Miracle-dz/UniFAR-FTUs huggingface dataset:
Campus perspective on the National Institutes of Health public access policy: University of California, San Francisco, library experience.

1. To what extent are you aware of the National Institutes of Health (NIH) public access policy? (Not aware/Aware/Highly aware) 2. Have you received an NIH grant within the last 3 years? (Yes/No) 3. Within the past year, have you taken steps to deposit articles to PubMed Central in accordance with the NIH public access policy? (Yes/No/I don’t know) 4. Have you sought assistance from any person or organization to help you understand how to comply with the NIH public access policy? (Yes/No) 5. If yes to # 4, who did you contact? [Check all that apply] (University of California, San Francisco [UCSF] Library/UCSF Office of Contracts and Grants/Departmental grant administrator or similar staff in your department/Publisher-Editor-Journal/Other) 6. “Open access” publishing involves making research articles freely available online without any subscription fees. To what extent are you aware of the concept of open access publishing? (Not aware/Aware/Highly aware) 7. Do you consider a journal’s open access policy when you are selecting where to publish? (Yes/No) 8. In what ways do you feel that open access is a positive development? [Check all that apply] (Increased reach of research articles/Easy access to articles/Members of public should have access to taxpayer funded research/Neutral/Other) 9. In what ways do you feel that open access is a negative development? [Check all that apply] (Could harm publishers/Could harm scholarly societies/One for administrative burden for already busy researchers/Neutral/Other) Check if you are: Faculty/Postdoctoral fellow/Other academic/Staff/Student
Inter-aural attenuation with insert earphones

Abstract The aim of the present study was to determine inter-aural attenuation (IA) values for pure tones and a broadband click obtained using an ER-3A insert earphone with a foam plug and with a customized hard acrylic earmould. Participants were 15 adults with a longstanding unilateral dead ear. IA was operationally defined as the difference between the good-ear and poorer-ear not-masked air conduction threshold. Minimum IA values for the foam earplug were 50 dB and 55 dB for pure tones and broadband click, respectively. Minimum IA values for the hard acrylic earmould were 45 dB and 50 dB for pure tones and broadband click, respectively. Sumario El objetivo de este estudio fue determinar los valores de IA para tonos puros y para un clic de banda ancha utilizando los audífonos de inserción ER-3A con oclusión de esponja y con un molde de acrílico duro a la medida. Participaron 15 adultos con un oído muerto unilateral de larga evolución. Desde el punto de vista operacional se definió IA como la diferencia de umbral por conducción aérea sin enmascarar, entre el oído sano y el dañado. Los valores mínimos de IA con el tapón de esponja fue de 50dB y 55dB para los tonos puros y para el clic de banda ancha respectivamente. Los valores IA mínimos con el molde de acrílico duro fueron de 45dB y 50dB para tonos y clic de banda ancha respectivamente.
Oscillator strengths and integral cross sections of the ÃA2″1← X̃1A1 excitation of ammonia studied by fast electron impact.

The vibrationally resolved generalized oscillator strengths of the first and strongest singlet excitation ÃA2″1← X̃1A1 of ammonia have been determined at an impact electron energy of 1500 eV with an energy resolution of 80 meV. The comprehensive comparison of the present results with the previous experimental and theoretical ones shows that the high-energy limit, where the first Born approximation holds, has been reached at an impact electron energy of 1500 eV in K2 < 1 a.u. , while it is still not satisfied in the K2 > 1 a.u. even at 1500 eV. It is also observed that the minimum position of the generalized oscillator strength of the vibronic state shifts toward the larger squared momentum transfer with the increasing vibrational quantum number. By extrapolating the generalized oscillator strength to the zero momentum transfer, the optical oscillator strength of the ÃA2″1 state has been obtained, which gives an independent cross check to the previous results. The integral cross sections of the ÃA2″1 state have been obtained systematically from the threshold to 5000 eV with the aid of the BE-scaling method.
Molecular Identification and Disease Management of Date Palm Sudden Decline Syndrome in the United Arab Emirates

Date palm orchards suffer from serious diseases, including sudden decline syndrome (SDS). External symptoms were characterized by whitening on one side of the rachis, progressing from the base to the apex of the leaf until the whole leaf dies; while the internal disease symptoms included reddish roots and highly colored vascular bundles causing wilting and death of the tree. Although three Fusarium spp. (F. oxysporum, F. proliferatum and F. solani) were isolated from diseased root samples, the fungal pathogen F. solani was associated with SDS on date palm in the United Arab Emirates (UAE). Fusarium spp. were identified based on their cultural and morphological characteristics. The internal transcribed spacer regions and large subunit of the ribosomal RNA (ITS/LSU rRNA) gene complex of the pathogens was further sequenced. Pathogenicity assays and disease severity indices confirm the main causal agent of SDS on date palm in the UAE is F. solani. Application of Cidely® Top (difenoconazole and cyflufenamid) significantly inhibited the fungal mycelial growth in vitro and reduced SDS development on date palm seedlings pre-inoculated with F. solani under greenhouse conditions. This is the first report confirming that the chemical fungicide Cidely® Top is strongly effective against SDS on date palm.
Temporal clustering of exacerbations in chronic obstructive pulmonary disease.

RATIONALE Exacerbations are important events in chronic obstructive pulmonary disease. Preventing exacerbations is a key treatment goal. Observational data suggest that after a first exacerbation, patients may be at increased risk of a second exacerbation, but this has not been specifically studied. We hypothesized that exacerbations may cluster together in time, a finding that would have important implications for targeting preventative interventions and the analysis of clinical trial data. OBJECTIVES To assess whether exacerbations are random events, or cluster in time. METHODS A total of 297 patients in the London chronic obstructive pulmonary disease cohort recorded daily symptoms and were assessed for a total of 904 patient-years. The observed timing of second exacerbations after an initial exacerbation was compared with that expected should exacerbations occur randomly. MEASUREMENTS AND MAIN RESULTS The observed timing distribution of second exacerbations differed significantly (P < 0.001) from the expected exponential function (shape parameter of the fitted Weibull function, 0.966 [95% confidence interval, 0.948-0.985]), suggesting that more second exacerbations occurred sooner than later and that exacerbations cluster together in time. Twenty-seven percent of first exacerbations were followed by a second recurrent event within 8 weeks. Approximately one third of exacerbations were recurrent exacerbations. Although initial exacerbations were milder than isolated events, they were not less likely to receive treatment, and under-treatment of initial events is not a plausible explanation for exacerbation recurrence. Recurrent exacerbations contribute significantly to overall exacerbation frequency (rho = 0.81; P < 0.0001). CONCLUSIONS Exacerbations are not random events but cluster together in time such that there is a high-risk period for recurrent exacerbation in the 8-week period after an initial excerbation.
Dynamic Prediction of Financial Distress Using Malmquist DEA

This paper is the first to apply dynamic time-varying efficiency scores in distress prediction.Malmquist DEA is used to produce dynamic efficiency scores over several periods.Various efficiency scores are compared in discrete time hazard models.A comparison is made between generic and industry-specific models. Creditors such as banks frequently use expert systems to support their decisions when issuing loans and credit assessment has been an important area of application of machine learning techniques for decades. In practice, banks are often required to provide the rationale behind their decisions in addition to being able to predict the performance of companies when assessing corporate applicants for loans. One solution is to use Data Envelopment Analysis (DEA) to evaluate multiple decision-making units (DMUs or companies) which are ranked according to the best practice in their industrial sector. A linear programming algorithm is employed to calculate corporate efficiency as a measure to distinguish healthy companies from those in financial distress. This paper extends the cross-sectional DEA models to time-varying Malmquist DEA, since dynamic predictive models allow one to incorporate changes over time. This decision-support system can adjust the efficiency frontier intelligently over time and make robust predictions. Results based on a sample of 742 Chinese listed companies observed over 10 years suggest that Malmquist DEA offers insights into the competitive position of a company in addition to accurate financial distress predictions based on the DEA efficiency measures.
Causal Inference in Environmental Epidemiology: Old and New Approaches

Copyright © 2019 Wolters Kluwer Health, Inc. Unauthorized reproduction of this article is prohibited. Epidemiology • Volume 30, Number 3, May 2019 www.epidem. com | 311 Editor’s Note: A related commentary appears on p. 317. London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands; Department of Clinical Epidemiology, Aarhus University, Denmark; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; and Population Health Science, Bristol Medical School, Bristol, United Kingdom. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement no 668954 and ERC grant agreement no 669545 and from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 733206. This commentary was sponsored by the International Society of Environmental Epidemiology (ISEE). The contents are the sole responsibility of the author(s) and do not necessarily reflect the official views of the ISEE. Correspondence: Neil Pearce, Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail: neil.pearce@lshtm.ac. uk.
Gastrointestinal capacity, gut hormones and appetite change during rat pregnancy and lactation.

Pregnancy and lactation increase maternal appetite and adiposity, which in humans can lead to long-term body mass retention. Previous rat reproduction studies suggest that appetite-inhibiting gut hormone, peptide-YY (PYY), is elevated, despite hyperphagia; also that gastrointestinal size increases. The present study characterised changes in orexigenic (appetite-stimulating) ghrelin and anorexigenic (appetite-inhibiting) PYY and glucagon-like peptide-1 (GLP-1), and gastrointestinal architecture during pregnancy and lactation, in matched fed and fasted plasma and gut tissue samples taken during the dark phase. Enteroendocrine cells were immunolabelled, and gut masses and lengths measured. Fasted plasma ghrelin reduced during pregnancy: it was lowest by day 18, recovered to control values at parturition, then increased by the end of lactation. Ghrelin-immunoreactive stomach cells and stomach ghrelin concentrations were highest at birth, prior to the onset of lactation-associated hyperphagia. Plasma fed GLP-1 concentrations were elevated during pregnancy; and together with higher colon concentrations of PYY and GLP-1 during early lactation, they were associated with gastrointestinal tissue expansion, not satiety. Body mass increased during lactation, whereas white adipose tissue depots depleted. Extensive gut remodelling coincided with elevated colon concentrations of PYY and GLP-1. Modifications included: stomach and caecum expansion, and duodenal, ascending and descending colon circumference increases, all peaking by day 10 of lactation; increased intestinal masses and lengths peaking at lactation day 10 for small intestine and lactation day 25 for large intestine. If these physical tissue increases persist post-partum, they could accelerate future nutrient assimilation and storage in dams, and may contribute to increased obesity risk.
Unnatural verticilide enantiomer inhibits type 2 ryanodine receptor-mediated calcium leak and is antiarrhythmic

Significance This report highlights a rare and exciting discovery of an unnatural enantiomer of a natural product [a cyclooligomeric depsipeptide (COD)] that potently inhibits ryanodine receptor type 2 (RyR2), a target for therapeutic development for which there are no known selective inhibitors. To our knowledge, there are no examples where the unnatural enantiomer of a natural product is highly potent at its protein target while the natural enantiomer is inactive. This discovery raises the question whether the enantiomers of other natural products harbor potent biological activity but will remain undiscovered until they are prepared or, alternatively, a mirror-image protein is used to screen natural product libraries. Ca2+ leak via ryanodine receptor type 2 (RyR2) can cause potentially fatal arrhythmias in a variety of heart diseases and has also been implicated in neurodegenerative and seizure disorders, making RyR2 an attractive therapeutic target for drug development. Here we synthesized and investigated the fungal natural product and known insect RyR antagonist (−)-verticilide and several congeners to determine their activity against mammalian RyR2. Although the cyclooligomeric depsipeptide natural product (−)-verticilide had no effect, its nonnatural enantiomer [ent-(+)-verticilide] significantly reduced RyR2-mediated spontaneous Ca2+ leak both in cardiomyocytes from wild-type mouse and from a gene-targeted mouse model of Ca2+ leak-induced arrhythmias (Casq2−/−). ent-(+)-verticilide selectively inhibited RyR2-mediated Ca2+ leak and exhibited higher potency and a distinct mechanism of action compared with the pan-RyR inhibitors dantrolene and tetracaine and the antiarrhythmic drug flecainide. ent-(+)-verticilide prevented arrhythmogenic membrane depolarizations in cardiomyocytes without significant effects on the cardiac action potential and attenuated ventricular arrhythmia in catecholamine-challenged Casq2−/− mice. These findings indicate that ent-(+)-verticilide is a potent and selective inhibitor of RyR2-mediated diastolic Ca2+ leak, making it a molecular tool to investigate the therapeutic potential of targeting RyR2 hyperactivity in heart and brain pathologies. The enantiomer-specific activity and straightforward chemical synthesis of (unnatural) ent-(+)-verticilide provides a compelling argument to prioritize ent-natural product synthesis. Despite their general absence in nature, the enantiomers of natural products may harbor unprecedented activity, thereby leading to new scaffolds for probe and therapeutic development.
Activation of GCN2 by the ribosomal P-stalk

Significance General control nonderepressible 2 (GCN2) phosphorylates eIF2α, regulating translation in response to nutritional stress. Here, we show that although tRNA stimulates purified, recombinant human GCN2 in vitro, mammalian ribosomes are even more potent GCN2 activators. Hydrogen/deuterium exchange–mass spectrometry (HDX-MS) showed GCN2 interacting with domain II of the uL10 P-stalk protein. The P-stalk is a uL10/P12/P22 pentameric complex that is part of the ribosomal GTPase-associated center. Recombinant human P-stalk greatly stimulates GCN2. Both domain II of uL10 and the C-terminal tails of P1 and P2 are necessary for maximal GCN2 activation. On actively translating ribosomes, the C-terminal tails of P1 and P2 are sequestered by elongation factors, suggesting P-stalk availability could link translational stress to GCN2 activation. Cells dynamically adjust their protein translation profile to maintain homeostasis in changing environments. During nutrient stress, the kinase general control nonderepressible 2 (GCN2) phosphorylates translation initiation factor eIF2α, initiating the integrated stress response (ISR). To examine the mechanism of GCN2 activation, we have reconstituted this process in vitro, using purified components. We find that recombinant human GCN2 is potently stimulated by ribosomes and, to a lesser extent, by tRNA. Hydrogen/deuterium exchange–mass spectrometry (HDX-MS) mapped GCN2–ribosome interactions to domain II of the uL10 subunit of the ribosomal P-stalk. Using recombinant, purified P-stalk, we showed that this domain of uL10 is the principal component of binding to GCN2; however, the conserved 14-residue C-terminal tails (CTTs) in the P1 and P2 P-stalk proteins are also essential for GCN2 activation. The HisRS-like and kinase domains of GCN2 show conformational changes upon binding recombinant P-stalk complex. Given that the ribosomal P-stalk stimulates the GTPase activity of elongation factors during translation, we propose that the P-stalk could link GCN2 activation to translational stress, leading to initiation of ISR.
Effects of Nitrogen Dioxide on Biochemical Responses in 41 Garden Plants

Nitrogen dioxide (NO2) at a high concentration is among the most common and harmful air pollutants. The present study aimed to explore the physiological responses of plants exposed to NO2. A total of 41 plants were classified into 13 functional groups according to the Angiosperm Phylogeny Group classification system. The plants were exposed to 6 μL/L NO2 in an open-top glass chamber. The physiological parameters (chlorophyll (Chl) content, peroxidase (POD) activity, and soluble protein and malondialdehyde (MDA) concentrations) and leaf mineral ion contents (nitrogen (N+), phosphorus (P+), potassium (K+), calcium (Ca2+), magnesium (Mg2+), manganese (Mn2+), and zinc (Zn2+)) of 41 garden plants were measured. After NO2 exposure, the plants were subsequently transferred to a natural environment for a 30-d recovery to determine whether they could recover naturally and resume normal growth. The results showed that NO2 polluted the plants and that NO2 exposure affected leaf Chl contents in most functional groups. Increases in both POD activity and soluble protein and MDA concentrations as well as changes in mineral ion concentrations could act as signals for inducing defense responses. Furthermore, antioxidant status played an important role in plant protection against NO2-induced oxidative damage. NO2 poses a pollution risk to plant systems, and antioxidant status plays an important role in plant protection against NO2-induced oxidative damage. In conditions of strong air pollution, more evergreen plants may be considered in landscape design, particularly in seasonal regions. The results of this study may provide useful data for the selection of landscaping plants in NO2 polluted areas.
Bone marrow adipose tissue-derived stem cell factor mediates metabolic regulation of hematopoiesis

Hematopoiesis is dynamically regulated by metabolic cues in homeostatic and stressed conditions; however, the cellular and molecular mechanisms mediating the metabolic sensing and regulation remain largely obscure. Bone marrow adipose tissue remodels in various metabolic conditions and has been recently proposed as a niche for hematopoietic stem cells after irradiation. Here, we investigated the role of marrow adipose tissue-derived hematopoietic cytokine stem cell factor in unperturbed hematopoiesis by selectively ablating the Kitl gene from adipocytes and bone marrow stroma cells using Adipoq-Cre and Osx1-Cre, respectively. We found that both Adipoq-Kitl knockout (KO) and Osx1-Kitl KO mice diminished hematopoietic stem and progenitor cells and myeloid progenitors in the bone marrow and developed macrocytic anemia at the steady-state. The composition and differentiation of hematopoietic progenitor cells in the bone marrow dynamically responded to metabolic challenges including high fat diet, β3-adrenergic activation, thermoneutrality, and aging. However, such responses, particularly within the myeloid compartment, were largely impaired in Adipoq-Kitl KO mice. Our data demonstrate that marrow adipose tissue provides stem cell factor essentially for hematopoiesis both at the steady state and upon metabolic stresses.
Concise Review: Modeling Neurodegenerative Diseases with Human Pluripotent Stem Cell‐Derived Microglia

Inflammation of the brain and the consequential immunological responses play pivotal roles in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia (FTD). Microglia, the resident macrophage cells of the brain, have also emerged as key players in neuroinflammation. As primary human microglia from living subjects are normally not accessible to researchers, there is a pressing need for an alternative source of authentic human microglia which allows modeling of neurodegeneration in vitro. Several protocols for induced pluripotent stem cell (iPSC)‐derived microglia have recently been developed and provide unlimited access to patient‐derived material. In this present study, we give an overview of iPSC‐derived microglia models in monoculture and coculture systems, their advantages and limitations, and how they have already been used for disease phenotyping. Furthermore, we outline some of the gene engineering tools to generate isogenic controls, the creation of gene knockout iPSC lines, as well as covering reporter cell lines, which could help to elucidate complex cell interaction mechanisms in the microglia/neuron coculture system, for example, microglia‐induced synapse loss. Finally, we deliberate on how said cocultures could aid in personalized drug screening to identify patient‐specific therapies against neurodegeneration. Stem Cells 2019;37:724–730
Factor analysis of the Spanish Multidimensional Attitudes Scale Toward Persons with Disabilities.

PURPOSE/OBJECTIVE To study the psychometric properties of a Spanish version of the Multidimensional Attitudes Scale toward Persons with Disabilities (MAS) and examine its factor structure using confirmatory and exploratory factor analyses on data from a Colombian collegiate sample. RESEARCH METHOD/DESIGN Five hundred students from Sur Colombia University in Neiva, Colombia, completed the Multidimensional Attitudes toward People with Disability scale. Forty-eight percent were male, and the average age for the entire sample was 21.25 years (SD = 3.50). Ninety-eight percent were undergraduates, 23% of whom were business majors and 33% of whom were education majors. RESULTS An exploratory factor analysis (EFA) of data from half of participants suggested the retention of 4 factors and the deletion of 4 items. A confirmatory factor analysis (CFA) on the data from the second half of participants using the 30 retained items and 4-factor structure suggested that the 4-factor model fit adequately with the remaining 30 items. High internal consistency was found for the overall scale (α = .77, .78) and for the 4 resulting subscales: Affect (α = .88, .87), Cognition (α = .92, .90), Behavior (α = .88, .88), and Calm (α = .90, .89). CONCLUSIONS/IMPLICATIONS This study modified the MAS to assess attitudes toward persons with disabilities in Colombia. The adequate reliability and fit of the factor structure of the Spanish MAS suggests that it holds promise to help researchers investigate attitudes toward persons with disabilities in Latin America, an important topic to the global disability community.