Miracle-dz/UniFAR-FTUs huggingface dataset:
An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host

RESEARCH ARTICLE 1 2 An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host 3 rRNA Genes by Altering Histone Acetylation 4 5 Paramasivan Vijayapalani,1 Tarek Hewezi,1,a Frederic Pontvianne,2,3 and Thomas J. Baum1* 6 1Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA 7 2CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, F-66860, Perpignan, France 8 3Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, F9 66860, Perpignan, France 10 11 Short title: Nematode effector alters host plant histone acetylation 12 13 One-sentence summary: The 32E03 effector epigenetically regulates plant rRNA gene dosage, which is a 14 crucial requirement to promote cyst nematode parasitism. 15 16 aPresent Address: Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA 17 *To whom correspondence should be addressed: Tel: +1 515-294-5420; Email: tbaum@iastate.edu 18 19 The author responsible for distribution of materials integral to the findings presented in this article in 20 accordance with the policy described in the Instructions for Authors (www.plantcell.org) is Thomas J. 21 Baum (tbaum@iastate.edu) 22 23 ABSTRACT 24 25 Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to 26
The acute and chronic effects of hot water immersion on inflammation and 1 metabolism in sedentary, overweight adults

Regular exercise-induced acute inflammatory responses are suggested to improve the 35 inflammatory profile and insulin sensitivity. As body temperature elevations partly mediate 36 this response, passive heating might be a viable tool to improve the inflammatory profile. This 37 study investigated the acute, and chronic effects of hot water immersion on inflammatory and 38 metabolic markers. Ten sedentary, overweight males (BMI: 31.0±4.2 kg/m 2 ) were immersed 39 in water set at 39°C for 1 h (HWI) or rested for 1 h at ambient temperature (AMB). Venous 40 blood was obtained prior to, immediately post and 2 h post-session for assessment of 41 monocyte intracellular heat shock protein 72 (iHsp72) and plasma concentrations of 42 extracelullar heat shock protein 72 (eHsp72), interleukin-6 (IL-6), fasting glucose, insulin and 43 nitrite. Thereafter, participants underwent a 2-week intervention period, consisting of 10 hot 44 water immersion sessions (INT). Eight BMI-matched participants (BMI: 30.0±2.5 kg/m 2 ) 45 were included as control (CON). Plasma IL-6 and nitrite concentrations were higher 46 immediately following HWI compared to AMB (IL-6 p <0.001, HWI: 1.37±0.94 to 2.51±1.49 47 pg/ml; nitrite p =0.04, HWI: 271±52 to 391±72 nM), while iHsp72 expression was unchanged 48 ( p =0.57). In contrast to resting iHsp72 expression ( p =0.59), fasting glucose ( p =0.04, INT: 49 4.44±0.93 to 3.98±0.98 mmol/l), insulin ( p =0.04, INT: 68.1±44.6 to 55.0±29.9 pmol/l) and 50 eHsp72 ( p =0.03, INT: 17±41% reduction) concentrations were lowered after INT compared 51 to CON. HWI induced an acute inflammatory response and increased nitric oxide 52 bioavailability. The reductions in fasting glucose and insulin concentrations The Hsp72 and Hsp90a mRNA responses to hot downhill running are reduced following a prior bout of hot downhill running, and occur concurrently within leukocytes and the vastus
Soil organic carbon storage and distribution in Arctic Tundra, Barrow, Alaska

Soil organic C (SOC) levels were determined to a depth of 100 cm for the nine units designated on a 1957 1:20 000 soil map of Barrow, AK prepared by J.V. Drew. The legend was updated by converting Drew's map units into the recently adopted Gelisol order in U.S. soil taxonomy and field verified. The SOC varied from 2.5 kg m -3 in modern beach sediments to >73 kg m -3 in Typic Sapristels in high-centered, ice-wedge polygons developed in reworked organic-rich lake sediments. The SOC averaged 50 kg m -3 for the entire 64-km 2 area (excluding open water). Considerable variability in SOC exists within individual soil map units. For example, SOC levels in a Typic Aquiturbel (formerly classified as a Meadow Tundra, Normal Phase soil) ranged from 24 to 109 kg m -3 (average = 48 ± 23 kg m 3 ). Substantial variation in SOC occurs within individual patterned-ground units. For a high-centered, ice-wedge polygon with a diameter of 15 m, SOC levels are 24, 32, and 64 kg m - 3 for the wedge trough, rim, and center, respectively. In a low-centered, ice-wedge polygon, SOC levels are 28 and 83 kg m -3 for the trough and center. The variation in SOC within soil map units and individual patterned-ground units is due primarily to differences in the amount of ground ice. Active-layer thickness varies within and between soil map units, ranging from 31 cm in Typic Sapristels to >100 cm in modern beach sediments. About 47% of the SOC in the upper meter of soil was in the active layer at the time of sampling; the remainder occurring in frozen ground, much of it meeting the definition of permafrost. Some of the SOC originates from past reworking of organic-rich lake sediments. Carbon stocks in near-surface permafrost may be of global significance and should be inventoried in other tundra regions.
Understanding the Contrast of Australian Springtime Rainfall of 1997 and 2002 in the Frame of Two Flavors of El Niño

AbstractThis study investigates the causes and predictability of the different springtime rainfall responses over Australia for El Nino in 1997 and 2002. The rainfall deficit over Australia is generally assumed to be linearly related to the strength of El Nino. However, Australia received near-normal springtime rainfall during the record strong El Nino in 1997, whereas it suffered from severe drought, especially in the east, during the weak El Nino of 2002.Statistical reconstruction of the rainfall anomalies and forecasts produced from the Australian Bureau of Meteorology’s dynamical seasonal forecast system [Predictive Ocean and Atmosphere Model for Australia (POAMA)] demonstrated that the eastward and westward shifts of the maximum SST warming of El Nino contributed to the near-normal and dry responses of Australian spring rainfall in 1997 and 2002, respectively. Hence, the contrasting rainfall responses were largely predictable. However, the dry conditions in 2002 were significantly amplified by the oc.
Fat Politics: The Real Story Behind America's Obesity Epidemic

Introduction: A Big, Fat Problem 1. What Is Fat? 2. How Obesity Became an Epidemic Disease 3. Why We Hate Fat People 4. Women, Fat, and the Sexual Market 5. Fat Genes and the Obesity Blame Game 6. Food and Weight Gain: Super Sized Misperceptions 7. Sloth, Capitalism, and the Paradox of Freedom 8. Obesity Policy: The Fix Is In 9. Unmaking the Obesity Epidemic
Vegetation response to the "African Humid Period" termination in Central Cameroon (7° N) – new pollen insight from Lake Mbalang

Abstract. A new pollen sequence from the Lake Mbalang (7°19´ N, 13°44´ E, 1110 m a.s.l.) located on the eastern Adamawa plateau, in Central Cameroon, is presented in this paper to analyze the Holocene African Humid Period (AHP) termination and related vegetation changes at 7° N in tropical Africa, completing an important transect for exploring shifts in the northern margin of the African Monsoon. This sequence, spanning the last 7000 cal yr BP, shows that the vegetation response to this transitional climatic period was marked by significant successional changes within the broad context of long-term aridification. Semi-deciduous/sub-montane forest retreat in this area is initially registered as early as ca. 6100 cal yr BP and modern savannah was definitely established at ca. 3000 cal yr BP and stabilized at ca. 2400 cal yr BP; but a slight forest regeneration episode is observed between ca. 5200 and ca. 4200 cal yr BP. In this area with modern high rainfall, increasing in the length of the dry season during the AHP termination linked to a contraction of the northern margin of the Intertropical Convergence Zone (ITCZ) from ca. 6100 cal yr BP onward, probably associated with decreasing in cloud cover and/or fog frequency, has primarily controlled vegetation dynamics and above all the disappearance of the forested environment on the Adamawa plateau. Compared to previous studies undertaken in northern tropical and Central Africa, this work clearly shows that the response of vegetation to transitional periods between climatic extremes such as the AHP termination might be different in timing, mode and amplitude according to the regional climate of the study sites, but also according to the stability of vegetation before and during these climatic transitions.
Validation of Respiratory Inductive Plethysmography Using Different Calibration Procedures1–3

We devised a new calibration procedure [least squares method (LSQ)] for respiratory inductive plethysmography (RIP) and compared it with our previously reported simultaneous equation method (SEQ) of analyzing data in 2 body positions and with the method of Stagg and associates using the analysis of individual breaths in a single body position. The values from RIP were compared with simultaneous spirometry (SP) in 20 normal subjects placed in the standing (STD), supine (SUP), sitting, prone, semi-recumbent, right lateral decubitus, and left lateral decubitus postures. The LSQ gave the most accurate results followed closely by SEQ. In addition, LSQ was compared with the isovolume angle maneuver (ISV) calibration procedure in supine (ISV-SUP) and standing (ISV-STD) postures. Each of the 10 normal subjects breathed at tidal volumes of 250, 750, and 1,250 ml in the SUP and STD postures. Of the values obtained by the LSQ method, 93% were within ± 10% of SP in SUP and STD positions. Without a change in the postu.
The quality of maize stored using roof and sack storage methods in Katumba Ward, Rungwe District, Tanzania: Implications on household food security

6Alliance for a Green Revolution in Africa (AGRA), Nairobi, Kenya. The quality of maize stored using sack and roof storage methods was studied by investigating the presence of Fusarium , Aspergillus and Penicillium infections using qualitative methods in 130 maize samples that were randomly collected from the roof and sack storage facilities in Katumba ward, Rungwe district, Tanzania. Levels of fumonisins, aflatoxins, ochratoxins and T-2 toxins were determined using quantitative methods on selected 77 maize samples. It was found that 86% of the selected maize samples were infected by one, two or all of the three pathogenic fungi investigated, whereas 88% were contaminated by one, two or three types of the investigated mycotoxins. The average concentrations of the mycotoxins were as follows: 596.48 ± 38.85 µg/kg of aflatoxins, 745.73 ± 105.57 µg/kg of ochratoxins 87717.95 ± 14984.32 µg/kg (or 87.2 ± 15 mg/kg) of fumonisins, and 1803.77 ± 244.56 µg/kg (or 1.8 ± 0.241 mg/kg) of T-2 toxins. The concentrations of the mycotoxins were a lot higher than the internationally accepted levels. These observations indicated that in Katumba ward, maize stored using roof and sack storage methods was exposed to infection by Fusarium , Aspergillus and Penicillium species, and that the farm households were at risk of ill health due to the mycotoxins.
Clothing gift expenditures : the influence of gender, ethnicity, and age

"The study's purpose was to understand better the role of clothing in gift giving, specifically to estimate the probabilities associated between gender, ethnicity, and age and CU (household) clothing and clothing gift expenditures, as well as to identify mean differences between CU clothing and clothing gift expenditures based on the gender, ethnicity, and age of CU heads. The study data were drawn from the 2001 Consumer Expenditure Survey (CEX) and probabilities were estimated using Bayesian statistical analysis. Analysis of variance (ANOVA) was used to test for mean expenditure differences. The findings indicated that male-headed CUs had a higher probability and higher mean expenditures relative to clothing and clothing gifts than female-headed CUs for the adult and infant clothing categories. African-American-headed CUs had the highest mean clothing expenditure for the adult and infant clothing categories, although Caucasian- and Hispanic-headed CUs had higher probabilities for purchasing clothing. CUs with heads 45~54 and 55~64 had the highest mean expenditures for adult clothing, while, CUs with heads 14~19 and 20~24 had the highest mean expenditures for infant clothing. A comparison of the study results and the literature suggests there may be differences between individual and CU expenditure behaviors relative to clothing and clothing gift giving. "--Abstract from author supplied metadata.
Lipoprotein Z, a hepatotoxic lipoprotein, predicts outcome in alcohol- associated hepatitis

[8] The current study examines the specificity of LP- Z in diagnosing AH, the mechanism for its accumulation, and the diagnostic and therapeutic implications of LP- Z for patients with AH. Abstract Background and Aims: Lipoprotein Z (LP- Z) is an abnormal free cholesterol (FC)– enriched LDL- like particle discovered from patients with cholestatic liver disease. This study aims to define the diagnostic value of LP- Z in alcohol-associated hepatitis (AH) and interrogate the biology behind its formation. Approach and Results: We measured serum levels of LP- Z using nuclear magnetic resonance spectroscopy, a well- established clinical assay. Serum levels of LP- Z were significantly elevated in four AH cohorts compared with control groups, including heavy drinkers and patients with cirrhosis. We defined a Z- index, calculated by the ratio of LP- Z to total apolipoprotein B– containing lipoproteins, representing the degree of deviation from normal VLDL metabolism. A high Z- index was associated with 90- day mortality independent from the Model for End- Stage Liver Disease (MELD) and provided added prognosticative value. Both a Z- index ≤ 0.6 and a decline of Z- index by ≥0.1 in 2 weeks predicted 90- day survival. RNA- sequencing analyses of liver tissues demonstrated an inverse association in the expression of enzymes responsible for the extrahepatic conversion of VLDL to LDL and AH disease severity, which was further confirmed by the measurement of serum enzyme activity. To evaluate whether the FC in LP- Z could contribute to the pathogenesis of AH, we found significantly altered FC levels in liver explant of patients with AH. Furthermore, FC in reconstituted LP- Z particles caused direct toxicity to human hepatocytes in a concentration- dependent manner, supporting a pathogenic role of FC in LP- Z. Conclusions: Impaired lipoprotein metabolism in AH leads to the accumulation of LP- Z in the circulation, which is hepatotoxic from excessive FC. A Z- index ≤ 0.6 predicts 90- day survival independent from conventional bio markers for disease prognostication.
Development of an Evidence-Based Risk Assessment Framework.

Assessment of potential human health risks associated with environmental and other agents requires careful evaluation of all available and relevant evidence for the agent of interest, including both data-rich and data-poor agents. With the advent of new approach methodologies in toxicological risk assessment, guidance on integrating evidence from multiple evidence streams is needed to ensure that all available data is given due consideration in both qualitative and quantitative risk assessment. The present report summarizes the discussions among academic, government, and private sector participants from North America and Europe in an international workshop convened to explore the development of an evidence-based risk assessment framework, taking into account all available evidence in an appropriate manner in order to arrive at the best possible characterization of potential human health risks, and associated uncertainty. Although consensus among workshop participants was not a specific goal, there was general agreement on the key considerations involved in evidence-based risk assessment incorporating 21st century science into human health risk assessment. These considerations have been embodied into an overarching prototype framework for evidence integration that will be explored in more depth in a follow-up meeting.
Pacific Northwest National Laboratory Facility Radionuclide Emissions Units and Sampling Systems

Battelle-Pacific Northwest Division operates numerous research and development (R and D) laboratories in Richland, WA, including those associated with Pacific Northwest National Laboratory (PNNL) on the U.S. Department of Energy (DOE)'s Hanford Site and PNNL Site that have the potential for radionuclide air emissions. The National Emission Standard for Hazardous Air Pollutants (NESHAP 40 CFR 61, Subparts H and I) requires an assessment of all emission units that have the potential for radionuclide air emissions. Potential emissions are assessed annually by PNNL staff members. Sampling, monitoring, and other regulatory compliance requirements are designated based upon the potential-to-emit dose criteria found in the regulations. The purpose of this document is to describe the facility radionuclide air emission sampling program and provide current and historical facility emission unit system performance, operation, and design information. For sampled systems, a description of the buildings, exhaust units, control technologies, and sample extraction details is provided for each registered emission unit. Additionally, applicable stack sampler configuration drawings, figures, and photographs are provided. Deregistered emission unit details are provided as necessary for up to 5 years post closure.
The Effects of Extended Unemployment Insurance over the Business Cycle: Evidence from Regression Discontinuity Estimates Over Twenty Years

One goal of extending the duration of unemployment insurance (UI) in recessions is to increase UI coverage in the face of longer unemployment spells. Although it is a common concern that such extensions may themselves raise nonemployment durations, it is not known how recessions would affect the magnitude of this moral hazard. To obtain causal estimates of the differential effects of UI in booms and recessions, this paper exploits the fact that, in Germany, potential UI benefit duration is a function of exact age which is itself invariant over the business cycle. We implement a regression discontinuity design separately for twenty years and correlate our estimates with measures of the business cycle. We find that the nonemployment effects of a month of additional UI benefits are, at best, somewhat declining in recessions. Yet, the UI exhaustion rate, and therefore the additional coverage provided by UI extensions, rises substantially during a downturn. The ratio of these two effects represents the nonemployment response of workers weighted by the probability of being affected by UI extensions. Hence, our results imply that the effective moral hazard effect of UI extensions is significantly lower in recessions than in booms. Using a model of job search with liquidity constraints, we also find that, in the absence of market-wide effects, the net social benefits from UI extensions can be expressed either directly in terms of the exhaustion rate and the nonemployment effect of UI durations, or as a declining function of our measure of effective moral hazard.
A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting

5 Lanying Du, Guangyu Zhao, Yang Yang, Hongjie Qiu, Lili Wang, Zhihua Kou, Xinrong 6 Tao, Hong Yu, Shihui Sun, Chien-Te K Tseng, Shibo Jiang, Fang Li, Yusen Zhou 7 Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA 8 State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and 9 Epidemiology, Beijing, China 10 Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, 11 USA 12 Department of Microbiology and Immunology, and Center for Biodefense and Emerging Disease, 13 University of Texas Medical Branch, Galveston, Texas, USA 14 Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai 15 Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China 16 These authors contributed equally to this work. 17 Correspondence. E-mail: lifang@umn.edu (F. Li); yszhou@bmi.ac. cn (Y. Zhou). 18
Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Fornicata

Giardia lamblia, a parasitic protist of the metamonada supergroup, has evolved one of the most diverged endocytic compartment systems investigated so far. Peripheral endocytic compartments, currently known as peripheral vesicles or vacuoles (PVs), perform bulk uptake of fluid phase material which is then digested and sorted either to the cell cytosol or back to the extracellular space. Here, we present a quantitative morphological characterization of these organelles using volumetric electron microscopy and super-resolution microscopy (SRM). We defined a morphological classification for the heterogenous population of PVs and performed a comparative analysis of PVs and endosome-like organelles in representatives of phylogenetically-related taxa, Spironucleus spp. and Tritrichomonas foetus. To investigate the as-yet insufficiently understood connection between PVs and clathrin assemblies in G. lamblia, we further performed an in-depth search for two key elements of the endocytic machinery, clathrin heavy chain (CHC) and clathrin light chain (CLC) across different lineages in Metamonada. Our data point to the loss of a bona fide CLC in the last Fornicata common ancestor (LFCA) with the emergence of a protein analogous to CLC (GlACLC) in the Giardia genus. Taken together, this provides the first comprehensive nanometric view of Giardia’s endocytic system architecture and sheds light on the evolution of GLACLC analogues in the Fornicata supergroup and, specific to Giardia, as a possible adaptation to the formation and maintenance of stable clathrin assemblies at PVs.
Measuring the development patterns of urban villages in Shenzhen

Urban villages are widespread in many Chinese cities, providing affordable and accessible housing for rural migrants. These urban villages are developed by the indigenous village population base on a self-help approach and in an unauthorized style. Consequently, urban villages are characterized by rapid physical development. This paper uses GIS applications and Municipal building surveys as instruments to examine the development patterns of urban villages in Shenzhen, one of the most dynamic cities in China. Analyses reveal significant variation in development patterns and trends across urban villages, which can provide informative support for policy making associated with urban village (re)development.
Modeling tissue-specific breakpoint proximity of structural variations from 2,382 whole-genomes to identify cancer drivers

Structural variations (SVs) in cancer cells often impact large genomic regions with functional consequences. However, little is known about the genomic features related to the breakpoint distribution of SVs in different cancers, a prerequisite to distinguish loci under positive selection from those with neutral evolution. We developed a method that uses a generalized additive model to investigate the breakpoint proximity curves from 2,382 whole-genomes of 32 cancer types. We find that a multivariate model, which includes linear and nonlinear partial contributions of various tissue-specific features and their interaction terms, can explain up to 57% of the observed deviance of breakpoint proximity. In particular, three-dimensional genomic features such as topologically associating domains (TADs), TAD-boundaries and their interaction with other features show significant contributions. The model is validated by identification of known cancer genes and revealed putative drivers in novel cancers that have previous evidence of therapeutic relevance in other cancers.