Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of genetic trends in dairy cattle populations.

Abstract Usefulness of full sisters and paternal half-sisters to estimate genetic trends was investigated, with 34,380 first lactation Holstein Herd Improvement Registry (HHIR) records reported in 335 herds from 1953 to 1961. Paternal half-sister families comprised one-third and full-sister families one-seventh of the data. All records were analyzed to obtain least-squares constants for year of calving. A weighted regression of these constants on years provided an estimate of the annual trend, genetic plus environmental, (63 ± 11 kg for milk and 0.007 ± 0.001 for per cent fat). Full sisters were analyzed to obtain least-squares year constants adjusted for sire and dam effects and corrected for selection. Weighted regression of these constants on years indicated the environmental trend in the population, and comparison with the genetic plus the environmental trend provided an estimate of annual genetic trend (45 ± 16 kg for milk and 0.018 ± 0.003 for per cent fat). A second estimate of the annual genetic trend (55 ± 26 kg for milk and 0.016 ± 0.005 for per cent fat) was obtained by comparing the over-all trend with one-half the genetic, plus the environmental trend estimated from records of paternal half-sisters adjusted for sire effects.
Polymorphisms in the Innate Immune IFIH1 Gene, Frequency of Enterovirus in Monthly Fecal Samples during Infancy, and Islet Autoimmunity

Interferon induced with helicase C domain 1 (IFIH1) senses and initiates antiviral activity against enteroviruses. Genetic variants of IFIH1, one common and four rare SNPs have been associated with lower risk for type 1 diabetes. Our aim was to test whether these type 1 diabetes-associated IFIH1 polymorphisms are associated with the occurrence of enterovirus infection in the gut of healthy children, or influence the lack of association between gut enterovirus infection and islet autoimmunity. After testing of 46,939 Norwegian newborns, 421 children carrying the high risk genotype for type 1 diabetes (HLA-DR4-DQ8/DR3-DQ2) as well as 375 children without this genotype were included for monthly fecal collections from 3 to 35 months of age, and genotyped for the IFIH1 polymorphisms. A total of 7,793 fecal samples were tested for presence of enterovirus RNA using real time reverse transcriptase PCR. We found no association with frequency of enterovirus in the gut for the common IFIH1 polymorphism rs1990760, or either of the rare variants of rs35744605, rs35667974, rs35337543, while the enterovirus prevalence marginally differed in samples from the 8 carriers of a rare allele of rs35732034 (26.1%, 18/69 samples) as compared to wild-type homozygotes (12.4%, 955/7724 samples); odds ratio 2.5, p = 0.06. The association was stronger when infections were restricted to those with high viral loads (odds ratio 3.3, 95% CI 1.3–8.4, p = 0.01). The lack of association between enterovirus frequency and islet autoimmunity reported in our previous study was not materially influenced by the IFIH1 SNPs. We conclude that the type 1 diabetes-associated IFIH1 polymorphisms have no, or only minor influence on the occurrence, quantity or duration of enterovirus infection in the gut. Its effect on the risk of diabetes is likely to lie elsewhere in the pathogenic process than in the modification of gut infection.
Histone H3R17me2a mark recruits human RNA Polymerase-Associated Factor 1 Complex to activate transcription

The histone coactivator-associated arginine methyltransferase 1 (CARM1) is a coactivator for a number of transcription factors, including nuclear receptors. Although CARM1 and its asymmetrically deposited dimethylation at histone H3 arginine 17 (H3R17me2a) are associated with transcription activation, the mechanism by which CARM1 activates transcription remains unclear. Using an unbiased biochemical approach, we discovered that the transcription elongation-associated PAF1 complex (PAF1c) directly interacts with H3R17me2a. PAF1c binds to histone H3 tails harboring dimethylation at R17 in CARM1-methylated histone octamers. Knockdown of either PAF1c subunits or CARM1 affected transcription of CARM1-regulated, estrogen-responsive genes. Furthermore, either CARM1 knockdown or CARM1 enzyme-deficient mutant knockin resulted in decreased H3R17me2a accompanied by the reduction of PAF1c occupancy at the proximal promoter estrogen-responsive elements. In contrast, PAF1c knockdown elicited no effects on H3R17me2a but reduced the H3K4me3 level at estrogen-responsive elements. These observations suggest that, apart from PAF1c's established roles in directing histone modifications, PAF1c acts as an arginine methyl histone effector that is recruited to promoters and activates a subset of genes, including targets of estrogen signaling.
Designs on the Contemporary: Anthropological Tests

Designs on the Contemporary pursues the challenge of how to design and put into practice strategies for inquiring into the intersections of philosophy and anthropology. Drawing on the conceptual repertoires of Weber, Foucault, and Dewey, among others, Paul Rabinow and Anthony Stavrianakis reflect on and experiment with how to give form to anthropological inquiry and its aftermath, with special attention to the ethical formation and ramifications of this mode of engagement. The authors continue their explorations of the contemporary from past works: how to conceptualize, test, and give form to breakdowns of truth and conduct, as well as how to open up possibilities for the remediation of such breakdowns. They offer a surprising and contrasting pair of case studies of two figures who engaged with contemporary breakdowns: Salman Rushdie and Gerhard Richter, showing how both men formulated different new approaches to anthropology for the twenty-first century.
More than just child’s play: A study on sibling incest

This article outlines some of the findings of a study of ten women who experienced sibling incest as children. Using qualitative research methods, this study explores the nature of the sibling incest relationship, how the incest occurred, the family environment, the effects suffered and the participants’ experience of intervention. For the majority of women, the effects of unwanted sibling incest were similar to the effects of parent-child incest. The participants provided important perspectives on both intervention and prevention strategies that would assist with the problem of sibling incest. This study aims to link the perspective of those who have experienced sibling incest with some implications for professional practice.
Osteoprotegerin, s-RANKL, and selected interleukins in the pathology of bone metabolism in patients with Crohn's disease

Introduction Crohn's disease (CD) promotes the development of osteopaenia/osteoporosis, the cytokine background of which is not fully known. Aim Evaluation of bone mineral density (BMD), the prevalence of osteopaenia and osteoporosis, and the determination of the levels of selected interleukins (IL), osteoprotegerin (OPG), and s-RANKL proteins in patients with CD in relation to a control group and assessment of the relationship between the tested cytokines, OPG, s-RANKL, and BMD. Material and methods Thirty-seven CD patients and 37 healthy volunteers (control group) were enrolled into the study. Densitometry of the lumbar spine (L2–L4) and of the femoral neck using the DXA technique was carried out. Serum levels of: IL-13, IL-4, IL-17, IL-1β, OPG, and s-RANKL were determined using the ELISA method. Progression-of-disease questionnaires were collected. Results The prevalence of osteoporosis and osteopaenia in the CD group was: 18.92% and 32.43% in L2–L4; 13.51% and 35.13% in the neck, respectively. The IL-13 and IL-1β concentrations were significantly higher and OPG was significantly lower in CD patients when compared to controls. In the case of all subjects: IL-13 correlated negatively with the BMD of the neck, IL-17 correlated negatively with the Z-score of L2–L4, and OPG correlated negatively with the IL-13. In the case of CD patients, IL-4 correlated negatively with the BMD of L2–L4. Conclusions The incidence of osteopaenia and osteoporosis in Polish CD patients is high. IL-13, IL-1β, and IL-4 seem to be connected with the pathology of decreased BMD in CD. It can be hypothesised that IL-13 may lower BMD by modulating OPG.
Distribution of Attention Modulates Salience Signals in Early Visual Cortex

Previous research has shown that the extent to which people spread attention across the visual field plays a crucial role in visual selection and the occurrence of bottom-up driven attentional capture. Consistent with previous findings, we show that when attention was diffusely distributed across the visual field while searching for a shape singleton, an irrelevant salient color singleton captured attention. However, while using the very same displays and task, no capture was observed when observers initially focused their attention at the center of the display. Using event-related fMRI, we examined the modulation of retinotopic activity related to attentional capture in early visual areas. Because the sensory display characteristics were identical in both conditions, we were able to isolate the brain activity associated with exogenous attentional capture. The results show that spreading of attention leads to increased bottom-up exogenous capture and increased activity in visual area V3 but not in V2 and V1.
FDSOI molecular flash cell with reduced variability for low power flash applications

In this work we present a modeling study of a conceptual low power non-volatile memory cell based on inorganic molecular metal oxide clusters (polyoxometalates (POM)) as a storage media embedded in the gate dielectric of a Fully Depleted SOI (FD SOI) with reduced statistical variability. The simulations were carried out using a multi-physics simulation framework, which allows us to evaluate the variability in the programming window of the molecular based flash cell with an 18 nm gate length. We have focused our study on the threshold voltage variability influenced by random dopant fluctuations and random special fluctuations of the molecules in the floating gate of the flash-cell. Our simulation framework and conclusions can be applied not only to POM-based flash cell but also to flash cells based on alternative molecules used as a storage media.
Cost-Efficient and Application SLA-Aware Client Side Request Scheduling in an Infrastructure-as-a-Service Cloud

Providers of applications deployed in an Infrastructure-as-a-Service cloud permanently face the decision of whether it is more cost-efficient to scale up(i.e., rent more resources from the cloud) or to delay incoming requests, even though doing so may lead to dissatisfied customers and broken service level agreements. This decision is further complicated by the fact that not all customers have the same agreements, and not all requests require the same amount of resources devoted to them. In this paper, we present an approach for optimally scheduling incoming requests to virtual computing resources in the cloud, so that the sum of payments for resources and loss incurred by service level agreement violations is minimized. We discuss our approach based on an illustrative use case. Furthermore, we present a numerical evaluation based on real-life request data, which shows that our agreement-aware algorithm improves upon earlier work, which does not take service level agreements into account.
Orientation Measurement Based on Magnetic Inductance by the Extended Distributed Multi-Pole Model

This paper presents a novel method to calculate magnetic inductance with a fast-computing magnetic field model referred to as the extended distributed multi-pole (eDMP) model. The concept of mutual inductance has been widely applied for position/orientation tracking systems and applications, yet it is still challenging due to the high demands in robust modeling and efficient computation in real-time applications. Recently, numerical methods have been utilized in design and analysis of magnetic fields, but this often requires heavy computation and its accuracy relies on geometric modeling and meshing that limit its usage. On the other hand, an analytical method provides simple and fast-computing solutions but is also flawed due to its difficulties in handling realistic and complex geometries such as complicated designs and boundary conditions, etc. In this paper, the extended distributed multi-pole model (eDMP) is developed to characterize a time-varying magnetic field based on an existing DMP model analyzing static magnetic fields. The method has been further exploited to compute the mutual inductance between coils at arbitrary locations and orientations. Simulation and experimental results of various configurations of the coils are presented. Comparison with the previously published data shows not only good performance in accuracy, but also effectiveness in computation.
Using Text Messages to Bridge the Intention-Behavior Gap? A Pilot Study on the Use of Text Message Reminders to Increase Objectively Assessed Physical Activity in Daily Life

Sedentarism is a serious health concern in industrialized countries throughout the world. We examined whether a text message-based intervention, targeted at increasing daily levels of physical activity, would be more effective than a standard psychoeducational intervention and a control condition. Sixty-three individuals (43 women) with a mean age of 23.7 years participated in the study. They were randomly assigned to a psychoeducational standard intervention; an augmented intervention with additional short text messages sent to the mobile phones to remind participants of their action plans, and a control condition. Objectively assessed physical activity and self-efficacy were assessed pre- and post-intervention. Participants in the control condition showed a significant decline in physical activity from pre-assessment to post-assessment, whereas participants in both intervention arms exhibited a slight increase. Moreover, the augmented intervention resulted in a marginally significant increase in self-efficacy, whereas the standard intervention resulted in a significant decrease. The findings suggest that short text messages reminding individuals of their action plans are not more effective than an intervention without text messages, although there seems to be a beneficial effect on self-efficacy, which might facilitate behavior change in the long-term. Challenging aspects of the research design (e.g., reactivity of the assessment protocol) are discussed and suggestions for future research are highlighted.
Screen-based identification and validation of four new ion channels as regulators of renal ciliogenesis

ABSTRACT To investigate the contribution of ion channels to ciliogenesis, we carried out a small interfering RNA (siRNA)-based reverse genetics screen of all ion channels in the mouse genome in murine inner medullary collecting duct kidney cells. This screen revealed four candidate ion channel genes: Kcnq1, Kcnj10, Kcnf1 and Clcn4. We show that these four ion channels localize to renal tubules, specifically to the base of primary cilia. We report that human KCNQ1 Long QT syndrome disease alleles regulate renal ciliogenesis; KCNQ1-p.R518X, -p.A178T and -p.K362R could not rescue ciliogenesis after Kcnq1-siRNA-mediated depletion in contrast to wild-type KCNQ1 and benign KCNQ1-p.R518Q, suggesting that the ion channel function of KCNQ1 regulates ciliogenesis. In contrast, we demonstrate that the ion channel function of KCNJ10 is independent of its effect on ciliogenesis. Our data suggest that these four ion channels regulate renal ciliogenesis through the periciliary diffusion barrier or the ciliary pocket, with potential implication as genetic contributors to ciliopathy pathophysiology. The new functional roles of a subset of ion channels provide new insights into the disease pathogenesis of channelopathies, which might suggest future therapeutic approaches. Highlighted Article: We present here the findings of a screen for ion channels regulating cilia in renal cells. The properties of four ion channels suggest a role for membrane subdomains at the base of the cilium.
[The nuclear hardness and associated factors of age-related cataract].

OBJECTIVE To determine the nuclear hardness and associated factors of age-related cataract. METHODS Forty-seven eyes of 47 patients with age-related cataract aged > 50 years were studied. The opacity of lenses was assessed and classified by the LOCS II pre-operatively. The lens nucleus obtained during extracapsular cataract extraction (ECCE) was measured. By means of a fine conical probe and dynamometer, the resistance to penetration of different lens layers was transferred to an electric signal and recorded by a function recorder. The hardness to the penetration of different lens layers was calculated. Multivariate regression analysis was applied to the parameters including age, color of the nucleus, duration of symptoms and other factors. RESULTS The mean force required to penetrate the lens was (0.51 +/- 0.29) Newtons (N) for grade I, (1.41 +/- 0.35) N for grade II and (1.95 +/- 0.42) N for grade III; it increased to (2.96 +/- 0.62) N for grade IV. The hardest part of the lens was located at the nucleus center. Multivariate analysis of the data showed that 85% of the variation in hardness could be explained in terms of color and opacity. The patients with myopia and diabetics had an increased incidence of grading IV nuclear sclerosis. Regression analysis revealed a positive correlation between nucleus color and weight (r = 0.4565), diameter (r = 0.5263), thickness (r = 0.5552) and hardness (r = 0.8969), P < 0.001. There was a weak positive correlation between age and the weight of nucleus (r = 0.3239, P < 0.05). CONCLUSIONS The results indicate that the color can be used more reliably to predict physical characteristics of lens nucleus, the preoperative knowledge of which would help the surgeon in planning small-incision surgery including phacoemulsification.
A Comprehensive Analysis of Deep Learning Based Representation for Face Recognition

Deep learning based approaches have been dominating the face recognition field due to the significant performance improvement they have provided on the challenging wild datasets. These approaches have been extensively tested on such unconstrained datasets, on the Labeled Faces in the Wild and YouTube Faces, to name a few. However, their capability to handle individual appearance variations caused by factors such as head pose, illumination, occlusion, and misalignment has not been thoroughly assessed till now. In this paper, we present a comprehensive study to evaluate the performance of deep learning based face representation under several conditions including the varying head pose angles, upper and lower face occlusion, changing illumination of different strengths, and misalignment due to erroneous facial feature localization. Two successful and publicly available deep learning models, namely VGG-Face and Lightened CNN have been utilized to extract face representations. The obtained results show that although deep learning provides a powerful representation for face recognition, it can still benefit from preprocessing, for example, for pose and illumination normalization in order to achieve better performance under various conditions. Particularly, if these variations are not included in the dataset used to train the deep learning model, the role of preprocessing becomes more crucial. Experimental results also show that deep learning based representation is robust to misalignment and can tolerate facial feature localization errors up to 10% of the interocular distance.
Deep Neural Network Embeddings for Text-Independent Speaker Verification

This paper investigates replacing i-vectors for text-independent speaker veriﬁcation with embeddings extracted from a feed-forward deep neural network. Long-term speaker characteristics are captured in the network by a temporal pooling layer that aggregates over the input speech. This enables the network to be trained to discriminate between speakers from variable-length speech segments. After training, utterances are mapped directly to ﬁxed-dimensional speaker embeddings and pairs of embeddings are scored using a PLDA-based backend. We compare performance with a traditional i-vector baseline on NIST SRE 2010 and 2016. We ﬁnd that the embeddings outperform i-vectors for short speech segments and are competitive on long duration test conditions. Moreover, the two representations are complementary, and their fusion improves on the baseline at all operating points. Similar systems have recently shown promising results when trained on very large proprietary datasets, but to the best of our knowledge, these are the best results reported for speaker-discriminative neural networks when trained and tested on publicly available corpora.
Technical and scale efficiency in the delivery of child health services in Zambia: results from data envelopment analysis

Objective Despite tremendous efforts to scale up key maternal and child health interventions in Zambia, progress has not been uniform across the country. This raises fundamental health system performance questions that require further investigation. Our study investigates technical and scale efficiency (SE) in the delivery of maternal and child health services in the country. Setting The study focused on all 72 health districts of Zambia. Methods We compiled a district-level database comprising health outcomes (measured by the probability of survival to 5 years of age), health outputs (measured by coverage of key health interventions) and a set of health system inputs, namely, financial resources and human resources for health, for the year 2010. We used data envelopment analysis to assess the performance of subnational units across Zambia with respect to technical and SE, controlling for environmental factors that are beyond the control of health system decision makers. Results Nationally, average technical efficiency with respect to improving child survival was 61.5% (95% CI 58.2% to 64.8%), which suggests that there is a huge inefficiency in resource use in the country and the potential to expand services without injecting additional resources into the system. Districts that were more urbanised and had a higher proportion of educated women were more technically efficient. Improved cooking methods and donor funding had no significant effect on efficiency. Conclusions With the pressing need to accelerate progress in population health, decision makers must seek efficient ways to deliver services to achieve universal health coverage. Understanding the factors that drive performance and seeking ways to enhance efficiency offer a practical pathway through which low-income countries could improve population health without necessarily seeking additional resources.