′ UTR contains one structured region, which lies within a known internal ribosome entry site. The 3′ UTR contains eight structured regions, including one that contains a polyadenylation signal. A series of functional experiments were carried out to assess the effects of mutations associated with mis-regulation of alternative splicing of exon 10 and to identify regions of the 3′ UTR that contain cis-regulatory elements. These studies defined novel structural regions within the mRNA that affect stability and pre-mRNA splicing and may lead to new therapeutic targets for treating tau-associated diseases. [ABSTRACT FROM AUTHOR]

A 110-kDa type II transmembrane glycoprotein with dipeptidyl peptidase IV (DPPIV) activity in its extracellular region, CD26 has a multitude of biological functions and plays an important role in the regulation of inflammatory responses and tumor biology. Our work has focused on CD26 as a novel therapeutic target for various tumors and immune disorders, and we have recently developed a humanized anti-CD26 monoclonal antibody (mAb), YS110, which has promising safety profile and clinical activity in patients with malignant pleural mesothelioma. The development of an anti-human CD26 mAb that can clearly and reliably detect the denatured CD26 molecule in formalin-fixed paraffin-embedded (FFPE) tissues in the clinical setting is therefore of the utmost importance. To develop novel anti-CD26 mAbs capable of binding to denatured CD26, we immunized mice with urea-treated CD26 protein. Hybridoma supernatants were screened for specific reactivity with human CD26 by immunostaining through the use of a set of FFPE human CD26-positive or negative tumor cell lines. This screening method enables us to develop novel anti-human CD26 mAbs suitable for immunohistochemical staining of CD26 in FFPE non-tumor and tumor tissue sections with reliable clarity and intensity. Specifically, these mAbs display strong binding affinity to denatured human CD26 rather than undenatured human CD26, and are capable of detecting denatured human CD26 in decalcified specimens. These novel anti-CD26 mAbs are potentially useful for the analysis of CD26 expression in cancer patients with bony metastasis, and may help decide the appropriateness of YS110 therapy for future cancer patients. [ABSTRACT FROM AUTHOR]

Growth differentiation factor 11 (GDF11) belongs to the TGF-β superfamily of proteins and is closely related to myostatin. Recent findings show that GDF11 has rejuvenating properties with pronounced effects on the cardiovascular system, brain, skeletal muscle, and skeleton in mice. Several human studies were also conducted, some implicating decreasing levels of circulating GDF11 with age. To date, however, there have not been any reports on its role in human skin. This study examined the impact of GDF11 on human skin, specifically related to skin aging. The effect of recombinant GDF11 on the function of various skin cells was examined in human epidermal keratinocytes, dermal fibroblasts, melanocytes, dermal microvascular endothelial cells and 3D skin equivalents, as well as in ex vivo human skin explants. GDF11 had significant effects on the production of dermal matrix components in multiple skin models in vitro and ex vivo. In addition, it had a pronounced effect on expression of multiple skin related genes in full thickness 3D skin equivalents. This work, for the first time, demonstrates an important role for GDF11 in skin biology and a potential impact on skin health and aging. [ABSTRACT FROM AUTHOR]

As an important part of the comprehensive treatment methods, the urate-lowering Chinese herbs could provide favorable clinical effects on hyperuricemia in its ability to invigorate spleen and remove dampness. Owing to the long-term duration, it brought up the potential adverse reactions (ADRs) and concerns about the drug-induced liver injury from these herbs. To address this problem, the bioinformatics approaches which combined the network pharmacology, computer simulation and molecular biology experiments were undertaken to elucidate the underlying drug-induced liver injury molecular mechanisms of urate-lowering Chinese herbs. Several electronic databases were searched to identify the potential liver injury compounds in published research. Then, the putative target profile of liver injury was predicted, and the interaction network was constructed based on the links between the compounds, corresponding targets and core pathways. Accordingly, the molecular docking simulation was performed to recognize the representative compounds with hepatotoxicity. Finally, the cell experiments were conducted to investigate the biochemical indicators and expression of the crucial protein that were closely associated with liver injury. In conclusion, the current research revealed that the compounds with potential liver injury including diosgenin, baicalin, saikosaponin D, tetrandrine, rutaecarpine and evodiamine from urate-lowering Chinese herbs, could lead to decline the survival rate of L-02 cell, increase the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and alkaline phosphatase (ALP) in cell-culture medium, enhance the expression of p-p38/p38, while the p38 inhibitor could achieve the trend of regulating and controlling liver injury. These research findings bring further support to the growing evidence that the mechanism of the liver injury induced by the compounds from urate-lowering Chinese herbs may be associated with the activation of p38α. [ABSTRACT FROM AUTHOR]

Background: The subtyping of breast cancer based on features of tumour biology such as hormonal receptor and HER2 status has led to increasingly patient-specific treatment and thus improved outcomes. However, such subgroups may not be sufficiently informed to best predict outcome and/or treatment response. The incorporation of multi-modal data may identify unexpected and actionable subgroups to enhance disease understanding and improve outcomes. Methods: This retrospective cross-sectional study used the cancer registry Surveillance, Epidemiology and End Results (SEER), which represents 28% of the U.S. population. We included adult female patients diagnosed with breast cancer in 2010. Latent class analysis (LCA), a data-driven technique, was used to identify clinically homogeneous subgroups (“endophenotypes”) of breast cancer from receptor status (hormonal receptor and HER2), clinical, and demographic data and each subgroup was explored using Bayesian networks. Results: Included were 44,346 patients, 1257 (3%) of whom had distant organ metastases at diagnosis. Four endophenotypes were identified with LCA: 1) “Favourable biology” had entirely local disease with favourable biology, 2) “HGHR-” had the highest incidence of HR- receptor status and highest grade but few metastases and relatively good outcomes, 3) “HR+ bone” had isolated bone metastases and uniform receptor status (HR+/HER2-), and 4) “Distant organ spread” had high metastatic burden and poor survival. Bayesian networks revealed clinically intuitive interactions between patient and disease features. Conclusions: We have identified four distinct subgroups of breast cancer using LCA, including one unexpected group with good outcomes despite having the highest average histologic grade and rate of HR- tumours. Deeper understanding of subgroup characteristics can allow us to 1) identify actionable group properties relating to disease biology and patient features and 2) develop group-specific diagnostics and treatments. [ABSTRACT FROM AUTHOR]

One of the biggest challenges in analyzing high throughput omics data in biological studies is extracting information that is relevant to specific biological mechanisms of interest while simultaneously restricting the number of false positive findings. Due to random chances with numerous candidate targets and mechanisms, computational approaches often yield a large number of false positives that cannot easily be discerned from relevant biological findings without costly, and often infeasible, biological experiments. We here introduce and apply an integrative bioinformatics approach, Biologically Anchored Knowledge Expansion (BAKE), which uses sequential statistical analysis and literature mining to identify highly relevant network genes and effectively removes false positive findings. Applying BAKE to genomic expression data collected from mouse (Mus musculus) adipocytes during insulin resistance progression, we uncovered the transcription factor Krueppel-like Factor 4 (KLF4) as a regulator of early insulin signaling. We experimentally confirmed that KLF4 controls the expression of two key insulin signaling molecules, the Insulin Receptor Substrate 2 (IRS2) and Tuberous Sclerosis Complex 2 (TSC2). [ABSTRACT FROM AUTHOR]

Recessive genic male sterility (RGMS) has great potential for F1 hybrid seeds production in sesame (Sesamum indicum L.). However, it is not yet widely used in practice due to poor understanding of the underlying mechanism in RGMS. Previously, we have developed a novel sesame RGMS line (D248A) controlled by a single recessive gene. To elucidate its cytological mechanism, histological observations were carried out in sterile and fertile buds. The results indicated that abnormality in D248A began at microspore mother cell stage and persisted until microspore stage. The microsporocytes had less cytoplasm and no obvious nucleus. Normal meiosis failed in microspore mother cells. Cytoplasm condensation and vacuolation frequently occurred in tetrads, leading to the production of crumpled and abortive microspores. To develop molecular markers for breeding of hybrid lines, InDel and SSR markers were analyzed in a fertility segregating NIL population constructed by sib-mating D248A with D248B. Five markers were identified for the male sterile gene (Ms), with a respective genetic distance of 1.47 and 5.17 cM for the two closest markers (SB2993 and LG1-170) on both sides. The Ms gene was further anchored into a 108-kb interval in the downstream of chromosome 1, within which 15 genes were predicted and four were likely to be responsible for male sterility. These findings provide a deeper understanding of the mechanism underlying RGMS in sesame. [ABSTRACT FROM AUTHOR]

The study reports the response to herbicide of the 2,4-dichlorophenoxyacetic acid (2,4-D)–degrading fungal strain Umbelopsis isabellina. A comparative analysis covered 41 free amino acids as well as 140 lipid species of fatty acids, phospholipids, acylglycerols, sphingolipids, and sterols. 2,4-D presence led to a decrease in fungal catalase activity, associated with a higher amount of thiobarbituric acid-reactive substances (TBARS). Damage to cells treated with the herbicide resulted in increased membrane permeability and decreased membrane fluidity. Detailed lipidomic profiling showed changes in the fatty acids composition such as an increase in the level of linoleic acid (C18:2). Moreover, an increase in the phosphatidylethanolamine/phosphatidylcholine ratio was observed. Analysis of fungal lipid profiles revealed that the presence of 2,4-D was accompanied by the accumulation of triacylglycerols, a decrease in ergosterol content, and a considerable rise in the level of sphingolipid ceramides. In the exponential phase of growth, increased levels of leucine, glycine, serine, asparagine, and hydroxyproline were found. The results obtained in our study confirmed that in the cultures of U. isabellina oxidative stress was caused by 2,4-D. The herbicide itself forced changes not only to membrane lipids but also to neutral lipids and amino acids, as the difference of tested compounds profiles between 2,4-D—containing and control samples was consequently lower as the pesticide degradation progressed. The presented findings may have a significant impact on the basic understanding of 2,4-D biodegradation and may be applied for process optimization on metabolomic and lipidomic levels. [ABSTRACT FROM AUTHOR]

In omics experiments, variable selection involves a large number of metabolites/ genes and a small number of samples (the n < p problem). The ultimate goal is often the identification of one, or a few features that are different among conditions- a biomarker. Complicating biomarker identification, the p variables often contain a correlation structure due to the biology of the experiment making identifying causal compounds from correlated compounds difficult. Additionally, there may be elements in the experimental design (blocks, batches) that introduce structure in the data. While this problem has been discussed in the literature and various strategies proposed, the over fitting problems concomitant with such approaches are rarely acknowledged. Instead of viewing a single omics experiment as a definitive test for a biomarker, an unrealistic analytical goal, we propose to view such studies as screening studies where the goal of the study is to reduce the number of features present in the second round of testing, and to limit the Type II error. Using this perspective, the performance of LASSO, ridge regression and Elastic Net was compared with the performance of an ANOVA via a simulation study and two real data comparisons. Interestingly, a dramatic increase in the number of features had no effect on Type I error for the ANOVA approach. ANOVA, even without multiple test correction, has a low false positive rates in the scenarios tested. The Elastic Net has an inflated Type I error (from 10 to 50%) for small numbers of features which increases with sample size. The Type II error rate for the ANOVA is comparable or lower than that for the Elastic Net leading us to conclude that an ANOVA is an effective analytical tool for the initial screening of features in omics experiments. [ABSTRACT FROM AUTHOR]

Modeling the basic structure of metabolic machinery is a challenge for modern biology. Some models based on complex networks have provided important information regarding this machinery. In this paper, we constructed metabolic networks of 17 plants covering unicellular organisms to more complex dicotyledonous plants. The metabolic networks were built based on the substrate-product model and a topological percolation was performed using the kcore decomposition. The distribution of metabolites across the percolation layers showed correlations between the metabolic integration hierarchy and the network topology. We show that metabolites concentrated in the internal network (maximum kcore) only comprise molecules of the primary basal metabolism. Moreover, we found a high proportion of a set of common metabolites, among the 17 plants, centered at the inner kcore layers. Meanwhile, the metabolites recognized as participants in the secondary metabolism of plants are concentrated in the outermost layers of the network. This data suggests that the metabolites in the central layer form a basic molecular module in which the whole plant metabolism is anchored. The elements from this central core participate in almost all plant metabolic reactions, which suggests that plant metabolic networks follows a centralized topology. [ABSTRACT FROM AUTHOR]

In the animal world, various kinds of collective motions have been found and proven to be efficient ways of carrying out some activities such as searching for food and avoiding predators. Many scholars research the interactions of collective behaviors of human beings according to the rules of collective behaviors of animals. Based on the Lennard-Jones potential function and a self-organization process, our paper proposes a topological communication model to simulate the collective behaviors of human beings. In the results of simulations, we find various types of collective behavior and fission behavior and discover the threshold for the emergence of collective behavior, which is the range five to seven for the number of topology K. According to the analysis of network properties of the model, the in-degree of individuals is always equal to the number of topology. In the stable state, the out-degrees of individuals distribute around the value of the number of topology K, except that the out-degree of a single individual is approximately double the out-degrees of the other individuals. In addition, under different initial conditions, some features of different kinds of networks emerge from the model. We also find the leader and herd mentality effects in the characteristics of the behaviors of human beings in our model. Thus, this work could be used to discover how to promote the emergence of beneficial group behaviors and prevent the emergence of harmful behaviors. [ABSTRACT FROM AUTHOR]

Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms. [ABSTRACT FROM AUTHOR]

Non-verbal communication has important implications for inter-individual relationships and negotiation success. However, to what extent humans can spontaneously use rhythm and prosody as a sole communication tool is largely unknown. We analysed human ability to resolve a conflict without verbal dialogs, independently of semantics. We invited pairs of subjects to communicate non-verbally using whistle sounds. Along with the production of more whistles, participants unwittingly used a subtle prosodic feature to compete over a resource (ice-cream scoops). Winners can be identified by their propensity to accentuate the first whistles blown when replying to their partner, compared to the following whistles. Naive listeners correctly identified this prosodic feature as a key determinant of which whistler won the interaction. These results suggest that in the absence of other communication channels, individuals spontaneously use a subtle variation of sound accentuation (prosody), instead of merely producing exuberant sounds, to impose themselves in a conflict of interest. We discuss the biological and cultural bases of this ability and their link with verbal communication. Our results highlight the human ability to use non-verbal communication in a negotiation process. [ABSTRACT FROM AUTHOR]

Digital processing and analysis of high resolution images of 30 individuals of the orb web spider Verrucosa arenata were performed to extract and quantify human visible colors present on the dorsal abdomen of this species. Color extraction was performed with minimal user intervention using an unsupervised algorithm to determine groups of colors on each individual spider, which was then analyzed in order to quantify and classify the colors obtained, both spatially and using energy and entropy measures of the digital images. Analysis shows that the colors cover a small region of the visible spectrum, are not spatially homogeneously distributed over the patterns and from an entropic point of view, colors that cover a smaller region on the whole pattern carry more information than colors covering a larger region. This study demonstrates the use of processing tools to create automatic systems to extract valuable information from digital images that are precise, efficient and helpful for the understanding of the underlying biology. [ABSTRACT FROM AUTHOR]

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina’s HiSeq and MiSeq, Roche’s 454 GS FLX, and Life Technologies’ Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case. [ABSTRACT FROM AUTHOR]

Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because many shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genera Opisthostoma and Plectostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approach for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology. [ABSTRACT FROM AUTHOR]

Objective: To investigate if a virtual laboratory simulation (vLAB) could be used to replace a face to face tutorial (demonstration) to prepare students for a laboratory exercise in microbiology. Methods: A total of 189 students who were participating in an undergraduate biology course were randomly selected into a vLAB or demonstration condition. In the vLAB condition students could use a vLAB at home to ‘practice’ streaking out bacteria on agar plates in a virtual environment. In the demonstration condition students were given a live demonstration from a lab tutor showing them how to streak out bacteria on agar plates. All students were blindly assessed on their ability to perform the streaking technique in the physical lab, and were administered a pre and post-test to determine their knowledge of microbiology, intrinsic motivation to study microbiology, and self-efficacy in the field of microbiology prior to, and after the experiment. Results: The results showed that there were no significant differences between the two groups on their lab scores, and both groups had similar increases in knowledge of microbiology, intrinsic motivation to study microbiology, as well as self-efficacy in the field of microbiology. Conclusion: Our data show that vLABs function just as well as face to face tutorials in preparing students for a physical lab activity in microbiology. The results imply that vLABs could be used instead of face to face tutorials, and a combination of virtual and physical lab exercises could be the future of science education. [ABSTRACT FROM AUTHOR]

Bashar Ibrahim is not affiliated with #1 but with #2: Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait. Reference 1 Almasri F, Hewapathirana GI, Ghaddar F, Lee N, Ibrahim B (2021) Measuring attitudes towards biology major and non-major: Effect of students' gender, group composition, and learning environment. [Extracted from the article]

Because the frequency of heterospecific interactions inevitably increases with species richness in a community, biodiversity effects must be expressed by such interactions. However, little is understood how heterospecific interactions affect ecosystem productivity because rarely are biodiversity ecosystem functioning experiments spatially explicitly manipulated. To test the effect of heterospecific interactions on productivity, direct evidence of heterospecific neighborhood interaction is needed. In this study we conducted experiments with a detailed spatial design to investigate whether and how heterospecific neighborhood interactions promote primary productivity in a grassland community. The results showed that increasing the heterospecific: conspecific contact ratio significantly increased productivity. We found there was a significant difference in the variation in plant height between monoculture and mixture communities, suggesting that height-asymmetric competition for light plays a central role in promoting productivity. Heterospecific interactions make tall plants grow taller and short plants become smaller in mixtures compared to monocultures, thereby increasing the efficiency of light interception and utilization. Overyielding in the mixture communities arises from the fact that the loss in the growth of short plants is compensated by the increased growth of tall plants. The positive correlation between species richness and primary production was strengthened by increasing the frequency of heterospecific interactions. We conclude that species richness significantly promotes primary ecosystem production through heterospecific neighborhood interactions. [ABSTRACT FROM AUTHOR]