Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs

While the effects of climate (long‐term, prevailing weather) on species abundance, range and genetic diversity have been widely studied, short‐term, localized variations in atmospheric conditions (i.e., weather) can also rapidly alter species’ geographical ranges and population sizes, but little is known about how they affect genetic diversity. We investigated the relationship between weather and range‐wide genetic diversity in a marsupial, Bettongia gaimardi, using dynamic species distribution models (SDMs). Genetic diversity was lower in parts of the range where the weather‐based SDM predicted high variability in probability of B. gaimardi occurrence during 1950–2009. This is probably an effect of lower population sizes and extinction–recolonization cycles in places with highly variable weather. Spatial variation in genetic diversity was also better predicted by mean probabilities of B. gaimardi occurrence from weather‐ than climate‐based SDMs. Our results illustrate the importance of weather in driving population dynamics and species distributions on decadal timescales and thereby in affecting genetic diversity. Modelling the links between changing weather patterns, species distributions and genetic diversity will allow researchers to better forecast biological impacts of climate change.
Bacteria and bioburden and healing in complex wounds: A prognostic systematic review

The wound microbiome may play an important role in the wound healing process. We conducted the first systematic prognosis review investigating whether aspects of the wound microbiome are independent prognostic factors for the healing of complex wounds. We searched Medline, Embase, CINAHL and the Cochrane Library to February 2019. We included longitudinal studies which assessed the independent association of aspects of wound microbiome with healing of complex wounds while controlling for confounding factors. Two reviewers extracted data and assessed risk of bias and certainty of evidence using the GRADE approach. We synthesised studies narratively due to the clinical and methodological heterogeneity of included studies and sparse data. We identified 28 cohorts from 21 studies with a total of 38,604 participants, including people with diabetes and foot ulcers, open surgical wounds, venous leg ulcers and pressure ulcers. Risk of bias varied from low (2 cohorts) to high (17 cohorts); the great majority of participants were in cohorts at high risk of bias. Most evidence related to the association of baseline clinical wound infection with healing. Clinical infection at baseline may be associated with less likelihood of wound healing in foot ulcers in diabetes (HR from cohort with moderate risk of bias 0.53, 95% CI 0.33 to 0.83) or slower healing in open surgical wounds (HR 0.65, 95% CI 0.51 to 0.83); evidence in other wounds is more limited. Most other associations assessed showed no clear relationship with wound healing; evidence was limited and often sparse; and we documented gaps in the evidence. There is low certainty evidence that a diagnosis of wound infection may be prognostic of poorer healing in foot ulcers in diabetes, and some moderate certainty evidence for this in open surgical wounds. Low certainty evidence means that more research could change these findings.
Phylogeography and demographic expansion in the widely distributed horned passalus beetle, Odontotaenius disjunctus (coleoptera: Passalidae)

Abstract Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.
Role of Diet in Colorectal Cancer Incidence

Key Points Question How credible is the evidence behind the association of dietary factors with colorectal cancer (CRC) risk in published meta-analyses of prospective observational studies? Findings This umbrella review of 45 meta-analyses describing 109 associations found convincing evidence for an association between lower CRC risk and higher intakes of dietary fiber, dietary calcium, and yogurt and lower intakes of alcohol and red meat. Meaning This study suggests that dietary factors may have a role in the development and prevention of CRC, but more research is needed on specific foods for which the evidence remains suggestive.
Dynamics of concentrated polymer systems. Part 1.—Brownian motion in the equilibrium state

In this series of papers, the dynamics of polymers in melts and concentrated solutions are discussed with the eventual aim of constructing the rheological constitutive equation. The basic ideas are introduced in this paper. A mathematical model chain which describes the motion of the polymer in the fully entangled state is presented and its Brownian motion in equilibrium is studied. The model chain, called the primitive chain, shows much qualitatively different behaviour from that of the Rouse chain used in dilute solution theory.
Regional anesthesia in pediatric patients with preexisting neurological disease

Preexisting neurological disease in pediatric patients presents unique challenges to the anesthesiologist. In‐depth knowledge of the disease processes and awareness of sequalae that uniquely influence the risks and benefits of anesthetics are needed to make informed decisions. Because these vulnerable populations are often susceptible to perioperative airway or cardiopulmonary complications, the use of regional anesthesia can be advantageous. However, these clinical conditions already involve compromised neural tissue and, as such, create additional concern that regional anesthesia may result in new or worsened deficits. The following discussion is not intended to be a full review of each disease process, but rather provides a concise, yet thorough, discussion of the available literature on regional anesthesia in the more common, but still rare, pediatric neurological disorders. We aim to provide a framework for pediatric anesthesiologists to reengage in a healthy discussion about the risks and benefits of utilizing regional anesthesia in this vulnerable population.
The transition state method

According to our present notions, the theory of reaction rates involves three steps. First, one should know the behaviour of all molecules present in the system during the reaction, how they will move, and which products they will yield when colliding with definite velocities, etc. Practically, this amounts in most cases to the construction of the energy surface for the reacting system. Professor Eyring told us about the results which can be obtained by the application of quantum mechanics to molecular systems for this part of the theory. The second step in the theory I would call the statistical part. It endeavours to solve the problem of the rate of elementary reactions. Assuming only the material on the left side of a chemical equation to be present in a vessel, and the molecules of these to have the Maxwell-Boltzman energy and velocity distribution, one wants to know how many molecules corresponding to the right side of the equation will be formed in unit time. The elementary properties of the molecules are supposed to be known in this second step and one wants to express the reaction rate of elementary reactions in terms of these. The present paper will be devoted entirely to this second step. The third step is the consideration of the co-operation of the various elementary reactions, which may occur beside and must occur after each other in order to complete a real reaction. In especially favourable cases there is only one important chain of reactions leading to the final products and this has one link which is so much slower than all the others, that it is made responsible for the observed rate. The others are then assumed to be so much faster that one has practically equilibrium between the two sides of their chemical equations.
Juvenile Psychopathy and Community Treatment Response in Youth Adjudicated for Sexual Offenses

The present study examined the association of juvenile psychopathy features and treatment response in a sample of 102 youth, court adjudicated for sexual offenses and followed up more than 11 years in the community. The Psychopathy Checklist: Youth Version (PCL: YV) was rated from comprehensive archival sources, along with a youth sexual offense risk assessment and treatment planning measure scored pre-and posttreatment. The PCL: YV converged with domains of sexual offense risk and change in conceptually meaningful ways, and significantly predicted nonsexual violent, general violent, and any recidivism; it did not significantly predict sexual recidivism. Higher levels of psychopathy-related personality features were significantly associated with noncompletion of youth sexual offense-specific treatment, while changes in risk were associated with decreased recidivism controlling for PCL: YV score and baseline risk at p < . 10. The findings underscore the importance of intervention and support services for youth convicted of sexual offenses as well as the clinical and risk relevance of the juvenile psychopathy construct to decrease violent victimization to others.
VA-MENGOC-BC Vaccination Induces Serum and Mucosal Anti Neisseria gonorrhoeae Immune Responses and Reduces the Incidence of Gonorrhea

Background: Overall, there are over 30 different sexually transmitted infections with Neisseria gonorrhoeae being the third most frequent with a reported 78 million cases per year. Gonococcal infection causes genital inflammation, which can be a risk factor for others sexually transmitted infections, particularly human immunodeficiency virus. Gonorrhea is a treatable disease, but recently an increase in antibiotic resistance has been of concern. There are currently no vaccines available. However, parenteral vaccination with anti N. meningitidis serogroup B vaccine has been reported to decrease the incidence of gonococcal burden in New Zealand and in Cuba despite the fact that parenteral vaccination is not deemed to induce mucosal IgA. Here we explore possible mechanisms of protection against gonococcal infection through parenteral meningococcal B vaccination. Methods: Ninety-two serum, saliva and oropharyngeal swabs samples of young adults (healthy and Neisseria carriers) of the internal higher school were obtained. They have been vaccinated with VA-MENGOC-BC (MBV) during their infancy and boosted with a third dose during this study. Serum and saliva samples were analyzed by ELISA and Western blot to measured IgG and IgA antibodies against N. meningitidis and N. gonorrhoeae antigens. N. meningitidis carriers were determined by standard microbiologic test. In addition, we reviewed epidemiologic data for N. meningitidis and N. gonorrhoeae infections in Cuba. Results: Epidemiologic data show the influence of MBV over gonorrhea incidence suggesting to be dependent of sexual arrival age of vaccines but not over syphilis. Laboratorial data permit the detection of 70 and 22 noncarriers and carriers of N. meningitidis, respectively. Serum anti-MBV antigens (PL) responses were boosted by a third dose and were independent of carriage stages, but saliva anti-PL IgA responses were only present and were significant induced in carriers subjects. Carriers boosted with a third dose of MBV induced similar antigonococcal and -PL saliva IgA and serum IgG responses; meanwhile, serum antigonococcal IgG was significantly lower. In saliva, at least 2 gonococcal antigens were identified by Western blot. Finally, gonococcal-specific mucosal IgA antibody responses, in addition to the serum IgG antibodies, might contributed to the reduction of the incidence of N. gonorrhoeae. We hypothesize that this might have contributed to the observed reductions of the incidence of N. gonorrhoeae. Conclusion: These results suggest a mechanism for the influence of a Proteoliposome-based meningococcal BC vaccine on gonococcal incidence.
Analysis of Global Methylome and Gene Expression during Carbon Reserve Mobilization in Stems under Soil Drying1[OPEN]

DNA methylation and gene expression in carbon reserve mobilization of rice stems occurs during grain filling under moderate soil drying. In rice (Oryza sativa), a specific temporary source organ, the stem, is important for grain filling, and moderate soil drying (MD) enhanced carbon reserve flow from stems to increase grain yield. The dynamics and biological relevance of DNA methylation in carbon reserve remobilization during grain filling are unknown. Here, we generated whole-genome single-base resolution maps of the DNA methylome in the stem. During grain filling under MD, we observed an increase in DNA methylation of total cytosines, with more hypomethylated than hypermethylated regions. Genes responsible for DNA methylation and demethylation were up-regulated, suggesting that DNA methylation changes in the stem were regulated by antagonism between DNA methylation and demethylation activity. In addition, methylation in the CG and CHG contexts was negatively associated with gene expression, while that in the CHH context was positively associated with gene expression. A hypermethylated/up-regulated transcription factor of MYBS2 inhibited MYB30 expression and possibly enhanced β-Amylase5 expression, promoting subsequent starch degradation in rice stems under MD treatment. In addition, a hypermethylated/down-regulated transcription factor of ERF24 was predicted to interact with, and thereby decrease the expression of, abscisic acid 8′-hydroxylase1, thus increasing abscisic acid concentration under MD treatment. Our findings provide insight into the DNA methylation dynamics in carbon reserve remobilization of rice stems, demonstrate that MD increased this remobilization, and suggest a link between DNA methylation and gene expression in rice stems during grain filling.
The human‐in‐the‐loop: an evaluation of pathologists’ interaction with artificial intelligence in clinical practice

One of the major drivers of the adoption of digital pathology in clinical practice is the possibility of introducing digital image analysis (DIA) to assist with diagnostic tasks. This offers potential increases in accuracy, reproducibility, and efficiency. Whereas stand‐alone DIA has great potential benefit for research, little is known about the effect of DIA assistance in clinical use. The aim of this study was to investigate the clinical use characteristics of a DIA application for Ki67 proliferation assessment. Specifically, the human‐in‐the‐loop interplay between DIA and pathologists was studied.
Diagnosis and Treatment of Metastatic Colorectal Cancer: A Review.

Importance Colorectal cancer (CRC) is the third most common cause of cancer mortality worldwide with more than 1.85 million cases and 850 000 deaths annually. Of new colorectal cancer diagnoses, 20% of patients have metastatic disease at presentation and another 25% who present with localized disease will later develop metastases. Observations Colorectal cancer is the third most common cause of cancer mortality for men and women in the United States, with 53 200 deaths projected in 2020. Among people diagnosed with metastatic colorectal cancer, approximately 70% to 75% of patients survive beyond 1 year, 30% to 35% beyond 3 years, and fewer than 20% beyond 5 years from diagnosis. The primary treatment for unresectable metastatic CRC is systemic therapy (cytotoxic chemotherapy, biologic therapy such as antibodies to cellular growth factors, immunotherapy, and their combinations.) Clinical trials completed in the past 5 years have demonstrated that tailoring treatment to the molecular and pathologic features of the tumor improves overall survival. Genomic profiling to detect somatic variants is important because it identifies the treatments that may be effective. For the 50% of patients with metastatic CRC with KRAS/NRAS/BRAF wild-type tumors, cetuximab and panitumumab (monoclonal antibodies to the epithelial growth factor receptor [EGFR]), in combination with chemotherapy, can extend median survival by 2 to 4 months compared with chemotherapy alone. However, for the 35% to 40% of patients with KRAS or NRAS sequence variations (formerly termed mutations), effective targeted therapies are not yet available. For the 5% to 10% with BRAF V600E sequence variations, targeted combination therapy with BRAF and EGFR inhibitors extended overall survival to 9.3 months, compared to 5.9 months for those receiving standard chemotherapy. For the 5% with microsatellite instability (the presence of numerous insertions or deletions at repetitive DNA units) or mismatch repair deficiency, immunotherapy may be used in the first or subsequent line and has improved treatment outcomes with a median overall survival of 31.4 months in previously treated patients. Conclusions and Relevance Advances in molecular profiling of metastatic CRC facilitate the ability to direct treatments to the biologic features of the tumor for specific patient subsets. Although cures remain uncommon, more patients can anticipate extended survival. Genomic profiling allows treatment selection so that more patients derive benefit and fewer are exposed to toxicity from ineffective therapies.
Inbreeding depression contributes to the maintenance of habitat segregation between closely related monkeyflower species

Incompletely reproductively isolated species often segregate into different microhabitats, even when they are able to survive and reproduce in both habitats. Longer term evolutionary factors may contribute to this lack of cross‐habitat persistence. When reproductive interference reduces immigrant fitness, assortative mating, including self‐fertilization, increases immigrants’ fitness in a single generation, but longer term, inbreeding depression may reduce the chance of population persistence. Two California monkeyflower species repeatedly segregate into drier and wetter areas in their zone of sympatry. To test whether inbreeding depression may contribute to the maintenance of this segregation pattern, we transplanted outbred and successively inbred Mimulus guttatus and Mimulus nudatus into their native habitats and heterospecific habitats. We measured germination, survival, and seed set and found that recurrent selfing reduced all aspects of fitness in both species, most strongly in foreign habitats. A simulation model, parameterized from the transplant experiment, found that inbreeding reduced fitness to such an extent that sequentially inbred populations of either species would be unable to persist in heterospecific‐occupied habitats in the absence of continued gene flow. These results demonstrate that individual immigrants are unlikely to form persistent populations and thus, inbreeding depression contributes to the absence of fine‐scale coexistence in this species pair.
Mortality, reoperation and hospital stay within 90 days of primary and secondary antireflux surgery in a population-based multinational study.

BACKGROUND AND AIMS Absolute rates and risk factors of short-term outcomes after antireflux surgery remain largely unknown. We aimed to clarify absolute risks and risk factors for poor 90-day outcomes of primary laparoscopic and secondary antireflux surgery. METHODS This population-based cohort study included patients who had primary laparoscopic or secondary antireflux surgery in the five Nordic countries in 2000-2018. In addition to absolute rates, we analyzed age, sex, comorbidity, hospital volume, and calendar period in relation to all-cause 90-day mortality (main outcome), 90-day reoperation, and prolonged hospital stay (≥2 days over median stay). Multivariable logistic regression provided odds ratios (ORs) with 95% confidence intervals (95%CI), adjusted for confounders. RESULTS Among 26,193 patients who underwent primary laparoscopic antireflux surgery, postoperative 90-day mortality and 90-day reoperation rates were 0.13% (n=35) and 3.0% (n=750), respectively. The corresponding rates after secondary antireflux surgery (n=1,618) were 0.19% (n=3) and 6.2% (n=94). Higher age (56-80 years vs 18-42 years: OR=2.66, 95%CI 1.03-6.85) and comorbidity (Charlson Comorbidity Index ≥2 vs 0: OR=6.25, 95%CI 2.42-16.14) increased risk of 90-day mortality after primary surgery, and higher hospital volume suggested a decreased risk (highest vs lowest tertile: OR 0.58, 95% CI 0.22-1.57). Comorbidity increased the risk of 90-day reoperation. Higher age and comorbidity increased risk of prolonged hospital stay after both primary and secondary surgery. Higher annual hospital volume decreased the risk of prolonged hospital stay after primary surgery (highest vs lowest tertile: OR=0.74, 95%CI 0.67-0.80). CONCLUSION These findings suggest that laparoscopic antireflux surgery has an overall favorable safety profile in the treatment of GERD, particularly in younger patients without severe comorbidity who undergo surgery at high-volume centers.
Orientation-dependent mechanical response of graphene/BN hybrid nanostructures

Graphene-based hybrid van der Waals structures have emerged as a new class of materials for novel multifunctional applications. In such a vertically-stacked heterostructure, it is expected that its mechanical strength can be tailored by the orientation of the constituent monolayers relative to each other. In this paper, we explore this hypothesis by investigating the orientation dependence of the mechanical properties of graphene/h-BN heterostructures together with that of graphene and h-BN bilayers. The calculated results simulating the pull-out experiment show a noticeable dependence of the (out-of-plane) transverse mechanical response, which is primarily governed by the interlayer strength, on the stacking configurations. The degree of the dependence is directly related to the nature of the interlayer interactions, which change from covalent to covalent polar in going from graphene bilayer to graphene/BN to BN bilayer. In contrast, molecular dynamics simulations mimicking nanoindentation experiments predict that the in-plane mechanical response, which mainly depends on the intra-layer interactions, shows little or no dependence on the stacking-order. The BN monolayer is predicted to fracture before graphene regardless of the stacking pattern or configuration in the graphene/BN heterostructure, affirming the mechanical robustness of graphene. Thus, the graphene-based hybrid structures retain both stiffness and toughness required for a wide range of optoelectromechanical applications.