Miracle-dz/UniFAR-FTUs huggingface dataset:
Changing primary production and biomass in heterogeneous landscapes: Estimation and uncertainty based on multi-scale remote sensing and GIS data

Changes in vegetation gross primary production (GPP) and forest aboveground standing biomass C (biomass) were investigated to better understand the impacts of human and natural disturbances on carbon uptake and storage in two northern hemisphere terrestrial ecosystems, which represent primarily forest-dominated and primarily urbanizing landscapes, respectively. Research focused on evaluating changes in (a) GPP in Southeastern Michigan, where the dynamics of vegetation carbon flux are tied closely to urbanization and human development characteristics; and (b) biomass in Eastern Siberia, where biomass changes are strongly affected by disturbance and regrowth. Both projects exploited remotely sensed data and biophysical or ecosystem models to estimate GPP and biomass. Altering the scale of spatial data and summary units may generate different results. The scaling effects need to be characterized to evaluate scale-related uncertainties associated with carbon estimates. In Michigan, sensitivity of inferences about productivity trends among several development types to levels of aggregation in the Census housing data were examined from the block-group to county scales. In Siberia, impacts of changes in the remote sensing observational scale (i.e., sensor resolution) on the estimated biomass trends were analyzed at resolutions from 60 to 960 meters. Results showed that GPP increased by 53 g C m-1 in Southeastern Michigan and biomass increased by 3.9 Mg C ha-1 in Eastern Siberia between 1990 and 2000, and that more productive landscapes resulted from tree-cover expansion and forest recovery, respectively. These results corroborate previous findings of increased vegetation activity throughout the northern hemisphere in 1990s. With respect to scaling effects on carbon estimates, in Michigan, relationships between the estimated GPP trends and development types remained consistent across Census scales; and, in Siberia, degradation of remote sensing resolution resulted in the overestimation of changes in biomass by 9-69% at the 960-meter resolution. Results suggested that, for carbon analysis across broader geographic extents (e.g., regional- to national-scale estimation), coarser Census scales up to the county level may be used to evaluate carbon trends by development intensities, while remote sensing data at coarser resolutions may not maintain accuracy of the estimated carbon trends relative to finer resolution data.
Cytoscape 2.8: new features for data integration and network visualization

Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. Availability and implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org. Contact: msmoot@ucsd.edu
PRINCIPLE: a tool for associating genes with diseases via network propagation

SUMMARY PRINCIPLE is a Java application implemented as a Cytoscape plug-in, based on a previously published algorithm, PRINCE. Given a query disease, it prioritizes disease-related genes based on their closeness in a protein-protein interaction network to genes causing phenotypically similar disorders to the query disease. AVAILABILITY Implemented in Java, PRINCIPLE runs over Cytoscape 2.7 or newer versions. Binaries, default input files and documentation are freely available at http://www.cs. tau.ac. il/~bnet/software/PrincePlugin/. CONTACT roded@tau.ac. il; assafgot@tau.ac. il.
Gestational Exposure to Bisphenol A Affects the Function and Proteome Profile of F1 Spermatozoa in Adult Mice

Background: Maternal exposure to the endocrine disruptor bisphenol A (BPA) has been linked to offspring reproductive abnormalities. However, exactly how BPA affects offspring fertility remains poorly understood. Objectives: The aim of the present study was to evaluate the effects of gestational BPA exposure on sperm function, fertility, and proteome profile of F1 spermatozoa in adult mice. Methods: Pregnant CD-1 mice (F0) were gavaged with BPA at three different doses (50 μg/kg bw/day, 5 mg/kg bw/day, and 50 mg/kg bw/day) on embryonic days 7 to 14. We investigated the function, fertility, and related processes of F1 spermatozoa at postnatal day 120. We also evaluated protein profiles of F1 spermatozoa to monitor their functional affiliation to disease. Results: BPA inhibited sperm count, motility parameters, and intracellular ATP levels in a dose-dependent manner. These effects appeared to be caused by reduced numbers of stage VIII seminiferous epithelial cells in testis and decreased protein kinase A (PKA) activity and tyrosine phosphorylation in spermatozoa. We also found that BPA compromised average litter size. Proteins differentially expressed in spermatozoa from BPA treatment groups are known to play a critical role in ATP generation, oxidative stress response, fertility, and in the pathogenesis of several diseases. Conclusions: Our study provides mechanistic support for the hypothesis that gestational exposure to BPA alters sperm function and fertility via down-regulation of tyrosine phosphorylation through a PKA-dependent mechanism. In addition, we anticipate that the BPA-induced changes in the sperm proteome might be partly responsible for the observed effects in spermatozoa. Citation: Rahman MS, Kwon WS, Karmakar PC, Yoon SJ, Ryu BY, Pang MG. 2017. Gestational exposure to bisphenol-A affects the function and proteome profile of F1 spermatozoa in adult mice. Environ Health Perspect 125:238–245; http://dx.doi. org/10.1289/EHP378
Protective Effect of Edaravone on Cyclophosphamide Induced Oxidative Stress and Neurotoxicity in Rats

Background: Cyclophosphamide (CPA) is the most widely prescribed cancer chemotherapeutic agent which shows serious neurotoxic side effect. Generation of reactive oxygen species at the cellular level is the basic mechanism of cyclophosphamide induced neurotoxicity. Edaravone is the synthetic drug used for brain stroke and has potent antioxidant property. Objective: This study aimed to investigate the effect of edaravone on neurobehavioral and neuropathological alteration induced by cyclophosphamide in male rats. Methods: Twenty eight Sprague-Dawley rats were equally divided into four groups of seven rats in each. The control group received saline, and other groups were given CPA intraperitoneally (100 mg/kg), CPA (100 mg/kg) intraperitoneally + Edaravone (10 mg/kg) orally, or Edaravone (10 mg/kg) orally for one month. Results: Our data showed that CPA significantly elevated brain AChE activity in the hippocampal region. A decrease in the total antioxidant capacity and a reduction in the CAT, SOD, and GPX activity occurred in the brains of the rats exposed to CPA. CPA-treated rats showed a significant impairment in long-term-memory and motor coordination. These results were supported by histopathological observations of the brain. Results revealed that administration of edaravone reversed AChE activity alternation and ameliorated behavioral and histopathological changes induced by CPA. Conclusion: This study suggests that co-administration of edaravone with cyclophosphamide may be a useful intriguing therapeutic approach to overcome cyclophosphamide induced neurotoxicity.
Modeling Ground‐Water Flow at Love Canal, New York

A ground‐water modeling study was conducted at the Love Canal area, Niagara Falls, New York, as part of a comprehensive evaluation of contamination at the area. The hydrogeology underlying Love Canal consists of a shallow system of silts and fine sands, underlain by confining layers of lacustrine clays and glacial till, which are underlain by the Lockport Dolomite. A two‐dimensional computer model of the Lockport Dolomite was constructed to help define the ground‐water flow system. Both history matching and a sensitivity analysis were conducted. Assuming the dolomite was contaminated, Monte Carlo simulation and uncertainty analysis were used to estimate contaminant travel times to the upper Niagara River. Results indicate that travel times would average 1,000 days with less than 5% probability of less than 100 days or greater than 10,000 days. Analysis of remedial action for the Lockport Dolomite using best estimates of hydrologic parameters indicates that three interceptor wells at the south end of the c.
LINC00238 inhibits hepatic carcinoma progression by activating TMEM106C-mediated apoptosis pathway

The present study aimed to explore the regulatory mechanism of long intergenic non-protein coding (LINC)00238 in hepatocellular carcinoma (HCC). LINC00238 expression in HCC tissues and cell lines was measured using reverse transcription-quantitative PCR. LncTar was used to predict the binding sites between LINC00238 and transmembrane protein 106C (TMEM106C). Survival analysis of LINC00238, TMEM106C and activating transcription factor 3 (ATF3) in patients with HCC was performed based on TCGA data. The proliferation, apoptosis, migration, and invasion of HCC cells were measured by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay, flow cytometer, wound healing and Transwell assays, respectively. LINC00238 promoted apoptosis and inhibited proliferation, migration and invasion of HCC cells. LINC00238 was downregulated in HCC. TMEM106C was a target of LINC00238 and TMEM106C expression was negatively regulated by LINC00238. TMEM106C suppressed the apoptosis pathway and decreased the expression of caspase-7, tissue inhibitor of metalloproteinase 2, programmed cell death 4 and ATF3. Notably, ATF3 was the upstream promoter of LINC00238 and positively regulated LINC00238 expression. In conclusion, LINC00238 inhibited HCC progression by inhibiting TMEM106 expression and activating the TMEM106C-mediated apoptosis pathway.
Modeling of Heat and Mass Transfer in Soil Plant-Atmosphere. Influence of the Spatial Variability of Soil Hydrodynamic

The modeling of water transfer in the unsaturated zone uses techniques and methods of the soil physics to solve the Richards’s equation. However, there is a disaccord between the size of the measurements provided by the soil physics and the size of the fields of hydrological modeling problem, to which is added the strong spatial variability of soil hydraulic properties. The objective of this work was to develop a methodology to estimate the hydrodynamic parameters for modeling water transfers at different hydrological scales in the soil-plant atmosphere systems. Keywords—Hydraulic properties, Modeling, Unsaturated zone, Transfer, Water
Opening-wedge high tibial osteotomy with a locked low-profile plate.

BACKGROUND High tibial osteotomy has been recognized as a beneficial treatment for osteoarthritis of the medial compartment of the knee. The purpose of this prospective study was to assess the short-term results of opening-wedge high tibial osteotomies with locked plate fixation. METHODS From September 2002 to November 2005, fifty-one consecutive medial opening-wedge high tibial osteotomies were performed. The mean age of the patients at the time of the index operation was forty-nine years. The preoperative and postoperative factors analyzed included the grade of arthritis of the tibiofemoral compartment (the Ahlbäck radiographic grade), the anatomic tibiofemoral angle, patellar height, the Hospital for Special Surgery rating system score, and the Lysholm and Gillquist knee score. RESULTS Postoperatively, one superficial wound infection occurred. Fifty of the fifty-one osteotomies healed after an average period of 12.9 weeks (range, eight to sixteen weeks) without bone grafts. A nonunion developed in a sixty-two-year-old patient who was a cigarette smoker. The average postoperative tibiofemoral angle was 9 degrees of valgus. Forty-nine patients were followed for a mean of fifty-two months. The average score on the Hospital for Special Surgery rating system was 86 points at the time of the most recent follow-up. The rating was excellent in twenty-eight patients (57%), good in twelve (24%), fair in four (8%), and poor in five (10%). The average score on the Lysholm and Gillquist knee-scoring scale was 83 points. According to these scores, the outcome was excellent in nine patients (18%), good in thirty-one (63%), fair in three (6%), and poor in six (12%). Four knees failed after an average of thirty-six months. CONCLUSIONS Our results suggest that an opening-wedge high tibial osteotomy with locked plate fixation allows a correct valgus angle to be achieved with good short-term results.
Automated analysis of SKS splitting to infer upper mantle anisotropy beneath Germany using more than 20 yr of GRSN and GRF data

S U M M A R Y Upper mantle anisotropy beneath Germany is investigated through the measurements and analysis of shear-wave splitting using SKS phases. We analysed teleseismic events recorded by 24 broadband stations of the German Regional Seismic Network (GRSN) and three broadband stations of the Gräfenberg-Array (GRF). These permanent German networks cover an area extending from the Alps in the south up to the Northern German basin towards north. In comparison to several former studies that are based either on short observation periods or that are restricted to limited areas of Germany, we resort to 22 yr of the GRSN (1991–2012) and 34 yr of GRF data archive (1979–2012). Due to the huge amount of data, we applied a fully automatic procedure to determine SKS splitting parameters from archived recordings and also applied strong quality constraints to obtain reliable solutions. From our analysis, two main features are obvious: For the stations in the middle and southern part of Germany we found homogeneous E–W to ENE–WSW fast-axis directions. In contrast, stations in NE-Germany exhibit a NW–SE oriented fast axis. Both findings can be correlated to major tectonic features in Central Europe. The E–W to ENE–WSW orientations in the middle and southern part of Germany are nearly parallel to the strike of the Variscan mountain belts, whereas the NW–SE direction in NE-Germany corresponds to the orientation of the nearby Tornquist-Teisseyre suture zone. For the southern part of Germany, there are indications for an alignment of the fast axis parallel to the curvature of the nearby Alps. Apart from the more large-scale features there are two stations (BFO and CLZ) which seem to have an imprint related to the regional geodynamic setting, namely the rifting in the Southern Rhine Graben and the formation of the Harz Mountains, respectively. We conclude that the observed regional variations of splitting parameter over Germany advocate for a mostly lithospheric route of the anisotropy. Furthermore, variations of the splitting parameters with respect to the azimuths of the incoming waves, as observed at some stations, point to vertical varying anisotropy. For some stations (BFO, RUE) the inversions for two anisotropic layers revealed directions of the fast axes that are similar to the strike directions of the surrounding tectonic units. For other stations, the confidence regions are too large for a tectonic interpretation.
Current Research in Ecological and Social Psychology A ﬁve-nation study of the impact of political leaning and perception of crisis severity on the preference for female and minority leaders during the COVID-19 pandemic

Research on underrepresented groups in leadership has shown that women and ethnic minorities are preferred as leaders during a crisis. In the present study, we investigated factors that shape voter preferences for minority political leaders in the COVID-19 crisis. We examined participant perceptions of the severity of the COVID-19 crisis in health, social, and economic domains and self-reported political leaning, and their impact on preference for a female (vs male) or minority political leader. We collected survey data in autumn 2020 using online platforms in France, Japan, the United Kingdom, the United States, and a snowball sample in Germany (total N = 1,259). Results showed that female leaders were generally more preferred by politically left- than right-leaning partici- pants independent of severity perceptions of the social or economic crisis. In addition, we found that preference for female leaders amongst right-leaning participants increased when their current regional leader’s actions were judged insuﬃcient to manage the health crisis, an eﬀect primarily driven by participants in Germany and the United Kingdom. Left-leaning political orientation also predicted the preference for minority leaders across coun- tries. Moreover, a more severe perception of the social aspects of the crisis increased minority preference, as expected, but mostly in Germany and the United States. We discuss cross-country variation of our results. Over- all, our ﬁndings aﬃrm and expand prior research showing the importance of political leaning and changing leadership demands in a crisis and their impact on the preference for minority leaders.
Development of 14 polymorphic microsatellite loci for Ficus tikoua (Moraceae)

Premise of the study: Polymorphic microsatellite markers were developed to facilitate studies on the fine-scale population genetic structure of Ficus tikoua (Moraceae), a prostrate shrub known to have highly restricted gene flow. Methods and Results: Microsatellite primers were developed using the biotin-streptavidin capture method and scanned for polymorphism within 76 individuals sampled from three natural F. tikoua populations. Fourteen loci were shown to be polymorphic, with allele numbers ranging from three to 16. The observed and expected heterozygosity in the three populations ranged from 0 to 1 and from 0 to 0.87, respectively. Substantial divergence was found among the populations at some loci. All loci can be successfully amplified in at least eight other Ficus species, indicating good transferability within the genus. Conclusions: The 14 microsatellite loci will be a helpful tool for assessing the fine-scale genetic structure of F. tikoua.
Treatment of diarrhea in young children: results from surveys on the perception and use of oral rehydration solutions, antibiotics, and other therapies in India and Kenya

Background Diarrheal disease is a leading cause of morbidity and mortality among children under five. Although oral rehydration solution (ORS) has tremendous therapeutic benefits, coverage of and demand for this product have remained low in many developing countries. This study surveyed caregivers and health care providers in India and Kenya to gather information about perceptions and use of various diarrhea treatments, assess reasons for low ORS use, and identify opportunities for expanding ORS use. Methods The project team conducted two rounds of semi–structured, quantitative surveys with more than 2000 caregivers in India and Kenya in 2012. A complementary survey covered more than 500 pharmacy staff and health care workers in both countries. In Kenya, the team also surveyed rural pharmacies to gather pricing and sales data. Results Although caregivers generally had very positive perceptions of ORS, they typically ranked antibiotics ahead of ORS as the strongest medicine for diarrhea (in India 62% ranked antibiotics first and 23% ranked ORS first, n = 404; in Kenya results were 55% and 29%, n = 401). Many caregivers had misconceptions about the purpose and effectiveness of various treatments. For example, most caregivers who gave ORS at last episode expected it to stop their child’s diarrhea (65% in India, n = 190; 73% in Kenya, n = 154). There were noteworthy differences between India and Kenya in the selection and sourcing of treatments. Much of the money spent by families during the last episode of diarrhea was for inappropriate treatments. This was especially true in India, where rural households typically spent US$ 2.29 (median for the 79% of rural households that paid for health care services or treatments, n = 199) with most of this going to pay fees of private health workers and/or for antibiotics. Conclusions Caregivers’ primary treatment goal is to stop diarrhea, and many believe that antibiotics or ORS will accomplish this goal. Inappropriate treatment – and especially overuse of antibiotics – is common. Satisfaction with ORS is high, but dosing is a challenge for caregivers. The results provide valuable insight into treatment behaviors and suggest significant opportunities to enhance use of ORS in developing countries.
Loss of Liver Kinase B1 (LKB1) in Beta Cells Enhances Glucose-stimulated Insulin Secretion Despite Profound Mitochondrial Defects

Background: LKB1 regulates multiple aspects of pancreatic β cell biology. Results: LKB1 loss in β cells leads to profound mitochondrial defects yet increases glucose-stimulated insulin secretion in a mitochondria-independent mechanism. Conclusion: LKB1 is essential for mitochondrial maintenance and negatively regulates a distal step of insulin secretion. Significance: LKB1 loss exposes powerful mechanisms of insulin secretion that can override defects in the classic triggering pathway. The tumor suppressor liver kinase B1 (LKB1) is an important regulator of pancreatic β cell biology. LKB1-dependent phosphorylation of distinct AMPK (adenosine monophosphate-activated protein kinase) family members determines proper β cell polarity and restricts β cell size, total β cell mass, and glucose-stimulated insulin secretion (GSIS). However, the full spectrum of LKB1 effects and the mechanisms involved in the secretory phenotype remain incompletely understood. We report here that in the absence of LKB1 in β cells, GSIS is dramatically and persistently improved. The enhancement is seen both in vivo and in vitro and cannot be explained by altered cell polarity, increased β cell number, or increased insulin content. Increased secretion does require membrane depolarization and calcium influx but appears to rely mostly on a distal step in the secretion pathway. Surprisingly, enhanced GSIS is seen despite profound defects in mitochondrial structure and function in LKB1-deficient β cells, expected to greatly diminish insulin secretion via the classic triggering pathway. Thus LKB1 is essential for mitochondrial homeostasis in β cells and in parallel is a powerful negative regulator of insulin secretion. This study shows that β cells can be manipulated to enhance GSIS to supra-normal levels even in the face of defective mitochondria and without deterioration over months.
Inverse borehole coupling theory and its application to hydrophone vertical seismic profiling

In 1953, J. E. White developed the theory of borehole coupling which describes how low-frequency elastic waves in the formation produce a pressure response in the fluid-filled borehole. The essence of this theory is that formation elastic waves squeeze the borehole, and that this squeezing action creates upand downgoing tube waves in the fluid. A key result of White’s theory is an integral expression for pressure in terms of a Quantity that is contenient o call squeeze strain: the fractional change in crosssectional area of the borehole, if it were empty, due to formation elastic waves. Consider a uniform. smooth fluid-filled borehole in 2 homogeneous elastic formation over the depth interval [zl,zZ]