Miracle-dz/UniFAR-FTUs huggingface dataset:
Decline in Natural Fisheries — A Genetic Analysis and Suggestion for Recovery

Overfishing and pollution of the aquatic environment, in addition to their direct effects on natural fisheries, may have also influenced natural fish populations genetically. Overfishing drastically reduces population size and, since the larger individuals are selectively removed, is equivalent to selection for smaller sized fish. Adaptation of natural fish populations to their environment must have been reduced by rapid environmental changes resulting from pollution and infestation. Inbreeding, negative selection, and lack of adaption are here considered as the genetic causes for the decline of natural fisheries and lack of recovery. Restocking programs involving hatchery stocks are unlikely to solve this problem, since these stocks were selected for adaptation to hatchery environments and not to natural environments. A series of studies have demonstrated heterosis of interstrain crossbreds, mainly between hatchery and wild stocks of salmonids, for performance in natural waters. Two strategies could be i.
WORKER POLYMORPHISM AND NEST STRUCTURE IN MYRMECIA BREVINODA FOREL (HYMENOPTERA: FORMICIDAE)

A large nest of Myrmecia brevinoda (with a soil mound 70 cm tall) contained 2576 workers and 1 queen. Other small ants, termites and various insect larvae were also found in uninhabited parts of the mound. Although workers exhibit considerable size variation (length: 13–36 mm), relative growth (head length versus head width) among workers is not allometric. Thus workers are monomorphic although they fall into 2 obvious size classes which overlap broadly. Small workers were abundant in the lower parts of the nest while larger workers prevailed in the upper parts. Field observations confirmed the occurrence of size polyethism, i.e. larger workers were engaged in hunting, defence and extranidal building, while smaller workers excavated soil from inside the nest.
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

Abstract Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity—a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei. polsl.pl/.
Functional Properties of Carotenoids in Human Health

Carotenoids are compounds of great dietery importance. Recent interest in carotenoids has been stimulated by epidemiological studies that strongly suggest that consumption of carotenoid-rich foods reduces the incidence of several diseases such as cancers, cardiovascular diseases, age-related macular degeneration, cataracts, diseases related to low immune function, and other degenerative diseases. Health benefits of carotenoids are derived from the fruits and vegetables in the diet, particularly from cooked products containing oil, or from supplements of their extracts, such as tomato sauce, dried tomatoes, or those suspended in oil. This article provides a brief overview of the chemistry of carotenoids—their absorption, transport, bioavailability, metabolism, and their action as antioxidants, and in the prevention of a number of common diseases.
Population Structure of Columbia River Basin Chinook Salmon and Steelhead Trout

The population structure of chinook salmon and steelhead trout is presented as an assimilation of the life history forms that have evolved in synchrony with diverse and complex environments over their Pacific range. As poikilotherms, temperature is described as the overwhelming environmental influence that determines what life history options occur. The different populations represent ecological types referred to as spring-, summer-, fall, and winter-run segments, as well as stream- and ocean-type, or stream- and ocean-maturing life history forms. However, they are more correctly described as a continuum of forms that fall along a temporal cline related to incubation and rearing temperatures that determine spawn timing and juvenile residence patterns. Population structure of chinook salmon and steelhead in the Columbia Basin, therefore, is the reflection of the genetic composition of the founding source or sources within the respective region, shaped by the environment, principally temperature, that defines life history evolutionary strategy to maximize fitness under the conditions delineated. The key in developing an effective recovery program for chinook salmon and steelhead is to recognize that measures taken must address the genetic and biological requirements of the population unit within the environmental template identified.
Changes in mucociliary clearance over time in children with cystic fibrosis

(a) To quantify changes in mucociliary clearance (MCC) over time in children with cystic fibrosis (CF) and the relationship between MCC and rate of infection with Pseudomonas aeruginosa (PA); (b) to determine the impact of MCC on the evolution of CF lung disease; and (c) to explore the role of mucus composition as a determinant of MCC.
Can We Predict the Evolution of Depressive Symptoms, Adjustment, and Perceived Social Support of Pregnant Women from Their Personality Characteristics? a Technology-Supported Longitudinal Study

Background: Research exploring the relationship between personality and important pregnancy outcomes (i.e., depressive symptoms, adjustment, and perceived social support) tends to be cross-sectional, arguably due to the difficulties of conducting longitudinal and mental health research in this population. The objective of this study is to use a web-based solution to longitudinally explore how personality traits are associated, not only with the co-occurrence of these outcomes but also with their evolution during pregnancy. Stability and change of these outcomes will also be investigated. Methods: The sample included 85 pregnant women attending several medical centers in Spain. The web-based assessment included sociodemographic and obstetric variables (ad hoc) and personality (at the second trimester only), and outcomes at both the second and the third trimester (i.e., depressive symptoms, adjustment, and perceived social support). Results: The results showed that adjustment worsened from the second to the third trimester of pregnancy. Neuroticism (N), low extraversion (E), and psychoticism (P) were cross-sectionally and longitudinally associated with outcomes. In addition, N and, to a lesser extent P, uniquely contributed to the evolution of these outcomes in the multivariate analyses, including autoregressions. Conclusion: Personality and especially N and P should be evaluated early during pregnancy mental health screening. The use of a web page appears to be a useful tool for that purpose. Technologies might also help disseminate mental health prevention programs for these women, which would be especially recommended for those with a personality profile characterized by high N and P and, to a lesser extent, low E.
Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.
The subcellular organization of stomatal initials in sugarcane leaves: the guard and subsidiary mother cells

The subcellular organization of guard and subsidiary mother cells in sugarcane leaves was examined by electron microscopy. Guard and subsidiary mother cells assume a characteristic shape before mitosis and contain variable numbers of mitochondria, proplastids, dictyosomes, and cisternae of rough endoplasmic reticulum. In guard mother cells, the nucleus occupies a central position, whereas in subsidiary mother cells, the nucleus is located toward one end of the cell, near the guard mother cell. Microtubules are found in both guard and subsidiary mother cells and are either closely grouped to form defined preprophase bands or randomly dispersed between the nucleus and the preprophase bands. Many of the dispersed microtubules occur in close association with the nucleus in both guard and subsidiary mother cells. Possible functions for these preprophase microtubules are discussed in relation to their organization in the preprophase band, their orientation, and their distribution within guard and subsidiary mot.
Use of Artificial Intelligence as an Innovative Method for Liver Graft Macrosteatosis Assessment

The worldwide implementation of a liver graft pool using marginal livers (ie, grafts with a high risk of technical complications and impaired function or with a risk of transmitting infection or malignancy to the recipient) has led to a growing interest in developing methods for accurate evaluation of graft quality. Liver steatosis is associated with a higher risk of primary nonfunction, early graft dysfunction, and poor graft survival rate. The present study aimed to analyze the value of artificial intelligence (AI) in the assessment of liver steatosis during procurement compared with liver biopsy evaluation. A total of 117 consecutive liver grafts from brain‐dead donors were included and classified into 2 cohorts: ≥30 versus <30% hepatic steatosis. AI analysis required the presence of an intraoperative smartphone liver picture as well as a graft biopsy and donor data. First, a new algorithm arising from current visual recognition methods was developed, trained, and validated to obtain automatic liver graft segmentation from smartphone images. Second, a fully automated texture analysis and classification of the liver graft was performed by machine‐learning algorithms. Automatic liver graft segmentation from smartphone images achieved an accuracy (Acc) of 98%, whereas the analysis of the liver graft features (cropped picture and donor data) showed an Acc of 89% in graft classification (≥30 versus <30%). This study demonstrates that AI has the potential to assess steatosis in a handy and noninvasive way to reliably identify potential nontransplantable liver grafts and to avoid improper graft utilization.
Characteristics and Outcomes of Patients Referred to an Emergency Department-Based End-of-Life Care Service in Hong Kong: A Retrospective Cohort Study

Background: This study describes the characteristics and outcomes of patients referred to an emergency department (ED)-based end-of-life (EOL) service in a tertiary acute hospital in Hong Kong. We examine how emergency physicians (EPs) perform in recognizing and managing dying patients. Methods: From September 2010 to April 2018, patients referred to this EOL service in this hospital were included. A group of 5 EPs assessed whether the referred patient would die within a few days. Dying patients (EOL group) were admitted to ED-based EOL service whereas those not likely dying within few days (non-EOL group) would continue management in respective specialty wards. Baseline characteristics of these 2 groups were compared. The time-to-death and use of opioids and anticholinergics were compared. Results: In total, 783 of 830 patients assessed were recognized as being in dying phase, with 688 admitted under ED-based EOL care. Their demographics and characteristics were described. Mean time from assessment to death (time-to-death) was significantly less in EOL group (38.93 hours) than in non-EOL group (250.36 hours; P = .004). Mean time-to-death was not significantly different between those under EP-based EOL service or not. The ED-based EOL care had significantly more patients receiving symptomatic treatment. Interpretation: The characteristics of patients under an ED-based EOL service are described. Emergency physicians are capable of recognizing dying patients. Emergency department-based EOL service does not alter the dying process and offers adequate palliation of symptoms. Emergency physician should assume a more active role in providing adequate EOL care to suitable patients.
Further studies on puffinosis, a disease of the manx shearwater (Puffinus puffinus)

Epizootics of puffinosis occurred on Skomer Island during the period from late August to mid-September 1978, 1979, and 1980. They affected shearwater fledglings in well-defined areas on the island which were the same for each of the 3 years of study. In contrast to previous reports puffinosis was also recorded in young chicks and full-grown birds.
Extracts of Thai Perilla frutescens nutlets attenuate tumour necrosis factor-α-activated generation of microparticles, ICAM-1 and IL-6 in human endothelial cells

Abstract Elevation of endothelial microparticles (EMPs) play an important role in the progression of inflammation-related vascular diseases such as cardiovascular diseases (CVDs). Thai perilla (Perilla frutescens) nutlets are rich in phenolic compounds and flavonoids that exert potent antioxidant and anti-inflammatory effects. We found that the ethyl acetate (EA) and ethanol (Eth) extracts of Thai perilla nutlets contain phenolic compounds such as luteolin, apigenin, chryseoriol and their glycosides, which exhibit antioxidant activity. The goal of the present study was to investigate the effects of the extracts on endothelial activation and EMPs generation in tumour necrosis factor-α (TNF-α)-induced EA.hy926 cells. We found that TNF-α (10 ng/ml) activated EA.hy926 cells and subsequently generated EMPs. Pre-treatment with the extracts significantly attenuated endothelial activation by decreasing the expression of the intracellular adhesion molecule-1 (ICAM-1) in a dose-dependent manner. Only the Eth extract showed protective effects against overproduction of interleukin-6 (IL-6) in the activated cells. Furthermore, the extracts significantly reduced TNF-α-enhanced EMPs generation in a dose-dependent manner. In conclusion, Thai perilla nutlet extracts, especially the Eth extract, may have potential to protect endothelium against vascular inflammation through the inhibition of endothelial activation and the generation of endothelial microparticles (EMPs).
microRNAs as Promising Biomarkers of Platelet Activity in Antiplatelet Therapy Monitoring

Given the high morbidity and mortality of cardiovascular diseases (CVDs), novel biomarkers for platelet reactivity are urgently needed. Ischemic events in CVDs are causally linked to platelets, small anucleate cells important for hemostasis. The major side-effect of antiplatelet therapy are life-threatening bleeding events. Current platelet function tests are not sufficient in guiding treatment decisions. Platelets host a broad spectrum of microRNAs (miRNAs) and are a major source of cell-free miRNAs in the blood stream. Platelet-related miRNAs have been suggested as biomarkers of platelet activation and assessment of antiplatelet therapy responsiveness. Platelets release miRNAs upon activation, possibly leading to alterations of plasma miRNA levels in conjunction with CVD or inadequate platelet inhibition. Unlike current platelet function tests, which measure platelet activation ex vivo, signatures of platelet-related miRNAs potentially enable the assessment of in vivo platelet reactivity. Evidence suggests that some miRNAs are responsive to platelet inhibition, making them promising biomarker candidates. In this review, we explain the secretion of miRNAs upon platelet activation and discuss the potential use of platelet-related miRNAs as biomarkers for CVD and antiplatelet therapy monitoring, but also highlight remaining gaps in our knowledge and uncertainties regarding clinical utility. We also elaborate on technical issues and limitations concerning plasma miRNA quantification.
ZSCAN4+ mouse embryonic stem cells have an oxidative and flexible metabolic profile

Cultured mouse embryonic stem cells are a heterogeneous population with diverse differentiation potential. In particular, the subpopulation marked by Zscan4 expression has high stem cell potency and shares with 2 cell stage preimplantation embryos both genetic and epigenetic mechanisms that orchestrate zygotic genome activation. Although embryonic de novo genome activation is known to rely on metabolites, a more extensive metabolic characterization is missing. Here we analyze the Zscan4+ mouse stem cell metabolic phenotype associated with pluripotency maintenance and cell reprogramming. We show that Zscan4+ cells have an oxidative and adaptable metabolism, which, on one hand, fuels a high bioenergetic demand and, on the other hand, provides intermediate metabolites for epigenetic reprogramming. Our findings enhance our understanding of the metastable Zscan4+ stem cell state with potential applications in regenerative medicine.
Primed CRISPR DNA uptake in Pyrococcus furiosus

Abstract CRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of ‘spacers’ which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called ‘adaptation’. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it (‘interference’). Adaptation can be ‘naïve’, i.e. independent of any existing spacer matches, or it can be ‘primed’, i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.
Desirability and acceptability of a treatment-sequencing model in relapsing-remitting multiple sclerosis: A health technology assessment perspective

Objective Gather health technology assessment (HTA) experts' insights on the desirability and acceptability of treatment-sequencing models applied to relapsing-remitting multiple sclerosis (RRMS). Data source/study setting Primary data. Study design In-depth double-blind semi-structured telephone interviews. Data collection/extraction methods General themes were extracted from qualitative interviews. Principal findings Although experts confirmed the importance of evaluating the clinical and cost-effectiveness of treatments as part of a sequence, the current HTA decision making framework is not conducive to this. Developing an RRMS treatment-sequencing model that meets HTA requirements is difficult, in particular due to scarcity of effectiveness data in later treatment lines. Conclusions At present, a treatment-sequencing model for RRMS may be desirable yet not requested by HTA bodies for their decision making. However, there could be other areas where a treatment-sequencing model for RRMS is of use.
Mental Health and Weather Extremes in a Southeastern U.S. City: Exploring Group Differences by Race

The connection between mental health and weather extremes is a public health concern, but less studied to date than physical health. This exploratory study examines the mental health impacts of two kinds of weather extremes increasingly linked to climate change—summer heat waves and extreme winter weather—in a low- to middle-income population in the Southeastern U.S. The distribution of mental health impacts, and potential pathways to them, are examined with a focus on race. Data are from a random-sample survey of 426 participants and are analyzed with bivariate statistics and path analysis. Self-reported mental health impacts, in both seasons, were common in our study, with White participants tending to report worse impacts than participants who identified with other racial groups. Physical health had direct effects on mental health across several models, overall and by racial group. For summer heat waves, concern about climate change and social cohesion had direct and indirect effects, respectively, on mental health in White participants only. For extreme winter weather, preparedness had a direct negative effect on mental health in White, but not Black, participants. Results suggest that there may be racial differences in the influence of human and social capital factors on mental health related to weather extremes, warranting further study of this critical topic and with larger racial subgroup samples.
“It Wasn’t Like We Expected”: Analyzing (Non-)Participation of Family Caregivers of People With Dementia in Sports Activities From Different Perspectives

Family caregivers of people with dementia represent a physically and psychologically burdened target group, which can benefit from offers of health promotion, but rarely use existing services. This article deals with the motives and conditions that induce this target group to be (not) active in sports. For this purpose, the perspectives of family caregivers and local sports clubs in Germany are compared to uncover similarities and discrepancies with the aim of developing target group-specific health promotion services. Results were classified into three dimensions for (non-)participation in sports activities. People who participated in sports club programs generally confirmed its positive effects. Among other things, the sports clubs and family caregivers surveyed emphasized the compatibility of the care situation with possible leisure activities as very important components for (non-)participation. The results show that the subjective health attitudes must be taken into account in the design of health promotion offers.