Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpreting genomic data via entropic dissection

Since the emergence of high-throughput genome sequencing platforms and more recently the next-generation platforms, the genome databases are growing at an astronomical rate. Tremendous efforts have been invested in recent years in understanding intriguing complexities beneath the vast ocean of genomic data. This is apparent in the spurt of computational methods for interpreting these data in the past few years. Genomic data interpretation is notoriously difficult, partly owing to the inherent heterogeneities appearing at different scales. Methods developed to interpret these data often suffer from their inability to adequately measure the underlying heterogeneities and thus lead to confounding results. Here, we present an information entropy-based approach that unravels the distinctive patterns underlying genomic data efficiently and thus is applicable in addressing a variety of biological problems. We show the robustness and consistency of the proposed methodology in addressing three different biological problems of significance—identification of alien DNAs in bacterial genomes, detection of structural variants in cancer cell lines and alignment-free genome comparison.
Microstructure and enhanced corrosion resistance of biodegradable Mg–Gd–Cu–Zr alloy by solution treatment

Abstract Mg-6.0Gd-1.2Cu-1.2Zr (wt-%) alloy was designed and prepared by gravity casting, then the ingots were solution treated at different temperatures. The microstructures of the as-cast and solution-treated alloys were observed by optical microscopy (OM) and scanning electron microscopy (SEM). Corrosion behaviors were evaluated by immersion tests in simulated body fluid. It is indicated that the as-cast alloy is composed of α-Mg matrix, eutectic phase and lamellar long period stacking ordered (LPSO) structure. After solution treatment, the volume fraction of the LPSO structure increases first, then decreases and vanishes finally. The eutectic phase is distributed discontinuously in the alloys. The solution-treated alloys exhibit enhanced corrosion resistance compared with the as-cast alloy. In addition, the alloy after solution treatment at 360 °C shows the lowest corrosion rate. Quasi in situ corrosion tests demonstrate that the corrosion sequence is α-Mg, followed by the LPSO structure, and the eutectic phase in all alloys exhibits inappreciable variations during the corrosion test for 30 min.
Dynamic Measurement of Polymorphism

Measuring "reuse" and "reusability" is difficult because there are so many different facets to these concepts. Before we can effectively measure reuse and reusability, we must first be able to effectively measure these different facets. One such facet is the programming language constructs that are available. For example whether or not a language supports polymorphism is believed to affect how reusable a developer can make a code artifact. Effectively measuring polymorphism is a challenge because its behaviour is only observable at run-time. In this paper, we present a metric for polymorphism based on the dynamic behaviour of the code. We evaluate the usefulness of the metric through two case studies.
Detection of environmental endocrine‐disruptor effects on gene expression in live Rana catesbeiana tadpoles using a tail fin biopsy technique

We describe a novel method of rapidly assessing exposure of premetamorphic Rana catesbeiana tadpoles to endocrine‐disrupting chemicals. Tail fin biopsy and reverse transcription–polymerase chain reaction analyses of the thyroid hormone (TH)–responsive gene, TH receptor β (TRβ), demonstrate for the first time that a known accelerant of TH‐induced metamorphosis, acetochlor, can significantly enhance TH‐induced TRβ mRNA levels within 24 h at an environmentally relevant dose. Although we focus on laboratory exposures in this study, this method easily can be adapted for use in field studies.
Developmental vulnerability of synapses and circuits associated with neuropsychiatric disorders

Psychiatric and neurodegenerative disorders, including intellectual disability, autism spectrum disorders (ASD), schizophrenia (SZ), and Alzheimer's disease, pose an immense burden to society. Symptoms of these disorders become manifest at different stages of life: early childhood, adolescence, and late adulthood, respectively. Progress has been made in recent years toward understanding the genetic substrates, cellular mechanisms, brain circuits, and endophenotypes of these disorders. Multiple lines of evidence implicate excitatory and inhibitory synaptic circuits in the cortex and hippocampus as key cellular substrates of pathogenesis in these disorders. Excitatory/inhibitory balance – modulated largely by dopamine – critically regulates cortical network function, neural network activity (i.e. gamma oscillations) and behaviors associated with psychiatric disorders. Understanding the molecular underpinnings of synaptic pathology and neuronal network activity may thus provide essential insight into the pathogenesis of these disorders and can reveal novel drug targets to treat them. Here, we discuss recent genetic, neuropathological, and molecular studies that implicate alterations in excitatory and inhibitory synaptic circuits in the pathogenesis of psychiatric disorders across the lifespan.
Verification of responses of Japanese medaka (Oryzias latipes) to anti‐androgens, vinclozolin and flutamide, in short‐term assays

Various testing methods for the detection of the endocrine disruptive activities of chemicals have been developed in freshwater fish species. However, a few relatively easier specific methods for detecting anti‐androgenic activities are available for fish. The aim of this study was to verify the papillary process in Japanese medaka (Oryzias latipes) as an indicator of the anti‐androgenic activity of chemicals. Japanese medaka were exposed to two types of anti‐androgenic compounds, vinclozolin and flutamide, using two short‐term assays; one was conformed to the existing short‐term reproduction assay using adult fish (adult test) and the other was a test based on the same methods but using juvenile fish at the beginning of exposure (juvenile test). Significant decreases in male papillary processes were observed in the juvenile test treated with the highest concentration of both antiandrogens (640 µg l–1 vinclozolin and 1000 µg l–1 flutamide); however, no significant effects were observed in the adult test. Consequently, our results indicate that papillary processes in Japanese medaka can be used as the end‐point for screening the anti‐androgenic activity of chemicals using juvenile fish for a specific period based on the existing short‐term reproduction assay. Copyright © 2013 John Wiley & Sons, Ltd.
Coding theorems for the nonsynchronized channel

Capacity and error bounds are derived for a memoryless binary symmetric channel with the receiver having no a priori information as to the starting time of the code words. The channel capacity is the same as the capacity of the synchronized channel. For all rates below capacity, the minimum probability of error for the nonsynchronized channel decreases exponentially with the code-block length. For rates near channel capacity, the exponent in the upper bound on the probability of error for the nonsynchronized channel is the same as the corresponding exponent for the synchronized channel. For low rates, the largest exponent obtained for the nonsynchronized channel with conventional block coding is inferior to the exponent obtained for the synchronized channel. Stronger results are obtained for a new form of coding that allows for a Markov dependency between successive code words. Bounds on the minimum probability of error are obtained for unconstrained binary codes and for several classes of parity-check codes and are used to obtain asymptotic distance properties for various classes of binary codes. At certain rates there exist codes whose minimum distance, in the comma-free sense, is not only greater than one, but is proportional to the block length.
Ammonia sensing properties of centimeter scaled CVD graphene in ambient condition

The present work reports ammonia (NH3) gas sensing properties of Graphene film synthesized by chemical vapor deposition (CVD) in ambient condition. Graphene with a large area as centimeter scale was synthesized on Cu foils by chemical vapor deposition under ambient pressure and has transferred onto Si/SiO2 wafer. By fabricating ohmic contact to both side of graphene layer, we measured DC resistance changes with respect to NH3 gas flow. The gas molecules are absorbed on graphene by chemisorption and causes resistance change of graphene which is increasing by electron injection from ammonia molecules. The sensing characteristics of graphene has been examined by changing the inlet gas flow and the sensor shows better performance with large flow, such as fast response time and high sensitivity.
Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012*

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.
Boundary formation in the development of the vertebrate hindbrain

The formation of a sharp interface of adjacent subdivisions is important for establishing the precision of tissue organization, and at specific borders it serves to organize key signaling centers. We discuss studies of vertebrate hindbrain development that have given important insights into mechanisms that underlie the formation and maintenance of sharp borders. The hindbrain is subdivided into a series of segments with distinct anteroposterior identity that underlies the specification of distinct neuronal cell types. During early stages of segmentation, cell identity switching contributes to the refinement of borders and enables homogenous territories to be maintained despite intermingling of cells between segments. At later stages, there is a specific restriction to cell intermingling between segments that is mediated by Eph receptor and ephrin signaling. Eph–ephrin signaling can restrict cell intermingling and sharpen borders through multiple mechanisms, including the regulation of cell adhesion and contact inhibition of cell migration. WIREs Dev Biol 2013, 2:735–745. doi: 10.1002/wdev.106
Suicide and the not-so-innocent bystander

See article on page 332 Functional dyspepsia is a clinical syndrome defined by chronic or recurrent symptoms of pain or discomfort centred upon the upper abdomen without a cause being identified by conventional diagnostic means.1 The pathophysiology of functional dyspepsia is unknown but a number of mechanisms have been proposed, such as delayed gastric emptying, hypersensitivity to gastric distension, impaired accommodation to a meal, Helicobacter pylori gastritis, or central nervous system dysfunction. Dyspeptic symptoms occur in approximately 25% of the general population and only about one quarter of these seek medical attention.2 The reasons underlying health care seeking behaviour in functional dyspepsia are unknown, and may relate both to symptom severity and psychological factors.2 Except for the possible involvement of H pylori , the symptom pattern and underlying mechanisms in non-consulters with dyspepsia have received little attention. Recent developments of less invasive techniques, such as gastric emptying breath tests or a caloric satiety test,3 may facilitate studies in non-consulting subjects in the general population. Because of its presumed pivotal role in the occurrence of functional gastrointestinal disorders, visceral sensitivity and its modulation is a topic of intense ongoing research. In this issue of Gut , Holtmann and colleagues used a gastric barostat procedure …
Nature Contact and Human Health: A Research Agenda

Background: At a time of increasing disconnectedness from nature, scientific interest in the potential health benefits of nature contact has grown. Research in recent decades has yielded substantial evidence, but large gaps remain in our understanding. Objectives: We propose a research agenda on nature contact and health, identifying principal domains of research and key questions that, if answered, would provide the basis for evidence-based public health interventions. Discussion: We identify research questions in seven domains: a) mechanistic biomedical studies; b) exposure science; c) epidemiology of health benefits; d) diversity and equity considerations; e) technological nature; f) economic and policy studies; and g) implementation science. Conclusions: Nature contact may offer a range of human health benefits. Although much evidence is already available, much remains unknown. A robust research effort, guided by a focus on key unanswered questions, has the potential to yield high-impact, consequential public health insights. https://doi.org/10.1289/EHP1663
Contractibility of deformation spaces of G-trees

Forester has defined spaces of simplicial tree actions for a finitely generated group, called deformation spaces. Culler and Vogtmann's Outer space is an example of a deformation space. Using ideas from Skora's proof of the contractibility of Outer space, we show that under some mild hypotheses deformation spaces are contractible.
Organization based access control

None of the classical access control models such as DAC, MAC, RBAC, TBAC or TMAC is fully satisfactory to model security policies that are not restricted to static permissions but also include contextual rules related to permissions, prohibitions, obligations and recommendations. This is typically the case of security policies that apply to the health care domain. We suggest a new model that provides solutions to specify such contextual security policies. This model, called organization based access control, is presented using a formal language based on first-order logic.
Animal models of post-traumatic stress disorder and recent neurobiological insights

Post-traumatic stress disorder (PTSD) is a complex psychiatric disorder characterized by the intrusive re-experiencing of past trauma, avoidant behavior, enhanced fear, and hyperarousal following a traumatic event in vulnerable populations. Preclinical animal models do not replicate the human condition in its entirety, but seek to mimic symptoms or endophenotypes associated with PTSD. Although many models of traumatic stress exist, few adequately capture the complex nature of the disorder and the observed individual variability in susceptibility of humans to PTSD. In addition, various types of stressors may produce different molecular neuroadaptations that likely contribute to the various behavioral disruptions produced by each model, although certain consistent neurobiological themes related to PTSD have emerged. For example, animal models report traumatic stress-induced and trauma reminder-induced alterations in neuronal activity in the amygdala and prefrontal cortex, in agreement with the human PTSD literature. Models have also provided a conceptual framework for the often-observed combination of PTSD and comorbid conditions such as alcohol use disorder. Future studies will continue to refine preclinical PTSD models in hope of capitalizing on their potential to deliver new and more efficacious treatments for PTSD and associated psychiatric disorders.
The Mitochondrial Calcium Uniporter (MCU): Molecular Identity and Physiological Roles*

The direct measurement of mitochondrial [Ca2+] with highly specific probes demonstrated that major swings in organellar [Ca2+] parallel the changes occurring in the cytosol and regulate processes as diverse as aerobic metabolism and cell death by necrosis and apoptosis. Despite great biological relevance, insight was limited by the complete lack of molecular understanding. The situation has changed, and new perspectives have emerged following the very recent identification of the mitochondrial Ca2+ uniporter, the channel allowing rapid Ca2+ accumulation across the inner mitochondrial membrane.
Evolving Strategies for Focused Web Crawling

The rapid growth of the World Wide Web has created many challenges for both general purpose crawling, search engines and web directories, making it difficult to find, index, and classify web pages based on a topic. Topic driven crawlers can complement search engines because they pre-classify the pages retrieved by the crawl. To implement such a focused crawler, a strategy for ordering the crawl frontier is required. Such a strategy can only use information gleaned from previously crawled pages to estimate the relevance of a newly observed URL. Because the best strategy for ranking URLsin the crawl frontier is not immediately apparent, we discover strategies by evolving them using a genetic algorithm. Strategies are learned by evaluating the results of crawls simulated using a database generated by a previous, more general crawl. We conclude that a rank function that combines analysis of text and link structure yields effective strategies. The evolved strategies perform better than the commonly used Best First strategy.
BRDF recovering and scene re-lighting using an environment map

A rendering algorithm based on physical phenomenon and well-defined model data are needed to generate a synthetic image realistically. In this paper, inverse rendering based on an environment map is proposed to obtain BRDF of objects. Many researchers try to find BRDF by analyzing many pictures taken with well-controlled camera and light position. But this method is available at a laboratory environment. Limits of previous works can be conquered by using inverse rendering based on an environment map and it is possible to get BRDF of objects at a general environment. Inputs are an image, an environment map and 3D geometry data of models. Objects of an input image are divided into three parts - diffuse reflection, glossy reflection and diffuse texture -and BRDF of objects are recovered. Using BRDF of objects, it is possible to add virtual objects and to remove real objects from an input image.
Prediction of Organic Anion-Transporting Polypeptide 1B1- and 1B3-Mediated Hepatic Uptake of Statins Based on Transporter Protein Expression and Activity Data

Organic anion-transporting polypeptides (OATP) 1B1 and OATP1B3 are drug transporters mediating the active hepatic uptake of their substrates. Because they exhibit overlapping substrate specificities, the contribution of each isoform to the net hepatic uptake needs to be considered when predicting drug-drug interactions. The relative contribution of OATP1B1- and OATP1B3-mediated uptake of statins into hepatocytes was estimated based on either relative transporter protein expression data or relative activity data. Therefore, kinetics of eight statins and OATP1B1- and OATP1B3-specific reference substrates was determined in OATP1B1- and OATP1B3-expressing human embryonic kidney 293 cells and in human cryopreserved hepatocytes. Absolute OATP1B1 and OATP1B3 protein abundance was determined by liquid chromatography-tandem mass spectrometry in all expression systems. Transporter activity data generated in recombinant cell lines were extrapolated to hepatocyte values using relative transporter expression factors (REF) or relative activity factors (RAF). Our results showed a pronounced OATP1B1 and comparatively low OATP1B3 protein expression in the investigated hepatocyte lot. Based on REF scaling, we demonstrated that the active hepatic uptake clearances of reference substrates, atorvastatin, pravastatin, rosuvastatin, and simvastatin were well predicted within twofold error, demonstrating that OATP1B1 and OATP1B3 were major contributors. For other statins, the net hepatic uptake clearance was underpredicted, suggesting the involvement of other hepatic uptake transporters. Summarized, we showed that REF- and RAF-based predictions were highly similar, indicating a direct transporter expression-activity relationship. Moreover, we demonstrated that the REF-scaling method provided a powerful tool to quantitatively assess the transporter-specific contributions to the net uptake clearance of statins in hepatocytes
Marbled Inflation From Population Structure in Gene‐Based Association Studies With Rare Variants

Accurate genetic association studies are crucial for the detection and the validation of disease determinants. One of the main confounding factors that affect accuracy is population stratification, and great efforts have been extended for the past decade to detect and to adjust for it. We have now efficient solutions for population stratification adjustment for single‐SNP (where SNP is single‐nucleotide polymorphisms) inference in genome‐wide association studies, but it is unclear whether these solutions can be effectively applied to rare variation studies and in particular gene‐based (or set‐based) association methods that jointly analyze multiple rare and common variants. We examine here, both theoretically and empirically, the performance of two commonly used approaches for population stratification adjustment—genomic control and principal component analysis—when used on gene‐based association tests. We show that, different from single‐SNP inference, genes with diverse composition of rare and common variants may suffer from population stratification to various extent. The inflation in gene‐level statistics could be impacted by the number and the allele frequency spectrum of SNPs in the gene, and by the gene‐based testing method used in the analysis. As a consequence, using a universal inflation factor as a genomic control should be avoided in gene‐based inference with sequencing data. We also demonstrate that caution needs to be exercised when using principal component adjustment because the accuracy of the adjusted analyses depends on the underlying population substructure, on the way the principal components are constructed, and on the number of principal components used to recover the substructure.