Miracle-dz/UniFAR-FTUs huggingface dataset:
Why aren't warning signals everywhere? On the prevalence of aposematism and mimicry in communities

Warning signals are a striking example of natural selection present in almost every ecological community – from Nordic meadows to tropical rainforests, defended prey species and their mimics ward off potential predators before they attack. Yet despite the wide distribution of warning signals, they are relatively scarce as a proportion of the total prey available, and more so in some biomes than others. Classically, warning signals are thought to be governed by positive density‐dependent selection, i.e. they succeed better when they are more common. Therefore, after surmounting this initial barrier to their evolution, it is puzzling that they remain uncommon on the scale of the community. Here, we explore factors likely to determine the prevalence of warning signals in prey assemblages. These factors include the nature of prey defences and any constraints upon them, the behavioural interactions of predators with different prey defences, the numerical responses of predators governed by movement and reproduction, the diversity and abundance of undefended alternative prey and Batesian mimics in the community, and variability in other ecological circumstances. We also discuss the macroevolution of warning signals. Our review finds that we have a basic understanding of how many species in some taxonomic groups have warning signals, but very little information on the interrelationships among population abundances across prey communities, the diversity of signal phenotypes, and prey defences. We also have detailed knowledge of how a few generalist predator species forage in artificial laboratory environments, but we know much less about how predators forage in complex natural communities with variable prey defences. We describe how empirical work to address each of these knowledge gaps can test specific hypotheses for why warning signals exhibit their particular patterns of distribution. This will help us to understand how behavioural interactions shape ecological communities.
Mechanical Complications of Acute Myocardial Infarction: A Scientific Statement From the American Heart Association

Over the past few decades, advances in pharmacological, catheter-based, and surgical reperfusion have improved outcomes for patients with acute myocardial infarctions. However, patients with large infarcts or those who do not receive timely revascularization remain at risk for mechanical complications of acute myocardial infarction. The most commonly encountered mechanical complications are acute mitral regurgitation secondary to papillary muscle rupture, ventricular septal defect, pseudoaneurysm, and free wall rupture; each complication is associated with a significant risk of morbidity, mortality, and hospital resource utilization. The care for patients with mechanical complications is complex and requires a multidisciplinary collaboration for prompt recognition, diagnosis, hemodynamic stabilization, and decision support to assist patients and families in the selection of definitive therapies or palliation. However, because of the relatively small number of high-quality studies that exist to guide clinical practice, there is significant variability in care that mainly depends on local expertise and available resources.
Loss of SDHB Promotes Dysregulated Iron Homeostasis, Oxidative Stress, and Sensitivity to Ascorbate

Loss of different succinate dehydrogenase subunits can lead to different cell and tumor phenotypes, linking stronger 2-OG–dependent dioxygenases inhibition, iron overload, and ROS accumulation following SDHB mutation. Succinate dehydrogenase is a key enzyme in the tricarboxylic acid cycle and the electron transport chain. All four subunits of succinate dehydrogenase are tumor suppressor genes predisposing to paraganglioma, but only mutations in the SDHB subunit are associated with increased risk of metastasis. Here we generated an Sdhd knockout chromaffin cell line and compared it with Sdhb-deficient cells. Both cell types exhibited similar SDH loss of function, metabolic adaptation, and succinate accumulation. In contrast, Sdhb−/− cells showed hallmarks of mesenchymal transition associated with increased DNA hypermethylation and a stronger pseudo-hypoxic phenotype compared with Sdhd−/− cells. Loss of SDHB specifically led to increased oxidative stress associated with dysregulated iron and copper homeostasis in the absence of NRF2 activation. High-dose ascorbate exacerbated the increase in mitochondrial reactive oxygen species, leading to cell death in Sdhb−/− cells. These data establish a mechanism linking oxidative stress to iron homeostasis that specifically occurs in Sdhb-deficient cells and may promote metastasis. They also highlight high-dose ascorbate as a promising therapeutic strategy for SDHB-related cancers. Significance: Loss of different succinate dehydrogenase subunits can lead to different cell and tumor phenotypes, linking stronger 2-OG–dependent dioxygenases inhibition, iron overload, and ROS accumulation following SDHB mutation.
Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site

Microbial pathogens bind host complement regulatory proteins to evade the immune system. The bacterial pathogen Neisseria meningitidis, or meningococcus, binds several complement regulators, including human Factor H (FH). FH binding protein (FHbp) is a component of two licensed meningococcal vaccines and in mice FHbp elicits antibodies that inhibit binding of FH to FHbp, which defeat the bacterial evasion mechanism. However, humans vaccinated with FHbp develop antibodies that enhance binding of FH to the bacteria, which could limit the effectiveness of the vaccines. In the present study, we show that two vaccine-elicited antibody fragments (Fabs) isolated from different human subjects increase binding of complement FH to meningococcal FHbp by ELISA. The two Fabs have different effects on the kinetics of FH binding to immobilized FHbp as measured by surface plasmon resonance. The 1.7- and 2.0-Å resolution X-ray crystal structures of the Fabs in complexes with FHbp illustrate that the two Fabs bind to similar epitopes on the amino-terminal domain of FHbp, adjacent to the FH binding site. Superposition models of ternary complexes of each Fab with FHbp and FH show that there is likely minimal contact between the Fabs and FH. Collectively, the structures reveal that the Fabs enhance binding of FH to FHbp by altering the conformations and mobilities of two loops adjacent to the FH binding site of FHbp. In addition, the 1.5 Å-resolution structure of one of the isolated Fabs defines the structural rearrangements associated with binding to FHbp. The FH-enhancing human Fabs, which are mirrored in the human polyclonal antibody responses, have important implications for tuning the effectiveness of FHbp-based vaccines.
Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach

ABSTRACT The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T. awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.
DGLinker: flexible knowledge-graph prediction of disease–gene associations

Abstract As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind. kcl.ac. uk. The webserver is free and open to all users without the need for registration.
Association Between Vitamin E and Handgrip Strength in the Korean General Population in KNHANES VII (2018)

Objective To investigate the association between vitamin E and handgrip strength (HGS) with multiple factors. Methods A total of 1,814 participants were included (822 men and 981 women) from the Korean subjects of the 7th Korea National Health and Nutrition Examination Survey in 2018. Data were analyzed using multiple logistic regression to determine the correlation between vitamin E and HGS with potential confounding factors. Results In the multiple logistic regression model, only the young age group (19–40 years) of men showed a positive relationship between vitamin E and HGS. However, in older age groups (41–80 years) of men and all age groups of women, there was no statistically significant result. After adjusting for confounding factors, young men showed higher vitamin E levels and higher HGS. Conversely, women and older age groups did not show significant results after adjusting for confounding factors. Conclusion In this study, the serum vitamin E level had a positive effect on HGS in young men (<40 years). Further research is needed on this topic regarding vitamin E intake and other objective measures.
Overcoming stochastic variations in culture variables to quantify and compare growth curve data

The comparison of growth, whether it is between different strains or under different growth conditions, is a classic microbiological technique that can provide genetic, epigenetic, cell biological, and chemical biological information depending on how the assay is used. When employing solid growth media, this technique is limited by being largely qualitative and low throughput. Collecting data in the form of growth curves, especially automated data collection in multi‐well plates, circumvents these issues. However, the growth curves themselves are subject to stochastic variation in several variables, most notably the length of the lag phase, the doubling rate, and the maximum expansion of the culture. Thus, growth curves are indicative of trends but cannot always be conveniently averaged and statistically compared. Here, we summarize a simple method to compile growth curve data into a quantitative format that is amenable to statistical comparisons and easy to graph and display.
WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and IAA-conjugating genes and by inhibiting NH4 + efflux in the root elongation zone.

Ammonium (NH4 + ) is toxic to root growth in most plants already at moderate levels. Transcriptional regulation is one of the most important mechanisms in plant's response to NH4 + toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear. Here, RNA-seq analysis in Arabidopsis roots was performed to screen ammonium-responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH4 + , was selected. We define the role of WRKY46 by using mutation and overexpression assays, and characterize the regulation of NUDX9 and IAA-conjugating genes by WRKY46 via yeast one-hybrid and electrophoretic mobility shift assays and ChIP-quantitative PCR. Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH4 + -suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA-conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and inhibits their transcription, thus positively regulating free IAA content and stabilizing protein N-glycosylation, leading to an inhibition of NH4 + efflux in the root elongation zone (EZ). We identify TF involvement in regulating NH4 + efflux in the EZ, and show that WRKY46 inhibits NH4 + efflux by negative regulation of NUDX9 and IAA-conjugating genes.
A case report of prenatal diagnosis of fetal alloimmune thrombocytopenia

Abstract Rationale: Fetal alloimmune thrombocytopenia (FAIT) is a serious life-threatening disease caused by platelet-antigen incompatibility between the mother and fetus. FAIT can lead to fetal thrombocytopenia, intracranial hemorrhage (ICH), fetal death and severe neurological disorders after birth. Noninvasive prenatal diagnosis technology has not been widely used in China, and thus few cases of FAIT can be diagnosed prenatally. In this study, we report a case of prenatal diagnosis and treatment of FAIT. Patient concerns: A 29-year-old female was admitted at 32 weeks’ gestational age (GA). Fetal ultrasound at 32 weeks’ GA showed a hemorrhagic focus area in the left lateral ventricle and the sign of severe fetal anemia. Hence, fetal umbilical cord puncture was ordered to identify the etiology. Diagnoses: The fetal cord blood test revealed a normal hemoglobin level but severe fetal thrombocytopenia (platelet count, 23 × 109/L). Antibodies of human platelet antigens and human leukocyte antigens between mother and fetus were positive, and thus the diagnosis of FAIT was confirmed. Interventions: The patient refused intravenous immunoglobulin (IVIG) therapy owing to financial consideration. She was treated with dexamethasone acetate tablets (Xianju Company, China) 0.75 mg twice a day until delivery and cesarean section was performed at 34 weeks’ GA. The newborn received postnatal anti-platelet antibody treatment. Outcomes: The platelet count of the newborn progressively decreased until the third day after birth and it increased to normal level after postnatal treatment. The neonatal cerebral ultrasound showed the area of hemorrhage was in the process of absorption. During the postnatal one-year follow-up, the neonate showed normal developmental milestones and had no abnormal signs of neurological symptoms. Lessons: For FAIT, the fetal umbilical cord puncture can be carried out by skilled fetal medical teams. Dexamethasone acetate tablets can be an alternative choice for patients from underdeveloped areas.
Subliminal perception is continuous with conscious vision and can be predicted from prestimulus electroencephalographic activity

Individuals are able to discriminate visual stimuli they report not consciously seeing. This phenomenon is known as “subliminal perception. ” Such capacity is often assumed to be relatively automatic in nature and rely on stimulus‐driven activity in low‐level cortical areas. Instead, here we asked to what extent neural activity before stimulus presentation influences subliminal perception. We asked participants to discriminate the location of a briefly presented low‐contrast visual stimulus and then rate how well they saw the stimulus. Consistent with previous studies, participants correctly discriminated with slightly above chance‐level accuracy the location of a stimulus they reported not seeing. Signal detection analyses indicated that while subjects categorized their percepts as “unconscious,” their capacity to discriminate these stimuli lay on the same continuum as conscious vision. We show that the accuracy of discriminating the location of a subliminal stimulus could be predicted with relatively high accuracy (AUC = 0.70) based on lateralized electroencephalographic (EEG) activity before the stimulus, the hemifield where the stimulus was presented, and the accuracy of previous trial's discrimination response. Altogether, our results suggest that rather than being a separate unconscious capacity, subliminal perception is based on similar processes as conscious vision.
Production planning of a furniture manufacturing company with random demand and production capacity using stochastic programming

In this article two multi-stage stochastic linear programming models are developed, one applying the stochastic programming solver integrated by Lingo 17.0 optimization software that utilizes an approximation using an identical conditional sampling and Latin-hyper-square techniques to reduce the sample variance, associating the probability distributions to normal distributions with defined mean and standard deviation; and a second proposed model with a discrete distribution with 3 values and their respective probabilities of occurrence. In both cases, a scenario tree is generated. The models developed are applied to an aggregate production plan (APP) for a furniture manufacturing company located in the state of Hidalgo, Mexico, which has important clients throughout the country. Production capacity and demand are defined as random variables of the model. The main purpose of this research is to determine a feasible solution to the aggregate production plan in a reasonable computational time. The developed models were compared and analyzed. Moreover, this work was complemented with a sensitivity analysis; varying the percentage of service level, also, varying the stochastic parameters (mean and standard deviation) to test how these variations impact in the solution and decision variables.
Sustained viremia suppression by SHIVSF162P3CN-recalled effector-memory CD8+ T cells after PD1-based vaccination

HIV-1 functional cure requires sustained viral suppression without antiretroviral therapy. While effector-memory CD8+ T lymphocytes are essential for viremia control, few vaccines elicit such cellular immunity that could be potently recalled upon viral infection. Here, we investigated a program death-1 (PD1)-based vaccine by fusion of simian immunodeficiency virus capsid antigen to soluble PD1. Homologous vaccinations suppressed setpoint viremia to undetectable levels in vaccinated macaques following a high-dose intravenous challenge by the pathogenic SHIVSF162P3CN. Poly-functional effector-memory CD8+ T cells were not only induced after vaccination, but were also recalled upon viral challenge for viremia control as determined by CD8 depletion. Vaccine-induced effector memory CD8+ subsets displayed high cytotoxicity-related genes by single-cell analysis. Vaccinees with sustained viremia suppression for over two years responded to boost vaccination without viral rebound. These results demonstrated that PD1-based vaccine-induced effector-memory CD8+ T cells were recalled by AIDS virus infection, providing a potential immunotherapy for functional cure.
The prevalence and break down of narrow anterior chamber angle pathology presenting to a general ophthalmology clinic

Abstract To approximate the breakdown of narrow anterior chamber angle conditions, on general ophthalmology clinics, in the predominantly white population of the South East Kent region in the United Kingdom. A review was done of all patients attending a secondary care ophthalmology general clinic over a 3-year period. Patients were assessed with: slitlamp biomicroscopy with indentation gonioscopy; SD optical coherence tomography, Humphrey visual field analyzer, and high frequency ultrasound and categorized into various narrow angle conditions. These were: narrow Van Herrick but open angle; primary narrow angle but nonoccludable; primary angle closure suspect; primary angle closure; chronic narrow angle glaucoma; plateau iris configuration; plateau iris syndrome, and phacomorphic narrow angle. A total of 14,520 patients were referred to the clinic, of those 10,491 attended and were analyzed. Six hundred seventy four (6.4%) of the patients had some form of narrow angle condition in at least 1 eye. The majority of these patients were at relative low risk of pathology such as nonoccludable narrow angles (359/53.3%) and narrow Van Herrick but open angles (93/13.8%). 8.8% of all the narrow angle patients had primary angle closure suspect or primary angle closure. Plateau iris pathology was seen in 68 (10.1%) of patients with 18 (26%) having confirmed plateau iris syndrome after peripheral iridotomy. Phacomorphic pathology was confirmed in 75 (11.1%) patients. Narrow angle patients form a significant proportion (6.4%) of those attending general ophthalmology clinic in the predominantly white population in the South East Kent Region of the United Kingdom. The majority of these (67.1%) are at a relatively low risk of developing acute or chronic angle closure glaucoma. Of the remaining patients 8.8% have primary angle closure suspect or primary angle closure and 2.9% have already progressed to chronic narrow angle closure glaucoma. Plateau iris pathology and phacomorphic glaucoma account for the remainder of the presentations.
Transition to Widowhood Among Older Adults in Rural Areas: A Study From the Faroe Islands

Studies have shown that losing a spouse can cause both physical and mental suffering for the bereaved. This qualitative study aimed to gather knowledge about how men and women in the Faroe Islands, a small-scale society in the North Atlantic Ocean, managed the transition to widowhood. Five women and three men were interviewed, their age varying from 67 to 74 years. A hermeneutic analytic method was applied. Our findings showed that managing the transition to widowhood followed two tracks, namely the process of loss and the process of restoration. For participants locked in either process, the transition caused severe disruption in daily living, while participants who managed to oscillate between the two processes appeared to manage the transition to widowhood and get on with their lives. Our findings, and those from other studies, point to the need to offer structured individual support for people who have lost their life partner.