Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting demographic processes in cattle with genome-wide population genetic analysis

The domestication of the aurochs took place approximately 10,000 years ago giving rise to the two main types of domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near the Fertile Crescent, and indicine (Bos indicus) domesticated in the Indus Valley. However, although cattle have historically played a prominent role in human society the exact origin of many extant breeds is not well known. Here we used a combination of medium and high-density Illumina Bovine SNP arrays (i.e., ~54,000 and ~770,000 SNPs, respectively), genotyped for over 1300 animals representing 56 cattle breeds, to describe the relationships among major European cattle breeds and detect patterns of admixture among them. Our results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin. We use these data to identify signatures of selection reflecting both domestication (hypothesized to produce a common signature across breeds) and local adaptation (predicted to exhibit a signature of selection unique to a single breed or group of related breeds with a common history) to uncover additional demographic complexity of modern European cattle.
Racial differences in clinical outcomes from metastatic breast cancer: a pooled analysis of CALGB 9342 and 9840--Cancer and Leukemia Group B.

PURPOSE African American women are more likely to be diagnosed with metastatic breast cancer at the time of presentation than whites, and have shorter survival once diagnosed. This study examines racial differences in clinical outcomes in the setting of two large cooperative group randomized clinical trials. PATIENTS AND METHODS The study cohort consisted of 787 white (80%) and 195 African American (20%) patients with metastatic breast cancer enrolled in two successive Cancer and Leukemia Group B (CALGB) trials using taxanes in the metastatic setting. Differences in overall survival (OS), response incidence, and time to treatment failure (TTF) were examined by race. In addition, differences in the incidence of baseline and treatment-related toxicities were examined. RESULTS With 779 deaths (166 African Americans and 613 whites), median OS was 14.3 months for African Americans and 18.75 months for whites (hazard ratio [HR] = 1.37; 95% CI, 1.15 to 1.63). When adjusted for prognostic factors, African Americans had a 24% increase in the hazard of death compared with whites (HR = 1.24; 95% CI, 1.02 to 1.51). No significant differences in TTF or overall response to therapy were seen. No clinically significant toxicity differences were seen. CONCLUSION African Americans with metastatic breast cancer have an increased hazard of death compared with whites despite the receipt of similar per-protocol treatment, but experience no differences in TTF or overall response to therapy. We hypothesize that more direct and robust measures of comorbidities, and perhaps other factors such as receipt of subsequent therapy could help further explain the observed survival difference.
Paternal inheritance of the primary sex ratio in a copepod

Uniparentally inherited genetic elements are under strong selection to manipulate sex determination in their host and shift the host sex ratio towards the transmitting sex. For any sex‐ratio trait, lineage analysis and quantitative genetics are important tools for characterizing the mode of inheritance (biparental vs. maternal vs. paternal) thereby narrowing the field of possible sex‐determining mechanisms (e.g. polygenic, sex chromosomes with meiotic drive, cytoplasmic microorganisms). The primary sex ratio of the harpacticoid copepod, Tigriopus californicus is often male‐biased and is highly variable among full sib families. We found that this extra‐binomial variation for the primary sex ratio is paternally but not maternally transmitted in T. californicus. Paternal transmission of the primary sex ratio has been well documented in the haplo–diploid hymenoptera but is relatively rare in diplo–diploid organisms. If the sex‐ratio trait is paternally transmitted in other closely related harpacticoid copepods it would explain why male biased primary sex ratios are so common in this group.
Semliki Forest Virus Expressing Interleukin-12 Induces Antiviral and Antitumoral Responses in Woodchucks with Chronic Viral Hepatitis and Hepatocellular Carcinoma

ABSTRACT A vector based on Semliki Forest virus (SFV) expressing high levels of interleukin-12 (SFV-enhIL-12) has previously demonstrated potent antitumoral efficacy in small rodents with hepatocellular carcinoma (HCC) induced by transplantation of tumor cells. In the present study, the infectivity and antitumoral/antiviral effects of SFV vectors were evaluated in the clinically more relevant woodchuck model, in which primary HCC is induced by chronic infection with woodchuck hepatitis virus (WHV). Intratumoral injection of SFV vectors expressing luciferase or IL-12 resulted in high reporter gene activity within tumors and cytokine secretion into serum, respectively, demonstrating that SFV vectors infect woodchuck tumor cells. For evaluating antitumoral efficacy, woodchuck tumors were injected with increasing doses of SFV-enhIL-12, and tumor size was measured by ultrasonography following treatment. In five (83%) of six woodchucks, a dose-dependent, partial tumor remission was observed, with reductions in tumor volume of up to 80%, but tumor growth was restored thereafter. Intratumoral treatment further produced transient changes in WHV viremia and antigenemia, with ≥1.5-log10 reductions in serum WHV DNA in half of the woodchucks. Antitumoral and antiviral effects were associated with T-cell responses to tumor and WHV antigens and with expression of CD4 and CD8 markers, gamma interferon, and tumor necrosis factor alpha in peripheral blood mononuclear cells, suggesting that immune responses against WHV and HCC had been induced. These experimental observations suggest that intratumoral administration of SFV-enhIL-12 may represent a strategy for treatment of chronic HBV infection and associated HCC in humans but indicate that this approach could benefit from further improvements.
Remifentanil Prevents Withdrawal Movements Caused by Intravenous Injection of Rocuronium

Purpose The incidence of pain induced withdrawal movement following intravenous injection of rocuronium is high. This randomized, double-blind, placebo-controlled study was designed to evaluate the effect of pretreatment of remifentanil on the withdrawal movements due to intravenous injection of rocuronium during anesthetic induction. Materials and Methods Ninety adult female patients undergoing thyroidectomy were randomly allocated to three groups. Each patient intravenously received one of three solutions of equal volume (4 mL): normal saline (Group I, n = 30), 0.5 µg/kg remifentanil (Group II, n = 30) or 1 µg/kg remifentanil (Group III, n = 30). Thirty seconds after remifentanil administration, anesthesia was induced with 5 mg/kg IV thiopental. Twenty seconds after thiopental injection, 0.6 mg/kg IV rocuronium was administered (injection rate of 0.5 mL/sec) and patients' withdrawal movements were assessed. Mean arterial pressure (MAP) and heart rate were assessed on arrival in the operation room, before the tracheal intubation and immediately, 1 and 2 min after the tracheal intubation. Results The incidence of withdrawal movements was significantly lower in both of the remifentanil groups (3 and 0% in Group II and III, respectively) than in the saline group (70%). Remifentanil attenuated the increase of heart rate and MAP immediately and 1 min after the tracheal intubation. Conclusion The pretreatment with 0.5 and 1.0 µg/kg remifentanil of bolus doses prevented the withdrawal movements caused by rocuronium injection, and effectively blunted cardiovascular activation following tracheal intubation.
Piloting and producing a map of Millennium Cohort Study Data usage: Where are data underutilised and where is granularity lost?

The UK Millennium Cohort Study (MCS) is a longitudinal interdisciplinary study following the lives of 19,000 children born in the UK in 2000/1. Information has been collected at 9 months, 3, 5, 7 and 11 years, with the next sweep of data collection underway among study members who are aged 14 years. A wide range of data have been collected from children, parents and guardians, the partners of parents/guardians, older siblings and teachers, as well as sub-studies that collected data from health visitors; these include self-reported and objectively measured/verified data. This study sets out to examine how MCS data are utilised. To fit within the remit of the study, we hone in on ten priority question areas (Strengths and Difficulties Questionnaire, Child Social Behaviour Questionnaire, Diet, BMI, Immunisations, School Dis/like, Self-reported Friendships, Self-reported feelings, Screen Time, Hobbies). In total we found 481 unique studies that were using MCS data and undertaking primary analysis up to July 2015. Data that are collected through a recognised scale with defined thresholds or cut-off points for identifying constructs of interest and/or data that can provide a unique insight into a policy-relevant issue, are those most widely used in the MCS data. Measures that have been collected across sweeps – diet, BMI, SDQ and screen time - are all comparatively well used. Those measures that have started to be collected at age 7 (and first made available in 2010) have had lower usage. Data that were collected from the child’s own reports (e.g. friendships and feelings) have seldom been utilised in comparison to data collected through parental reports (e.g. SDQ). Collection of data from multiple informants did not always correlate with higher levels of usage. Imposing thresholds on data was found to be problematic in some cases, for example for BMI, where a number of different thresholds for overweight and obesity were in use. The use of different thresholds can lead to substantial differences in the results obtained. This is the first review using systematic methods that has explored MCS data use. We set out a number of ideas for good practice around the use of and reporting of MCS data.
Confocal microscopy of corneal sub-basal nerve plexus: a quantitative and qualitative analysis in healthy and pathologic eyes.

PURPOSE To validate corneal sub-basal nerve plexus examination by in vivo corneal confocal microscopy. METHODS Five parameters of corneal sub-basal nerve plexus in 250 human eyes (nerve fiber length, number of fibers, number of beadings, branching pattern, fiber tortuosity) acquired using in vivo corneal confocal microscopy (Confoscan 4.0; NIDEK Co Ltd) were analyzed. The first operator repeated the parameter analysis twice, performing the 2 evaluations 4 weeks apart. The second operator analyzed the cases once. RESULTS Intraoperator reproducibility of nerve fiber length, number of fibers, and number of beadings (intraclass correlation coefficient [ICC] = 0.96, 0.96, and 0.93, respectively) and interoperator reproducibility (ICC = 0.94, 0.95, and 0.87, respectively) were very good. Intraoperator reproducibility for branching pattern was good (ICC = 0.74), whereas interoperator reproducibility was very good (ICC = 0.81). Reproducibility of fiber tortuosity was good both at intra- and interoperator levels (ICC = 0.69 and 0.60, respectively). CONCLUSIONS Corneal confocal microscopy with the NIDEK Confoscan 4.0 represents an in vivo, noninvasive, and reproducible diagnostic technique for the analysis of sub-basal corneal nerve plexus. Methods used to analyze quantitative and qualitative variables were highly reproducible.
Courtship raises male fertilization success through post-mating sexual selection in a spider

Courtship is well known for its positive effects on mating success. However, in polyandrous species, sexual selection continues to operate after copulation. Cryptic female choice is expected under unpredictable mating rates in combination with sequential mate encounters. However, there are very few accounts of the effects of courtship on cryptic female choice, and the available evidence is often correlative. Mature Argiope bruennichi females are always receptive and never attack or reject males before mating, although sexual cannibalism after mating occurs regularly. Still, males usually perform an energetic vibratory display prior to copulation. We tested the hypothesis that beneficial effects of courtship arise cryptically, during or after mating, resulting in increased paternity success under polyandry. Manipulating courtship duration experimentally, we found that males that mated without display had a reduced paternity share even though no differences in post-copulatory cannibalism or copulation duration were detected. This suggests that the paternity advantage associated with courtship arose through female-mediated processes after intromission, meeting the definition of cryptic female choice.
Demonstration of a novel optical transmitter for high-speed differential phase-shift-keying/inverse-return-to-zero (DPSK/inv-RZ) orthogonally modulated signals

We propose and experimentally demonstrate a simple and novel optical transmitter for superimposing 10-Gb/s differential phase-shift-keying signals on a 10-Gb/s inverse-return-to-zero signal. The proposed transmitter comprises a dual-drive Mach-Zehnder intensity modulator and an optical phase modulator. Its performance has been experimentally characterized.
Automatic Data Partitioning Applied to Multigrid PDE Solvers

This paper studies the impact of using automatic data-layout techniques on the process of coding the well-known multigrid MG NAS parallel benchmark. We describe the sequential problem in detail, and discuss the parallel version and its optimizations. Then, we implement the parallel algorithm using Hit map, a highly-efficient modular library for hierarchical tiling and mapping of arrays. We describe how to use the library plug-in system to add a new data-layout module that encapsulates a generalization of the data-alignment policy of the MG benchmark. The module system applies this policy to automatically adapt the data distribution and communication code to any grain level. The impact of using these techniques is qualitatively and quantitatively described in terms of development effort and performance. Our results show that it is possible to introduce flexible automatic data-layout techniques in current parallel compiler technology, without sacrificing performance.
Quantum loop modules

We classify the simple infinite dimensional integrable modules with finite dimensional weight spaces over the quantized enveloping algebra of an untwisted affine algebra. We prove that these are either highest (lowest) weight integrable modules or simple submodules of a loop module of a finite-dimensional simple integrable module and describe the latter class. Their characters and crystal bases theory are discussed in a special case.
Anthropometrics and Body Composition by Dual Energy X-Ray in Children of Obese Women: A Follow-Up of a Randomized Controlled Trial (the Lifestyle in Pregnancy and Offspring [LiPO] Study)

Objective In obese women, 1) to assess whether lower gestational weight gain (GWG) during pregnancy in the lifestyle intervention group of a randomized controlled trial (RCT) resulted in differences in offspring anthropometrics and body composition, and 2) to compare offspring outcomes to a reference group of children born to women with a normal Body Mass Index (BMI). Research design and methods The LiPO (Lifestyle in Pregnancy and Offspring) study was an offspring follow-up of a RCT with 360 obese pregnant women with a lifestyle intervention during pregnancy including dietary advice, coaching and exercise. The trial was completed by 301 women who were eligible for follow-up. In addition, to the children from the RCT, a group of children born to women with a normal BMI were included as a reference group. At 2.8 (range 2.5–3.2) years, anthropometrics were measured in 157 children of the RCT mothers and in 97 reference group children with Body Mass Index (BMI) Z-score as a primary outcome. Body composition was estimated by Dual Energy X-ray (DEXA) in 123 successful scans out of 147 (84%). Results No differences between randomized groups were seen in mean (95% C.I.) BMI Z-score (intervention group 0.06 [−0.17; 0.29] vs. controls −0.18 [−0.43; 0.05]), in the percentage of overweight or obese children (10.9% vs. 6.7%), in other anthropometrics, or in body composition values by DEXA. Outcomes between children from the RCT and the reference group children were not significantly different. Conclusions The RCT with lifestyle intervention in obese pregnant women did not result in any detectable effect on offspring anthropometrics or body composition by DEXA at 2.8 years of age. This may reflect the limited difference in GWG between intervention and control groups. Offspring of obese mothers from the RCT were comparable to offspring of mothers with a normal BMI. Trial registration clinicaltrials.gov NCT00530439, NCT01918319 and NCT01918423. URL: NCT00530439? term = NCT00530439&rank = 1, NCT01918319? term = NCT00530439&rank = 2 and NCT01918423? term = NCT00530439&rank = 3.
Developmental changes in evoked Purkinje cell complex spike responses.

The development of synaptic interconnections between the cerebellum and inferior olive, the sole source of climbing fibers, could contribute to the ontogeny of certain forms of motor learning (e.g., eyeblink conditioning). Purkinje cell complex spikes are produced exclusively by climbing fibers and exhibit short- and long-latency activity in response to somatosensory stimulation. Previous studies have demonstrated that evoked short- and long-latency complex spikes generally occur on separate trials and that this response segregation is regulated by inhibitory feedback to the inferior olive. The present experiment tested the hypothesis that complex spikes evoked by periorbital stimulation are regulated by inhibitory feedback from the cerebellum and that this feedback develops between postnatal days (PND) 17 and 24. Recordings from individual Purkinje cell complex spikes in urethan-anesthetized rats indicated that the segregation of short- and long-latency evoked complex spike activity emerges between PND17 and PND24. In addition, infusion of picrotoxin, a GABAA-receptor antagonist, into the inferior olive abolished the response pattern segregation in PND24 rats, producing evoked complex spike response patterns similar to those characteristic of younger rats. These data support the view that cerebellar feedback to the inferior olive, which is exclusively inhibitory, undergoes substantial changes in the same developmental time window in which certain forms of motor learning emerge.
The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate healthcare interventions: explanation and elaboration

Systematic reviews and meta-analyses are essential to summarise evidence relating to efficacy and safety of healthcare interventions accurately and reliably. The clarity and transparency of these reports, however, are not optimal. Poor reporting of systematic reviews diminishes their value to clinicians, policy makers, and other users. Since the development of the QUOROM (quality of reporting of meta-analysis) statement—a reporting guideline published in 1999—there have been several conceptual, methodological, and practical advances regarding the conduct and reporting of systematic reviews and meta-analyses. Also, reviews of published systematic reviews have found that key information about these studies is often poorly reported. Realising these issues, an international group that included experienced authors and methodologists developed PRISMA (preferred reporting items for systematic reviews and meta-analyses) as an evolution of the original QUOROM guideline for systematic reviews and meta-analyses of evaluations of health care interventions. The PRISMA statement consists of a 27-item checklist and a four-phase flow diagram. The checklist includes items deemed essential for transparent reporting of a systematic review. In this explanation and elaboration document, we explain the meaning and rationale for each checklist item. For each item, we include an example of good reporting and, where possible, references to relevant empirical studies and methodological literature. The PRISMA statement, this document, and the associated website (www.prisma-statement.org/) should be helpful resources to improve reporting of systematic reviews and meta-analyses.
Top-Eye: top-k evolving trajectory outlier detection

The increasing availability of large-scale location traces creates unprecedent opportunities to change the paradigm for identifying abnormal moving activities. Indeed, various aspects of abnormality of moving patterns have recently been exploited, such as wrong direction and wandering. However, there is no recognized way of combining different aspects into an unified evolving abnormality score which has the ability to capture the evolving nature of abnormal moving trajectories. To that end, in this paper, we provide an evolving trajectory outlier detection method, named TOP-EYE, which continuously computes the outlying score for each trajectory in an accumulating way. Specifically, in TOP-EYE, we introduce a decay function to mitigate the influence of the past trajectories on the evolving outlying score, which is defined based on the evolving moving direction and density of trajectories. This decay function enables the evolving computation of accumulated outlying scores along the trajectories. An advantage of TOP-EYE is to identify evolving outliers at very early stage with relatively low false alarm rate. Finally, experimental results on real-world location traces show that TOP-EYE can effectively capture evolving abnormal trajectories.
Dual-Main-Drain Suction-Entrapment Test Report

Life-threatening suction-entrapment events have been recorded in swimming pools and spas since before World War II, although formal documentation and investigation did not occur until the Consumer Product Safety Commission began maintaining National Electronic Incident Surveillance System data. Of 147 incidents documented between 1985 and 2002, 36 incidents, 1 in 4, were fatal. Suction entrapment occurs in wading pools, spas, or swimming pools when a person’s body blocks the flow of water from a pool or spa to the circulation pump. When the source of suction to the pump is blocked, the pump continues to operate, creating a strong suction on whatever is blocking the water flow. The dual-main-drain suction-entrapment tests were developed to determine the effectiveness of dual main drains as a means of avoiding suction-entrapment accidents.