Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex‐biased dispersal and a density‐independent mating system in the Australian brushtail possum, as revealed by minisatellite DNA profiling

Natal dispersal can have important effects on mammal population structure and dynamics following a local population crash. Such dispersal is of practical importance when applied to the control of pest species because dispersal may significantly, and undesirably, reduce the population recovery time following a control operation. The relative dispersal rate of the sexes is also critical because that too will affect the rate of population increase. Here, we describe a field experiment in which we reduce the density of two populations of the Australian brushtail possum, and use genetic similarity, as estimated by minisatellite DNA profiles, to investigate dispersal in the original (undisturbed) and recovering populations. Our results show that the genetic similarity within the undisturbed populations was lower between males than between females. Conversely, the genetic similarities between males and females in the two recovering populations were not significantly different, while relatedness among males was significantly higher in the recovering populations when compared with those in the pre‐removal populations. These data indicate two important characteristics of dispersal in possums: (i) that dispersal in established populations is sex biased towards males; and (ii) that within the first 3 years following population control, ‘the vacuum effect’, whereby individuals from areas adjacent to a control area expand their home range and invade the depopulated area, is the most important factor in the re‐colonization process for possums. We found no evidence that the mating system, which is polygynous, varied when the density was markedly reduced. These results indicate that drastic reductions in population density by conventional control will not affect the rate of spread of biological control agents that rely on sexual transmission for dissemination.
Transcriptome sequencing of the anterior cingulate in bipolar disorder: dysregulation of G protein-coupled receptors.

OBJECTIVE Gene expression dysregulation in the brain has been associated with bipolar disorder through candidate gene and microarray expression studies, but questions remain about isoform-specific dysregulation and the role of noncoding RNAs whose importance in the brain has been suggested recently but not yet characterized for bipolar disorder. METHOD The authors used RNA sequencing, a powerful technique that captures the complexity of gene expression, in postmortem tissue from the anterior cingulate cortex from 13 bipolar disorder case subjects and 13 matched comparison subjects. Differential expression was computed, and a global pattern of downregulation was detected, with 10 transcripts significant at a false discovery rate ≤5%. Importantly, all 10 genes were also replicated in an independent RNA sequencing data set (N=61) from the anterior cingulate cortex. RESULTS Among the most significant results were genes coding for class A G protein-coupled receptors: SSTR2 (somatostatin receptor 2), CHRM2 (cholinergic receptor, muscarinic 2), and RXFP1 (relaxin/insulin-like family peptide receptor 1). A gene ontology analysis of the entire set of differentially expressed genes pointed to an overrepresentation of genes involved in G protein-coupled receptor regulation. The top genes were followed up by querying the effect of treatment with mood stabilizers commonly prescribed in bipolar disorder, which showed that these drugs modulate expression of the candidate genes. CONCLUSIONS By using RNA sequencing in the postmortem bipolar disorder brain, an interesting profile of G protein-coupled receptor dysregulation was identified, several new bipolar disorder genes were indicated, and the noncoding transcriptome in bipolar disorder was characterized. These findings have important implications with regard to fine-tuning our understanding of the bipolar disorder brain, as well as for identifying potential new drug target pathways.
Identifying Hosts of Families of Viruses: A Machine Learning Approach

Identifying emerging viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to an epidemic. Phylogenetics, though currently the most popular tool used to characterize the likely host of a virus, can be ambiguous when studying species very distant to known species and when there is very little reliable sequence information available in the early stages of the outbreak of disease. Motivated by an existing framework for representing biological sequence information, we learn sparse, tree-structured models, built from decision rules based on subsequences, to predict viral hosts from protein sequence data using popular discriminative machine learning tools. Furthermore, the predictive motifs robustly selected by the learning algorithm are found to show strong host-specificity and occur in highly conserved regions of the viral proteome.
Two-Tier Multiple Query Optimization for Sensor Networks

When there are multiple queries posed to the resource-constrained wireless sensor network, it is critical to process them efficiently. In this paper, we propose a two-tier multiple query optimization (TTMQO) scheme. The first tier, called base station optimization, adopts a cost-based approach to rewrite a set of queries into an optimized set that shares the commonality and eliminates the redundancy among the queries in the original set. The optimized queries are then injected into the wireless sensor network. In the second tier, called in-network optimization, our scheme efficiently delivers query results by taking advantage of the broadcast nature of the radio channel and sharing the sensor readings among similar queries over time and space at a finer granularity. Our experimental results indicate that our proposed TTMQO scheme offers significant improvements over the traditional single query optimization technique.
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

Concept recognition tools rely on the availability of textual corpora to assess their performance and enable the identification of areas for improvement. Typically, corpora are developed for specific purposes, such as gene name recognition. Gene and protein name identification are longstanding goals of biomedical text mining, and therefore a number of different corpora exist. However, phenotypes only recently became an entity of interest for specialized concept recognition systems, and hardly any annotated text is available for performance testing and training. Here, we present a unique corpus, capturing text spans from 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference standard for free text annotation of human phenotypes. Furthermore, we developed a test suite for standardized concept recognition error analysis, incorporating 32 different types of test cases corresponding to 2164 HPO concepts. Finally, three established phenotype concept recognizers (NCBO Annotator, OBO Annotator and Bio-LarK CR) were comprehensively evaluated, and results are reported against both the text corpus and the test suites. The gold standard and test suites corpora are available from http://bio-lark.org/hpo_res. html. Database URL: http://bio-lark.org/hpo_res. html
Virologic Outcome of Using Tenofovir/Emtricitabine to Treat Hepatitis B in HIV-Coinfected Patients

Goal. To study the effect of combination antiviral therapy with tenofovir and emtricitabine or lamivudine with and without prior monotherapy with lamivudine. Study. We reviewed charts of 31 HIV-/HBV-coinfected patients. Twelve 3TC-naïve patients initially received tenofovir plus emtricitabine. Nineteen epivir experienced patients who had previously failed epivir were given tenofovir plus emtricitabine. Results. Baseline median HBV DNA was similar in the epivir-naïve (5.8×107 copies/mL) and experienced group (7.3×107 copies/mL, P = .65). The median time to complete suppression of HBV was 466 days in the naïve group and 877 days in the experienced (P = .001). After 12 months, 6/10 (60%) naïve patients and 3/14 (21%) experienced patients had HBV DNA below the detectionlimit (P = .067). After 24 months, 5/5 (100%) naïve patients and 4/13 (31%) experienced patients had an undetectable HBV DNA level (P = .015). Conclusions. The median time to suppression of HBV DNA was significantly shorter among treatment naïve patients. There was a significantly greater proportion of naïve patients with suppressed HBV DNA at 24 months. Our results support using initial dual therapy in those with HIV/HBV coinfection.
Predicting Speech-in-Noise Recognition From Performance on the Trail Making Test: Results From a Large-Scale Internet Study

Objective: The aim of the study was to investigate the utility of an internet-based version of the trail making test (TMT) to predict performance on a speech-in-noise perception task. Design: Data were taken from a sample of 1509 listeners between ages 18 and 91 years old. Participants completed computerized versions of the TMT and an adaptive speech-in-noise recognition test. All testing was conducted via the internet. Results: The results indicate that better performance on both the simple and complex subtests of the TMT are associated with better speech-in-noise recognition scores. Thirty-eight percent of the participants had scores on the speech-in-noise test that indicated the presence of a hearing loss. Conclusions: The findings suggest that the TMT may be a useful tool in the assessment, and possibly the treatment, of speech-recognition difficulties. The results indicate that the relation between speech-in-noise recognition and TMT performance relates both to the capacity of the TMT to index processing speed and to the more complex cognitive abilities also implicated in TMT performance.
Characterization of Pseudomonas spp. and Associated Proteolytic Properties in Raw Milk Stored at Low Temperatures

Milk spoilage is caused by the presence of proteolytic enzymes produced by Pseudomonas spp. during storage at low temperatures. The aim of this study was to identify Pseudomonas spp. in raw milk and investigate their associated proteolytic properties at low temperatures. Raw milk samples (n = 87) were collected from 87 bulk tanks in Shaanxi Province in China. Pseudomonas spp. were identified using Pseudomonas specific 16S, universal 16S rRNA sequencing, and rpoB gene sequencing. The proteolytic properties of Pseudomonas spp. were examined using milk agar, quantitative trinitrobenzenesulfonic acid assay, and by the presence of alkaline metallopeptidase gene (aprX). A total 143 isolates from all 87 samples were confirmed as Pseudomonas, and were identified as belonging to 14 Pseudomonas species. Of these, 40 (28.0%) isolates revealed proteolysis on milk agar at 2°C, 74 (51.8%) at 4°C, 104 (72.7%) at 7°C, and 102 (71.3%) at 10°C. However, proteolytic activity of 45 (31.5%) isolates exceeded 2 μmol of glycine equivalents per mL at 7°C, followed by 43 (30.1%) at 10°C, 18 (12.6%) at 4°C, and 7 (4.9%) at 2°C. The results reveal proteolytic activity of Pseudomonas spp. present in milk and their spoilage potential at different temperatures.
Cytokine inflammation state in non-alcoholic steatohepatitis surpasses that of chronic hepatits C and alcoholic liver disease

Increased serum levels of cytokines were reported in persistent inflammatory conditions such as non-alcoholic steatohepatitis (NASH), chronic hepatitis C (CHC) and alcoholic liver disease (ALD). The aim of this study was to compare cytokines IL-6, TNF-α, VEGF, EG-VEGF, BB-PDGF and ICAM-1 levels in these patients. Ninety patients seen in two Mexican outpatient clinics (Liver Unit, UANL and HIPAM and UNAM) were included: NASH (30), CHC (30) and ALD (30). Serum cytokines IL-6, TNF-α, VEGF, EG-VEGF, BB-PDGF and ICAM-1 were measured by ELISA. A statistically significant difference was found in 5/6 mediators studied in NASH patients vs. CHC and ALD. Regarding ICAM-1 (5.482±613 vs. 2.145±1011 vs. 1.830±1224 pg/mL; P<0.05; respectively), IL-6 (2.430±1506 vs. 726±735 vs. 516±603 pg/mL; P<0.05, respectively), TNF-α (3686±1409 vs. 677±747 vs. 437±70 pg/mL; P<0.05; respectively), VEFG (2.267±486 vs. 421±557 vs. 554±619 pg/mL; P<0.05; respectively) and EG-VEGF (2.146±1914 vs. 1.225±1388 vs. 799±1046 pg/mL; P<0.05; respectively). VEGF positively correlated with TNF-α(r+0.51 and P=0.004) in NASH and negatively in CHC (r-0.44 and P=0.01). The only positive correlation for BB-PDGF was with EG-VEGF levels (r=+0.41 and P=0.02). IL-6 exhibited a positive correlation vs. ICAM-1 in ALD (r+0.42 and P=0.02). We demonstrated a significant increase in pro-inflammatory cytokines (TNF-α, IL-6, VEGF and EG-VEGF) and ICAM-1 in patients with NASH. Correlations showed differential cytokine and adhesion molecule patterns on the basis of the liver disease etiology. These abnormalities in cytokine profile can influence the pathophysiology of liver injury.
Why do women complain of vaginal discharge? A population survey of infectious and pyschosocial risk factors in a South Asian community.

BACKGROUND Vaginal discharge is a common complaint, particularly among women in Asia. Although presumed to be caused by reproductive tract infections (RTIs), the association between the complaint and the presence of RTIs is weak. This study aimed to investigate the risk factors of the complaint of vaginal discharge. METHODS We conducted a community-based survey of 3000 women aged 18-50 years, randomly sampled from a population in Goa, India. Women who gave informed consent were invited to participate in a structured interview, which elicited data on the primary outcome (the experience of current abnormal vaginal discharge) and psychosocial exposures: gender adversity; symptoms of somatoform disorders; and common mental disorders (CMD). All women were required to provide vaginal and/or urine samples for diagnosis of RTIs using gold standard laboratory tests. Risk factors were analysed using logistic regression with the binary outcome of the complaint of vaginal discharge. RESULTS Of the 2494 women (83%) who agreed to participate, 14.5% complained of having an abnormal vaginal discharge. Stress was the most common causal attribution for the complaint. The final multivariate model found that high scores for CMD (OR 2.16, 1.4-3.2) and somatoform disorders (6.23, 4.0-9.7) and the use of an intrauterine contraceptive device (1.86, 1.0-3.4) were independently associated with the complaint. Low literacy (0.54, 0.4-0.8) and age >40 years (0.29, 0.2-0.4) were associated with a reduced risk. RTI were not associated with the complaint (1.24, 0.9-1.6). CONCLUSIONS Psychosocial factors have the strongest association with the complaint of vaginal discharge. Syndromic management algorithms need refinement so that women with complaints that are non-infectious in aetiology are offered psychosocial interventions.
Partisanship, Not Spanish: Explaining Municipal Ordinances Affecting Undocumented Immigrants *

This chapter seeks to advance our understanding of local government ordinances on issues related to unauthorized immigrant residents including day labor markets, housing, unlicensed businesses, and cooperation with federal immigration authorities. We attempt to answer the question of why such ordinances are considered, passed, or fail to pass in some municipalities and not others. Some factors expected to explain the consideration and passage of restrictionist ordinances were demographic changes, labor market outcomes, and political factors. One of the strongest explanations for restrictionist versus " pro-immigrant " proposals is the proportion of Republicans and Democrats in the county. Controlling for demographic characteristics, Republican areas are twice as likely to propose restrictionist ordinances, and one half as likely to propose " pro-immigrant " ones. Similar effects can be found when examining passage of such legislation as the relevant outcome. Other factors, such as the growth of the Latino population and the size of linguistically-isolated Spanish-speaking households, were not associated with a greater likelihood of proposing or passing restrictionist legislation. Thus, demographic factors are not as important as political factors in accounting for ordinances passed by local governments related to unauthorized immigration, either pro or con. Though there is widespread recognition that localities are playing a more significant role in regulating the lives of low-skilled immigrant residents, there is little systematic understanding of why some localities may adopt restrictionist policies while others may adopt more permissive policies or do nothing at all. Part of the difficulty in understanding why these ordinances are being proposed in some places but not in others is the fact that many of the localities considering restrictionist ordinances are small municipalities that rarely get coverage in state newspapers and wire stories, let alone in national outlets such as the New York Times and Washington Post or more regional newspapers like the Chicago Tribune. Thus, as suggested by a number of chapters * We thank the ACLU, Migration Policy Institute, and Fair Immigration Reform Movement for sharing their data on local ordinances, and we are grateful for comments from participants in the 2007 Omaha Cumbre,
Facial Nerve Outcomes in Facial Nerve Schwannomas

Objective To better understand the characteristics and outcomes of facial nerve schwannomas (FNSs) over a 30-year period. Study Design Retrospective study. Setting Subspecialty practice at a tertiary hospital. Patients Fifty-six patients diagnosed with FNS over a 30-year period. Methods Preoperative data (audiologic data, facial nerve [FN] function, and patient symptoms), intraoperative data (tumor location, total versus subtotal resection, and FN status), and postoperative data (audiologic data, FN function, and recurrence) were collected. Mann-Whitney and &khgr;2 analyses were done to determine which factors correlated with poor FN outcomes (defined as House-Brackmann ≥4). Results Of the 56 patients in this study, 53 (94.6%) underwent surgical resection of their FNS. Of those patients, 45 (84.9%) underwent total resection, and 8 (15.1%) underwent subtotal resection. Subtotal resection was associated with a statistically significant decreased risk of having postoperative HB grade ≥4 (odds ratio, 0.09; 95% confidence interval, 0.01–0.77; p = 0.028). Of those undergoing a subtotal resection, no patient had further tumor growth seen on postoperative magnetic resonance imaging (average time of last magnetic resonance imaging since operation, 44.9 mo). Tumor location was not statistically associated with poor FN outcome (all p > 0.05). Preoperative FN paralysis was the only preoperative clinical finding statistically associated with poor FN outcomes (p = 0.004). Conclusion We have identified multiple characteristics of FNS as well as multiple factors associated with increased statistical risk of poor FN outcomes.
Cell‐surface nucleolin is involved in lipopolysaccharide internalization and signalling in alveolar macrophages

C23 (nucleolin) shuttling between the nucleus, cytoplasm and cell surface has been implicated in controlling regulatory processes and may play a role in pathogen infection and autoimmune diseases. It has been reported that cell surface‐expressed C23 on THP‐1 monocytes is involved in the inflammatory response induced by LPS (lipopolysaccharide). This study investigates whether C23 is a membrane receptor for LPS during LPS‐induced AMs (alveolar macrophages) activation. First, using immunofluorescence and microscopy, we detected the expression of C23 on the surface of AMs. Second, using LPS affinity columns, we demonstrated that C23 directly binds to LPS. Third, we found that LPS colocalized with C23 on both the cell surface and in the cytoplasm. Finally, knockdown of C23 expression on the cell surface using siRNA (small interfering RNA) led to significant reductions in the internalization of LPS, in LPS‐induced NF‐κB (nuclear factor κB)–DNA binding and in the protein expression of TNF (tumour necrosis factor)‐α and IL‐6 (interleukin‐6). These findings provide evidence that cell‐surface C23 on AMs may serve as a receptor for LPS and are essential for internalization and transport of LPS. Furthermore, C23 participates in the regulation of LPS‐induced inflammation of AMs, which indicates that cell‐surface C23 is a new and promising therapeutic target for the treatment of bacterial infections.
Caloric restriction in grouped rats: aggregate influence on behavioural and hormonal data

The majority of studies in short- and middle-term caloric restriction (CR) have been primarily focused on physiological parameters, improvements in aging, modulation of oxidative stress, and long-term negative effects on cognitive functions. However, single-housing associated with CR may pose many logistical problems. Thus, it is necessary to study the effects of CR under conditions in which animals are group-housed. The aims of this study were to (i) observe the possible differences in the proportion of the weights and social behaviour under ad libitum and CR (at 70%) conditions; (ii) examine the eventual inequalities in the proportion of the weights and social behaviour (the time spent eating under the feeder as an indicator of dominance and empathy, and the number of ‘pushes’ as an indicator of aggressiveness) in sibling and non-sibling rats under CR conditions; and (iii) compare the concentrations of corticosterone (stress biomarker) in serum under ad libitum and CR conditions. The results indicated the effectiveness of CR in different groups independent of the relationship between the rats. No extreme changes in weight were observed in the CR rats. Behavioural observations also indicated the differences in the total time spent under the feeder and in the number of pushes (higher in both cases for the sibling rats). However, no significant differences in corticosterone levels were observed. Our results suggest the viability of group-housing rats during long periods of CR maintenance.
Network Security and Contagion

This paper develops a theoretical model of investments in security in a network of interconnected agents. The network connections introduce the possibility of cascading failures depending on exogenous or endogenous attacks and the profile of security investments by the agents. The general presumption in the literature, based on intuitive arguments or analysis of symmetric networks, is that because security investments create positive externalities on other agents, there will be underinvestment in security. We show that this reasoning is incomplete because of a first-order economic force: security investments are also strategic substitutes. In a general (non-symmetric) network, this implies that underinvestment by some agents will encourage overinvestment by others. We demonstrate by means of examples that not only there will be overinvestment by some agents but also aggregate probabilities of infection can be lower in equilibrium than in the social optimum. We then provide sufficient conditions for underinvestment. This requires both sufficiently convex cost functions (just convexity is not enough) and networks that are either symmetric or locally tree-like (i.e., either trees or in the case of stochastic networks, without local cycles with high probability). We also characterize the impact of network structure on equilibrium and optimal investments. Finally, we show that when the attack location is endogenized (by assuming that the attacker chooses a probability distribution over the location of the attack in order to maximize damage), there is another reason for overinvestment: greater investment by an agent shifts the attack to other parts of the network.