Miracle-dz/UniFAR-FTUs huggingface dataset:
Gender disparities in screening for congenital hypothyroidism using thyroxine as a primary screen.

OBJECTIVE Newborn screening for congenital hypothyroidism (CH) is based on testing for the markers thyroxine (T4) and/or thyroid-stimulating hormone (TSH). Diagnosis of CH is complicated because many factors affect the levels of these hormones including infant birth weight, prematurity and age at specimen collection. We investigated whether the sex of the newborn affected the levels of T4 and TSH and consequently the outcome of newborn screening. DESIGN In New York State, the Newborn Screening program initially tests all infants for T4 and any baby with a result in the lowest 10% is triaged for TSH screening. We analyzed data from 2008 to 2016 to determine mean and median T4 and TSH values and how these results correlate with the sex of infants who are reported as borderline, referred and confirmed with CH. METHODS T4 and TSH concentrations in dried blood spots were measured using commercially available fluoroimmunoassays. RESULTS From 2008 to 2016, of the 2.4 million specimens tested for thyroxine, 51.5% were from male and 48.5% were from female infants. Male infants constituted 60% of specimens triaged for TSH testing, 64.9% of repeat requests and 59.6% of referrals, but only 49% of confirmed CH cases. The mean and median T4 values were lower (a difference of approximately 0.8-1.1 μg/dL each year) and the median TSH values were higher in male compared to female infants. CONCLUSIONS Natural differences in thyroid hormone levels in male and female infants leads to male infants being disproportionately represented in the false-positive category.
Plasticity and Susceptibility of Brain Morphometry Alterations to Insufficient Sleep

Background: Insufficient sleep is common in daily life and can lead to cognitive impairment. Sleep disturbance also exists in neuropsychiatric diseases. However, whether and how acute and chronic sleep loss affect brain morphology remain largely unknown. Methods: We used voxel-based morphology method to study the brain structural changes during sleep deprivation (SD) at six time points of rested wakefulness, 20, 24, 32, 36 h SD, and after one night sleep in 22 healthy subjects, and in 39 patients with chronic primary insomnia relative to 39 status-matched good sleepers. Attention network and spatial memory tests were performed at each SD time point in the SD Procedure. The longitudinal data were analyzed using one-way repeated measures ANOVA, and post-hoc analysis was used to determine the between-group differences. Results: Acute SD is associated with widespread gray matter volume (GMV) changes in the thalamus, cerebellum, insula and parietal cortex. Insomnia is associated with increased GMV in temporal cortex, insula and cerebellum. Acute SD is associated with brain atrophy and as SD hours prolong more areas show reduced GMV, and after one night sleep the brain atrophy is restored and replaced by increased GMV in brain areas. SD has accumulative negative effects on attention and working memory. Conclusions: Acute SD and insomnia exhibit distinct morphological changes of GMV. SD has accumulative negative effects on brain morphology and advanced cognitive function. The altered GMV may provide neurobiological basis for attention and memory impairments following sleep loss. Statement of significance Sleep is less frequently studied using imaging techniques than neurological and psychiatric disorders. Whether and how acute and chronic sleep loss affect brain morphology remain largely unknown. We used voxel-based morphology method to study brain structural changes in healthy subjects over multiple time points during sleep deprivation (SD) status and in patients with chronic insomnia. We found that prolonged acute SD together with one night sleep recovery exhibits accumulative atrophic effect and recovering plasticity on brain morphology, in line with behavioral changes on attentional tasks. Furthermore, acute SD and chronic insomnia exhibit distinct morphological changes of gray matter volume (GMV) but they also share overlapping GMV changes. The altered GMV may provide structural basis for attention and memory impairments following sleep loss.
Placental weight and birthweight: the relations with number of daily cigarettes and smoking cessation in pregnancy. A population study

Abstract Background We studied associations of number of daily cigarettes in the first trimester with placental weight and birthweight in women who smoked throughout pregnancy, and in women who stopped smoking after the first trimester. Methods We included all women with delivery of a singleton in Norway (n = 698 891) during 1999–2014, by using data from the Medical Birth Registry of Norway. We assessed dose-response associations by applying linear regression with restricted cubic splines. Results In total, 12.6% smoked daily in the first trimester, and 3.7% stopped daily smoking. In women who smoked throughout pregnancy, placental weight and birthweight decreased by number of cigarettes; however, above 11–12 cigarettes we estimated no further decrease (Pnon-linearity < 0.001). Maximum decrease in placental weight in smokers compared with non-smokers was 18.2 g [95% confidence interval (CI): 16.6 to 19.7], and for birthweight the maximum decrease was 261.9 g (95% CI: 256.1 to 267.7). In women who stopped smoking, placental weight was higher than in non-smokers and increased by number of cigarettes to a maximum of 16.2 g (95% CI: 9.9 to 22.6). Birthweight was similar in women who stopped smoking and non-smokers, and we found no change by number of cigarettes (Pnon-linearity < 0.001). Conclusions In women who smoked throughout pregnancy, placental weight and birthweight decreased non-linearly by number of cigarettes in the first trimester. In women who stopped smoking, placental weight was higher than in non-smokers and increased linearly by number of cigarettes; birthweight was almost similar to that of non-smokers.
p4v: practical verification for programmable data planes

We present the design and implementation of p4v, a practical tool for verifying data planes described using the P4 programming language. The design of p4v is based on classic verification techniques but adds several key innovations including a novel mechanism for incorporating assumptions about the control plane and domain-specific optimizations which are needed to scale to large programs. We present case studies showing that p4v verifies important properties and finds bugs in real-world programs. We conduct experiments to quantify the scalability of p4v on a wide range of additional examples. We show that with just a few hundred lines of control-plane annotations, p4v is able to verify critical safety properties for switch.p4, a program that implements the functionality of on a modern data center switch, in under three minutes.
Health champions in South London: evaluation of training, and impact on public health

The Healthy Living Pharmacy framework, introduced in England in 2008, provides a tailored approach to the implementation of pharmacy services locally, facilitated by qualified ‘Health Champions’ (HCs). The study aimed to evaluate the perceived value of the 1‐day level 2 HC training by assessing knowledge and confidence of HC pre‐ and post‐training, and changes in practice. The views of additional stakeholders on factors that either obstructed or facilitated pharmacy engagement are also explored.
The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease

Abstract Coenurosis, caused by the larval coenurus of the tapeworm Taenia multiceps, is a fatal central nervous system disease in both sheep and humans. Though treatment and prevention options are available, the control of coenurosis still faces presents great challenges. Here, we present a high-quality genome sequence of T. multiceps in which 240 Mb (96%) of the genome has been successfully assembled using Pacbio single-molecule real-time (SMRT) and Hi-C data with a N50 length of 44.8 Mb. In total, 49.5 Mb (20.6%) repeat sequences and 13, 013 gene models were identified. We found that Taenia spp. have an expansion of transposable elements and recent small-scale gene duplications following the divergence of Taenia from Echinococcus, but not in Echinococcus genomes, and the genes underlying environmental adaptability and dosage effect tend to be over-retained in the T. multiceps genome. Moreover, we identified several genes encoding proteins involved in proglottid formation and interactions with the host central nervous system, which may contribute to the adaption of T. multiceps to its parasitic life style. Our study not only provides insights into the biology and evolution of T. multiceps, but also identifies a set of species-specific gene targets for developing novel treatment and control tools for coenurosis.
A Survey of Major Techniques for Combating Link Spamming

To access exponentially growing information on today’s Web, search engines serve people as the main portal of the Web. Web spamming becomes a major cause of search engine quality deterioration. One of the most dreadful spam techniques is based on manipulating hyperlinks on the Web according to the Web ranking algorithm. This paper presents an overview of present status of link spamming technique, and a summary of several combating techniques. We also present a classification of those techniques.
LPS-Challenged Macrophages Release Microvesicles Coated With Histones

Histones are the protein component of nucleosomes, which are the basic packing unit of chromatin. However, histones are also found in the blood, both as components of nucleosomes leaked out from dead cells, or expelled from neutrophils in the active process of NET formation. Circulating histones contribute to inflammation, and to lethality in sepsis, a hyperinflammatory condition, by interacting with specific receptors, notably toll-like receptor 4 (TLR4). Here, we show that histones are also actively released by LPS-activated macrophages in association with extracellular vesicles. Vesicle-associated histones can be recovered from the plasma of mice with sepsis. Actively released histones are on the outer surface of vesicles and can interact with TLR4. Thus, activated macrophages release histones without dying, at the same time, making their DNA more accessible and communicating to other cells that infection is present.
Early antipsychotic treatment in juvenile rats elicits long-term alterations to the adult serotonin receptors

Background Antipsychotic drug (APD) prescription/use in children has increased significantly worldwide, despite limited insight into potential long-term effects of treatment on adult brain functioning. While initial long-term studies have uncovered alterations to behaviors following early APD treatment, further investigations into potential changes to receptor density levels of related neurotransmitter (NT) systems are required. Methods The current investigation utilized an animal model for early APD treatment with aripiprazole, olanzapine, and risperidone in male and female juvenile rats to investigate potential long-term changes to the adult serotonin (5-HT) NT system. Levels of 5-HT1A, 5-HT2A, and 5-HT2C receptors were measured in the prefrontal cortex (PFC), caudate putamen (CPu), nucleus accumbens (NAc), and hippocampus via Western Blot and receptor autoradiography. Results In the male cohort, long-term changes to 5-HT2A and 5-HT2C receptors were found mostly across hippocampal and cortical brain regions following early aripiprazole and olanzapine treatment, while early risperidone treatment changed 5-HT1A receptor levels in the NAc and PFC. Lesser effects were uncovered in the female cohort with aripiprazole, olanzapine and risperidone to alter 5-HT1A and 5-HT2A receptors in NAc and hippocampal brain regions, respectively. Conclusion The results of this study suggest that early treatment of various APDs in juvenile rats may cause gender and brain regional specific changes in 5-HT2A and 5-HT2C receptors in the adult brain.
LP-based Scheduler Work fl ows with Deadlines Jobs with Deadlines Deadline Decomposition YARN Scheduling Decisions Job / Cluster Statuses

With rapidly increasing volumes of data to be processed in modern data analytics, it is commonplace to run multiple data processing jobs with inter-job dependencies in a datacenter cluster, typically as recurring data processing workloads. Such a group of inter-dependent data analytic jobs is referred to as a workflow, and may have a deadline due to its mission-critical nature. In contrast, non-recurring ad-hoc jobs are typically best-effort in nature, and rather than meeting deadlines, it is desirable to minimize their average job turnaround time. The state-of-the-art scheduling mechanisms focused on meeting deadlines for individual jobs only, and are oblivious to workflow deadlines. In this paper, we present FlowTime, a new system framework designed to make scheduling decisions for workflows so that their deadlines are met, while simultaneously optimizing the performance of ad-hoc jobs. To achieve this objective, we first adopt a divide-and-conquer strategy to transform the problem of workflow scheduling to a deadline-aware job scheduling problem, and then design an efficient algorithm that tackles the scheduling problem with both deadline-aware jobs and ad-hoc jobs by solving its corresponding optimization problem directly using a linear program solver. Our experimental results have clearly demonstrated that FlowTime achieves the lowest deadline-miss rates for deadline-aware workflows and 210 times shorter average job turnaround time, as compared to the state-of-the-art scheduling algorithms.
Neonatal Contrast Sensitivity and Visual Acuity: Basic Psychophysics

Purpose This research was prospectively designed to determine whether a 0.083 cycles per degree (cy/deg) (20/7200) square-wave stimulus is a good choice for clinical measurement of newborn infants' contrast sensitivity and whether the contrast sensitivity function (CSF) of the newborn infant is band-pass. The results were retrospectively analyzed to determine whether the method of constant stimuli (MCS) and the descending method of limits (dLIM) yielded similar results. Methods In across-subjects experimental designs, a pilot experiment used MCS (N = 47 visual acuity; N = 38 contrast sensitivity at 0.083 cy/deg), and a main experiment used dLIM (N = 22 visual acuity; N = 22 contrast sensitivity at 0.083 cy/deg; N = 21 at 0.301 cy/deg) to measure visual function in healthy newborn infants. Three candidate CSFs estimated maximum neonatal contrast sensitivity. MCS and dLIM psychometric functions were compared while taking the stimulus presentation protocols into account. Results The band-pass CSF fit the data best, with a peak sensitivity near 0.31 at 0.22 cy/deg. However, the 0.083 cy/deg square-wave stimulus underestimated the best performance of newborn infants by less than 0.15 log10 units. MCS and dLIM data agreed well when the stimulus presentation contingencies were taken into account. Conclusions Newborn contrast sensitivity is well measured using a 0.083 cy/deg square-wave target, regardless of which CSF shape is correct. MCS and dLIM yield wholly comparable results, with no evidence to suggest effects of other factors such as infant inattention or examiner impatience. Translational Relevance These measurements open the way for clinical behavioral measurement of infant visual acuity and contrast sensitivity in the neonatal period.
Rebuttal from Luc J. Teppema

In the view of this author, it is confusing to state that the only CNS contribution to the isocapnic HVR is depression of ventilation (Funk & Gourine, 2018). The term decline may be preferred over depression (hypoxic ventilatory decline; HVD; Teppema & Dahan, 2010). After 20 min of sustained isocapnic hypoxia, ventilation reaches a level 25–40% above control. Is this a true depression or is HVD, apart from energy-sparing, simply caused by a rise in cerebral blood flow (CBF) and the hyperadditive way the peripheral and central chemoreceptors interact? A lower central PCO2 will impact the effect of a given output of the carotid bodies that thus operate at lower gain (Wilson & Teppema, 2016). In the anaesthetized cat the dynamics of ventilatory depression by central hypoxia equals that of an isolated decrease in central PCO2 (Teppema & Dahan, 2010). Together with the increase in ventilation, the rise in CBF may be sufficient to ensure adequate brain oxygenation. I thus disagree with the statement that HVD is maladaptive. During poikilocapnic hypoxia, HVD is much smaller and can be considered to be due to a limited rise in carotid body (CB) activity resulting from the peripheral O2–CO2 interaction (Teppema & Dahan, 2010). In contrast to Funk and Gourine (2018), I do not consider the literature concerning the HVR after carotid body denervation (CBD) confusing. The small stimulation that is sometimes observed has a time profile indicating a peripheral, not central, origin, likely the aortic bodies (Swanson et al. 1978; Honda et al. 1979). While carotid body stimulation does not influence CBF, there is also no evidence for a CB role in the hypoxaemia-induced cerebral vasodilatation (Heistad et al. 1976; Myabe et al. 1989; Awar et al. 1990), so in this respect a confounding effect of CBD is minimal. Rather than ascribing the maintenance of ventilation during hypoxia in CBD patients to a central stimulation (Funk & Gourine, 2018), it may be preferable to circumscribe it as resulting from an absence of both an increased CB activity and HVD. Due to the abolishment of a peripheral–central interaction and the known decrease in central CO2 sensitivity, hypoxia in these patients results in only a limited change (if any, but sometimes decrease) in ventilation despite an intact CBF response. Also, the fact that brain O2 sensing mechanisms require facilitatory inputs (Funk & Gourine, 2018) inevitably implies that they cannot be considered real O2 sensors that can operate independently of synaptic input. Finally, an impairment of respiratory O2/CO2 and exercise responses by compromising astrocyte function in the integrating preBötzinger complex (Sheikhbahaei et al. 2018) does not provide a valuable argument to revise the current concept concerning the mechanisms underlying the HVR.
Phylodynamic Model Adequacy Using Posterior Predictive Simulations

Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy (TMA), a package for the popular BEAST2 software, that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analysing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data was best described by the birth-death SIR model.
Using a Virtual Reality Social Network During Awake Craniotomy to Map Social Cognition: Prospective Trial

Background In awake craniotomy, it is possible to temporarily inactivate regions of the brain using direct electrical stimulation, while the patient performs neuropsychological tasks. If the patient shows decreased performance in a given task, the neurosurgeon will not remove these regions, so as to maintain all brain functions. Objective The objective of our study was to describe our experience of using a virtual reality (VR) social network during awake craniotomy and discuss its future applications for perioperative mapping of nonverbal language, empathy, and theory of mind. Methods This was a single-center, prospective, unblinded trial. During wound closure, different VR experiences with a VR headset were proposed to the patient. This project sought to explore interactions with the neuropsychologist’s avatar in virtual locations using a VR social network as an available experience. Results Three patients experienced VR. Despite some limitations due to patient positioning during the operation and the limitation of nonverbal cues inherent to the app, the neuropsychologist, as an avatar, could communicate with the patient and explore gesture communication while wearing a VR headset. Conclusions With some improvements, VR social networks can be used in the near future to map social cognition during awake craniotomy. Trial Registration ClinicalTrials.gov NCT03010943; https://clinicaltrials.gov/ct2/show/NCT03010943 (Archived at WebCite at http://www.webcitation.org/70CYDil0P)
Gradient Acceleration in Activation Functions

Dropout has been one of standard approaches to train deep neural networks, and it is known to regularize large models to avoid overfitting. The effect of dropout has been explained by avoiding co-adaptation. In this paper, however, we propose a new explanation of why dropout works and propose a new technique to design better activation functions. First, we show that dropout is an optimization technique to push the input towards the saturation area of nonlinear activation function by accelerating gradient information flowing even in the saturation area in backpropagation. Based on this explanation, we propose a new technique for activation functions, gradient acceleration in activation function (GAAF), that accelerates gradients to flow even in the saturation area. Then, input to the activation function can climb onto the saturation area which makes the network more robust because the model converges on a flat region. Experiment results support our explanation of dropout and confirm that the proposed GAAF technique improves performances with expected properties.
An Elevated Platelet Count Increases the Risk of Relapse in Ulcerative Colitis Patients with Mucosal Healing

Background/Aims Although mucosal healing (MH) has been considered a treatment goal for patients with ulcerative colitis (UC), the risk factors predictive of relapse in patients who achieve MH are unknown. Because the platelet count has been shown to be a marker of inflammation in inflammatory bowel diseases, this study aimed to assess whether the platelet count could predict relapse in UC patients with MH. Methods A prospective observational study was performed. UC patients with MH were consecutively enrolled in the study and monitored for at least 2 years or until relapse. The correlation between the incidence of relapse and the platelet count at the time of study enrollment was examined. Results In total, 43 patients were enrolled, and 14 patients (33%) relapsed. The median platelet count at the time of enrollment in the patients who relapsed significantly differed from that in the patients who did not relapse (27.2×104/μL vs 23.8×104/μL, respectively; p=0.016). A platelet count >25.0×104/μL was a significant risk factor for relapse based on a multivariate analysis (hazard ratio, 4.85; 95% confidence interval, 1.07 to 25.28), and according to the Kaplan-Meier analysis, this cutoff could identify patients susceptible to relapse (p=0.041, log-rank test). Conclusions The platelet count could be used as a predictor of relapse in UC patients with MH.