Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of the Human Placenta and Fetal Heart: Synergic or Independent?

The placenta is the largest fetal organ, and toward the end of pregnancy the umbilical circulation receives at least 40% of the biventricular cardiac output. It is not surprising, therefore, that there are likely to be close haemodynamic links between the development of the placenta and the fetal heart. Development of the placenta is precocious, and in advance of that of the fetus. The placenta undergoes considerable remodeling at the end of the first trimester of pregnancy, and its vasculature is capable of adapting to environmental conditions and to variations in the blood supply received from the mother. There are two components to the placental membranes to consider, the secondary yolk sac and the chorioallantoic placenta. The yolk sac is the first of the extraembryonic membranes to be vascularized, and condensations in the mesenchyme at ~17 days post-conception (p.c.) give rise to endothelial and erythroid precursors. A network of blood vessels is established ~24 days p.c. , with the vitelline vein draining through the region of the developing liver into the sinus venosus. Gestational sacs of early pregnancy failures often display aberrant development of the yolk sac, which is likely to be secondary to abnormal fetal development. Vasculogenesis occurs in the villous mesenchyme of the chorioallantoic placenta at a similarly early stage. Nucleated erythrocytes occupy the lumens of the placental capillaries and end-diastolic flow is absent in the umbilical arterial circulation throughout most of the first trimester, indicating a high resistance to blood flow. Resistance begins to fall in the umbilico-placental circulation around 12–14 weeks. During normal early pregnancy the placental capillary network is plastic, and considerable remodeling occurs in response to the local oxygen concentration, and in particular to oxidative stress. In pregnancies complicated by preeclampsia and/or fetal growth restriction, utero-placental malperfusion induces smooth muscle cells surrounding the placental arteries to dedifferentiate and adopt a proliferative phenotype. This change is associated with increased umbilical resistance measured by Doppler ultrasound, and is likely to exert a major effect on the developing heart through the afterload. Thus, both the umbilical and maternal placental circulations may impact on development of the heart.
Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates

Legumain is a dual-function protease–peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform γ (AtLEGγ) in complex with the covalent peptidic Ac-YVAD chloromethyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate-cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGγ structures disclosed a substrate-induced disorder–order transition with synergistic rearrangements in the substrate-recognition sites. Docking and in vitro studies with an AtLEGγ ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate–like binding to the active site–binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2′–S2′, to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGγ active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.
Edge Caching With Transmission Schedule for Multiuser Multirelay Networks

We propose an edge caching scheme with transmission schedule for multiuser multirelay networks, where the communication from the source to users is assisted by intermediate relays. We assume that each intermediate relay has a capacity-limited cache which can cache the contents that users request from the source. To improve the outage performance in this network, contents are cached at all relays or at a cluster formed by partial relays according to their popularities. Furthermore, transmissions for contents with different popularities are scheduled. We optimize the cache placement by minimizing the average outage. Therefore, cache placement can be dynamically updated according to the optimization outcome. The performance of our method is compared with the existing schemes via numerical studies.
Neural Text Generation: Past, Present and Beyond

This paper presents a systematic survey on recent development of neural text generation models. Specifically, we start from recurrent neural network language models with the traditional maximum likelihood estimation training scheme and point out its shortcoming for text generation. We thus introduce the recently proposed methods for text generation based on reinforcement learning, re-parametrization tricks and generative adversarial nets (GAN) techniques. We compare different properties of these models and the corresponding techniques to handle their common problems such as gradient vanishing and generation diversity. Finally, we conduct a benchmarking experiment with different types of neural text generation models on two well-known datasets and discuss the empirical results along with the aforementioned model properties.
Analysis and Development of a Novel Algorithm for the In-vehicle Hand-Usage of a Smartphone

Smartphone usage while driving is unanimously considered to be a really dangerous habit due to strong correlation with road accidents. In this paper, the problem of detecting whether the driver is using the phone during a trip is addressed. To do this, high-frequency data from the triaxial inertial measurement unit (IMU) integrated in almost all modern phone is processed without relying on external inputs so as to provide a self-contained approach. By resorting to a frequency-domain analysis, it is possible to extract from the raw signals the useful information needed to detect when the driver is using the phone, without being affected by the effects that vehicle motion has on the same signals. The selected features are used to train a Support Vector Machine (SVM) algorithm. The performance of the proposed approach are analyzed and tested on experimental data collected during mixed naturalistic driving scenarios, proving the effectiveness of the proposed approach.
Regularised CSP for Sensor Selection in BCI

The Common Spatial Pattern (CSP) algorithm is a highly successful method for efficiently calculating spatial filters for brain signal classification. Spatial filtering can improve classification performance considerably, but demands that a large number of electrodes be mounted, which is inconvenient in day-to-day BCI usage. The CSP algorithm is also known for its tendency to overfit, i.e. to learn the noise in the training set rather than the signal. Both problems motivate an approach in which spatial filters are sparsified. We briefly sketch a reformulation of the problem which allows us to do this, using 1-norm regularisation. Focusing on the electrode selection issue, we present preliminary results on EEG data sets that suggest that effective spatial filters may be computed with as few as 10– 20 electrodes, hence offering the potential to simplify the practical realisation of BCI systems significantly.
EXPERIMENTAL INVESTIGATION AND ANALYSIS OF MICROSTRUCTURE AND MECHANICAL PROPERTIES ON TWIST EXTRUSION FORMING PROCESS OF AA7075-T6 ALUMINIUM ALLOY

The objective of this study is to investigate the twist extrusion forming behaviour of AA 7075-T6 Aluminium alloy. Samples of 28x18x70 mm cross sections were subjected to twist extrusion forming with the aim to decrease the grain size and improve the mechanical properties. Four different temperatures and three passes were employed to conduct the experiments. The mechanical and microstructure properties of the as received and twist extruded samples at different temperatures and passes were examined. The results reveal that Twist Extrusion (TE) can refine the grain structure, with increasing number of passes, the hardness increase with structure homogeneity improvement but with decrease in the tensile strength at high temperatures. SEM micrographs show that the twist extrusion passes reduces the sizes of the second phase particles which enhance the improvement in mechanical properties.
Mortality risk in patients on hemodiafiltration versus hemodialysis: a ‘real-world’ comparison from the DOPPS

Abstract Background With its convective component, hemodiafiltration (HDF) provides better middle molecule clearance compared with hemodialysis (HD) and is postulated to improve survival. A previous analysis of Dialysis Outcomes and Practice Patterns Study (DOPPS) data in 1998–2001 found lower mortality rates for high replacement fluid volume HDF versus HD. Randomized controlled trials have not shown uniform survival advantage for HDF; in secondary (non-randomized) analyses, better outcomes were observed in patients receiving the highest convection volumes. Methods In a ‘real-world’ setting, we analyzed patients on dialysis >90 days from seven European countries in DOPPS Phases 4 and 5 (2009–15). Adjusted Cox regression was used to study HDF (versus HD) and mortality, overall and by replacement fluid volume. Results Among 8567 eligible patients, 2012 (23%) were on HDF, ranging from 42% in Sweden to 12% in Germany. Median follow-up was 1.5 years during which 1988 patients died. The adjusted mortality hazard ratio (95% confidence interval) was 1.14 (1.00–1.29) for any HDF versus HD and 1.08 (0.92–1.28) for HDF >20 L replacement fluid volume versus HD. Similar results were found for cardiovascular and infection-related mortality. In an additional analysis aiming to avoid treatment-by-indication bias, we did not observe lower mortality rates in facilities using more HDF (versus HD). Conclusions Our results do not support the notion that HDF provides superior patient survival. Further trials designed to test the effect of high-volume HDF (versus lower volume HDF versus HD) on clinical outcomes are needed to adequately inform clinical practices.
Amygdala, Childhood Adversity and Psychiatric Disorders

Above 10% of children in the U.S. are subjected to some form of maltreatment (Table 1) [1]. Childhood adversity can take the form of abuse, neglect, or loss, with examples including but not limited to: sexual abuse, physical abuse, emotional/psychological abuse, neglect, parental death, and bullying. Childhood adversity has been shown to have lifelong impact on the victim‘s physical and mental well-being (Table 2).
Nutrition Therapy Diabetes Canada Clinical Practice Guidelines Expert Committee

• People with diabetes should receive nutrition counselling by a registered dietitian. • Nutrition therapy can reduce glycated hemoglobin (A1C) by 1.0% to 2.0% and, when used with other components of diabetes care, can further improve clinical and metabolic outcomes. • Reduced caloric intake to achieve and maintain a healthier body weight should be a treatment goal for people with diabetes with overweight or obesity. • The macronutrient distribution is flexible within recommended ranges and will depend on individual treatment goals and preferences. • Replacing high-glycemic-index carbohydrates with low-glycemic-index carbohydrates in mixed meals has a clinically significant benefit for glycemic control in people with type 1 and type 2 diabetes. • Consistency in spacing and intake of carbohydrate intake and in spacing and regularity in meal consumption may help control blood glucose and weight. • Intensive healthy behaviour interventions in people with type 2 diabetes can produce improvements in weight management, fitness, glycemic control and cardiovascular risk factors. • A variety of dietary patterns and specific foods have been shown to be of benefit in people with type 1 and type 2 diabetes. • People with diabetes should be encouraged to choose the dietary pattern that best aligns with their values, preferences and treatment goals, allowing them to achieve the greatest adherence over the long term.
Mitochondrial Reactive Oxygen Species Control the Transcription Factor CHOP-10/GADD153 and Adipocyte Differentiation

Recent reports emphasize the importance of mitochondria in white adipose tissue biology. In addition to their crucial role in energy homeostasis, mitochondria are the main site of reactive oxygen species generation. When moderately produced, they function as physiological signaling molecules. Thus, mitochondrial reactive oxygen species trigger hypoxia-dependent gene expression. Therefore the present study tested the implication of mitochondrial reactive oxygen species in adipocyte differentiation and their putative role in the hypoxia-dependent effect on this differentiation. Pharmacological manipulations of mitochondrial reactive oxygen species generation demonstrate a very strong and negative correlation between changes in mitochondrial reactive oxygen species and adipocyte differentiation of 3T3-F442A preadipocytes. Moreover, mitochondrial reactive oxygen species positively and specifically control expression of the adipogenic repressor CHOP-10/GADD153. Hypoxia (1% O2) strongly increased reactive oxygen species generation, hypoxia-inducible factor-1 and CHOP-10/GADD153 expression, and inhibited adipocyte differentiation. All of these hypoxia-dependent effects were partly prevented by antioxidants. By using hypoxia-inducible factor-1α (HIF-1α)-deficient mouse embryonic fibroblasts, HIF-1α was shown not to be required for hypoxia-mediated CHOP-10/GADD153 induction. Moreover, the comparison of hypoxia and CoCl2 effects on adipocyte differentiation of wild type or HIF-1α deficient mouse embryonic fibroblasts suggests the existence of at least two pathways dependent or not on the presence of HIF-1α. Together, these data demonstrate that mitochondrial reactive oxygen species control CHOP-10/GADD153 expression, are antiadipogenic signaling molecules, and trigger hypoxia-dependent inhibition of adipocyte differentiation.
Impaired retrograde transport of axonal autophagosomes contributes to autophagic stress in Alzheimer’s disease neurons

Neurons face unique challenges of transporting nascent autophagic vacuoles (AVs) from distal axons toward the soma, where mature lysosomes are mainly located. Autophagy defects have been linked to Alzheimer’s disease (AD). However, the mechanisms underlying altered autophagy remain unknown. Here, we demonstrate that defective retrograde transport contributes to autophagic stress in AD axons. Amphisomes predominantly accumulate at axonal terminals of mutant hAPP mice and AD patient brains. Amyloid-β (Aβ) oligomers associate with AVs in AD axons and interact with dynein motors. This interaction impairs dynein recruitment to amphisomes through competitive interruption of dynein-Snapin motor-adaptor coupling, thus immobilizing them in distal axons. Consistently, deletion of Snapin in mice causes AD-like axonal autophagic stress, whereas overexpressing Snapin in hAPP neurons reduces autophagic accumulation at presynaptic terminals by enhancing AV retrograde transport. Altogether, our study provides new mechanistic insight into AD-associated autophagic stress, thus establishing a foundation for ameliorating axonal pathology in AD. DOI: http://dx.doi. org/10.7554/eLife.21776. 001
Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models

Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).
Comparing a Scanning Ambiguous Keyboard to the On-screen QWERTY Keyboard

This paper explores text entry on a scanning ambiguous keyboard (SAK) and the Windows onscreen keyboard (OSK) operating in scanning mode. The SPACEBAR was used for physical input with both keyboards. Testing involved 12 participants entering five phrases of text with each keyboard. On entry speed, the means were 5.06 wpm for the SAK and 2.67 wpm for the OSK, thus revealing a significant speed advantage for the SAK. However, the character-level error rate of 13.3% for the SAK was significantly higher than the error rate of 2.4% for the OSK. On subjective preference, 7 of 12 participants preferred the Windows OSK over the SAK, citing familiarity with the QWERTY layout as the most common reason. However, participants appreciated the efficiency of the SAK keyboard. A limitation of the results is the small amount of text entered.
Lightweight Deep Convolutional Network for Tiny Object Recognition

Object recognition is an important problem in Computer Vision with many applications such as image search, autonomous car, image understanding, etc. In recent years, Convolutional Neural Network (CNN) based models have achieved great success on object recognition, especially VGG, ResNet, Wide ResNet, etc. However, these models involve a large number of parameters that should be trained with large-scale datasets on powerful computing systems. Thus, it is not appropriate to train a heavy CNN with small-scale datasets with only thousands of samples as it is easy to be over-fitted. Furthermore, it is not efficient to use an existing heavy CNN method to recognize small images, such as in CIFAR-10 or CIFAR-100. In this paper, we propose a Lightweight Deep Convolutional Neural Network architecture for tiny images codenamed “DCTI” to reduce significantly a number of parameters for such datasets. Additionally, we use batch-normalization to deal with the change in distribution each layer. To demonstrate the efficiency of the proposed method, we conduct experiments on two popular datasets: CIFAR-10 and CIFAR-100. The results show that the proposed network not only significantly reduces the number of parameters but also improves the performance. The number of parameters in our method is only 21.33% the number of parameters of Wide ResNet but our method achieves up to 94.34% accuracy on CIFAR-10, comparing to 96.11% of Wide ResNet. Besides, our method also achieves the accuracy of 73.65% on CIFAR-100.
Disability and health outcomes – from a cohort of people on long-term anti-retroviral therapy

Abstract Human-immunodeficiency virus (HIV)/Acquired immunodeficiency Syndrome (AIDS) remains a major health problem in South Africa – even after two decades since the introduction of antiretroviral therapy (ART). Long-term survival with HIV is associated with new health-related issues and a risk of functional limitation/disability. The aim of this study was to assess functional limitation associated with HIV/AIDS among people living with HIV (PLHIV) in South Africa. This study is a cross-sectional survey using a cohort in an urban area in Gauteng province, South Africa. Data were collected using questionnaires through an interview process. The information collected included aspects such as demographics, livelihood, the state of mental and physical health, adherence and disability. A total of 1044 participants with an average age of 42 ± 12 years were included in the study, with 51.9% of the participants reporting functional limitations (WHODAS ≥ 2). These were reported mainly in the domains of participation (40.2%) and mobility (38.7%). In addition, adherence to ART, symptoms of poor physical health and depression were strongly associated with their functional limitations/disability. HIV as a chronic disease is associated with functional limitations that are not adequately addressed and pose a risk of long-term disability and negative adherence outcomes. Therefore, wellness for PLHIV/AIDS needs to include interventions that can prevent and manage disability.
Clinical and pathological phenotype of genetic causes of focal segmental glomerulosclerosis in adults

Abstract Focal segmental glomerulosclerosis (FSGS) is a histologic lesion resulting from a variety of pathogenic processes that cause injury to the podocytes. Recently, mutations in more than 50 genes expressed in podocyte or glomerular basement membrane were identified as causing genetic forms of FSGS, the majority of which are characterized by onset in childhood. The prevalence of adult-onset genetic FSGS is likely to be underestimated and its clinical and histological features have not been clearly described. A small number of studies of adult-onset genetic FSGS showed that there is heterogeneity in clinical and histological findings, with a presentation ranging from sub-nephrotic proteinuria to full nephrotic syndrome. A careful evaluation of adult-onset FSGS that do not have typical features of primary or secondary FSGS (familial cases, resistance to immunosuppression and absence of evident cause of secondary FSGS) should include a genetic evaluation. Indeed, recognizing genetic forms of adult-onset FSGS is of the utmost importance, given that this diagnosis will have major implications on treatment strategies, selecting of living-related kidney donor and renal transplantation success.
FEVER: a Large-scale Dataset for Fact Extraction and VERification

In this paper we introduce a new publicly available dataset for verification against textual sources, FEVER: Fact Extraction and VERification. It consists of 185,445 claims generated by altering sentences extracted from Wikipedia and subsequently verified without knowledge of the sentence they were derived from. The claims are classified as Supported, Refuted or NotEnoughInfo by annotators achieving 0.6841 in Fleiss kappa. For the first two classes, the annotators also recorded the sentence(s) forming the necessary evidence for their judgment. To characterize the challenge of the dataset presented, we develop a pipeline approach and compare it to suitably designed oracles. The best accuracy we achieve on labeling a claim accompanied by the correct evidence is 31.87%, while if we ignore the evidence we achieve 50.91%. Thus we believe that FEVER is a challenging testbed that will help stimulate progress on claim verification against textual sources.