Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole‐genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole‐genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome‐wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome‐wide pattern, we uncovered a 50‐kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
Dormancy and endozoochorous dispersal ofOpuntia rastreraseeds in the southern Chihuahuan Desert

Abstract Seed dormancy and endozoochorous dispersal have important effects on population dynamics, i.e. seed bank formation, spatial and temporal bet-hedging, avoidance of crowding and decreased sib-competition. Seeds having primary dormancy do not germinate, even if adequate environmental and dispersal conditions are met, until an after-ripening period is completed. This study examined the effects on germination rates of seed dispersal by vertebrates and primary dormancy (i.e. how germination rates changed in time) in the prickly pear Opuntia rastrera from the southern Chihuahuan Desert. Ripe fruits, scats of coyote, mule deer, woodrat, common pig and pellets of the northern raven were collected in 1992 during the ripe fruit peak (August). A factorial design was used to assess the effect of disperser and seed age on germination rates using these seeds collected in 1992. In 1992, 1993 and 1994 (fresh, 1- and 2-year-old seeds, respectively) germination success after 3 months was determined for 100 seeds of each disperser, plus a control of uneaten seeds. We found differences in germination rates both between dispersers and years. All but one disperser (deer) decreased germination rates with respect to the control. Germination steadily increased with ageing of seeds, implying the presence of primary dormancy (embryo immaturity). Our results show that despite the large disperser coterie associated with Opuntia rastrera , seeds have an obligate primary dormancy which seems to result in seed bank formation. Seed germination and seedling establishment will depend on selection pressures caused mainly by environmental variability in deserts (unpredictable rainfall, extreme temperatures, safe-site availability). Nevertheless, endozoochorous dispersal provides some additional advantages (e.g. habitat colonization, genetic variability, avoidance of long-term local extinction) that needs further research.
The timing of child physical maltreatment: A cross-domain growth analysis of impact on adolescent externalizing and internalizing problems

In a sample of 578 children assessed in kindergarten through the eighth grade, we used growth modeling to determine the basic developmental trajectories of mother-reported and teacher-reported externalizing and internalizing behaviors for three physical maltreatment groups of children—early-harmed (prior to age 5 years), later-harmed (age 5 years and over), and nonharmed—controlling for SES and gender. Results demonstrated that the earlier children experienced harsh physical treatment by significant adults, the more likely they were to experience adjustment problems in early adolescence. Over multiple domains, early physical maltreatment was related to more negative sequelae than the same type of maltreatment occurring at later periods. In addition, the fitted growth models revealed that the early-harmed group exhibited somewhat higher initial levels of teacher-reported externalizing problems in kindergarten and significantly different rates of change in these problem behaviors than other children. as reported by mothers over the 9 years of this study. The early-harmed children were also seen by teachers, in kindergarten, as exhibiting higher levels of internalizing behaviors. The later-harmed children were seen by their teachers as increasing their externalizing problem behaviors more rapidly over the 9 years than did the early- or nonharmed children. These findings indicate that the timing of maltreatment is a salient factor in examining the developmental effects of physical harm.
Microglia play a role in ethanol-induced oxidative stress and apoptosis in developing hypothalamic neurons.

BACKGROUND Animals exposed to alcohol during the developmental period develop many physiological and behavioral problems because of neuronal loss in various brain areas including the hypothalamus. Because alcohol exposure is known to induce oxidative stress in developing neurons, we tested whether hypothalamic cells from the fetal brain exposed to ethanol (EtOH) may alter the cell-cell communication between neurons and microglia, thereby leading to increased oxidative stress and the activation of apoptotic processes in the neuronal population in the hypothalamus. METHODS Using enriched neuronal and microglial cells from fetal rat hypothalami, we measured cellular levels of various oxidants (O2 -, reactive oxygen species, nitrite), antioxidants (glutathione [GSH]), antioxidative enzymes (glutathione peroxidase [GSH-Px], catalase, superoxide dismutase) and apoptotic death in neurons in the presence and absence of EtOH or EtOH-treated microglial culture medium. Additionally, we tested the effectiveness of antioxidative agents in preventing EtOH or EtOH-treated microglial conditioned medium actions on oxidative stress and apoptosis in neuronal cell cultures. RESULTS Neuronal cell cultures showed increased oxidative stress, as demonstrated by higher cellular levels of oxidants but lower levels of antioxidant and antioxidative enzymes, as well as, increased apoptotic death following treatment with EtOH. These effects of EtOH on oxidative stress and cell death were enhanced by the presence of microglia. Antioxidative agents protected developing hypothalamic neurons from oxidative stress and cellular apoptosis which is caused by EtOH or EtOH-treated microglial culture medium. CONCLUSIONS These data suggest that exposure of developing hypothalamic neurons to EtOH increases cellular apoptosis via the effects on oxidative stress of neurons directly and via increasing production of microglial-derived factor(s).
The semantics of sexual behavior and their implications for HIV/AIDS research and sexual health: US and UK gay men's definitions of having “had sex”

Abstract Understanding the definition and meaning of the word “sex” has implications for sexual medicine, HIV/AIDS research, and clinical practices. Previous studies have reported variations in the definition of having “had sex” and the necessity of using behaviorally specific terminology when taking sexual histories and assessing sexual risk. The purpose of the current study is to assess gay men's definitions of what constitutes having “had sex. ” Two international convenience samples are compared: a UK sample of 180 self-identified gay men ranging from 18 to 56 years of age (M=36 years; SD=8.29) and a US sample of 190 self-identified gay men ranging 18–74 years of age (M=33.9 years; SD=12.49). Both groups were asked to indicate whether each of a list of sexual behaviors was considered having “had sex. ” Almost all participants (~95%) believed that penile–anal intercourse constituted having “had sex. ” US and UK gay men differed in defining the following as having “had sex”: giving oral–genital stimulation (US 71.6%, UK 84.9%, P=0.002); giving (G) and receiving (R) manual-anal stimulation (G: US 53.4%, UK 70.9%, P=0.001; R: US 53.7%, UK 71.2%, P=0.001); giving and receiving oral–anal stimulation (G: US 61.2%, UK 78.4%, P<0.001; R: US 59.3%, UK 78.1, P<0.001); and giving and receiving sex-toy stimulation (G: US 55%, UK 77.1%, P<0.001; R: US 56.1%, UK 77.7%, P<0.001). It is important to note that regardless of country there was not overall consensus on which behaviors constituted having “had sex. ” These findings reinforce the need for behavioral specificity in documenting sexual histories and assessing sexual risk. Further, researchers and clinicians should exercise caution by not assuming that their own definitions of the term “sex” is shared by their gay male participants or patients.
Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation.

BACKGROUND Proteomic techniques have recently become available for large-scale protein analysis. The utility of these techniques in identification of urinary proteins is poorly defined. We constructed a proteome map of normal human urine as a reference protein database by using two differential fractionated techniques to isolate the proteins. METHODS Proteins were isolated from urine obtained from normal human volunteers by acetone precipitation or ultracentrifugation, separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and identified by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry followed by peptide mass fingerprinting. RESULTS A total of 67 protein forms of 47 unique proteins were identified, including transporters, adhesion molecules, complement, chaperones, receptors, enzymes, serpins, cell signaling proteins and matrix proteins. Acetone precipitated more acidic and hydrophilic proteins, whereas ultracentrifugation fractionated more basic, hydrophobic, and membrane proteins. Bioinformatic analysis predicted glycosylation to be the most common explanation for multiple forms of the same protein. CONCLUSIONS Combining two differential isolation techniques magnified protein identification from human urine. Proteomic analysis of urinary proteins is a promising tool to study renal physiology and pathophysiology and to determine biomarkers of renal disease.
Neuronal mRNAs travel singly into dendrites

RNA transport granules deliver translationally repressed mRNAs to synaptic sites in dendrites, where synaptic activity promotes their localized translation. Although the identity of many proteins that make up the neuronal granules is known, the stoichiometry of their core component, the mRNA, is poorly understood. By imaging nine different dendritically localized mRNA species with single-molecule sensitivity and subdiffraction-limit resolution in cultured hippocampal neurons, we show that two molecules of the same or different mRNA species do not assemble in common structures. Even mRNA species with a common dendritic localization element, the sequence that is believed to mediate the incorporation of these mRNAs into common complexes, do not colocalize. These results suggest that mRNA molecules traffic to the distal reaches of dendrites singly and independently of others, a model that permits a finer control of mRNA content within a synapse for synaptic plasticity.
Comparisons of body image dimensions by race/ethnicity and gender in a university population.

OBJECTIVE We examined affective and cognitive components of body image related to physical appearance, weight, and health among 120 university men and women of three racial/ethnic groups: African American, European American, and Latino/a American. METHOD Participants completed a Background Information Sheet, the Multidimensional Body-Self Relations Questionnaire (MBSRQ), the Body-Esteem Scale (BES) with additional items, and the Balanced Inventory of Desirable Responding (BIDR). We tested for effects of race/ethnicity and gender on the body image measures while controlling for age, body size, social desirability, and socioeconomic status (SES). RESULTS African Americans reported greatest body satisfaction and least overestimation of weight. Latino/a Americans were equal to or higher than European Americans on all indices. Gender differences occurred on global body image, weight concerns, fitness, and health. There were no Gender x Race/Ethnicity interactions. DISCUSSION This pattern of racial/ethnic and gender differences shows a need for exploring a wider range of culturally relevant body image dimensions.
Improved Oxacillin Treatment Outcomes in Experimental Skin and Lung Infection by a Methicillin-Resistant Staphylococcus aureus Isolate with a vraSR Operon Deletion

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) strains are major pathogens causing infections of the skin and soft tissues and more serious, life-threatening diseases, including sepsis and necrotizing pneumonia. The vraSR operon encodes the key regulatory system that modulates the stress response of S. aureus elicited upon exposure to cell wall antibiotics. Mutation of vraS and vraR results in decreased oxacillin resistance in vitro. We investigated the effect of oxacillin treatment in experimental models employing a clinical USA300 MRSA strain (strain 923) and an isogenic vraSR deletion mutant (strain 923-M23). In a murine model of S. aureus necrotizing pneumonia, animals were treated with oxacillin, beginning 15 min after inoculation. Among mice infected with mutant strain 923-M23, oxacillin treatment significantly improved survival compared with saline treatment, whereas oxacillin treatment had no effect in mice infected with strain 923. Similarly, treatment with oxacillin decreased the bacterial burden among animals infected with strain 923-M23 but not among animals infected with strain 923. In a murine skin infection model, oxacillin eliminated the development of dermonecrosis among 923-M23-infected mice and decreased the bacterial burden in the lesions, but not among strain 923-infected mice. We conclude that deletion of the vraSR operon allowed an oxacillin regimen to be effective in murine models of MRSA pneumonia and skin infection. These findings provide proof-of-principle for development of a new antibiotic that could restore the usefulness of oxacillin against MRSA by inhibiting VraS or VraR.
On Benchmarking the Capability of Symbolic Execution Tools with Logic Bombs

Symbolic execution is an important software testing approach. It has been widely employed in program analysis, such as bug detection and malware analysis. However, the approach is not overwhelming because it suffers many issues, including the well-known scalability issue and other challenges, such as handling floating-point numbers and symbolic memories. Currently, several symbolic execution tools are available off-the-shelf, but they generally do not demonstrate their limitations clearly to users. Yet, we have no effective approach to benchmark their capabilities. Without such information, users would not know which tool to choose, or how reliable their program analysis results are based on particular symbolic execution tools. To address such concerns, this paper proposes a novel approach to benchmark symbolic execution tools. Our approach is based on logic bombs which are guarded by particular challenging problems. If a symbolic execution tool can find test cases to trigger such logic bombs during evaluation, it indicates that the tool can handle corresponding problems. Following the idea, we have designed an automated benchmark framework and a dataset of logic bombs covering 12 different challenges. Then we have conducted real-world experiments on benchmarking three popular symbolic execution tools: KLEE, Angr, and Triton. Experimental results show that our approach can reveal their limitations in handling particular issues accurately and efficiently. The benchmark process generally takes only a few minutes to evaluate a tool. To better serve the community, we release our toolset on GitHub as open source, and we hope it would serve as an essential tool to benchmark symbolic execution tools in the future.
Prognostic utility of the recently recommended histologic classification and revised TNM staging system of renal cell carcinoma

A new, internationally accepted histologic classification of renal cell carcinoma (RCC) and a new edition of the TNM staging system were introduced in 1997. In the latter, there was a dramatic change in the pT classification of organ‐confined renal cancer in which the break point between category pT1 and pT2 was increased from 2.5 cm to 7 cm.
Cost-effectiveness of routine coronary angiography after acute myocardial infarction.

BACKGROUND Coronary angiography is indicated for many patients after acute myocardial infarction (AMI). There are a number of subgroups of AMI patients, however, for whom the indication for coronary angiography is not well established. METHODS AND RESULTS We developed a decision-analytic model for AMI in representative patient subgroups based on relevant clinical characteristics. The model estimates quality-adjusted life expectancy and direct lifetime costs for two strategies: coronary angiography and treatment guided by its results versus initial medical therapy without angiography. Decision tree chance node probabilities were estimated with the use of pooled data from randomized clinical trials and other relevant literature, costs were estimated with the use of the Medicare Part A database, and quality of life adjustments were derived from a survey of 1051 patients who had had a recent AMI. In our analysis, incremental cost-effectiveness ratios for coronary angiography and treatment guided by its result, compared with initial medical therapy without angiography, ranged between $17,000 and > $1 million per quality-adjusted year of life gained. Patient subgroups with severe postinfarction angina or a strongly positive exercise tolerance test (ETT) typically had cost-effectiveness ratios of < $50,000 per quality-adjusted year of life gained. In addition, most patient subgroups with a prior AMI had cost-effectiveness ratios of < $50,000 per quality-adjusted year of life gained, even with a negative ETT result. CONCLUSIONS In many patient subgroups after AMI, the cost-effectiveness of routine coronary angiography and treatment guided by its results compares favorably with other treatment strategies for coronary heart disease.
Antibody Interactions with the Capsule ofCryptococcus neoformans

ABSTRACT Monoclonal antibodies to the encapsulated fungus Cryptococcus neoformans produce different immunofluorescence (IF) patterns after binding to the polysaccharide capsule. To explore the relationship between the IF pattern and the location of antibody binding, two immunoglobulin M (IgM) monoclonal antibodies (MAbs) (12A1 and 13F1) that differ in protective efficacy and IF pattern and one protective IgG1 MAb (2H1) were studied by IF and electron microscopy (EM). Fixing C. neoformans cells in lung tissue for EM resulted in significantly better preservation of the capsule than fixing yeast cells in suspension. The localization of MAbs 12A1 and 13F1 by immunogold EM differed depending on whether the MAb was bound to cells in cut tissue sections embedded in plastic or to cells in solution. In cut tissue sections, MAbs 12A1 and 13F1 bound throughout the capsule, whereas in solution both MAbs bound near the capsule surface. To investigate whether antibody binding to the C. neoformans capsule affected the binding of other primary or secondary reagents, various combinations of MAbs 12A1, 13F1, and 2H1 were studied by direct and indirect IF. The IF pattern and location of binding for MAbs 12A1, 13F1, and 2H1 varied depending on the presence of other capsule-binding MAbs and the method of detection. The results show that (i) binding of MAbs to the C. neoformanspolysaccharide capsule can modify the binding of subsequent primary or secondary antibodies; (ii) the IgM MAbs bind primarily to the outer capsule regions despite the occurrence of their epitopes throughout the capsule; and (iii) MAb 2H1 staining of newly formed buds is reduced, suggesting quantitative or qualitative differences in bud capsule.
Characteristics and sources of leadership culture of entrepreneurs

A study of comparison of leadership cultures of Chinese and German entrepreneurs was conducted. The result was compared with the results of the GLOBE leadership culture study and the Hofstedepsilas national culture study. The purpose of the comparison was to find out sources of the entrepreneurial leadership culture and their characteristics of Chinese and German. The analysis included three steps. First, the researcher used measurement equivalence test to ensure the comparability of Chinese and German samples. Second, the researcher used the mean structure model of SEM and explored leadership culture differences between China and Germany. Then at last, differences of the entrepreneurial leadership culture, the GLOBE leadership culture, and the Hofstedepsilas national culture in and across China and Germany were discussed. Two key sources of the entrepreneurial leadership culture were found: national culture value and group traits.
Experimental and Simulation Analysis of Radiation of the Beta Emitting Sources in a Magnetic Field

Objective: The behavior of beta particles under the magnetic field was investigated both theoretically and experimentally based on the assumption of reducing the damage to the normal tissues created by using magnetic field in radionuclide therapy. Methods: A water-filled spherical medium and a beta particle source was formed by using Geant4 simulation software for the theoretical study. After applying a homogenous magnetic field, the volume of points at which the particles interact with the medium was calculated by determining particle range. The range of beta particles was examined using yttrium-90 source and Gafchromic films for the experimental study. The setup was kept in normal room conditions and in the magnetic resonance imaging device. Then the irradiated films were analyzed by creating isodose curves. Results: With the increase of the magnetic field, the number of hits at the center was increased, but the number of hits at the outer boundaries decreased inversely proportional to the strength of the magnetic field. The change perpendicular to the magnetic field was greater as compared to the change parallel to the magnetic field. The volume of hits of beta particles got smaller with the increase of the magnetic field. Conclusion: When magnetic field is increased, the decrease in the number of interactions at the outer boundaries became more pronounced in the perpendicular direction to the magnetic field. The effect of magnetic field was more apparent for higher energy beta particles than lower energy particles.