Miracle-dz/UniFAR-FTUs huggingface dataset:
Water-Quality Assessment of the Trinity River Basin, Texas - Pesticides in a Coastal Prairie Agricultural Area, 1994-95

Agriculture is a major land use in the coastal prairie area located in the southern part of the Trinity River Basin. Crops grown in the area include rice, sorghum, and soybeans. Pesticide-use estimates for the area show that compounds with the highest use are the herbicides: molinate, propanil, thiobencarb, metolachlor, acifluorfen, bentazon, and atrazine and the insecticides: carbaryl and methyl parathion. More than 20 pesticide samples collected from each of three streams in the coastal prairie resulted in detections of 29 different pesticide compounds. The most frequently detected compounds were the herbicides: atrazine, metolachlor, and molinate, which were detected in more than 75 percent of the samples. Herbicides were detected more frequently than insecticides. Maximum concentrations of atrazine, metolachlor, and molinate occurred in the spring and were 4, 1.9, and 200 micrograms per liter (μg/L), respectively. Almost all concentrations of atrazine and metolachlor were below drinking water standards; no standard is available for molinate. Concentrations and estimated loads and percent of applied compound lost to the streams were generally higher in the watersheds where more of the pesticides were applied to crops.
Crystal structure of ethyl 2-({[(4Z)-3,5-dioxo-1-phenylpyrazolidin-4-ylidene]methyl}amino)acetate

The title compound, C14H15N3O4, is nearly planar, the dihedral angle between the planes of the phenyl and pyrazolidine rings being 1.13 (7) Å, and that between the plane of the pyrazolidine ring and the mean plane of the side chain [C—N—C–C(=O)—O; r.m.s. deviation = 0.024 Å] being 2.52 (7)°. This is due in large part to the presence of the intramolecular N—H⋯O and C—H⋯O hydrogen bonds. In the crystal, pairwise N—H⋯O hydrogen bonds form inversion dimers, which are further associated into layers, lying very close to plane (-120), via pairwise C—H⋯O hydrogen bonds. The layers are then weakly connected through C—H⋯O hydrogen bonds, forming a three-dimensional structure.
Intratumoral Decorin Gene Delivery by AAV Vector Inhibits Brain Glioblastomas and Prolongs Survival of Animals by Inducing Cell Differentiation

Glioblastoma multiforme (GBM) is the most malignant cancer in the central nervous system with poor clinical prognosis. In this study, we investigated the therapeutic effect of an anti-cancer protein, decorin, by delivering it into a xenograft U87MG glioma tumor in the brain of nude mice through an adeno-associated viral (AAV2) gene delivery system. Decorin expression from the AAV vector in vitro inhibited cultured U87MG cell growth by induction of cell differentiation. Intracranial injection of AAV-decorin vector to the glioma-bearing nude mice in vivo significantly suppressed brain tumor growth and prolonged survival when compared to control non-treated mice bearing the same U87MG tumors. Proteomics analysis on protein expression profiles in the U87MG glioma cells after AAV-mediated decorin gene transfer revealed up- and down-regulation of important proteins. Differentially expressed proteins between control and AAV-decorin-transduced cells were identified through MALDI-TOF MS and database mining. We found that a number of important proteins that are involved in apoptosis, transcription, chemotherapy resistance, mitosis, and fatty acid metabolism have been altered as a result of decorin overexpression. These findings offer valuable insight into the mechanisms of the anti-glioblastoma effects of decorin. In addition, AAV-mediated decorin gene delivery warrants further investigation as a potential therapeutic approach for brain tumors.
Feminization of Male Mouse Liver by Persistent Growth Hormone Stimulation: Activation of Sex-Biased Transcriptional Networks and Dynamic Changes in Chromatin States

ABSTRACT Sex-dependent pituitary growth hormone (GH) secretory profiles—pulsatile in males and persistent in females—regulate the sex-biased, STAT5-dependent expression of hundreds of genes in mouse liver, imparting sex differences in hepatic drug/lipid metabolism and disease risk. Here, we examine transcriptional and epigenetic changes induced by continuous GH infusion (cGH) in male mice, which rapidly feminizes the temporal profile of liver STAT5 activity. cGH repressed 86% of male-biased genes and induced 68% of female-biased genes within 4 days; however, several highly female-specific genes showed weak or no feminization, even after 14 days of cGH treatment. Female-biased genes already in an active chromatin state in male liver generally showed early cGH responses; genes in an inactive chromatin state often responded late. Early cGH-responsive genes included those encoding two GH/STAT5-regulated transcriptional repressors: male-biased BCL6, which was repressed, and female-specific CUX2, which was induced. Male-biased genes activated by STAT5 and/or repressed by CUX2 were enriched for early cGH repression. Female-biased BCL6 targets were enriched for early cGH derepression. Changes in sex-specific chromatin accessibility and histone modifications accompanied these cGH-induced sex-biased gene expression changes. Thus, the temporal, sex-biased gene responses to persistent GH stimulation are dictated by GH/STAT5-regulated transcription factors arranged in a hierarchical network and by the dynamics of changes in sex-biased epigenetic states.
Graph learning with a nearest neighbor approach

In this paper, we study how to traverse all edges of an unknown graph G = (V;E) that is bi-directed and strongly connected. This problem can be solved with a simple algorithm that traverses all edges at most twice, and no algorithm can do better in the worst case. Artificial Intelligence researchers, however, often use the following online nearest neighbor algorithm: “repeatedly take a shortest path to the closest unexplored edge and traverse it. ” We prove bounds on the worst-case complexity of this algorithm. We show, for example, that its worst-case complexity is close to optimal for some classes of graphs, such as graphs with linear or star topology and dense graphs with edge lengths one. In general, however, its complexity can grow faster than linear in the sum of all edge lengths, although not faster than log(V ) times the sum of all edge lengths.
Does cleanliness influence moral judgments? Response effort moderates the effect of cleanliness priming on moral judgments

Whether cleanliness influences moral judgments has recently become a topic of debate in the psychological literature. After the initial report that activating the notion of physical purity can result in less severe moral judgments (Schnall et al., 2008a), a direct replication (Johnson et al., 2014a) with much larger sample sizes failed to yield similar findings. The current paper examines the possibility that only non-conscious activation of the cleanliness concept, as achieved in participants with low response effort on priming materials, can produce the expected effect. An online replication (Study 1, N = 214) provided evidence that, when participants exerted low (yet still acceptable) levels of response effort to the experimental material, cleanliness priming led to more lenient moral judgments than neutral priming. An online experiment (Study 2, N = 440; replicated in Study 2a, N = 436) manipulating participants’ effort on the priming task (low vs. high) supported the hypothesized mechanism. Specifically, respondents in the low response effort group were instructed to complete the priming task as quickly as possible without too much attention, and the cleanliness priming resulted in less extreme moral judgments than the neutral condition as expected. In contrast, respondents in the high response effort group were instructed to perform to the best of their ability on the priming task, with a non-significant difference on moral ratings between cleanliness and neutral conditions. In addition to helping resolve the controversy regarding the cleanliness hypothesis, the current paper calls into attention the role of response effort in the execution and replication of priming studies.
Imaging of subvolcanic Mesozoics in the Saurashtra peninsula of India using traveltime inversion of wide-angle seismic data

Low-velocity Mesozoic sediments exposed in the northeastern part of the Saurashtra peninsula of western India are assumed to be below the high-velocity volcanic rock cover. Conventional seismic refraction and reflection profiling experiments often fail to map hidden low-velocity formations caused by inherent limitations of these methods. However, wide-angle seismics involving both refractions and reflections is an effective tool for imaging in such a geological setting. Inversion of wide-angle seismic traveltime data from a 45 km long profile reveals a three-layered velocity structure above the basement with Mesozoic sediments sandwiched between exposed volcanic rock and an underlying basalt flow. The derived velocity model closely matches the lithology of the nearby deep Lodhika well, demonstrating the potential of wide-angle seismics in mapping formations hidden below volcanic rock cover. The volcanic rock cover is almost flat, ∼ 1.4 km thick, with an average velocity of ∼5.1 km s - 1 . The Mesozoic sediments have a velocity of 4.3 km s - 1 and thickness variations from 0.9 to 1.6 km. The underlying basalt flow has a velocity of 5.15 km s - 1 and varies in thickness from 1 to 2 km. The basement, with a velocity of 5.80-5.95 km s - 1 , is at an average depth of 3.9 km. Shear wave analysis yielded velocities varying between 2.65-2.75 and 3.30-3.40 km s - 1 for the exposed volcanic rock and the subsurface basement, respectively, corresponding to Poisson ratios of 0.31 and 0.26. The high Poisson ratio in the volcanic rock cover is a result of rock fracturing as indicated by the fast decay of seismic energy with offset.
Role of a Mutation in Human Cytomegalovirus Gene UL104 in Resistance to Benzimidazole Ribonucleosides

ABSTRACT The benzimidazole d-ribonucleosides TCRB and BDCRB are potent and selective inhibitors of human cytomegalovirus (HCMV) replication. Two HCMV strains resistant to these compounds were selected and had resistance mutations in genes UL89 and UL56. Proteins encoded by these two genes are the two subunits of the HCMV “terminase” and are necessary for cleavage and packaging of viral genomic DNA, a process inhibited by TCRB and BDCRB. We now report that both strains also have a previously unidentified mutation in UL104, the HCMV portal protein. This mutation, which results in L21F substitution, was introduced into the genome of wild-type HCMV by utilizing a recently cloned genome of HCMV as a bacterial artificial chromosome. The virus with this mutation alone was not resistant to BDCRB, suggesting that this site is not involved in binding benzimidazole nucleosides. As in previous proposals for mutations in UL104 of murine cytomegalovirus and HCMV strains resistant to BAY 38-4766, we hypothesize that this mutation could compensate for conformational changes in mutant UL89 and UL56 proteins, since the HCMV terminase is likely to interact with the portal protein during cleavage and packaging of genomic DNA.
Representation of African Easterly Waves in CMIP5 Models

AbstractAfrican easterly waves (AEWs) can act as seed disturbances for tropical cyclones (TCs) in the Atlantic, and changes in future AEW activity may have important consequences for development of TCs. The simulation of AEWs was investigated using output from phase 5 of the Coupled Model Intercomparison Project (CMIP5) suite of experiments, including coupled historical and future simulations and atmosphere only (AMIP) simulations. Large biases exist in the simulation of low- (850 hPa) and midlevel (700 hPa) eddy kinetic energy (EKE, a proxy for AEW activity) in AMIP and historical simulations. CMIP5 models simulate excessive EKE and deficient rainfall south of 17°N. The same biases exist in historical and AMIP models and are not a consequence of errors in sea surface temperatures. The models also struggle to accurately couple AEWs and rainfall, with little improvement from CMIP3 models. CMIP5 models are unable to propagate AEWs across the coast and into the Atlantic, which is shown to be related to the r.
A 2.2/spl mu/W 94nV//spl radic/Hz, Chopper-Stabilized Instrumentation Amplifier for EEG Detection in Chronic Implants

A chopper-stabilized instrumentation amplifier is targeted for "deep-brain" human implants and consumes 2.2muW from a 1.8V supply. The integrated noise from 0.5 to 100 Hz is 0.94muV, providing a noise efficiency factor of 4.9. The use of chopper stabilization provides rail-to-rail inputs and 105dB CMRR. An integrated 0.5Hz HPF is used to suppress electrode offsets. The circuit is also used in micropower bridge interfaces for impedance measurement and pressure sensing.
MicroRNA Expression and Identification of Putative miRNA Targets in Ovarian Cancer

Background MicroRNAs (miRNAs) represent a class of small non-coding RNAs that control gene expression by targeting mRNAs and triggering either translation repression or RNA degradation. Emerging evidence suggests the potential involvement of altered regulation of miRNA in the pathogenesis of cancers, and these genes are thought to function as both tumor suppressors and oncogenes. Methodology/Principal Findings Using microRNA microarrays, we identify several miRNAs aberrantly expressed in human ovarian cancer tissues and cell lines. miR-221 stands out as a highly elevated miRNA in ovarian cancer, while miR-21 and several members of the let-7 family are found downregulated. Public databases were used to reveal potential targets for the highly differentially expressed miRNAs. In order to experimentally identify transcripts whose stability may be affected by the differentially expressed miRNAs, we transfected precursor miRNAs into human cancer cell lines and used oligonucleotide microarrays to examine changes in the mRNA levels. Interestingly, there was little overlap between the predicted and the experimental targets or pathways, or between experimental targets/pathways obtained using different cell lines, highlighting the complexity of miRNA target selection. Conclusion/Significance Our results identify several differentially expressed miRNAs in ovarian cancer and identify potential target transcripts that may be regulated by these miRNAs. These miRNAs and their targets may have important roles in the initiation and development of ovarian cancer.
Programmed Cell Death During Caenorhabditis elegans Development

Programmed cell death is an integral component of Caenorhabditis elegans development. Genetic and reverse genetic studies in C. elegans have led to the identification of many genes and conserved cell death pathways that are important for the specification of which cells should live or die, the activation of the suicide program, and the dismantling and removal of dying cells. Molecular, cell biological, and biochemical studies have revealed the underlying mechanisms that control these three phases of programmed cell death. In particular, the interplay of transcriptional regulatory cascades and networks involving multiple transcriptional regulators is crucial in activating the expression of the key death-inducing gene egl-1 and, in some cases, the ced-3 gene in cells destined to die. A protein interaction cascade involving EGL-1, CED-9, CED-4, and CED-3 results in the activation of the key cell death protease CED-3, which is tightly controlled by multiple positive and negative regulators. The activation of the CED-3 caspase then initiates the cell disassembly process by cleaving and activating or inactivating crucial CED-3 substrates; leading to activation of multiple cell death execution events, including nuclear DNA fragmentation, mitochondrial elimination, phosphatidylserine externalization, inactivation of survival signals, and clearance of apoptotic cells. Further studies of programmed cell death in C. elegans will continue to advance our understanding of how programmed cell death is regulated, activated, and executed in general.
Changes in seasonal maximum daily precipitation in China over the period 1961–2006

Daily rainfall data from 485 stations in China over the period 1961‐2006 are used to examine changes in seasonal extreme rainfall. We focus on the temporal changes in their distribution, together with examination of the dependence of seasonal extreme rainfall on elevation. The validity of the stationarity assumption is investigated by testing for nonstationarities in the form of abrupt and slowly varying changes. The nonparametric Pettitt test is used to detect change points in the mean and variance of the rainfall distribution, while the presence of monotonic trends and trend magnitude is tested using Mann‐Kendall test and Sen's slope estimator. Violation of the stationarity assumption is mostly associated with abrupt rather than gradual changes, and monotonic trends are generally not statistically significant. Most of the change points occurred in the 1980s, when China underwent a socioeconomic development. Extreme rainfall in autumn (spring and winter) points to a decreasing (increasing) tendency over the majority of the country, while summer extreme rainfall exhibits a ‘dipole‐like’ structure, with an overall tendency towards increasing trends in the south and decreasing in the north. The parameters of the Generalized Extreme Value (GEV) distribution are used to examine the dependence of extreme rainfall on elevation. The location and scale parameters are negatively correlated with elevation, while orography does not appear to be an important control on the shape parameter. The dependence of GEV parameters on elevation is more pronounced in northern rather than southern China. We also investigated the relation between summer extreme rainfall and climate variability, focusing on the East Asia Summer Monsoon (EASM) index. EASM is negatively (positively) correlated with summer extreme rainfall over South (North) China. Considering the weakening trend of EASM in recent years, there is a potential water shortage in the North China Plain and increasing flood risk in the south. Copyright © 2012 Royal Meteorological Society
Variability Mitigation in Nanometer CMOS Integrated Systems: A Survey of Techniques From Circuits to Software

Variation in performance and power across manufactured parts and their operating conditions is an accepted reality in modern microelectronic manufacturing processes with geometries in nanometer scales. This article surveys challenges and opportunities in identifying variations, their effects and methods to combat these variations for improved microelectronic devices. We focus on computing devices and their design at various levels to combat variability. First, we provide a review of key concepts with particular emphasis on timing errors caused by various variability sources. We consider methods to predict and prevent, detect and correct, and finally conditions under which such errors can be accepted; we also consider their implications on cost, performance and quality. We provide a comparative evaluation of methods for deployment across various layers of the system from circuits, architecture, to application software. These can be combined in various ways to achieve specific goals related to observability and controllability of the variability effects, providing means to achieve cross-layer or hybrid resilience. We then provide examples of real world resilient single-core and parallel architectures. We find that parallel architectures and parallelism in general provide the best means to combat and exploit variability to design resilient and efficient systems. Using programmable accelerator architectures such as clustered processing elements and GP-GPUs, we show how system designers can coordinate propagation of timing error information and its effects along with new techniques for memoization (i.e., spatial or temporal reuse of computation). This discussion naturally leads to use of these techniques into emerging area of “approximate computing,” and how these can be used in building resilient and efficient computing systems. We conclude with an outlook for the emerging field.
Multilocus Sequence Typing of Bartonella henselae in the United Kingdom Indicates that Only a Few, Uncommon Sequence Types Are Associated with Zoonotic Disease

ABSTRACT Bartonella henselae is one of the most common zoonotic agents acquired from companion animals (cats) in industrialized countries. Nonetheless, although the prevalence of infections in cats is high, the number of human cases reported is relatively low. One hypothesis for this discrepancy is that B. henselae strains vary in their zoonotic potential. To test this hypothesis, we employed structured sampling to explore the population structure of B. henselae in the United Kingdom and to determine the distribution of strains associated with zoonotic disease within this structure. A total of 118 B. henselae strains were delineated into 12 sequence types (STs) using multilocus sequence typing. We observed that most (85%) of the zoonosis-associated strains belonged to only three genotypes, i.e., ST2, ST5, and ST8. Conversely, most (74%) of the feline isolates belonged to ST4, ST6, and ST7. The difference in host association of ST2, ST5, and ST8 (zoonosis associated) and ST6 (feline) was statistically significant (P < 0.05), indicating that a few, uncommon STs were responsible for the majority of symptomatic human infections.
Identification of Amino Acid Residues Involved in Heme Binding and Hemoprotein Utilization in the Porphyromonas gingivalis Heme Receptor HmuR

ABSTRACT We have previously identified and characterized a heme/hemoglobin receptor, HmuR, in Porphyromonas gingivalis. To analyze the conserved amino acid residues of HmuR that may be involved in hemin/hemoprotein binding and utilization, we constructed a series of P. gingivalis A7436 hmuR mutants with amino acid replacements and characterized the ability of these mutants to utilize hemin and hemoproteins. Site-directed mutagenesis was employed to introduce mutations H95A, H434A, H95A-H434A, YRAP420-423YAAA, and NPDL442-445NAAA into HmuR in both P. gingivalis and Escherichia coli. Point mutations at H95 and H434 and in the NPDL motif of HmuR resulted in decreased binding to hemin, hemoglobin, and human serum albumin-hemin complex. Notably, mutations of these conserved sites and motifs led to reduced growth of P. gingivalis when human serum was used as the heme source. Analysis using a three-dimensional homology model of HmuR indicated that H95, H434, and the NPDL motif are present on apical or extracellular loops of HmuR, while the YRAP motif is present on the barrel wall. Taken together, these results support a role for H95, H434, and the NPDL motif of the P. gingivalis HmuR protein in heme binding and utilization of serum hemoproteins and the HmuR YRAP motif in serum hemoprotein utilization.