Miracle-dz/UniFAR-FTUs huggingface dataset:
A scalable, aggregated genotypic–phenotypic database for human disease variation

Abstract Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic–phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy. The database is composed of 50 000 individuals who were sequenced for 30 genes associated with hereditary cancer risk and provides useful information on allele frequency and variant classification, as well as associated phenotypic information such as demographics and personal and family history. Our user-friendly interface allows researchers to easily execute their own queries with filtering, and the results of queries can be shared and/or downloaded. The rapid and broad dissemination of these research results will help increase the value of, and reduce the waste in, scientific resources and data. Furthermore, the database is able to quickly scale and support integration of additional genes and human hereditary conditions. We hope that this database will help researchers and scientists explore genotype–phenotype correlations in hereditary cancer, identify novel variants for functional analysis and enable data-driven drug discovery and development.
Self-Compassion and Subjective Well-Being Mediate the Impact of Mindfulness on Balanced Time Perspective in Chinese College Students

Balanced time perspective is associated with optimal social functioning and provides psychological benefits in times of stress. Previous studies have found that mindfulness is positively associated with balanced time perspective and might promote it. However, the mechanism through which mindfulness affects balanced time perspective remains unexplored. The purpose of the present study was to investigate the mediating role of self-compassion and subjective well-being in the relationship between mindfulness and balanced time perspective. A total of 754 Chinese college students, aged 17–27 years, completed the Chinese versions of the Five-Facet Mindfulness Questionnaire, Self-Compassion Scale, Subjective Well-Being Scale, and Zimbardo Time Perspective Inventory. There were significant positive correlations between mindfulness, self-compassion, subjective well-being, and balanced time perspective. Structural equation modeling indicated that in addition to the direct influence of mindfulness on balanced time perspective, self-compassion and subjective well-being played a partial mediating role. On the basis of these findings, we conclude that mindfulness has an important positive influence on balanced time perspective, and highlights the crucial role of the self-compassion in cultivating a balanced time perspective. Limitations of the present study are also discussed.
Learned Step Size Quantization

Deep networks run with low precision operations at inference time offer power and space advantages over high precision alternatives, but need to overcome the challenge of maintaining high accuracy as precision decreases. Here, we present a method for training such networks, Learned Step Size Quantization, that achieves the highest accuracy to date on the ImageNet dataset when using models, from a variety of architectures, with weights and activations quantized to 2-, 3- or 4-bits of precision, and that can train 3-bit models that reach full precision baseline accuracy. Our approach builds upon existing methods for learning weights in quantized networks by improving how the quantizer itself is configured. Specifically, we introduce a novel means to estimate and scale the task loss gradient at each weight and activation layer's quantizer step size, such that it can be learned in conjunction with other network parameters. This approach works using different levels of precision as needed for a given system and requires only a simple modification of existing training code.
Enhanced antibacterial activity of capped zinc oxide nanoparticles: A step towards the control of clinical bovine mastitis

Background and Aim: Bovine mastitis is the costliest prevalent disease in the dairy sector due to the limitations of conventional treatments. Zinc oxide nanoparticles (ZnO-NPs) have been regarded as safe and economical antibacterial candidates against several microorganisms, but the tendency of these particles to aggregate is a major barrier to their application. This study aimed to enhance the antibacterial efficiency of ZnO-NPs against some bacterial agents, causing bovine mastitis. Materials and Methods: A total of 24 milk samples out of 300 cases from Nubaria farm, Beheira Governorate, Egypt, were collected from cows with clinical mastitis. ZnO-NPs were fabricated by a sonochemical method using starch as a capping agent and by an auto-combustion reaction using glycine as a fuel. The two preparations of synthesized ZnO-NPs at different concentrations were assessed for their antimicrobial activities in vitro against Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae isolated from milk of affected cows. Results: Sonochemically synthesized capped ZnO-NPs were dispersed and non-agglomerated in comparison with aggregated uncapped ZnO-NPs prepared by an auto-combustion reaction. Capped dispersed ZnO-NPs showed higher antibacterial activity against S. aureus, E. coli, and K. pneumoniae than particles synthesized by the auto-combustion reaction at same concentrations. However, the zone of inhibition for dispersed and agglomerated ZnO-NPs was concentration-dependent. In addition, Gram-positive S. aureus exhibited higher resistance to ZnO-NPs synthesized by both methods than Gram-negative E. coli and K. pneumoniae. Conclusion: Dispersed, non-agglomerated ZnO-NPs fabricated using starch as a capping agent under sonochemical irradiation could potentially be regarded as highly effective and inexpensive antimicrobial agents against S. aureus, E. coli, and K. pneumoniae for the management of bovine mastitis.
Deep Multi-Modal Object Detection and Semantic Segmentation for Autonomous Driving: Datasets, Methods, and Challenges

Recent advancements in perception for autonomous driving are driven by deep learning. In order to achieve robust and accurate scene understanding, autonomous vehicles are usually equipped with different sensors (e.g. cameras, LiDARs, Radars), and multiple sensing modalities can be fused to exploit their complementary properties. In this context, many methods have been proposed for deep multi-modal perception problems. However, there is no general guideline for network architecture design, and questions of “what to fuse”, “when to fuse”, and “how to fuse” remain open. This review paper attempts to systematically summarize methodologies and discuss challenges for deep multi-modal object detection and semantic segmentation in autonomous driving. To this end, we first provide an overview of on-board sensors on test vehicles, open datasets, and background information for object detection and semantic segmentation in autonomous driving research. We then summarize the fusion methodologies and discuss challenges and open questions. In the appendix, we provide tables that summarize topics and methods. We also provide an interactive online platform to navigate each reference: https://boschresearch.github. io/multimodalperception/.
The phyllostomid bat (Mammalia, Chiroptera) assemblage in a fragmented landscape in Midwestern Brazil

ABSTRACT Bats are the second largest order of mammals, with varying feeding habits and great ecological significance. Anthropization has several important effects on animal communities and the Brazilian Cerrado, a Neotropical savannah, has been severely affected by human activity. The objective of this study was to evaluate phyllostomid bat assemblage distributions in the different landscape formations of a modified savannah. Using mist nets, we performed 36 sampling nights between 2015 and 2016. The sampling effort was 23,328 m². h and was equally distributed over three landscape formations: a large fragment, riparian forest, and small fragments. We compared capture rates, richness, diversity, similarity, and feeding guilds for the three formations. We captured 418 bats of 12 species belonging to the family Phyllostomidae. The most abundant species was Artibeus planirostris (Spix, 1823) (n = 126). We found no significant differences in capture rate or diversity between the areas, but there were differences in feeding guild representation. Frugivores species were the most abundant in the three areas. No gleaning insectivore or carnivore species were captured in the small fragments, and the large fragment contained no hematophages. The large fragment and the small fragments had the greatest similarity whereas the riparian forest and small fragments had the least similarity.
Depression, Hematologic Parameters, and Blood Levels of Vitamin B12 in Patients With Laryngopharyngeal Reflux Under Use of Proton Pump Inhibitors

Objective: The objective of this study was to evaluate and correlate hematologic indices, vitamin B12 levels, and depression in patients with suspected laryngopharyngeal reflux (LPR) treated with proton pump inhibitor (PPI). Methods: This was a prospective study with a population (n = 23) consisted of patients with suspected LPR and treated with 2 daily doses of Omeprazole 40 mg (80 mg or full dose). The study volunteers performed a complete blood count and vitamin B12 dosage before and after 3 and 6 months of treatment, as well as depression screening using the Center of Epidemiologic Studies-Depression (CES-D) questionnaire before and after 6 months of treatment. Scores greater than 16 were considered as suggestive of depression. Results: The mean score on the CES-D scale of study participants at baseline significantly decreased after 6 months of treatment. A significant decrease was observed in the red blood cells count (RBC) after 6 months in relation to 3 months. Significant increases in mean corpuscular volume (MCV) and mean corpuscular hemoglobin (MCH) were observed from 3 months to 6 months in this study. Vitamin B12 levels increased significantly between baseline and after 6 months of treatment. Conclusion: Decreased scores on the CES-D scale were associated with increased MCV values, with no association with vitamin B12 levels. However, vitamin B12 levels also increased significantly after 6 months of treatment with PPI.
Refuge facilitates the preservation and accumulation of herbicide resistance traits in Conyza canadensis

Abstract: Herbicide resistance is selected for within a weed population through the recurrent use of an herbicide. Once the use of the herbicide is reduced or discontinued, the trait may persist in the population unless resistance endows a fitness penalty. Few studies have examined the long-term persistence of an herbicide resistance trait in a weed population once the selection pressure that led to its prevalence has been removed. The objective of this research was to re-survey the locations described by A.J.J. Smisek in her 1995 study of a paraquat resistant biotype of C. canadensis on the grounds of the Harrow Research and Development Centre. Results indicate that, ∼20 yr after paraquat use was significantly reduced, a glyphosate resistant biotype had replaced the paraquat resistant biotype at all but one of the original locations surveyed by Smisek. The sole location where the paraquat resistant biotype was observed was an old, un-treed orchard row currently managed by mowing. This location not only served as a refuge for the paraquat resistant biotype, ensuring its persistence in the face of strong selection for glyphosate resistance at all other locations, but it facilitated the co-occurrence of glyphosate and paraquat resistant biotypes. The observation of a multiple resistant biotype at this location alone, with resistance to both paraquat and glyphosate, suggests a role for refugia in the stacking of herbicide resistance traits. Given that this stacking occurred in the absence of either herbicide, we hypothesize that the multiple resistant biotype arose through pollen mediated gene flow among biotypes.
Wasserstein Adversarial Examples via Projected Sinkhorn Iterations

A rapidly growing area of work has studied the existence of adversarial examples, datapoints which have been perturbed to fool a classifier, but the vast majority of these works have focused primarily on threat models defined by $\ell_p$ norm-bounded perturbations. In this paper, we propose a new threat model for adversarial attacks based on the Wasserstein distance. In the image classification setting, such distances measure the cost of moving pixel mass, which naturally cover "standard" image manipulations such as scaling, rotation, translation, and distortion (and can potentially be applied to other settings as well). To generate Wasserstein adversarial examples, we develop a procedure for projecting onto the Wasserstein ball, based upon a modified version of the Sinkhorn iteration. The resulting algorithm can successfully attack image classification models, bringing traditional CIFAR10 models down to 3% accuracy within a Wasserstein ball with radius 0.1 (i.e., moving 10% of the image mass 1 pixel), and we demonstrate that PGD-based adversarial training can improve this adversarial accuracy to 76%. In total, this work opens up a new direction of study in adversarial robustness, more formally considering convex metrics that accurately capture the invariances that we typically believe should exist in classifiers. Code for all experiments in the paper is available at this https URL.
Genetic polymorphisms of the OLR1 and DGAT1 genes associated with milk components in Holstein Friesian dairy cattle under an intensive management in Central Java

Oxidized Low Density Lipoprotein Receptor 1 (OLR1) gene serves to encode the binding vascular surface receptors and to degrade the oxidized low-density lipoprotein. In dairy cattle a nucleotide mutation at 3′UTR location of the OLR1 gene results in C allele of which related to higher milk fat content than A allele. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has a K232A mutation of which K allele also associated with higher milk fat content against A allele. This study was aimed to study the association of variant genotypes of the OLR1 and DGAT1 genes on milk fat and other milk components in Holstein Friesian (HF) dairy cattle. The target of this research was to obtain genotypes of the OLR1 and DGAT1 gene affecting highly to milk fat content and other milk components in domestic HF cattle. Animals observed were Holstein Friesian (HF) lactating cows for 53 heads kept intensively at one government dairy station at BBPTU Baturraden, Central Java. Base mutations at 3′UTR location of the OLR1 gene and at K232A mutation of the DGAT1 gene were identified by PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism) techniques. Allele frequency of the base mutation of each gene was analyzed by PopGen 32 program. Milk components of fat, protein, solid non-fat (SNF) and lactose were generated from daily milk test for morning, afternoon and average of both. Study of the association of variant genotypes of the OLR1 and DGAT1 genes on individual milk component was analyzed by GLM considering the fixed effects of lactation period (1-3, 4-6), calving season (1-4 mo., and 5-8 mo.) and calving year (2011, 2012). Duncan Multiple Range Test was used to test significant differences of the averages among subclasses. The OLR1 gene resulted in A allele and C allele of whose the frequencies were respectively 0.457 and 0.543, while the DGAT1 gene resulted in A allele and K allele with the frequencies respectively 0.426 and 0.575. Variant genotypes of the OLR1 gene gave a significant different on milk fat production (P<0.05). Genetic polymorphism of the OLR1 gene had a significant effect on milk fat content in the noon, the highest was for CC genotype, followed by AC, and the lowest was AA, with the fat contents of CC and AC genotypes higher to AA one by 4.87% and 1.38% respectively. However variant genotypes of the OLR1 gene had no significant effect on other milk components (P>0.05). Similarly, variant genotypes of the DGAT1 gene consisting of genotype AK and genotype KK did not significantly affect on all of milk components. It was concluded that there was a fairly good control of the OLR1 gene to fat content in HF cows. The base mutation at the 3′UTR location of the OLR1 gene can be considered as an initial information in developing a genetic assisted selection (GAS) technique for milk fat content in domestic HF cows.
Studies of the Plymouth Brachyura. II. The Larval Stages of Ebalia and Pinnotheres

Further study of the larval crabs of the Plymouth district has resulted in the elucidation of many more life-histories. Amongst these perhaps some of the most interesting are Ebalia and Pinnotheres. These genera, placed by systematists in widely different groups, resemble one another closely in many details in their larval stages and are here purposely described together in order that a comparison may be made.
Standards in Pupillography

The number of research groups studying the pupil is increasing, as is the number of publications. Consequently, new standards in pupillography are needed to formalize the methodology including recording conditions, stimulus characteristics, as well as suitable parameters of evaluation. Since the description of intrinsically photosensitive retinal ganglion cells (ipRGCs) there has been an increased interest and broader application of pupillography in ophthalmology as well as other fields including psychology and chronobiology. Color pupillography plays an important role not only in research but also in clinical observational and therapy studies like gene therapy of hereditary retinal degenerations and psychopathology. Stimuli can vary in size, brightness, duration, and wavelength. Stimulus paradigms determine whether rhodopsin-driven rod responses, opsin-driven cone responses, or melanopsin-driven ipRGC responses are primarily elicited. Background illumination, adaptation state, and instruction for the participants will furthermore influence the results. This standard recommends a minimum set of variables to be used for pupillography and specified in the publication methodologies. Initiated at the 32nd International Pupil Colloquium 2017 in Morges, Switzerland, the aim of this manuscript is to outline standards in pupillography based on current knowledge and experience of pupil experts in order to achieve greater comparability of pupillographic studies. Such standards will particularly facilitate the proper application of pupillography by researchers new to the field. First we describe general standards, followed by specific suggestions concerning the demands of different targets of pupil research: the afferent and efferent reflex arc, pharmacology, psychology, sleepiness-related research and animal studies.
Fight them or feed them: how the intestinal mucus layer manages the gut microbiota

Abstract The intestinal tract is inhabited by a tremendous number of microorganisms, termed the gut microbiota. These microorganisms live in a mutualistic relationship with their host and assist in the degradation of complex carbohydrates. Although the gut microbiota is generally considered beneficial, the vast number of microbial cells also form a permanent threat to the host. Thus, the intestinal epithelium is covered with a dense layer of mucus to prevent translocation of the gut microbiota into underlying tissues. Intestinal mucus is an organized glycoprotein network with a host-specific glycan structure. While the mucus layer has long been considered a passive, host-designed barrier, recent studies showed that maturation and function of the mucus layer are strongly influenced by the gut microbiota. In return, the glycan repertoire of mucins can select for distinct mucosa-associated bacteria that are able to bind or degrade specific mucin glycans as a nutrient source. Because the intestinal mucus layer is at the crucial interface between host and microbes, its breakdown leads to gut bacterial encroachment that can eventually cause inflammation and infection. Accordingly, a dysfunctional mucus layer has been observed in colitis in mice and humans. Moreover, the increased consumption of a low-fiber Western-style diet in our modern society has recently been demonstrated to cause bacteria-mediated defects of the intestinal mucus layer. Here, I will review current knowledge on the interaction between gut bacteria and the intestinal mucus layer in health and disease. Understanding the molecular details of this host–microbe interaction may contribute to the development of novel treatment options for diseases involving a dysfunctional mucus layer, such as ulcerative colitis.
Modulation by Sigma-1 Receptor of Morphine Analgesia and Tolerance: Nociceptive Pain, Tactile Allodynia and Grip Strength Deficits During Joint Inflammation

Sigma-1 receptor antagonism increases the effects of morphine on nociceptive pain, even in morphine-tolerant animals. However, it is unknown whether these receptors are able to modulate morphine antinociception and tolerance during inflammatory pain. Here we used a mouse model to test the modulation of morphine effects by the selective sigma-1 antagonist S1RA (MR309), by determining its effect on inflammatory tactile allodynia (von Frey filaments) and on grip strength deficits induced by joint inflammation (a measure of pain-induced functional disability), and compared the results with those for nociceptive heat pain recorded with the unilateral hot plate (55°C) test. The subcutaneous (s.c.) administration of morphine induced antinociceptive effects to heat stimuli, and restored mechanical threshold and grip strength in mice with periarticular inflammation induced by Complete Freund’s Adjuvant. S1RA (80 mg/kg, s.c.) administered alone did not induce any effect on nociceptive heat pain or inflammatory allodynia, but was able to partially reverse grip strength deficits. The association of S1RA with morphine, at doses inducing little or no analgesic-like effects when administered alone, resulted in a marked antinociceptive effect to heat stimuli and complete reversion of inflammatory tactile allodynia. However, S1RA administration did not increase the effect of morphine on grip strength deficits induced by joint inflammation. When S1RA (80 mg/kg, s.c.) was administered to morphine-tolerant animals, it rescued the analgesic-like effects of this opioid in all three pain measures. However, when S1RA was repeatedly given during the induction of morphine tolerance (and not on the day of behavioral evaluation) it failed to affect tolerance to the effects of morphine on nociceptive heat pain or inflammatory allodynia, but completely preserved the effects of this opioid on grip strength deficits. These effects of S1RA on morphine tolerance cannot be explained by pharmacokinetic interactions, given that the administration of S1RA did not modify concentrations of morphine or morphine-3-glucuronide (a major morphine metabolite) in morphine-tolerant animals in plasma or brain tissue. We conclude that sigma-1 receptors play a pivotal role in the control of morphine analgesia and tolerance in nociceptive and inflammatory pain, although in a manner dependent on the type of painful stimulus explored.