Miracle-dz/UniFAR-FTUs huggingface dataset:
Sexual Selection and Life History Allocation

A comprehensive explanation for sexual trait diversity depends on integrating life history theory and sexual selection to compare costs and benefits of sexual traits. A universal cost for all sexual traits involves the resources required to create and maintain them, which are consequently unavailable to other life history characters. This resource trade-off typically causes covariance between an organism's resource budget and its level of sexual trait expression, which is known as condition-dependence. Condition-dependence has several implications. It may be particularly important for ornaments signalling genetic quality, by helping to maintain the genetic variation that favours mate choice. It may also reduce extinction risk in sexually selected populations. Further life history studies of sexually selected traits are required, mindful of the inherent difficulties in quantifying resource acquisition and allocation, not least of which is that these processes are not independent of one another. Key Concepts: Trait evolution is restricted by trade-offs, where the benefit of increased investment in a trait is opposed by the cost of investment. The acquisition and allocation of resources is central to life history theory, but these processes are extremely difficult to quantify. Phenotypic correlations are not necessarily good metrics for the strength or importance of a trade-off between traits. Condition-dependence in mating systems featuring choice for indirect genetic benefits can help to maintain genetic variation for ornamental traits. Sex-role reversed systems have life history features that may clarify some of the outstanding questions in sexual selection. Keywords: sexual selection; life history; condition-dependence; acquisition; allocation; fitness; trade-offs; genetic quality
The network structure of myrmecophilic interactions

1. Ants establish mutualistic interactions involving a wide range of protective relationships (myrmecophily), in which they provide defence against enemies and partners provide food rewards and/or refuge. Although similar in the general outcome, myrmecophilic interactions differ in some characteristics such as quantity and quality of rewards offered by partners which may lead to different specialisation levels and, consequently, to different network properties.
Diversidad genética y distribución regional de cepas de Mycobacterium bovis del ganado en México

The molecular fingerprints of 878 isolates of Mycobacterium bovis from cattle, mostly dairy cattle, collected from cattle between 2009 and 2010 in different regions of Mexico were obtained by spoligotyping. Seventy-two percent (72 %) of the spoligotypes fell into nine clusters, and 27 % of the isolates fell into only two spoligotypes; 149 were orphan spoligotypes. The two predominant spoligotypes, arbitrarily designated as SP1 and SP2, were found in almost all States in Mexico, especially in central Mexico, where a concentration of dairy cattle is known. In spite of the wide distribution of spoligotypes observed, some show high regional preference, especially those in geographically distant regions. Only a few spoligotypes show patterns completely different from those shown by the most frequent spoligotypes, suggesting strange sources of infection or the formation of new genetic lines derived from non-lethal mutations. Most States with predominantly high dairy cattle populations showed similar spoligotypes, suggesting exchange of animals between regions. Some spoligotypes are common to dairy and beef cattle, suggesting transmission between populations, most probably due to the movement of dairy cattle to non-dairy regions.
Polyextremophiles : life under multiple forms of stress

PART 1: OPENING CHAPTERS Introduction J. Seckbach et al. Foreword R.W. Castenholz Preface K. Horikoshi List of Authors and Their Addresses PART 2: GENERAL ASPECTS Polyextremophiles and the Constraints for Terrestrial Habitability M.C. Capece et al. Life on the Edge and Astrobiology: Who Is Who in the Polyextremophiles World J. Seckbach The Dynamic Genomes of Acidophiles F. J. Lopez de Saro et al. PART 3: HALOPHILES Two Centuries of Microbiological Research in the Wadi Natrun, Egypt: A Model System for the Study of the Ecology, Physiology, and Taxonomy of Haloalkaliphilic Microorganisms A. Oren Adaptation in Haloalkaliphiles and Natronophilic Bacteria H.L. Banciu and D.Y. Sorokin A Random Biogeochemical Walk into Three Soda Lakes of the Western USA: With an Introduction to a Few of their Microbial Denizens R.S. Oremland Halophilic, Acidophilic, and Haloacidophilic Prokaryotes H. Minegishi Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions A. Oren Survival Strategies of Halophilic Oligotrophic and Desiccation Resistant Prokaryotes H. Stan-Lotter and S. Fendrihan Radiation Resistance in Extremophiles: Fending Off Multiple Attacks K.M. Webb and J. DiRuggiero PART 4: THERMOPHILES Thermoalkaliphilic Microbes V. Kumar and T. Satyanarayana Acido- and Thermophilic Microorganisms, Their Features and Identification of Novel Enzymes or Pathways Y. Kawarabayasi Microbial Diversity in Acidic High Temperature Steam Vents R.L. Weiss Bizzoco and S.T. Kelley PART 5: PSYCHROPHILES Left Out in the Cold: Life in Cryoenvironments J. Goordial et al. Microbial Diversity and Enzymes in Ikaite Columns A Cold and Alkaline Environment in Greenland J.K. Vester et al. Microbial Communities Thriving in Various Ice Ecosystems B. Sattler and B. Post Snow Algae. Adaptation Strategies to Survive on Snow and Ice T. Leya Adaptation of Antarctic Freshwater Green Algae to the Extreme Environments H. Hu PART 6: PRESSURE Deep Sub-Surface Oil Reservoirs as Poly-Extreme Habitats for Microbial Life. A Current Review A. Wentzel et al. Expanding Limits for Life to a New Dimension: Microbial Growth at Hypergravity S. Deguchi and K. Horikoshi PART 7: OXYGEN RELATIONSHIPS Microbial Eukaryotes in Marine Oxygen Minimum Zones W.D. Orsi and V.P. Edgcomb Deep Hypersaline Anoxic Basins as Model Systems for Environmental Selection of Microbial Plankton A. Stock et al. Microbial Eukaryotes in Hypersaline Anoxic Deep Sea Basins V.P. Edgcomb and W.D. Orsi Life at High Salt and Low Oxygen: How Do the Halobacteriaceae Cope with Low Oxygen Concentrations in their Environment? A. Oren PART 8: SELECTED ORGANISMS Niches and Adaptations of Polyextremotolerant Black Fungi M. Grube et al. Polyextremophilic Photoautotrophic Eukaryotic Algae W. Reisser Extremophilic Magnetotactic Bacteria C.T. Lefevre and D. A. Bazylinski Multicellular Extremophiles - The Case of the Tardigrades D. Schulze-Makuch and J. Seckbach PART 9: FINAL COMMENTS Polyextremophiles - Summary and Conclusions J. Chela Flores Erratum Organism Index Subject Index Author Index
VARIABILITY IN TEMPERATURE AND HISTORICAL PATTERNS IN REPRODUCTION IN THE FUCUS DISTICHUS COMPLEX (HETEROKONTOPHYTA; PHAEOPHYCEAE): IMPLICATIONS FOR SPECIATION AND THE COLLECTION OF HERBARIUM SPECIMENS 1

Natural and anthropogenic‐induced fluctuations in temperature can have profound effects on an organism's reproduction. The potential of herbarium collections for detecting changes in the timing of reproduction associated with interannual fluctuations in temperature from 1905 to 2003 was assessed in several taxa in the Fucus distichus (L.) emend. Powell complex from northern New England. Data were also used to evaluate whether air and/or sea temperature and North Atlantic Oscillation indices can cause overlap in the reproductive seasonalities of these taxa, a potential mechanism that prevents speciation. For all taxa, there was much variability in reproductive seasonalities among years. Discerning potential correlations with air or sea temperature was difficult because of a suspected bias to collect reproductive specimens at times when most of the population was nonreproductive. Nevertheless, there was a trend for seawater temperature to explain aseasonal reproduction for some taxa. Moreover, the existing archive (1895–2003) shows that the reproductive seasons of these taxa often overlap, and we suggest that interannual variability in temperature may often inhibit speciation. Suggestions also include archive of both reproductive and vegetative materials as well as coordinated sampling in critical biogeographic regions. No one investigator or institution can accomplish this, but phycological societies could organize and sustain such efforts.
Distribuição do sistema radicular de porta-enxertos sob laranjeira ‘Folha Murcha’ em clima subtropical

Objetivou-se estudar a distribuicao do sistema radicular dos limoeiros ‘Cravo’ ( Citrus limonia Osbeck) e ‘Rugoso da Africa’ ( Citrus jambluri Lush.), tangerineira ‘Cleopatra’ ( Citrus reshni Hort ex Tan.) e ‘Trifoliata’ ( Poncirus trifoliata (L.) Ralf. ), sob a laranjeira ‘Folha Murcha’ em clima subtropical. As amostragens foram realizadas, pelo metodo do trado, paralelamente a linha de plantio (entre plantas) a 0,5; 1,0; 1,5 e 2,0 m de distância do tronco e perpendicularmente a linha de plantio (entrelinhas) a 0,5; 1,0; 1,5; 2,0; 2,5; 3,0 e 3,5 m de distância do tronco. Essas amostras foram estratificadas em 0 – 0,1; 0,1 – 0,2; 0,2 – 0,4; 0,4 – 0,6 m de profundidade. Foram determinadas: massa seca, profundidade e distâncias efetivas do sistema radicular das plantas. O delineamento experimental utilizado foi o de blocos ao acaso, com quatro tratamentos e quatro repeticoes, com uma planta por parcela. A tangerineira ‘Cleopatra’ apresentou maior massa total de raizes a 2,0, 2,5 e 3,0 m de distância do tronco na entrelinha e nas camadas superficiais dos seguintes locais de amostragem: 0,5 e 1,0 m de distância do tronco no sentido da linha e 1,5 e 2,0 m de distância do tronco no sentido da entrelinha. O limoeiro ‘Rugoso da Africa’ apresentou maior profundidade efetiva das raizes na linha de plantio.
A molecular dynamics approach on the Y393C variant of protein disulfide isomerase A1

Human protein disulfide isomerase A1 (PDIA1) shows both catalytic (i.e., oxidoreductase) and non‐catalytic (i.e., chaperone) activities and plays a crucial role in the oxidative folding of proteins within the endoplasmic reticulum. PDIA1 dysregulation is a common trait in numerous pathophysiological conditions, including neurodegenerative disorders and cancerous diseases. The 1178A>G mutation of the human PDIA1‐encoding gene is a non‐synonymous single nucleotide polymorphism detected in patients with Cole‐Carpenter syndrome type 1 (CSS1), a particularly rare bone disease. In vitro studies showed that the encoded variant (PDIA1 Y393C) exhibits limited oxidoreductase activity. To gain knowledge on the structure–function relationship, we undertook a molecular dynamics (MD) approach to examine the structural stability of PDIA1 Y393C. Results showed that significant conformational changes are the structural consequence of the amino acid substitution Tyr>Cys at position 393 of the PDIA1 protein. This structure‐based study provides further knowledge about the molecular origin of CCS1.
DSP: A tool for probabilistic sex diagnosis using worldwide variability in hip-bone measurements

Determination of the sex of human bone remains represents a crucial stage in any palaeoanthropological study. The palaeobiological or palaeoethnological interpretations depend on its reliability. It is acknowledged that the adult hip-bone (os coxae) is by far the best non-population-specific indicator for reliable sex determination of adults. However, we clarify here a certain number of limitations which lower the reliability and ease of application of the usual methods. We propose a new tool—Probabilistic Sex Diagnosis (DSP: Diagnose Sexuelle Probabiliste)—based on a worldwide hip-bone metrical database (2040 adult specimens of known sex from 12 different reference populations). Sex is determined by comparing the specimen’s measurements to those from the database and by computing the individual probability of being female or male, from any combination of at least four variables among ten. This method is very easy to learn and apply; it provides sex diagnosis for any anatomically modern human, whatever population the specimen belongs to. Numerous combinations allow sex diagnosis of either well—preserved hip-bones or damaged ones. DSP is thus useful for both archaeological and forensic purposes. Its accuracy is close to 100%. The DSP computing program is available at the following web link: http://www.pacea. u-bordeaux1.fr/publication/dspv1.html
miR-378a-5p and miR-630 induce lens epithelial cell apoptosis in cataract via suppression of E2F3

Cataract, an eye disease that threatens the health of millions of people, brings about severe economic burden for patients and society. MicroRNA (miR)-378a-5p and miR-630 were recognized as essential regulators in multiple cancers. However, the exact functions of miR-378a-5p and miR-630 in cataract are still unclear. The expression of miR-378a-5p, miR-630, and E2F transcription factor 3 (E2F3) in tissues and cells was measured by quantitative real-time polymerase chain reaction. The 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay was used to evaluate cell viability. Flow cytometry was conducted to analyze cell apoptosis. The interaction between E2F3 and miR-378a-5p or miR-630 was confirmed by dual-luciferase reporter assay. The expression of proteins E2F3, B cell lymphoma (Bcl-2), Bcl-2 associated X (Bax), and cleaved caspase 3 was detected by western blot assay. The expression of miR-378a-5p and miR-630 was up-regulated whereas E2F3 was down-regulated in human cataract lens tissues compared with normal lens tissues. Depletion of miR-378a-5p or miR-630 enhanced proliferation and reduced apoptosis of human lens epithelial cells. Interestingly, up-regulation of E2F3 exhibited the same trend. Next, dual-luciferase reporter assay validated the interaction between E2F3 and miR-378a-5p or miR-630. The rescue experiments further revealed that E2F3 knockdown could recover miR-378a-5p, and miR-630 inhibitor induced promotion of cell proliferation and inhibition of apoptosis in cataract. miR-378a-5p and miR-630 repressed proliferation and induced apoptosis of lens epithelial cells by targeting E2F3 in cataract, representing a prospective alternative therapy for cataract.
Clinical Aspects of Ruminal Acidosis in Dairy Cattle

Acute and subacute ruminal acidosis are well recognized as important diseases in beef feedlots.6,14,32,37 Acute ruminal acidosis has been long recognized in dairy cattle, although deaths due to acute ruminal acidosis are apparently less frequent in dairy cattle than in beef feedlot cattle. 35 Only recently has subacute ruminal acidosis (SARA) been described for dairy cattle.26 Although dairy cattle are typically fed diets higher in forage and fiber compared to beef feedlot cattle, total consumption of rapidly fermentable (non-fiber) carbohydrates is similar between these two livestock classes because lactating dairy cows have very high feed intakes. This principle is illustrated by the data presented in Table 1. Ruminal pH values measured by continuous data acquisition in feedlot steers and lactating dairy cattle were similar when the cattle consumed similar total amounts of non-fiber carbohydrates. The prevalence of SARA in dairy herds is probably about the same as it is in beef feedlots. The objectives of this paper are to review the pathophysiology, clinical signs, diagnostic methods and prevention of ruminal acidosis in dairy herds. The subacute form of ruminal acidosis will be emphasized.
Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients

Cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for therapy management in oncology. We aimed to establish a multimodal liquid biopsy strategy that is usable with minimized blood volume to deconvolute the genomic complexity of metastatic breast cancer. CTCs were isolated from 10ml blood of 18 hormone receptor-positive and human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer patients. cfDNA was isolated from plasma generated after CTC depletion and targeted sequencing analyses were conducted. PIK3CA and ESR1 variants were less common in CTC gDNA, while ERBB2 variants were only detected in CTC gDNA. A total of 62% of all cfDNA variants were recovered in the matched CTC gDNA, while 72% of all variants were unique in either cfDNA (14 variants) or CTC gDNA (104 variants). The percentage of patients with no detectable cfDNA variants or CTC gDNA variants was 17%/11%, but a combined analysis identified variants in 94% of all patients. In univariate and multivariate regression models, ESR1 variants in cfDNA and CTC gDNA correlated significantly with survival. We suggest a coordinated analysis of both fractions in order to provide a comprehensive genomic footprint that may contribute to identifying the most suitable therapy for each individual.
Detection of Atrial Fibrillation Using a Ring-Type Wearable Device (CardioTracker) and Deep Learning Analysis of Photoplethysmography Signals: Prospective Observational Proof-of-Concept Study

Background Continuous photoplethysmography (PPG) monitoring with a wearable device may aid the early detection of atrial fibrillation (AF). Objective We aimed to evaluate the diagnostic performance of a ring-type wearable device (CardioTracker, CART), which can detect AF using deep learning analysis of PPG signals. Methods Patients with persistent AF who underwent cardioversion were recruited prospectively. We recorded PPG signals at the finger with CART and a conventional pulse oximeter before and after cardioversion over a period of 15 min (each instrument). Cardiologists validated the PPG rhythms with simultaneous single-lead electrocardiography. The PPG data were transmitted to a smartphone wirelessly and analyzed with a deep learning algorithm. We also validated the deep learning algorithm in 20 healthy subjects with sinus rhythm (SR). Results In 100 study participants, CART generated a total of 13,038 30-s PPG samples (5850 for SR and 7188 for AF). Using the deep learning algorithm, the diagnostic accuracy, sensitivity, specificity, positive-predictive value, and negative-predictive value were 96.9%, 99.0%, 94.3%, 95.6%, and 98.7%, respectively. Although the diagnostic accuracy decreased with shorter sample lengths, the accuracy was maintained at 94.7% with 10-s measurements. For SR, the specificity decreased with higher variability of peak-to-peak intervals. However, for AF, CART maintained consistent sensitivity regardless of variability. Pulse rates had a lower impact on sensitivity than on specificity. The performance of CART was comparable to that of the conventional device when using a proper threshold. External validation showed that 94.99% (16,529/17,400) of the PPG samples from the control group were correctly identified with SR. Conclusions A ring-type wearable device with deep learning analysis of PPG signals could accurately diagnose AF without relying on electrocardiography. With this device, continuous monitoring for AF may be promising in high-risk populations. Trial Registration ClinicalTrials.gov NCT04023188; https://clinicaltrials.gov/ct2/show/NCT04023188
A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging

Abstract Motivation Probabilistic latent semantic analysis (pLSA) is commonly applied to describe mass spectra (MS) images. However, the method does not provide certain outputs necessary for the quantitative scientific interpretation of data. In particular, it lacks assessment of statistical uncertainty and the ability to perform hypothesis testing. We show how linear Poisson modelling advances pLSA, giving covariances on model parameters and supporting χ2 testing for the presence/absence of MS signal components. As an example, this is useful for the identification of pathology in MALDI biological samples. We also show potential wider applicability, beyond MS, using magnetic resonance imaging (MRI) data from colorectal xenograft models. Results Simulations and MALDI spectra of a stroke-damaged rat brain show MS signals from pathological tissue can be quantified. MRI diffusion data of control and radiotherapy-treated tumours further show high sensitivity hypothesis testing for treatment effects. Successful χ2 and degrees-of-freedom are computed, allowing null-hypothesis thresholding at high levels of confidence. Availability and implementation Open-source image analysis software available from TINA Vision, www.tina-vision.net. Supplementary information Supplementary data are available at Bioinformatics online.
A Phase 2 Multi-institutional Study of Nivolumab for Patients With Advanced Refractory Biliary Tract Cancer.

Importance Currently, there is no established second-line systemic treatment for biliary tract cancer (BTC). Preclinical data have demonstrated that the presence of tumor-infiltrating CD8 T cells and programmed cell death 1 ligand 1-expressing tumor cells in the tumor microenvironment of BTC supports the rationale of using programmed cell death 1 protein blockade immunotherapy in BTC. Objective To evaluate anticancer activity of nivolumab in patients with advanced refractory BTC. Design, Setting, and Participants In this single-group, multicenter phase 2 study of nivolumab, 54 patients with histologically confirmed BTC whose disease progressed while undergoing treatment with at least 1 line but no more than 3 lines of systemic therapy were enrolled between October 5, 2016, and December 26, 2018. Analysis was performed on an intention-to-treat basis. Interventions Nivolumab, 240 mg, was delivered intravenously every 2 weeks for 16 weeks, and then 480 mg was delivered intravenously every 4 weeks until disease progression or unacceptable toxic effects occurred. Main Outcomes and Measures The primary end point was investigator-assessed objective response rate, and the secondary end points were progression-free survival, overall survival, and incidence of adverse events. Results A total of 54 patients (27 men and 27 women; median age, 65 years [range, 28-86 years]) enrolled, and 46 (22 men and 24 women; median age, 65 years [range, 28-86 years]) were examined for objective response with radiologic imaging. The investigator-assessed objective response rate was 22% (10 of 46), including 1 unconfirmed partial response, with a disease control rate of 59% (27 of 46). Central independent review found an objective response rate of 11% (5 of 46), including 1 unconfirmed partial response, with a disease control rate of 50% (23 of 46). All patients who responded to treated (hereafter referred to as responders) had mismatch repair protein-proficient tumors. The median duration of investigator-assessed response was not reached, with a median follow-up of 12.4 months. Among the intention-to-treat population, median progression-free survival was 3.68 months (95% CI, 2.30-5.69 months) and median overall survival was 14.24 months (95% CI, 5.98 months to not reached). Programmed cell death 1 ligand 1 expression in tumors was associated with prolonged progression-free survival (hazard ratio, 0.23; 95% CI, 0.10-0.51; P < .001). The most common treatment-related grade 3 or 4 toxic effects were hyponatremia (3 of 54 [6%]) and increased alkaline phosphatase (2 of 54 [4%]). Conclusions and Relevance This study found that nivolumab was well tolerated and showed modest efficacy with durable response in patients with refractory BTC. Further studies are warranted to verify the findings and evaluate biomarkers for improved treatment selection for patients. Trial Registration ClinicalTrials.gov Identifier: NCT02829918.