Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungal involvement in bioweathering and biotransformation of rocks and minerals

Abstract In the Earth’s lithosphere, fungi are of fundamental importance as decomposer organisms, animal and plant pathogens and symbionts (e.g. lichens and mycorrhizas), being ubiquitous in sub-aerial and subsoil environments. The ability of fungi to interact with minerals, metals, metalloids and organic compounds through biomechanical and biochemical processes, makes them ideally suited as biological weathering agents of rock and building stone. They also play a fundamental role in biogeochemical cycling of nutrients, (e.g. C, N, P and S) and metals (e.g. Na, Mg, Ca, Mn, Fe, Cu, Zn, Co and Ni) essential for the growth of living organisms in the biosphere. In addition they play an integral role in the mobilization and immobilization of non-essential metals (e.g. Cs, Al, Cd, Hg and Pb). Most studies on mineral-microbe interactions and microbial involvement in geological processes have concentrated on bacteria and archaea (Prokaryota): fungi (Eukaryota) have, to a certain extent, been neglected. This article addresses the role of fungi in geomicrobiological processes, emphasizing their deteriorative potential on rock, building stone and mineral surfaces and involvement in the formation of secondary mycogenic minerals. Such roles of fungi are also of importance for the global carbon reservoir and have potential biotechnological applications, e.g. in the bioremediation of xenobiotic-, metal- and/or radionuclide-contaminated soils and wastes, and metal/radionuclide recovery.
Strategies to Prevent Clostridium difficile Infections in Acute Care Hospitals: 2014 Update

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections (HAIs). The intent of this document is to highlight practical recommendations in a concise format designed to assist acute care hospitals in implementing and prioritizing their Clostridium difficile infection (CDI) prevention efforts. This document updates “Strategies to Prevent Clostridium difficile Infections in Acute Care Hospitals,” published in 2008. This expert guidance document is sponsored by the Society for Healthcare Epidemiology of America (SHEA) and is the product of a collaborative effort led by SHEA, the Infectious Diseases Society of America (IDSA), the American Hospital Association (AHA), the Association for Professionals in Infection Control and Epidemiology (APIC), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise. The list of endorsing and supporting organizations is presented in the introduction to the 2014 updates.
Turbulent flow structures and aeolian sediment transport over a barchan sand dune

The turbulent structure of airflow over a barchan sand dune is determined using quadrant analysis of wind velocity data derived from sonic anemometers. Results indicate an increased frequency of ejection and sweep events in the toe region of the dune, characteristic of the turbulent bursting process. In contrast, at the crest there was a significant increase in the occurrence of outward interactions. Combined with high frequency saltation data our analyses show that turbulent structures characterised by a positive streamwise fluctuating velocity (+u′; sweeps at the toe and outward interactions at the crest) have a dominant influence on sand transport on the dune, together accounting for up to 83% and 95% of transporting events at the toe and crest respectively.
To what extent does climate change result in a shift in Alpine hydrology? A case study in the Austrian Alps

Abstract The quantification of the effect of climate change on the hydrological water balance components within a catchment is invaluable for future planning within the water sector (municipal and industrial water supply, hydropower, irrigation, snowmaking). As the regional effect of global warming is somewhat uncertain, the provision of quantitative estimates with error bands is essential. Many studies only take one or a very limited sample of climate change scenarios into account. In this paper, the hydrological response to a number of regional climate change model scenarios for the end of the 21st century within the catchment of the Kitzbüheler Ache in Austria is investigated by means of a distributed hydrological model. These regional climate scenarios originate from the European PRUDENCE project. The results show a shift from a rainfall and snowmelt-dominated flow regime to a rainfall-dominated flow regime for all scenarios. A future decrease in snowmelt and a shortening in snow cover duration is observed, with an increase in winter flow, and a decrease in spring, summer and autumn flow. The typical low-flow period during winter shifts to a low-flow period during late summer and autumn. However, the magnitude of the effects depends strongly on the choice of scenario. Average annual snowmelt reduction ranges from 31 to 81%, average annual runoff reduction from 6 to 33% and average annual evapotranspiration increase from 6 to 20%. These uncertainties are also presented for a monthly and a seasonal time step. These values and observations provide for a future vision within a mountainous catchment in the European Alps. Normal future planning is within a shorter time frame (20–30 years within the water sector), but this future vision puts realistic planning in a wider context. Editor Z.W. Kundzewicz; Associate editor R.L. Wilby Citation Laghari, A.N, Vanham, D. and Rauch, W. , 2012. To what extent does climate change result in a shift in Alpine hydrology? A case study in the Austrian Alps. Hydrological Sciences Journal, 57 (1), 103–117.
Increases in Methamphetamine Use among Heroin Treatment Admissions in the United States, 2008–2017

Background and Aims: Due to their small sample sizes, geographic specificity, and limited examination of sociodemographic characteristics, recent studies of methamphetamine use among people using heroin in the U.S. are limited in their ability to identify national and regional trends and to characterize populations at risk for using heroin and methamphetamine. This study aimed to examine trends and correlates of methamphetamine use among heroin treatment admissions in the U.S. Design: Longitudinal analysis of data from the 2008 through 2017 Treatment Episode Data Set. Descriptive statistics, trend analyses, and multivariable logistic regression were used to examine characteristics associated with methamphetamine use among heroin treatment admissions. Setting: United States Participants: Treatment admissions of people ≥12 years whose primary substance of use is heroin. Measurements: Primary measurement was heroin treatment admissions involving methamphetamine. Secondary measurements were demographics of sex, age, race/ethnicity, U.S. census region, living arrangement, and employment status. Findings: The percentage of primary heroin treatment admissions reporting methamphetamine use increased each year from 2.1% in 2008 to 12.4% in 2017, a relative percentage increase of 490% and an annual percent change (APC) of 23.4% (p<0.001). During the study period, increases were seen among males and females, and across all demographic and geographic groups examined. Among primary heroin treatment admissions reporting methamphetamine use in 2017, Corresponding Author: Christopher M. Jones, PharmD, MPH, Senior Advisor and Director of Strategy and Innovation, National Center for Injury Prevention and Control, Centers for Disease Control and Prevention. 4700 Buford Highway, Atlanta, GA, 30342, USA. Fjr0@cdc.gov 404-798-0756. Declarations of Competing Interests: Compton reports long-term holdings in General Electric Company, 3M Companies and Pfizer, Incorporated, unrelated to the present work. Publisher's Disclaimer: Disclaimer: The opinions expressed in this article are those of the authors and do not necessarily represent the opinions of the National Institute on Drug Abuse, the National Institutes of Health, or the Centers for Disease Control and Prevention or the U.S. Department of Health and Human Services. HHS Public Access Author manuscript Addiction. Author manuscript; available in PMC 2021 February 01. Published in final edited form as: Addiction. 2020 February ; 115(2): 347–353. doi:10.1111/add.14812. A uhor M anscript
Ocean ventilation and sedimentation since the glacial maximum at 3 km in the western North Atlantic

Stable isotope, sedimentological, and radiocarbon data from cores at ∼3 km water depth on the Blake Ridge, western subtropical North Atlantic, reveal the history of deep water ventilation since the last glacial maximum (LGM). Bulk sediment accumulation rates varied locally by a factor of 2 under the influence of bottom currents in this sediment drift environment, but the sand flux, mostly foraminifera, was nearly identical at a given time. This suggests that the rain rate of foraminifera (mostly planktonic) was constant, that transport of foraminifera was negligible, and that current‐controlled differences in clay and silt transport drive bulk accumulation. In two of the cores, flux peaks in the benthic foraminifera Cibicidoides and Uvigerina peregrina occurred during the Younger Dryas (YD) cold event, and at 18.2, 19.6, 21.1, 25.0, and 28.1 ka. Radiocarbon measurements on those benthic foraminifera show the ventilation age of bottom waters was ∼1000 years during the YD, and for older events it was as great as 2000 years. These results contrast with Holocene ventilation, which was ∼500 years and 700 years at 1500 years and ∼7100 years before present, respectively.
The Effects of Aging on Corneal and Ocular Surface Homeostasis in Mice.

Purpose Aging is a risk factor for dry eye disease. The aim of this study was to investigate if aging is associated with a range of signs of dry eye disease, including tear hyperosmolarity, reduced nerve density, and increased dendritic cell number, in mice. Method Healthy C57BL/6 female mice, aged 2 months (young, n = 10) and 22 months (aged, n = 11) were used. Clinical assessments included corneal sensitivity (Cochet-Bonnet esthesiometry), tear secretion (Phenol red thread test), tear film osmolarity (TearLab osmometer), and corneal thickness (optical coherence tomography). The sum length of the corneal superficial terminals and sub-basal nerves, density of vertical nerve projections, and density and tree area of resident epithelial dendritic cells, were assessed using immunofluorescence and confocal microscopy. Results Aged mice had significantly higher tear secretion, lower corneal sensitivity, and a thicker corneal stroma but thinner epithelium. There was no significant intergroup difference for tear osmolarity. Aged mice showed a significantly lower sum length of nerves in the superficial terminals and sub-basal plexus, relative to young mice. Dendritic cell density and morphology were similar in both groups. Conclusions In mice, aging is associated with higher tear secretion and corneal epithelial thinning, together with lower corneal nerve density and sensitivity. However, aging was not significantly associated with changes to tear osmolarity or dendritic cell density or size, despite a significant reduction in total nerve length. These findings demonstrate that aged mice exhibit some changes to ocular surface parameters that parallel the anomalies evident in dry eye disease.
Global hexachlorocyclohexane use trends and their impact on the Arctic atmospheric environment

The relationship between the global technical HCH use trends and their impact on the arctic atmospheric environment has been studied. Two significant drops in global technical HCH usage were identified. In 1983, China banned the use of technical HCH. This represented the largest drop ever in global use rates. In 1990 India stopped technical HCH usage in agriculture and the former Soviet Union banned the use of technical HCH. Since 1990, India has been the biggest user of technical HCH in the world. Significant drops in atmospheric α‐HCH in the arctic were observed between 1982 and 1983, and again between 1990 and 1992. The rapid response in atmospheric concentrations to usage is encouraging; however, since α‐HCH concentrations in the arctic waters have remained relatively unchanged, the decline in atmospheric α‐HCH has reversed the net direction of air‐sea gas flux. The accumulated mass in oceans and large lakes may represent a new source of HCH to the arctic atmosphere.
The French Accelerometric Network (RAP) and National Data Centre (RAP-NDC)

France is a country of low-to-moderate seismic hazard that has, in the past, suffered strong earthquakes that have caused damage and casualties (SisFrance historical catalog, http://www.sisfrance.net). More recently, it has experienced moderate earthquakes that have caused significant economic loss. One major earthquake occurred at the beginning of the 20th century (1909) and seriously affected the rural area of Aix-en-Provence (southeast France). In moderate-to-low seismic-hazard countries, even earthquakes that are not regarded as major can cause severe damage. This was the case with the earthquakes in Ossau-Arudy (Pyrenees area, 1980, M L = 5.1) and Annecy (northern Alps, 1996, M L = 4.8) which, in spite of their low magnitudes, resulting in damage of approximately €3 million (MEDD 1982) and €45 million (AFPS 1996), respectively. Since 1980 and the creation of the French national seismological network (ReNaSS, http://renass.u-strasbg.fr), more than 27,000 events have been recorded in the M L 1-5 magnitude range, corresponding to approximately 20 M L > 3.5 earthquakes per year (figure 1A), which are located in four main tectonic regions: the Pyrenees in the southwest, the Alps in the southeast, the Rhine Graben zone in the northeast, and the Massif Central and Brittany in the central and western regions. Moreover, France's overseas territories include Mayotte in the Indian Ocean, New Caledonia in the Pacific Ocean close to the Vanuatu subduction zone, and especially the French Antilles islands, which belong to the West Indies in the Caribbean Sea. While according to the national seismic building code mainland France is assigned seismic zones 0 to II ( aN = 2.5 m/s2), the French Antilles islands are assigned seismic zone III ( aN = 3.5 m/s2). The significant hazard level combined with the large population and the poorly designed buildings therefore make these islands the region of France with …
Point Adversarial Self Mining: A Simple Method for Facial Expression Recognition in the Wild

In this paper, the Point Adversarial Self Mining (PASM) approach, a simple yet effective way to progressively mine knowledge from training samples, is proposed to produce training data for CNNs to improve the performance and network generality in Facial Expression Recognition (FER) task. In order to achieve a high prediction accuracy under real-world scenarios, most of the existing works choose to manipulate the network architectures and design sophisticated loss terms. Although demonstrated to be effective in real scenarios, those aforementioned methods require extra efforts in network design. Inspired by random erasing and adversarial erasing, we propose PASM for data augmentation, simulating the data distribution in the wild. Specifically, given a sample and a pre-trained network, our proposed approach locates the informative region in the sample generated by point adversarial attack policy. The informative region is highly structured and sparse. Comparing to the regions produced by random erasing which selects the region in a purely random way and adversarial erasing which operates by attention maps, the located informative regions obtained by PASM are more adaptive and better aligned with the previous findings: not all but only a few facial regions contribute to the accurate prediction. Then, the located informative regions are masked out from the original samples to generate augmented images, which would force the network to explore additional information from other less informative regions. The augmented images are used to finetune the network to enhance its generality. In the refinement process, we take advantage of knowledge distillation, utilizing the pre-trained network to provide guidance and retain knowledge from old samples to train a new network with the same structural configuration.
Altered Repertoire Diversity and Disease- Associated Clonal Expansions Revealed by T Cell Receptor Immunosequencing in Ankylosing Spondylitis Patients

Objective. Ankylosing spondylitis (AS) is a common spondyloarthropathy primarily affecting the axial skeleton and strongly associated with HLA–B*27 carriage. Genetic evidence implicates both autoinflammatory processes and autoimmunity against an HLA–B*27 –restricted autoantigen in immunopathology. In addition to articular symptoms, up to 70% of AS patients present with concurrent bowel inflammation, suggesting that adverse interactions between a genetically primed host immune system and the gut microbiome contribute to the disease. Accordingly, this study aimed to characterize adaptive immune responses to antigenic stimuli in AS. Methods. The peripheral CD4 and CD8 T cell receptor (TCR) repertoire was profiled in AS patients (n = 47) and HLA–B*27 – matched healthy controls (n = 38). Repertoire diversity was estimated using the Normalized Shannon Diversity Entropy (NSDE) index, and univariate and multivariate statistical analyses were performed to characterize AS- associated clonal signatures. Furthermore, T cell proliferation and cytokine production in response to immunogenic antigen exposure were investigated in vitro in peripheral blood mononuclear cells from AS patients (n = 19) and HLA–B*27 –matched healthy controls (n = 14). Results. Based on the NSDE measure of sample diversity across CD4 and CD8 T cell repertoires, AS patients showed increased TCR diversity compared to healthy controls (for CD4 T cells, P = 7.8 × 10 −6 ; for CD8 T cells, P = 9.3 × 10 −4 ), which was attributed to a significant reduction in the magnitude of peripheral T cell expansions globally. Upon in vitro stimulation, fewer T cells from AS patients than from healthy controls expressed interferon- γ (for CD8 T cells, P = 0.03) and tumor necrosis factor (for CD4 T cells, P = 0.01; for CD8 T cells, P = 0.002). In addition, the CD8 TCR signature was altered in HLA–B*27 + AS patients compared to healthy controls, with significantly expanded Epstein-Barr virus–specific clonotypes ( P = 0.03) and cytomegalovirus- specific clonotypes ( P = 0.02). HLA–B*27 + AS patients also showed an increased incidence of “public” CD8 TCRs, representing identical clonotypes emerging in response to common antigen encounters, including homologous clonotypes matching those previously isolated from individuals with bacterial- induced reactive arthritis. Our results reveal fundamental differences in the landscape of antigen- restricted immunity in AS patients, including global reductions in T cell clonal expansion, altered T cell function, expanded viral- specific CD8 clonotypes and public HLA–B*27 + AS- associated CD8 clonotypes, and constitutive activation of cross- presenting DCs. These data suggest that AS is not simply an autoinflammatory disease, but one characterized by profound immunoregulatory imbalance.
Identifying Disordered Regions in Proteins from Amino Acid Sequence 1

A rule-based and several neural network predictors are developed for identifying disordered regions in proteins. The rule-based predictor was suitable only for very long disordered regions, whereas the neural network predictors were developed separately for short-, medium-, and long-disordered regions (S-, M-, and LDRs, respectively). The out-of-sample prediction accuracies on a residue-by-residue basis ranged from 69 to 74% for the neural network predictors when applied to the same length class, but fell to 59 to 67% when applied to diierent length classes. Application of both the rule-based and LDR neural network predictors to large databases of protein sequences provide strong evidence that disordered regions are very common in nature. These results are consistent with our recent proposal that disordered regions are crucial for the evolution of molecular recognition.
Use of agronomic conditions, genetics, and processing to improve utilization of sorghum grain.

Sorghum grain is an extremely important crop to both farmers and livestock feeders in the High-Plains states (e.g., from Nebraska to Texas). Kansas leads the nation in sorghum production, and as should be expected, Kansas State University has a long history of research to improve the utilization and marketability of this versatile and hardy crop. This paper is a synopsis of current research at KSU and other universities concerning production and use of sorghum grain for feeding swine. Topics addressed include the relatively small loss in nutritional value (4 to 11 %) as test weight decreases from 55 to 35 lb/ bu compared to the extreme discounts experienced by farmers trying to market light grain. Also, an experiment to quantitate yield of utilizable nutrients from com and sorghum was conducted to determine the relative merits of these grain sources when grown with different irrigation and N application strategies. Finally, sorghum parent lines have been identified with improved digestibility, and alternative milling procedures (e.g., fine-grinding and extrusion) have been identified that should greatly improve the competitiveness of sorghum grain as a feedstuff of choice for swine diets. ; Swine Day, Manhattan, KS, November 21. 1991
Validation of a Consumer Sleep Wearable Device With Actigraphy and Polysomnography in Adolescents Across Sleep Opportunity Manipulations.

STUDY OBJECTIVES To compare the quality and consistency in sleep measurement of a consumer wearable device and a research-grade actigraph with polysomnography (PSG) in adolescents. METHODS Fifty-eight healthy adolescents (aged 15-19 years; 30 males) underwent overnight PSG while wearing both a Fitbit Alta HR and a Philips Respironics Actiwatch 2 (AW2) for 5 nights, with either 5 hours or 6.5 hours time in bed (TIB) and for 4 nights with 9 hours TIB. AW2 data were evaluated using two different wake and immobility thresholds. Discrepancies in estimated total sleep time (TST) and wake after sleep onset (WASO) between devices and PSG, as well as epoch-by-epoch agreements in sleep/wake classification, were assessed. Fitbit-generated sleep staging was compared to PSG. RESULTS Fitbit and AW2 under default settings similarly underestimated TST and overestimated WASO (TST: medium setting (M10) ≤ 38 minutes, Fitbit ≤ 47 minutes; WASO: M10 ≤ 38 minutes; Fitbit ≤ 42 minutes). AW2 at the high motion threshold setting provided readings closest to PSG (TST: ≤ 12 minutes; WASO: ≤ 18 minutes). Sensitivity for detecting sleep was ≥ 90% for both wearable devices and further improved to 95% by using the high threshold (H5) setting for the AW2 (0.95). Wake detection specificity was highest in Fitbit (≥ 0.88), followed by the AW2 at M10 (≥ 0.80) and H5 thresholds (≤ 0.73). In addition, Fitbit inconsistently estimated stage N1 + N2 sleep depending on TIB, underestimated stage N3 sleep (21-46 min), but was comparable to PSG for rapid eye movement sleep. Fitbit sensitivity values for the detection of N1 + N2, N3 and rapid eye movement sleep were ≥ 0.68, ≥ 0.50, and ≥ 0.72, respectively. CONCLUSIONS A consumer-grade wearable device can measure sleep duration as well as a research actigraph. However, sleep staging would benefit from further refinement before these methods can be reliably used for adolescents. CLINICAL TRIAL REGISTRATION Registry: ClinicalTrials.gov; Title: The Cognitive and Metabolic Effects of Sleep Restriction in Adolescents; Identifier: NCT03333512; URL: https://clinicaltrials.gov/ct2/show/NCT03333512.