Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands

ABSTRACT Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States. This change coincided with a bacterial population shift toward human-pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43, and ST636) to nearshore areas off the Atlantic coast of the Northeast United States. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human-pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins or contained a chromosome I-inserted island we call VPaIβ that encodes a type 3 secretion system (T3SS2β) typical of Trh hemolysin producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaIγ that encodes both tdh and trh and that was inserted in chromosome II. VPaIγ was derived from VPaIβ but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaIγ-type islands containing tdh inserted adjacent to the ure cluster in the three introduced Pacific and most other emergent lineages that collectively cause 67% of infections in the Northeast United States as of 2016. IMPORTANCE The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in parallel from the same potentially benign lineage by independent VPaI acquisition is surprising considering the historically low prevalence of community members harboring VPaI in waters along the Northeast U.S. coast that could serve as the source of this material. This illustrates a possible predisposition of some lineages to not only acquire foreign DNA but also become human pathogens. Whereas the underlying cause for the expansion of V. parahaemolyticus lineages harboring VPaIγ along the U.S. Atlantic coast and spread of this element to multiple lineages that underlies disease emergence is not known, this work underscores the need to define the environment factors that favor bacteria harboring VPaI in locations of emergent disease.
The Relative Contributions of the X Chromosome and Autosomes to Local Adaptation

Models of sex chromosome and autosome evolution yield key predictions about the genomic basis of adaptive divergence, and such models have been. Models of sex chromosome and autosome evolution yield key predictions about the genomic basis of adaptive divergence, and such models have been important in guiding empirical research in comparative genomics and studies of speciation. In addition to the adaptive differentiation that occurs between species over time, selection also favors genetic divergence across geographic space, with subpopulations of single species evolving conspicuous differences in traits involved in adaptation to local environmental conditions. The potential contribution of sex chromosomes (the X or Z) to local adaptation remains unclear, as we currently lack theory that directly links spatial variation in selection to local adaptation of X-linked and autosomal genes. Here, we develop population genetic models that explicitly consider the effects of genetic dominance, effective population size, and sex-specific migration and selection on the relative contributions of X-linked and autosomal genes to local adaptation. We show that X-linked genes should nearly always disproportionately contribute to local adaptation in the presence of gene flow. We also show that considerations of dominance and effective population size—which play pivotal roles in the theory of faster-X adaptation between species—have surprisingly little influence on the relative contribution of the X chromosome to local adaptation. Instead, sex-biased migration is the primary mediator of the strength of spatial large-X effects. Our results yield novel predictions about the role of sex chromosomes in local adaptation. We outline empirical approaches in evolutionary quantitative genetics and genomics that could build upon this new theory.
The 2017 DAVIS Challenge on Video Object Segmentation

We present the 2017 DAVIS Challenge on Video Object Segmentation, a public dataset, benchmark, and competition specifically designed for the task of video object segmentation. Following the footsteps of other successful initiatives, such as ILSVRC and PASCAL VOC, which established the avenue of research in the fields of scene classification and semantic segmentation, the DAVIS Challenge comprises a dataset, an evaluation methodology, and a public competition with a dedicated workshop co-located with CVPR 2017. The DAVIS Challenge follows up on the recent publication of DAVIS (Densely-Annotated VIdeo Segmentation), which has fostered the development of several novel state-of-the-art video object segmentation techniques. In this paper we describe the scope of the benchmark, highlight the main characteristics of the dataset, define the evaluation metrics of the competition, and present a detailed analysis of the results of the participants to the challenge.
Below‐ and above‐ground effects of deadwood and termites in plantation forests

Deadwood is an important legacy structure in managed forests, providing continuity in shelter and resource availability for many organisms and acting as a vehicle by which nutrients can be passed from one stand to the next following a harvest. Despite existing at the interface between below- and above-ground systems, however, much remains unknown about the role woody debris plays in linking these zones. Moreover, it remains untested whether the accelerative effects of wood-feeding insects on wood decomposition influence tree growth or nutritional status in forests. In this study, we added different quantities of pine logs to the bases of saplings in two-year-old loblolly pine (Pinus taeda L.) plantations in Mississippi, USA. We included a treatment in which subterranean termites (Blattodea: Rhinotermitidae: Reticulitermes) were excluded from logs to determine how these insects affect the release of nutrients from wood and, in turn, tree growth. After 51 months of decomposition, we quantified below-ground effects by measuring microbial biomass, plant-available forms of N, and ectomycorrhizal diversity associated with fine tree roots. Meanwhile, above-ground measurements focused on the elemental concentrations in decomposing wood either protected or unprotected from termites and tree metrics related to growth and nutrient status. We found additions of wood to significantly increase nitrate and potential net nitrification relative to reference treatments but detected no significant effects on tree growth, needle nitrogen concentrations, or ectomycorrhizal diversity. Soil nitrate and potential net nitrification were higher under protected vs. unprotected logs, and plant-available forms of N were mostly more abundant short distances away from both protected and unprotected logs than directly under them. The wood of logs protected from termites had significantly lower concentrations of most elements compared to that of unprotected logs, largely due to the large amounts of soil imported into unprotected logs by termites. Termite exclusion had no measurable effect on tree growth, nutritional status, or ectomycorrhizal diversity, however. Our findings indicate that deadwood and termites both contribute to the spatial heterogeneity of soil properties but may have limited short-term local effects on tree growth. Longer-term studies and studies on less fertile sites are needed.
The psychophysiological mechanisms of alexithymia in autism spectrum disorder

Accumulating evidence indicates that co-occurring alexithymia underlies several facets of the social-emotional difficulties common in individuals with autism spectrum disorder. The mechanisms involved, however, remain poorly understood because measuring alexithymia relies heavily on self-report. To address this issue, carefully matched groups of individuals with autism spectrum disorder and comparison participants rated 70 emotion-inducing pictures on subjectively experienced arousal while skin conductance responses were monitored objectively. The results demonstrated reliable correlations between these subjective and objective measures, and in both groups, around 25% of individual differences in this correlation (i.e. in emotion-relevant interoception) were accounted for by self-reported alexithymia. In the context of the wider literature, this suggests that alexithymia involves a disruption in how physiological arousal modulates the subjective experience of feelings in those with and without a diagnosis of autism spectrum disorder. Since mindfulness-based therapies foster greater awareness of thoughts, feelings and bodily sensations, the findings also have implications for how the symptoms and consequences of alexithymia (e.g. anxiety) might be ameliorated.
Effects of telehealth by allied health professionals and nurses in rural and remote areas: A systematic review and meta-analysis.

OBJECTIVE To describe telehealth interventions delivered by allied health professionals and nurses in rural and remote areas, and to compare the effects of telehealth interventions with standard face-to-face interventions. DATA SOURCES CINAHL, Embase, PsycINFO and PubMed databases were searched. The content of relevant journals and published articles were also searched. STUDY SELECTION Studies examining the effectiveness of allied health and nursing telehealth interventions for rural and remote populations were included in descriptive analyses. Studies comparing telehealth intervention with standard face-to-face interventions grouped by type of intervention approach were used to examine between-groups effect sizes. DATA EXTRACTION Methodological quality of studies was rated using the QualSyst critical appraisal tool and the National Health and Medical Research Council (NHMRC) Evidence Hierarchy levels. DATA SYNTHESIS After quality ratings, 43 studies were included. A majority of studies had strong methodological quality. The disciplines of psychology and nursing were represented most frequently, as were studies using a cognitive intervention approach. Meta-analysis results slightly favoured telehealth interventions compared with face-to-face interventions, but did not show significant differences. Interventions using a combined physical and cognitive approach appeared to be more effective. CONCLUSION Telehealth services may be as effective as face-to-face interventions, which is encouraging given the potential benefits of telehealth in rural and remote areas with regards to healthcare access and time and cost savings.
Is online information on ecstasy tablet content safe?

BACKGROUND AND AIMS In recent years, the prevalence of ecstasy use has increased in most European countries. Users can acquire information on ecstasy tablet composition through the internet. This study compares online information from two websites, Pillreports and Partyflock, to the validated Dutch Drugs Information and Monitoring System (DIMS) database, and aims to measure its accuracy and potential danger or value. DESIGN, SETTING, PARTICIPANTS The drug-related information posted on Pillreports.net and Partyflock.nl between 1 January 2014 and 31 December 2015 was investigated for accuracy and several information characteristics such as picture inclusion and dose range inclusion. In total, 471 informatory statements on ecstasy tablet content were analysed relative to the Dutch ecstasy market. MEASUREMENTS Informatory statements on the content of specific ecstasy tablets were scored as 'too high' or 'too low' if their concentrations deviated > 10 mg from the entries in the DIMS database within a 12-week time-frame, and scored as 'dangerous' if their concentration was > 40 mg too low. Unreported substances were scored as 'dangerous' if listed as an illegal or dangerous substance in the DIMS database and if present in relevant quantities. Also scored were the report characteristics 'picture inclusion', 'spread inclusion' and 'website source', which were tested for their association with report safety/danger. FINDINGS On average, reports on ecstasy tablets from Pillreports and Partyflock show concentrations which are 10.6 mg too high [95% confidence interval (CI) = 6.7-14.4]. Qualitatively, 39.7% of the reports scored as 'too high' (95% CI = 35.2-44.4), 17.6% scored as 'too low' (95% CI = 14.0-21.2) and 15.5% had 'unreported substances' (95% CI = 12.3-18.9), resulting overall in 15.3% of the reports being scored as 'dangerous' (95% CI = 11.9-18.5). The report characteristic 'spread inclusion' associated inversely with report danger [Exp(b) = 0.511, 95% CI = 0.307-0.850, P = 0.01]. CONCLUSION Information from the popular Pillreports and Partyflock websites tends to overestimate 3,4-methylenedioxymethamphetamine (MDMA) concentrations in ecstasy tablets. In addition, 15.3% of the reports omit the relevant concentration spread, fail to report additional illegal or dangerous substances contained in the tablets or underestimate MDMA concentration by > 40 mg.
Sperm storage and transport following natural mating and artificial insemination.

Recent observations in turkey and chicken hens show that sperm storage in both species is a highly inefficient process. After artificial insemination (AI), less than 1% of spermatozoa inseminated are selected for transport to and enter the sperm storage tubules (SST). It has been shown that the sperm selection process is orchestrated within the vagina and not at the level of the SST. At least two mechanisms are involved in the selection of spermatozoa fit for sperm storage, one being mechanical (motility) and the other biochemical in nature (sperm-vaginal mucosa interactions). Furthermore, it was also observed that the sperm storage efficiency in the chicken is dependent upon the logarithm of the number of spermatozoa inseminated. From a practical standpoint, inseminations performed frequently with a moderate number of spermatozoa should be more efficient than inseminations performed with higher doses at longer intervals. Maximal filling of the SST of hens in egg production requires only 1 day for the chicken and 2 days for the turkey. By contrast, the release of sperm from the SST is about seven times faster in the chicken than the turkey hen. The efficiency of oviducal sperm storage is related to a number of factors including age of the hen, stage of the ovulatory cycle when inseminated, and, in the turkey, if the hen was inseminated before or after the onset of egg production. Two different categories should be considered among factors that affect sperm survival in vivo. 1) Factors affecting sperm storage. (ABSTRACT TRUNCATED AT 250 WORDS)
Regulation of gammaherpesvirus lytic replication by endoplasmic reticulum stress–induced transcription factors ATF4 and CHOP

The stress-induced unfolded protein response (UPR) in the endoplasmic reticulum (ER) involves various signaling cross-talks and controls cell fate. B-cell receptor (BCR) signaling, which can trigger UPR, induces gammaherpesvirus lytic replication and serves as a physiological mechanism for gammaherpesvirus reactivation in vivo. However, how the UPR regulates BCR-mediated gammaherpesvirus infection is unknown. Here, we demonstrate that the ER stressors tunicamycin and thapsigargin inhibit BCR-mediated murine gammaherpesvirus 68 (MHV68) lytic replication by inducing expression of the UPR mediator Bip and blocking activation of Akt, ERK, and JNK. Both Bip and the downstream transcription factor ATF4 inhibited BCR-mediated MHV68 lytic gene expression, whereas UPR-induced C/EBP homologous protein (CHOP) was required for and promoted BCR-mediated MHV68 lytic replication by suppressing upstream Bip and ATF4 expression. Bip knockout was sufficient to rescue BCR-mediated MHV68 lytic gene expression in CHOP knockout cells, and this rescue was blocked by ectopic ATF4 expression. Furthermore, ATF4 directly inhibited promoter activity of the MHV68 lytic switch transactivator RTA. Altogether, we show that ER stress–induced CHOP inhibits Bip and ATF4 expression and that ATF4, in turn, plays a critical role in CHOP-mediated regulation of BCR-controlled MHV68 lytic replication. We conclude that ER stress–mediated UPR and BCR signaling pathways are interconnected and form a complex network to regulate the gammaherpesvirus infection cycle.
Local resection of rectal neuroendocrine tumor with first clinical manifestation of giant liver metastasis by transanal endoscopic microsurgery

Rationale: Rectal neuroendocrine tumor (NET) is a relatively rare tumor. Well-differentiated NETs (G1 and G2) rarely display distant metastasis at initial diagnosis. Currently, treatment for the primary lesions of rectal NETs with liver metastasis remains controversial. The liver metastasis was resected in local hospital. Transanal endoscopic microsurgery (TEM) has emerged as an effective minimally invasive surgery for local resection of lower rectal lesions. Herein, we reported the initial application of TEM to remove the rectal primary lesion in patients with low rectal NETs (G2) with giant liver metastases. Patient concerns: The patient, a 45-year-old woman, was primarily diagnosed with hepatocellular carcinoma and underwent curative resection of a giant liver lesion in a local hospital. Nevertheless, the postoperative pathologic examination revealed that the lesion was an NET (G2). The colonoscopy then showed a nodule 1.4 cm in diameter, 4 cm above the anal verge, located on the anterior wall of the rectum. The biopsy revealed that the nodule was also an NET (G2). However, the patient did not consent to abdominoperineal resection based on concerns for quality of life. Diagnoses: Rectal NET with liver metastasis. Interventions: The patient underwent curative resection of liver metastasis. And, TEM was adopted to resect the primary tumor in rectum. Outcomes: The patient has been disease-free for 2 years with a good quality of life and presents no local recurrence in the rectum. Lessons: TEM is an appropriate palliative operation for therapy of rectal NETs with distant metastases, especially for primary rectal NETs located in low rectal.
Review of Smart Meter Data Analytics: Applications, Methodologies, and Challenges

The widespread popularity of smart meters enables an immense amount of fine-grained electricity consumption data to be collected. Meanwhile, the deregulation of the power industry, particularly on the delivery side, has continuously been moving forward worldwide. How to employ massive smart meter data to promote and enhance the efficiency and sustainability of the power grid is a pressing issue. To date, substantial works have been conducted on smart meter data analytics. To provide a comprehensive overview of the current research and to identify challenges for future research, this paper conducts an application-oriented review of smart meter data analytics. Following the three stages of analytics, namely, descriptive, predictive, and prescriptive analytics, we identify the key application areas as load analysis, load forecasting, and load management. We also review the techniques and methodologies adopted or developed to address each application. In addition, we also discuss some research trends, such as big data issues, novel machine learning technologies, new business models, the transition of energy systems, and data privacy and security.
A Bayesian method for detecting stellar flares

We present a Bayesian-odds-ratio-based algorithm for detecting stellar flares in light curve data. We assume flares are described by a model in which there is a rapid rise with a half-Gaussian profile, followed by an exponential decay. Our signal model also contains a polynomial background model required to fit underlying light curve variations in the data, which could otherwise partially mimic a flare. We characterize the false alarm probability and efficiency of this method under the assumption that any unmodelled noise in the data is Gaussian, and compare it with a simpler thresholding method based on that used in Walkowicz et al. (2011). We find our method has a significant increase in detection efficiency for low signal-to-noise ratio (S/N) flares. For a conservative false alarm probability our method can detect 95% of flares with S/N less than �20, as compared to S/N of �25 for the simpler method. We also test how well the assumption of Gaussian noise holds by applying the method to a selection of “quiet” Kepler stars. As an example we have applied our method to a selection of stars in Kepler Quarter 1 data. The method finds 687 flaring stars with a total of 1873 flares after vetos have been applied. For these flares we have made preliminary characterisations of their durations and and signal-to-noise ratios.
Developers' code context models for change tasks

To complete a change task, software developers spend a substantial amount of time navigating code to understand the relevant parts. During this investigation phase, they implicitly build context models of the elements and relations that are relevant to the task. Through an exploratory study with twelve developers completing change tasks in three open source systems, we identified important characteristics of these context models and how they are created. In a second empirical analysis, we further examined our findings on data collected from eighty developers working on a variety of change tasks on open and closed source projects. Our studies uncovered, amongst other results, that code context models are highly connected, structurally and lexically, that developers start tasks using a combination of search and navigation and that code navigation varies substantially across developers. Based on these findings we identify and discuss design requirements to better support developers in the initial creation of code context models. We believe this work represents a substantial step in better understanding developers' code navigation and providing better tool support that will reduce time and effort needed for change tasks.