Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution and abundance of Rhynchocinetes typus (Crustacea: Decapoda), in different benthic community structures in northern Chile

An evaluation was carried out on the distribution and abundance of the rock shrimp Rhynchocinetes typus in the inshore subtidal zone on the north-central coast of Chile. A number of different benthic community types occur in the region which have different degrees of spatial complexity provided by the primary substratum and by the biotic communities colonizing the substratum. Shrimp abundance was estimated in five different community types including shallow and deep ‘barren grounds’, low encrusting communities, erect suspension feeding associations, and kelp beds of Lessonia trabeculata. The abundance of shrimp was determined on three different types of primary substratum (stones, boulders, rock mass) within each community. Rhynchocinetes typus occurred in all the communities studied, showing the highest abundance on the deep barren grounds and lowest abundance on the shallow barren grounds. The shrimp was found to prefer the stony areas, as these offered the greatest degree of refuge. The abundance of predators was not significantly different among the different communities. However, a decline of abundance of predators was apparent over the deep barren grounds.
Novel function for AP-1B during cell migration

The epithelial cell-specific clathrin adaptor protein (AP)-1B has a well-established role in polarized sorting of cargos to the basolateral membrane. Here we show that β1 integrin was dependent on AP-1B and its coadaptor, autosomal recessive hypercholesterolemia protein (ARH), for sorting to the basolateral membrane. We further demonstrate an unprecedented role for AP-1B at the basal plasma membrane during collective cell migration of epithelial sheets. During wound healing, expression of AP-1B (and ARH in AP–1B-positive cells) slowed epithelial-cell migration. We show that AP-1B colocalized with β1 integrin in focal adhesions during cell migration using confocal microscopy and total internal reflection fluorescence microscopy on fixed specimens. Further, AP-1B labeling in cell protrusions was distinct from labeling for the endocytic adaptor complex AP-2. Using stochastic optical reconstruction microscopy we identified numerous AP–1B-coated structures at or close to the basal plasma membrane in cell protrusions. In addition, immunoelectron microscopy showed AP-1B in coated pits and vesicles at the plasma membrane during cell migration. Lastly, quantitative real-time reverse transcription PCR analysis of human epithelial-derived cell lines revealed a loss of AP-1B expression in highly migratory metastatic cancer cells suggesting that AP-1B’s novel role at the basal plasma membrane during cell migration might be an anticancer mechanism.
Risk of hematological malignancy in blood donors: A nationwide cohort study

There has been a concern that blood donations can increase the risk of hematological malignancies. We investigated if blood donations increase the risk of developing hematological malignancies, specifically acute lymphoblastic leukemia, acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myeloid leukemia, Hodgkin lymphoma, and myeloma, as well other non‐Hodgkin lymphoma.
Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins

Molecular dynamics (MD) simulations of six upgraded empirical force fields were compared and evaluated with short peptides, intrinsically disordered proteins and folded proteins using trajectories of 1, 1.5, 5 or 10μs (5 replicates of 200ns, 300ns, 1μs or 2 μs) for each system. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. Here, the MD simulations were done in an explicit solvent with RS-peptide, HEWL19, HIV-rev, Aβ-40, A-42, phosphodiesterase-γ, CspTm and Ubiquitin using ff99IDPs, ff14IDPs, ff14IDPSFF, ff03w, CHARMM36m and CHARMM22* force fields. The IDP ensembles generated by six all-atom empirical force fields were compared against NMR data. Despite using identical starting structures and simulation parameters, ensembles obtained with different force fields exhibit significant differences in NMR RMDs, secondary structure contents as well as the global properties such as radius of gyration. The IDPs-specific force fields could substantially reproduce the experimental observables in force field comparison: they have the lowest error in chemical shifts and J-couplings for short peptides/proteins, reasonably well for large IDPs and reasonably well with the radius of gyration. A high population of disorderness was observed in the IDPs-specific force field for IDPs ensemble with fraction of β sheets for β-amyloids. The CHARMM22* performs better for many observables, however, still has a preference towards the helicity for short peptides. The results of β amyloid-42 starting from two different initial structures (Aβ421Z0Q and Aβ42model) were also compared with DSSP and NMR data. Results obtained with IDPs-specific force fields within 2µs simulation time are similar, even though starting from different structures. The current force fields perform equally well for folded proteins. The results of currently developed or modified force fields for IDPs are capable of enlightening force field's overall performance for disordered as well as folded proteins, therefore contributing to force field development.
Chlamydia trachomatis Plasmid Gene Protein 3 Is Essential for the Establishment of Persistent Infection and Associated Immunopathology

Chlamydia trachomatis can cause persistent infection that drives damaging inflammatory responses resulting in infertility and blindness. Little is known about chlamydial genes that cause persistence or factors that drive damaging pathology. In this work, we show that the C. trachomatis plasmid protein gene 3 (Pgp3) is the essential virulence factor for establishing persistent female genital tract infection and provide supportive evidence that Pgp3 functions similarly in a nonhuman primate trachoma model. We further show that persistent Ppg3-dependent infection drives damaging immunopathology. These results are important advances in understanding the pathophysiology of chlamydial persistence. ABSTRACT Chlamydia trachomatis is an obligate intracellular bacterial pathogen that causes blinding trachoma and sexually transmitted disease afflicting hundreds of millions of people globally. A fundamental but poorly understood pathophysiological characteristic of chlamydial infection is the propensity to cause persistent infection that drives damaging inflammatory disease. The chlamydial plasmid is a virulence factor, but its role in the pathogenesis of persistent infection capable of driving immunopathology is unknown. Here, we show by using mouse and nonhuman primate infection models that the secreted plasmid gene protein 3 (Pgp3) is essential for establishing persistent infection. Ppg3-dependent persistent genital tract infection resulted in a severe endometritis caused by an intense infiltration of endometrial submucosal macrophages. Pgp3 released from the cytosol of lysed infected oviduct epithelial cells, not organism outer membrane-associated Pgp3, inhibited the chlamydial killing activity of antimicrobial peptides. Genetic Pgp3 rescue experiments in cathelin-related antimicrobial peptide (CRAMP)-deficient mice showed Pgp3-targeted antimicrobial peptides to subvert innate immunity as a pathogenic strategy to establish persistent infection. These findings provide important advances in understanding the role of Pgp3 in the pathogenesis of persistent chlamydial infection and associated immunopathology. IMPORTANCE Chlamydia trachomatis can cause persistent infection that drives damaging inflammatory responses resulting in infertility and blindness. Little is known about chlamydial genes that cause persistence or factors that drive damaging pathology. In this work, we show that the C. trachomatis plasmid protein gene 3 (Pgp3) is the essential virulence factor for establishing persistent female genital tract infection and provide supportive evidence that Pgp3 functions similarly in a nonhuman primate trachoma model. We further show that persistent Ppg3-dependent infection drives damaging immunopathology. These results are important advances in understanding the pathophysiology of chlamydial persistence.
Identification of skipjack tuna (Katsuwonus pelamis) pelagic hotspots applying a satellite remote sensing-driven analysis of ecological niche factors: A short-term run

Skipjack tuna (SJT) pelagic hotspots in the western North Pacific (WNP) were modelled using fishery and satellite remotely sensed data with Ecological Niche Factor Analysis (ENFA) models. Our objectives were to model and predict habitat hotspots for SJT and assess the monthly changes in sub-surface temperatures and mixed layer depths at fishing locations. SJT presence-only monthly resolved data, sea surface temperature, chlorophyll-a, diffuse attenuation coefficient, sea surface heights and surface wind speed were used to construct ENFA models and generate habitat suitability indices using a short-term dataset from March-November 2004. The suitability indices were then predicted for July-October (2007 and 2008). Monthly aggregated polygons of areas fished by skipjack tuna pole and line vessels were also overlaid on the predicted habitat suitability maps. Distributions of sub-surface temperatures and mixed layer depths (MLD) at fishing locations were also examined. Our results showed good fit for ENFA models, as indicated by the absolute validation index, the contrast validation index and the continuous Boyce index. The predicted hotspots showed varying concurrences when compared with 25-degree polygons derived from fished areas. Northward shifts in SJT hotspots corresponded with declining MLDs from March to September. The MLDs were shallower in summer and deeper in autumn and winter months. The habitat hotspots modeled using ENFA were consistent with the known ecology and seasonal migration pattern of SJT. The findings of this work, derived from a short-term dataset, enable identification of SJT hotspots in the WNP, thus contributing valuable information for future research on SJT habitat prediction models.
Demographic perspectives on the mortality of COVID-19 and other epidemics

Significance What would a hypothetical 1 million US deaths in the COVID-19 epidemic mean for mortality of individuals at the population level? Life expectancy for 2020 would drop by 2.9 y. Those dying would lose an average of 11.7 y of expected remaining life, while for the general population the loss of remaining life would be 0.2 y for elders (at age 80) and much less at younger ages. Mortality per person would be less than that of the Spanish flu, but closer to that of the opioid and HIV/AIDS epidemics, while far more concentrated in time. The standard valuation of averting 1.75 million deaths would be many trillions of dollars. To put estimates of COVID-19 mortality into perspective, we estimate age-specific mortality for an epidemic claiming for illustrative purposes 1 million US lives, with results approximately scalable over a broad range of deaths. We calculate the impact on period life expectancy (down 2.94 y) and remaining life years (11.7 y per death). Avoiding 1.75 million deaths or 20.5 trillion person years of life lost would be valued at $10.2 to $17.5 trillion. The age patterns of COVID-19 mortality in other countries are quite similar and increase at rates close to each country’s rate for all-cause mortality. The scenario of 1 million COVID-19 deaths is similar in scale to that of the decades-long HIV/AIDS and opioid-overdose epidemics but considerably smaller than that of the Spanish flu of 1918. Unlike HIV/AIDS and opioid epidemics, the COVID-19 deaths are concentrated in a period of months rather than spread out over decades.
Hierarchical dynamics as a macroscopic organizing principle of the human brain

Significance Accumulating evidence suggests that, during task performance, information is encoded at shorter timescales in primary sensory regions as compared to longer timescales in higher-order cortical regions. These encoding timescales correlate with the timescales of activity within these regions. Here, we test the hypothesis that a hierarchy of activity timescales represents a general organizing principle of brain function. Using functional imaging of the human brain in the eyes-open resting state, we find that the timescales of ongoing activity are hierarchically organized as gradients across the entire cerebral cortex. Further, whole-brain coverage permitted examination of subcortical structures, which exhibited hierarchical timescale gradients parallel to cerebral cortex. Altogether, our results support the existence of hierarchical gradients that globally organize human brain dynamics. Multimodal evidence suggests that brain regions accumulate information over timescales that vary according to anatomical hierarchy. Thus, these experimentally defined “temporal receptive windows” are longest in cortical regions that are distant from sensory input. Interestingly, spontaneous activity in these regions also plays out over relatively slow timescales (i.e., exhibits slower temporal autocorrelation decay). These findings raise the possibility that hierarchical timescales represent an intrinsic organizing principle of brain function. Here, using resting-state functional MRI, we show that the timescale of ongoing dynamics follows hierarchical spatial gradients throughout human cerebral cortex. These intrinsic timescale gradients give rise to systematic frequency differences among large-scale cortical networks and predict individual-specific features of functional connectivity. Whole-brain coverage permitted us to further investigate the large-scale organization of subcortical dynamics. We show that cortical timescale gradients are topographically mirrored in striatum, thalamus, and cerebellum. Finally, timescales in the hippocampus followed a posterior-to-anterior gradient, corresponding to the longitudinal axis of increasing representational scale. Thus, hierarchical dynamics emerge as a global organizing principle of mammalian brains.
Severe Maternal Morbidity and Infant Mortality in Canada

This population-based study has revealed an association of SMM with infant mortality and coupling tendency between maternal sepsis and infant death from sepsis. BACKGROUND: Severe maternal morbidity (SMM) comprises an array of conditions and procedures denoting an acutely life-threatening pregnancy-related condition. SMM may further compromise fetal well-being. Empirical data are lacking about the relation between SMM and infant mortality. METHODS: This population-based cohort study included 1 892 857 singleton births between 2002 and 2017 in Ontario, Canada, within a universal health care system. The exposure was SMM as an overall construct arising from 23 weeks’ gestation up to 42 days after the index delivery. The primary outcome was infant mortality from birth to 365 days. Multivariable modified Poisson regression generated relative risks and 95% confidence intervals (CIs), adjusted for maternal age, income, rurality, world region of origin, diabetes mellitus, and chronic hypertension. RESULTS: Infant mortality occurred among 174 of 19 587 live births with SMM (8.9 per 1000) vs 5289 of 1 865 791 live births without SMM (2.8 per 1000) (an adjusted relative risk of 2.93 [95% CI 2.51–3.41]). Of 19 587 pregnancies with SMM, 4523 (23.1%) had sepsis. Relative to births without SMM, the adjusted odds ratio for infant death from sepsis was 1.95 (95% CI 1.10–3.45) if SMM occurred without maternal sepsis and 6.36 (95% CI 3.50–11.55) if SMM included sepsis. CONCLUSIONS: SMM confers a higher risk of infant death. There is also coupling tendency (concurrent event of interest) between SMM with sepsis and infant death from sepsis. Identification of preventable SMM indicators, as well as the development of strategies to limit their onset or progression, may reduce infant mortality.
Effects of inoculation method of plant growth-promoting rhizobacteria and silicon rate on rice grain yield.

A field experiment was conducted in Lahijan, north of Iran, to determine the effects of inoculation method of plant growth-promoting rhizobacteria (Azosprilium + Azotobacter) and silicon rate on rice grain yield. The experimental design was a factorial based on randomized complete block with three replications. Factors were silicon rates (0, 150, 300, 450, and 600 kg ha -1 ), and bio-fertilizer application methods (un-inoculated, seed treatment, and seedling root dip). A liquid bio-fertilizer containing Azospirillum spp. and Azotobacter spp. bacteria was applied according to manufacture instruction. Analysis of variance showed that plant height, grain yield, tiller number per m 2 , grain number per panicle, 1000-grain weight, biological yield, and grain N uptake were significantly influenced by silicon rate and biofertilizer application method, but the interaction effects of two factors was not significant for all of the traits. Grain yield, averaged across silicon rates, was significantly increased by 27% and 16% when biofertilizer was applied as seed and seedling root dip treatment, respectively, compared to non inoculated treatment. Grain N uptake was higher for the seed inoculated plants than non inoculated plants averaged over silicon rates. Averaged across inoculation methods, rice grain yield was significantly increased as Si application rate increased from 0 to 450 Kg ha -1 , but did not significantly increase at higher Si rate. The trend in rice biological yield was similar to that of rice grain yield. With increasing Si rate from 0 to 450 kg ha -1 , grain N uptake increased from 47.4 to 94.8 kg ha -1 , but declined slightly at higher Si rate. This experiment illustrated that silicon fertilization and biofertilizer application, especially seed treatment method, can increase rice grain yield.
INTEGRATED MANAGEMENT OF MELOIDOGYNE INCOGNITA ON TOMATO

Paecilomyces lilacinus, Bacillus subtilis and green manuring with Eicchornia crassipes were used alone and in combination for the management of Meloidogyne incognita on tomato. Treatment of P. lilacinus to M. incognita inoculated plants caused greater plant growth than B. subtilis or E. crassipes. Use of B. subtilis plus P. lilacinus plus E. crassipes. The use of both biocontrol agents along with a green manure of E. crassipes resulted in greatest plant growth of M. incognita inoculated plants. Treatment of B. subtilis plus E. crassipes resulted in less growth of M. incognita inoculated plants compared to any other combined treatment of management agents.
User Acceptance of Electronic Medical Record System: Implementation at Marie Stopes International, Myanmar

Objectives This study assessed the technical feasibility and aimed to determine the factors influencing intention to use Electronic Medical Records (EMRs) at Marie Stopes International, Myanmar (MSI-M). Methods A cross-sectional survey was conducted among 112 participants who were working at the clinics and head office of MSI-M. Demographic information, type of office, technical feasibility, information communication technology knowledge, computer usage, and user acceptance towards the proposed system were obtained from the participants. Results The results indicated low health information technology usage and network availability at MSI-M clinics. Positive perception of EMRs was found among the staff members of MSI-M, which was reflected by positive responses regarding perceived usefulness (average score of 4.15), perceived ease of use (average score of 4.03), and intention to use (average score of 4.10) on a 5-point Likert scale. Statistically, staff from the head office expressed less desire to implement an EMR system (odds ratio = 0.07; 95% confidence interval, 0.01–0.97), especially when they do not perceive the usefulness of the system (odds ratio = 5.05; 95% confidence interval, 2.39–10.69). Conclusions Since health information technology usage and network availability were low in MSI-M, it is important to strengthen the information and communication technology infrastructure and introduce a policy for capacity building at MSI-M. Adequate training and strong leadership support are recommended for the successful initial implementation and sustainability of an EMR system at MSI-M.
Influence of State-Level Emergency Planning Policy Requirements on Secondary School Adoption.

CONTEXT Emergency action plans (EAPs) are a critical component in the management of catastrophic sport-related injury. Some state high school athletic associations and state legislation have required that schools develop EAPs, but little research exists on the influence of a statewide policy requirement on local adoption of these policies. OBJECTIVE To examine the efficacy of a statewide policy requirement on local adoption of an EAP. DESIGN Cross-sectional study. SETTING Online questionnaire. PATIENTS OR OTHER PARTICIPANTS High school athletic trainers were invited to complete a survey (n = 9642); 1136 completed the survey, yielding an 11.7% response rate. MAIN OUTCOME MEASURE(S) Survey responses on the adoption of EAPs along with cardiopulmonary resuscitation and automated external defibrillator (CPR/AED) requirements were cross-referenced with published statewide policies to determine the prevalence of EAP adoption. We evaluated the adoption of emergency action plan components based on the National Athletic Trainers' Association's emergency planning position statement along with CPR/AED requirements to determine component-specific prevalence. We compared the prevalence of EAP and component adoption between states that required EAPs and specific components of EAPs and states without such requirements. RESULTS Athletic trainers in states that required adoption of an EAP reported including more components of the emergency planning position statement (mean = 8 ± 4, median = 9) than in states without a requirement (mean = 7 ± 4, median = 8). The adoption of EAP components did not differ between states that required specific components of the EAP versus development of the EAP only. However, schools in states with both EAP and CPR/AED training requirements reported higher rates of CPR/AED training implementation (95.5%) than states that only required CPR/AED training (81.6%, prevalence ratio = 1.10, 95% confidence interval = 1.01, 1.20). CONCLUSIONS Based on these data, statewide policy requirements for the development of an EAP may be associated with increasing adoption of EAPs.