Miracle-dz/UniFAR-FTUs huggingface dataset:
Scale‐dependent home range optimality for a solitary omnivore

Abstract Spatial and temporal heterogeneity are fundamental mechanisms structuring home ranges. Under optimality, an individual should structure their space use economically to maximize fitness. We evaluated support for three hypotheses related to range optimality in American black bears (Ursus americanus), predicting (a) range location on a landscape will correspond with high vegetation productivity, (b) increasing forest fragmentation will result in larger ranges, and (c) increasing proportion of forest and/or mean vegetation productivity will result in smaller ranges. We used black bear radio telemetry data from Michigan (2009–2015), Missouri (2010–2016), and Mississippi (2008–2017), USA. Annual space use excluded winter, and we separated seasonal space use into spring, summer, and fall. We collected data from 143 bears (80 females, 63 males), resulting in 97 annual and 538 seasonal ranges. We used generalized linear mixed models to evaluate productivity (estimated through Normalized Difference Vegetation Index [NDVI]) selection, and range size (km2) variation between individuals. At the annual scale, black bears consistently selected areas with greater vegetation productivity than the surrounding landscape; yet selection weakened and was more variable seasonally. Opposite to our prediction, we found that increasing fragmentation consistently resulted in smaller ranges; non‐forested land covers and forest edges might provide greater abundance or more diverse foods for bears. Ranges with a greater proportion of forest were smaller, likely reflecting an increase in food and cover which could reduce movements, yet there was no support for more productive ranges also being smaller as expected from an area minimizing strategy. Black bears displayed a scale‐dependent space use strategy: at larger spatial and temporal scales, productivity acted as the strongest limiting factor and energy maximizing was the dominant strategy, while an area minimizing strategy was exhibited seasonally. We revealed consistent, scale‐dependent responses by black bears to environmental conditions, demonstrating the intrinsic plasticity of this adaptable omnivore.
Prognostic Value of Long Noncoding RNAs in Patients with Gastrointestinal Cancer: A Systematic Review and Meta-Analysis

Gastrointestinal cancers (GICs) are a huge threat to human health, which mainly include esophageal, gastric, and colorectal cancers. The purpose of this study was to clarify the prognostic value of long noncoding RNAs (lncRNAs) in GICs. A total of 111 articles were included, and 13103 patients (3123 with esophageal cancer, 4972 with gastric cancer, and 5008 with colorectal cancer) were enrolled in this study. The pooled hazard ratio (HR) values and corresponding 95% confidence interval (95% CI) of overall survival (OS) related to different lncRNA expressions in esophageal, gastric, colorectal, and gastrointestinal cancer patients were 1.92 (1.70–2.16), 1.96 (1.77–2.16), 2.10 (1.87–2.36), and 2.00 (1.87–2.13), respectively. We have identified 74 lncRNAs which were associated closely with poor prognosis of GIC patients, including 58 significantly upregulated lncRNA expression and 16 significantly downregulated lncRNA expression. In addition, 47 of the included studies revealed relative mechanisms and 12 of them investigated the correlation between lncRNAs and microRNAs. Taken together, this meta-analysis supports that specific lncRNAs are significantly related to the prognosis of GIC patients and may serve as novel markers for predicting the prognosis of GIC patients. Furthermore, lncRNAs may have a promising contribution to lncRNA-based targeted therapy and clinical decision-making in the future.
One thousand simple rules

What began as a one-off in 2005 as Ten Simple Rules for Getting Published [1] has, in thirteen years, now multiplied a hundredfold to become One Thousand Simple Rules for many aspects of one’s professional development and led to Quick Tips in the journal’s Education section. This milestone of a thousand rules has been reached thanks to the unselfish work of all stakeholders—authors, editors, reviewers, and readers. Let’s face it, writing, editing or reviewing a Ten Simple Rules (TSR) article is not the same as a publication that advances a scientific field. What it is going to get you is the satisfaction of knowing you have passed on a part of your experience in a form that is easily understood and acted upon by those following in your footsteps and hence have a very different kind of positive impact on science. Thank you. On the other hand, as a reader the TSRs might contribute in some small way to you getting tenure, or whatever else you care about in your professional life.
Long-term outcome of myotomy and fundoplication based on intraoperative real-time high-resolution manometry in achalasia patients

Background Current treatment options for achalasia of the esophagus predominantly consist of endoscopic myotomy or laparoscopic myotomy combined with a partial fundoplication. The intraoperative use of conventional manometry has previously been proposed with various results. The aim of the present study was to introduce the use of high-resolution manometry (HRM) during surgical treatment for achalasia and to assess the long-term outcome of this technique. Methods We enrolled achalasia patients within the time period November 2013 to July 2016 who underwent HRM and evaluation of Eckardt scores (ES) before and after tailored laparoscopic myotomy and fundoplication with intraoperative recording using HRM. Results Twenty patients were classified as having achalasia type I (20%), type II (55%), or type III (25%). During surgery, 9 myotomies were extended and 13 fundoplications were modified according to HRM findings. Mean resting (16.1 vs. 41.9 mmHg) and residual (9 vs. 28.7 mmHg) pressures of the lower esophageal sphincter and ES (0.7 vs. 6.9) were significantly eliminated postoperatively over a mean follow-up time of 17.7 months. Conclusions The use of intraoperative HRM gives us the advantage of simultaneous real-time estimation of intraluminal pressures of the esophagus and the ability to identify the exact points that produce pressure during laparoscopy. Consequently, it may be the key to the tailoring of the Heller-Dor technique and improving the outcomes for achalasia patients.
Formulating a model for the relationship between alexithymia, social support, loneliness, and marital satisfaction: Path analysis model

Aim: The present study was conducted in order to develop a relationship model of alexithymia, social support, loneliness, and marital satisfaction. Methods: One hundred eight couples who were parents of beginner students who participated in the assessment plan at the entrance to the primary school of Mahmoud Abad from Iran were selected using the accessible method to participate in this study; these couples completed self-reported questionnaires of alexithymia, social support, loneliness, and the Enrich's Couple Scales. Results: Findings showed that social support has a direct positive effect on marital satisfaction; additionally, alexithymia and social support have an indirect significant impact on marital satisfaction. Conclusion: The study provided additional evidence of the importance of alexithymia, social support, and loneliness in marital satisfaction.
Development and characterization of 30 microsatellite loci for Plagiorhegma dubium (Berberidaceae)

Premise of the Study Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats. In this study, 30 microsatellite loci, including 25 polymorphic loci, were developed for P. dubium for use in population‐level genetic analyses. Methods and Results We carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag–simple sequence repeat markers from P. dubium using Illumina HiSeq high‐throughput sequencing. To test utility of the developed markers, we genotyped 60 individuals from three populations and estimated the number of alleles and levels of observed and expected heterozygosity. Expected heterozygosity levels ranged from 0.000 to 0.594, 0.000 to 1.000, and 0.000 to 0.744 in the three populations, respectively. Conclusions These transcriptome‐derived simple sequence repeat markers are highly polymorphic and can be widely used in characterization of the endangered P. dubium. Population genetic studies with these markers will provide valuable insights for conservation by unraveling evolutionary patterns of P. dubium.
Development, characterization, and cross‐amplification of microsatellite markers for Psammosilene tunicoides (Caryophyllaceae)

Premise of the Study Psammosilene tunicoides (Caryophyllaceae) is a narrowly distributed and endemic plant species in southwestern China. The overexploitation of natural P. tunicoides has led to the destruction of many populations. Population and genetic studies will provide crucial data for the protection and management of P. tunicoides. In this study, we develop simple sequence repeat markers of P. tunicoides to analyze population diversity. Methods and Results Microsatellite loci of P. tunicoides were isolated with FIASCO. Eleven polymorphic and 10 monomorphic primers were developed. The 11 polymorphic primers were tested in three P. tunicoides populations, yielding two to nine alleles per locus. Levels of observed heterozygosity varied from 0.000 to 1.000, and levels of expected heterozygosity ranged from 0.000 to 0.615. In addition, three of these loci were successfully amplified, and showed polymorphism, in three Silene species. Conclusions These microsatellite markers can be valuable tools to investigate the genetic diversity and population structure of P. tunicoides.
The path to leadership: the career journey of academic health sciences library directors

Objective The authors examined the career journeys of academic health sciences library directors to better understand their leadership development and what led them to their leadership positions in libraries. Methods A qualitative phenomenological approach was employed due to its focus on exploring and understanding the meaning that individuals ascribe to a particular phenomenon or experience. Eleven library directors from academic health sciences libraries at public universities with very high research activity agreed to participate in the study. The research question guiding this study was: What was the library directors’ career journey that led them into library leadership? Results A major theme that emerged from the data was “Path to Leadership. ” Although each participant’s journey was unique, common elements surfaced as they chronicled their careers that were informative as to how they understood their emergence and development as library leaders. The four categories defining this theme were breadth of experience, focused preparation, mentors, and recognition and development of leadership potential. Conclusions Previous research suggests that leadership development and preparedness are important contributors to leadership effectiveness. It was encouraging to witness and understand the amount of preparation by participants to ready themselves for their roles as library directors. This study provides a comprehensive view of the path to library leadership that furthers understanding of the value of leadership development and preparedness and provides a model for aspiring library leaders.
Neutrophil-Lymphocyte Ratio Predicts Organ Salvage in Testicular Torsion with Marginal Diagnostic Delay

PURPOSE Though prompt diagnosis to minimize symptom duration (SD) is highly associated with organ salvage in cases of testicular torsion (TT), SD is subjective and hard to determine. We thus investigated the clinical implications of systemic inflammatory responses (SIRs) as potential surrogates of SD to improve testis survival. MATERIALS AND METHODS Sixty men with TT that underwent immediate operation among orchiectomy and orchiopexy following a visit to a single emergency department were retrospectively enrolled. Mandatory laboratory tests conducted included neutrophil, lymphocyte, and platelet counts. RESULTS Mean age and SD was 15.7±3.7 years and 8.27±4.98 hours, respectively. Thirty-eight (63.3%) underwent orchiectomy and the remaining 22 underwent orchiopexy. Leukocytosis (p=0.001) and neutrophil-lymphocyte ratio (NLR, p<0.001) were significantly lower in the orchiopexy group as was SD (3.27±1.88 vs. 11.16±3.80, p<0.001). Although multivariate model showed that the only single variable associated with receipt of orchiopexy was SD (odds ratio [OR]=0.259, p<0.001), it also revealed NLR as a sole SIR associated with SD (B=0.894, p<0.001). While 93.3% with a SD of within 3 hours underwent orchiopexy, only 26.6% of affected testes were preserved between 3 to 12 hours (n=30). When multivariable analysis was applied to those with window period, NLR alone predicted orchiopexy rather than orchiectomy (p=0.034, OR=0.635, p=0.013). The area under curve between SD (0.882) and NLR (0.756) was similar (p=0.14). CONCLUSIONS This study showed NLR independently predicted testis survival by proper surgical correction particularly for patients with marginally delayed diagnosis, which suggest the clinical usefulness for identifying candidates for orchiopexy in emergency setting.
The effects of diet and mating system on reproductive (and post‐reproductive) life span in a freshwater snail

Abstract The length of the reproductive life span, along with the number/frequency/magnitude of reproductive events, quantifies an individual's potential contribution to the next generation. By examining reproductive life span, and distinguishing it from somatic life span, we gain insight into critical aspects of an individual's potential fitness as well as reproductive and somatic senescence. Additionally, differentiating somatic and reproductive life spans can provide insight into the existence of a post‐reproductive period and factors that shape its duration. Given the known importance of diet and mating system on resource allocation, I reared individual freshwater snails (Physa acuta) from 22 full‐sib families under a 2 × 2 factorial design that crossed mate availability (available [outcrossing] or not [selfing]) and diet (Spirulina or lettuce) and quantified aspects of the entire life history enabling me to distinguish reproductive and somatic life spans, determine the total number of reproductive events, and evaluate how the reproductive rate changes with age. Overall, mated snails experienced shorter reproductive and somatic life spans; a diet of Spirulina also shortened both reproductive and somatic life spans. A post‐reproductive period existed in all conditions; its duration was proportional to somatic but not reproductive life span. I evaluate several hypotheses for the existence and duration of the post‐reproductive period, including a novel hypothesis that the post‐reproductive period may result from an increase in reproductive interval with age. I conclude that the post‐reproductive period may be indicative of a randomly timed death occurring as the interval between reproductive events continues to increase. As such, a “post‐reproductive” period can be viewed as a by‐product of a situation where reproductive senescence outpaces somatic senescence.
No support for cryptic choice by ovarian fluid in an external fertilizer

Abstract Whether the ovarian fluid (OF) represents a selective environment influencing cryptic female choice was tested using an external fertilizer experiencing intense sperm competition and large effects of OF on sperm swimming behavior—the Arctic charr (Salvelinus alpinus). We physically separated the OF from the eggs of reproductively active females and reintroduced either their own OF or fluid from another female to the eggs. The eggs were then fertilized in vitro in a replicated split‐brood design with sperm from two males under synchronized sperm competition trials, while also measuring sperm velocity of the individual males in the individual OFs. We found large effects of males, but no effect of females (i.e., eggs) on paternity, determined from microsatellites. More important, we found no effect of OF treatments on the relative paternity of the two competing males in each pair. This experimental setup does not provide support for the hypothesis that OF plays an important role as medium for cryptic female choice in charr. Power analyses revealed that our sample size is large enough to detect medium‐sized changes in relative paternity (medium‐sized effect sizes), but not large enough to detect small changes in relative paternity. More studies are needed before a conclusion can be drawn about OF's potential influence on paternity under sperm competition—even in charr.
Isolation and characterization of microsatellite loci from Pterocarya stenoptera (Juglandaceae)

Premise of the Study Microsatellite markers of Pterocarya stenoptera (Juglandaceae) were developed for future studies on the population genetic diversity and spatial genetic structure of the species. Methods and Results Based on Illumina sequencing of the transcriptome of P. stenoptera, a total of 2452 microsatellites were identified from 83,674 assembled unigenes. One hundred microsatellites were randomly selected to design amplification primer pairs. Of these, 15 were successfully amplified and displayed polymorphism. For these markers, the number of alleles per locus and population ranged from one to six. The levels of observed and expected heterozygosity varied from 0.000 to 1.000 and 0.000 to 0.718, respectively. Furthermore, all of the 15 loci were successfully cross‐amplified in another congeneric species (P. hupehensis) and were demonstrated to be polymorphic. Conclusions The microsatellite loci described here can be used for future population genetic and landscape genetic studies on P. stenoptera.
A C/EBPα–Wnt connection in gut homeostasis and carcinogenesis

This research reveals an antagonism between C/EBPα expression and activated Wnt signaling in the human and mouse gut and suggests a tumor suppressor function of C/EBPα in human and murine intestinal cancer. We explored the connection between C/EBPα (CCAAT/enhancer-binding protein α) and Wnt signaling in gut homeostasis and carcinogenesis. C/EBPα was expressed in human and murine intestinal epithelia in the transit-amplifying region of the crypts and was absent in intestinal stem cells and Paneth cells with activated Wnt signaling. In human colorectal cancer and murine APCMin/+ polyps, C/EBPα was absent in the nuclear β-catenin–positive tumor cells. In chemically induced intestinal carcinogenesis, C/EBPα KO in murine gut epithelia increased tumor volume. C/EBPα deletion extended the S-phase cell zone in intestinal organoids and activated typical proliferation gene expression signatures, including that of Wnt target genes. Genetic activation of β-catenin in organoids attenuated C/EBPα expression, and ectopic C/EBPα expression in HCT116 cells abrogated proliferation. C/EBPα expression accompanied differentiation of the colon cancer cell line Caco-2, whereas β-catenin stabilization suppressed C/EBPα. These data suggest homeostatic and oncogenic suppressor functions of C/EBPα in the gut by restricting Wnt signaling.
Polymorphic success types for Erlang ∗

Erlang is a dynamically typed concurrent functional language of increasing interest in industry and academia. Official Erlang distributions come equipped with Dialyzer, a useful static analysis tool able to anticipate runtime errors by inferring so-called success types, which are overapproximations to the real semantics of expressions. However, Dialyzer exhibits two main weaknesses: on the practical side, its ability to deal with functions that are typically polymorphic is rather poor; and on the theoretical side, a fully developed theory for its underlying type system –comparable to, say, Hindley-Milner system– does not seem to exist, something that we consider a regrettable circumstance. This work presents a type derivation system to obtain polymorphic success types for Erlang programs, along with correctness results with respect to a suitable semantics for the language.
The involutions-as-principal types/application-as-unification Analogy

In 2005, S. Abramsky introduced various universal models of computation based on Affine Combinatory Logic, consisting of partial involutions over a suitable formal language of moves, in order to discuss reversible computation in a game-theoretic setting. We investigate Abramsky’s models from the point of view of the model theory of λ-calculus, focusing on the purely linear and affine fragments of Abramsky’s Combinatory Algebras. Our approach stems from realizing a structural analogy, which had not been hitherto pointed out in the literature, between the partial involution interpreting a combinator and the principal type of that term, with respect to a simple types discipline for λ-calculus. This analogy allows for explaining as unification between principal types the somewhat awkward linear application of involutions arising from Geometry of Interaction (GoI). Our approach provides immediately an answer to the open problem, raised by Abramsky, of characterising those finitely describable partial involutions which are denotations of combinators, in the purely affine fragment. We prove also that the (purely) linear combinatory algebra of partial involutions is a (purely) linear λ-algebra, albeit not a combinatory model, while the (purely) affine combinatory algebra is not. In order to check the complex equations involved in the definition of affine λ-algebra, we implement in Erlang the compilation of λ-terms as involutions, and their execution.
Left-Handed Completeness for Kleene algebra, via Cyclic Proofs

We give a new proof that the axioms of left-handed Kleene algebra are complete with respect to language containments. This proof is significantly simpler than both the proof of Boffa (which relies on Krob’s completeness result), and the more recent proof of Kozen and Silva. Our proof builds on a recent non-wellfounded sequent calculus which makes it possible to explicitly compute the invariants required for left-handed Kleene algebra.
Loop Analysis by Quantification over Iterations

We present a framework to analyze and verify programs containing loops by using a first-order language of so-called extended expressions. This language can express both functional and temporal properties of loops. We prove soundness and completeness of our framework and use our approach to automate the tasks of partial correctness verification, termination analysis and invariant generation. For doing so, we express the loop semantics as a set of first-order properties over extended expressions and use theorem provers and/or SMT solvers to reason about these properties. Our approach supports full first-order reasoning, including proving program properties with alternation of quantifiers. Our work is implemented in the tool QuIt and successfully evaluated on benchmarks coming from software verification.