Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

A diversity of tools is available for identification of variants from genome sequence data. Given the current complexity of incorporating external software into a genome analysis infrastructure, a tendency exists to rely on the results from a single tool alone. The quality of the output variant calls is highly variable however, depending on factors such as sequence library quality as well as the choice of short-read aligner, variant caller, and variant caller filtering strategy. Here we present a two-part study first using the high quality ‘genome in a bottle’ reference set to demonstrate the significant impact the choice of aligner, variant caller, and variant caller filtering strategy has on overall variant call quality and further how certain variant callers outperform others with increased sample contamination, an important consideration when analyzing sequenced cancer samples. This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether the intersection or union, of all variant calls is used respectively. Second, we analyze a melanoma cell line derived from a control lymphocyte sample to determine whether software choices affect the detection of clinically important melanoma risk-factor variants finding that only one of the three such variants is unanimously detected under all conditions. Finally, we describe a cogent strategy for implementing a clinical variant detection pipeline; a strategy that requires careful software selection, variant caller filtering optimizing, and combined variant calls in order to effectively minimize false negative variants. While implementing such features represents an increase in complexity and computation the results offer indisputable improvements in data quality.
Low-Complexity Early Termination Method for Rateless Soft Decoder

We propose a new early termination method (ETM) with low computational complexity for Luby transform belief propagation (BP) decoder. The proposed method, which we call least reliable messages (LRM) ETM, observes only sign alterations of a small cluster in log-likelihood ratio messages passing between nodes in BP decoder. Simulation results and complexity analyzes show that LRM ETM has quite low computational complexity and small average iteration amounts without any performance degradation compared with conventional ETMs in literature. The method can be applied to code families which can be decoded by BP such as low density parity check codes, polar codes, and Raptor codes.
Assessment of language impairment in bilingual children using semantic tasks: two languages classify better than one.

BACKGROUND Significant progress has been made in the identification of language impairment in children are bilingual. Bilingual children's vocabulary knowledge may be distributed across languages. Thus, when testing bilingual children it is difficult to know how to weigh each language for diagnostic purposes. Even when conceptual scoring is used in vocabulary testing, bilingual children may score below that of their typical monolingual peers. AIMS The primary aim was to evaluate the classification accuracy of two approaches (total semantics score and two-dimensional bilingual coordinate score) that combined lexical-semantic knowledge across two languages. We investigated the classification accuracy of the English and Spanish semantics subtest using the experimental version of the Bilingual English Spanish Assessment (BESA) with bilingual children with and without language impairment. METHODS A total of 78 bilinguals with balanced exposure to English and Spanish (15 with language impairment, 63 with typical development) participated. Children were between 4;0 and 6;11 years old. Discriminant function analysis explored the extent to which these children were accurately classified when combining Spanish and English subtests. OUTCOMES & RESULTS Discriminant analysis yielded above 85% correct classification for balanced bilingual children for both approaches. CONCLUSIONS & IMPLICATIONS For the most accurate assessment and diagnostic decision-making for bilinguals, approaches that consider both languages together are recommended.
In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression

Abstract In vitro corticogenesis from embryonic stem cells (ESCs) is an attractive model of cortical development and a promising tool for cortical therapy. It is unknown to which extent epigenetic mechanisms crucial for cortex development and function, such as parental genomic imprinting, are recapitulated by in vitro corticogenesis. Here, using genome‐wide transcriptomic and methylation analyses on hybrid mouse tissues and cells, we find a high concordance of imprinting status between in vivo and ESC‐derived cortices. Notably, in vitro corticogenesis strictly reproduced the in vivo parent‐of‐origin‐dependent expression of 41 imprinted genes (IGs), including Mest and Cdkn1c known to control corticogenesis. Parent‐of‐origin‐dependent DNA methylation was also conserved at 14 of 18 imprinted differentially methylated regions. The least concordant imprinted locus was Gpr1‐Zdbf2, where the aberrant bi‐allelic expression of Zdbf2 and Adam23 was concomitant with a gain of methylation on the maternal allele in vitro. Combined, our data argue for a broad conservation of the epigenetic mechanisms at imprinted loci in cortical cells derived from ESCs. We propose that in vitro corticogenesis helps to define the still poorly understood mechanisms that regulate imprinting in the brain and the roles of IGs in cortical development.
Learning User Preference Patterns for Top-N Recommendations

In this paper, we observe that the user preference styles tend to change regularly following certain patterns. Therefore, we propose a Preference Pattern model to capture the user preference styles and their temporal dynamics, and apply this model to improve the accuracy of the Top-N recommendation. Precisely, a preference pattern is defined as a set of user preference styles sorted in a time order. The basic idea is to model user preference styles and their temporal dynamics by constructing a representative subspace with an Expectation-Maximization (EM)-like algorithm, which works in an iterative fashion by refining the global and the personal preference styles simultaneously. Then, the degree which the recommendations match the active user's preference styles, can be estimated by measuring its reconstruction error from its projection on the representative subspace. The experiment results indicate that the proposed model is robust to the data sparsity problem, and can significantly outperform the state-of-the-art algorithms on the Top-N recommendation in terms of accuracy.
Building by Syntax: The Neural Basis of Minimal Linguistic Structures

Abstract Language comes in utterances in which words are bound together according to a simple rule‐based syntactic computation (merge), which creates linguistic hierarchies of potentially infinite length—phrases and sentences. In the current functional magnetic resonance imaging study, we compared prepositional phrases and sentences—both involving merge—to word lists—not involving merge—to explore how this process is implemented in the brain. We found that merge activates the pars opercularis of the left inferior frontal gyrus (IFG; Brodmann Area [BA] 44) and a smaller region in the posterior superior temporal sulcus (pSTS). Within the IFG, sentences engaged a more anterior portion of the area (pars triangularis, BA 45)—compared with phrases—which showed activity peak in BA 44. As prepositional phrases, in contrast to sentences, do not contain verbs, activity in BA 44 may reflect structure‐building syntactic processing, while the involvement of BA 45 may reflect the encoding of propositional meaning initiated by the verb. The pSTS appears to work together with the IFG during thematic role assignment not only at the sentential level, but also at the phrasal level. The present results suggest that merge, the process of binding words together into syntactic hierarchies, is primarily supported by BA 44 in the IFG.
Automatic construction of jump-oriented programming shellcode (on the x86)

Return-Oriented Programming (ROP) is a technique which leverages the instruction gadgets in existing libraries/executables to construct Turing complete programs. However, ROP attack is usually composed with gadgets which are ending in ret instruction without the corresponding call instruction. Based on this fact, several defense mechanisms have been proposed to detect the ROP malicious code. To circumvent these defenses, Return-Oriented Programming without returns has been proposed recently, which uses the gadgets ending in jmp instruction but with much diversity. In this paper, we propose an improved ROP techniques to construct the ROP shellcode without returns. Meanwhile we implement a tool to automatically construct the real-world Return-Oriented Programming without returns shellcode, which as demonstrated in our experiment can bypass most of the existing ROP defenses.
Chronic Disease, Prescription Medications, and Food Purchases

Purpose: Diet-related chronic diseases like diabetes can be dangerous and expensive to treat, especially for patients who do not follow a recommended diet. Meanwhile, prescription drugs can alleviate the symptoms of or control many diet-related chronic diseases, but these drugs may also weaken the resolve to follow recommended diets (moral hazard). Design: We measure the effect of a diagnosis of chronic disease and subsequent pharmacological treatment on the dietary quality of food purchases using a large panel data set of US consumers. We estimate the effect of prescription drug utilization on food purchases for the following chronic diseases: type 2 diabetes, high cholesterol, heart disease, and obesity. Participants: Panelists of the Information Resources, Inc consumer panel. Measures: Dietary quality is measured as purchases of (1) food groups (ie, fruit, vegetables, and sweets) and (2) nutrients (ie, saturated fat, fiber, sodium, sugar, and total calories). Analysis: Linear regression with mixed effects on pooled panel (household random effects, city fixed effects). Results/Conclusion: We do not find strong effects of either diagnosis or pharmacological treatment of diet-related disease on food purchases.
Needs and Achievements of the Juvenile Justice System: Insights From Two Empirical Studies With Portuguese Young Adults

Over the last decade, studies have evaluated the effectiveness of interventions for juvenile offenders; nonetheless, those studies were more focused on recidivism than on the mechanisms associated with criminal perpetration. The current study explores the role of juvenile justice involvement and detention measures in a set of psychological, social, and criminal behavior characteristics in early adulthood. Seventy-five young adults with official records of juvenile delinquency in 2010-2011 and 240 young adults from the community filled out our protocol in 2014-2015. Young adults with juvenile justice involvement showed worse psychological, social, and criminal outcomes than those from community. Detention appears to be related to the number of deviant friends, delinquency, and school achievement in early adulthood. Our findings are in line with the labeling and deviant peer contagion theories and establish the main areas of interventions that affect the identified needs. A set of policy implications is provided.
HIPK2-Mediated Transcriptional Control of NMDA Receptor Subunit Expression Regulates Neuronal Survival and Cell Death

NMDA receptors are critical for neuronal communication. Dysfunction in NMDA receptors has been implicated in neuropsychiatric diseases. While it is well recognized that the composition of NMDA receptors undergoes a GluN2B-to-GluN2A switch in early postnatal life, the mechanism regulating this switch remains unclear. Using transcriptomic and functional analyses in brain tissues from male and female Hipk2+/+ and Hipk2−/− mice, we showed that the HIPK2-JNK–c-Jun pathway is important in suppressing the transcription of Grin2a and Grin2c, which encodes the GluN2A and GluN2C subunits of the NMDA receptors, respectively. Loss of HIPK2 leads to a significant decrease in JNK–c-Jun signaling, which in turn derepresses the transcription of Grin2a and Grin2c mRNA and upregulates GluN2A and GluN2C protein levels. These changes result in a significant increase of GluN2A/GluN2B ratio in synapse and mitochondria, a persistent activation of the ERK-CREB pathway and the upregulation of synaptic activity-regulated genes, which collectively contribute to the resistance of Hipk2−/− neurons to cell death induced by mitochondrial toxins. SIGNIFICANCE STATEMENT We identify HIPK2-JNK–c-Jun signaling as a key mechanism that regulates the transcription of NMDA receptor subunits GluN2A and GluN2C in vivo. Our results provide insights into a previously unrecognized molecular mechanism that control the switch of NMDA receptor subunits in early postnatal brain development. Furthermore, we provide evidence that changes in the ratio of NMDA subunits GluN2A/GluN2B can also be detected in the synapse and mitochondria, which contributes to a persistent activation of the prosurvival ERK-CREB pathway and its downstream target genes. Collectively, these changes protect HIPK2 deficient neurons from mitochondrial toxins.
Creating Virtual-hand and Virtual-face Illusions to Investigate Self-representation

Studies investigating how people represent themselves and their own body often use variants of "ownership illusions", such as the traditional rubber-hand illusion or the more recently discovered enfacement illusion. However, these examples require rather artificial experimental setups, in which the artificial effector needs to be stroked in synchrony with the participants' real hand or face—a situation in which participants have no control over the stroking or the movements of their real or artificial effector. Here, we describe a technique to establish ownership illusions in a setup that is more realistic, more intuitive, and of presumably higher ecological validity. It allows creating the virtual-hand illusion by having participants control the movements of a virtual hand presented on a screen or in virtual space in front of them. If the virtual hand moves in synchrony with the participants' own real hand, they tend to perceive the virtual hand as part of their own body. The technique also creates the virtual-face illusion by having participants control the movements of a virtual face in front of them, again with the effect that they tend to perceive the face as their own if it moves in synchrony with their real face. Studying the circumstances that illusions of this sort can be created, increased, or reduced provides important information about how people create and maintain representations of themselves.
Polymer Concentration and Solvent Variation Correlation with the Morphology and Water Filtration Analysis of Polyether Sulfone Microfiltration Membrane

Microfiltration flat sheet membranes of polyether sulfone (PES) were fabricated by incorporating varying concentrations of polymer and investigated the influence of substituting solvents. The membranes were prepared via immersion precipitation method. Different solvents that included NMP (N-methyl-2-pyrrolidone), DMF (dimethylformamide), and THF (tetrahydrofuran) were used to analyse their effect on the performance and morphology of the prepared membranes. Two different coagulation bath temperatures were used to investigate the kinetics of membrane formation and subsequent effect on membrane performance. The maximum water flux of 141 ml/cm2.h was observed using 21% of PES concentration in NMP + THF cosolvent system. The highest tensile strength of 29.15 MPa was observed using membrane prepared with 21% PES concentration in NMP as solvent and coagulation bath temperature of 25°C. The highest hydraulic membrane resistance was reported for membrane prepared with 21% PES concentration in NMP as solvent. Moreover, the lowest contact angle of 67° was observed for membrane prepared with 15% of PES concentration in NMP as solvent with coagulation bath temperature of 28°C. Furthermore, the Hansen solubility parameter was used to study the effect on the thermodynamics of membrane formation and found to be in good correlation with experimental observation and approach in the present work.
Synthetic cannabinoids: the hidden side of Spice drugs

Spice drugs are herbal mixtures sprayed with synthetic cannabinoids designed to mimic the psychoactive ingredient in marijuana [&Dgr;9-tetrahydrocannabinol (&Dgr;9-THC)] and synthesized by introducing modifications to the chemical structure of parental compounds aiming to circumvent legal regulations. Synthetic cannabinoid use/abuse can be devastating as toxicological effects and adverse reactions cannot be entirely predicted and may vary with the dose, route of administration, individual vulnerability and concomitant intake with other drugs. The absence of validated testing procedures in the clinical field makes difficult the adoption of a therapeutic approach effective in coping with the synthetic cannabinoid phenomenon, posing a significant challenge for prevention, treatment and public health in general. The aim of this review is to gain insights into the epidemiological, pharmacological and toxicological properties of synthetic cannabinoids, aiming to provide a reliable background needed for the management of synthetic cannabinoid-related adverse effects. Consumers, competent authorities and medical care professionals should be aware of the risks associated with synthetic cannabinoid use.
Study on temperature characteristics of triangular prisms ring cavity

The refractive indexes of prisms are affected by temperature, hence the optical characteristics of triangular prisms ring cavity is disturbed enough to affect the stability of the laser gyro. Considering the temperature perturbation, the transmission matrices of the reflected and refracted beams on the prism surfaces have been modified. The modified results are the old 2×2 beam transfer matrices are corrected to new 3×3 matrices and the temperature perturbations are added. According to the self-consistent theory of the laser ring cavity, a physical model of the ring cavity light transmission with the temperature disturbance has been established. The theoretical analysis shows that when the temperature varies from -40℃ to 70℃, the changes of the optical cavity-length, frequency offset, and scale factor are 49μm, 0.011MHz and 1.96×10-10, respectively. An experimental system of the prism laser gyroscope has been established whose temperature can be changed, and the experimental results agree with the theoretical values.
Traffic Controller: A Practical Approach to Block Network Covert Timing Channel

This paper discusses the network covert timing channel. This channel modulates network packet's time properties to transfer information secretly. Much work has been done in inventing and utilizing network covert timing channels, however, there is not so much work in other areas such as detecting and handling covert channels. Covert channel detection is difficult, what's more, it often needs human analysis to confirm whether a suspect is a real covert channel. However, we figured out that we can try to control covert channels without knowing whether there are covert channels in using, which means our approach does not rely on the detection of covert channels at all. A network traffic controller is proposed to undermine the network covert timing channel communication mechanism. We will show how our method works and why our traffic control strategy is especially efficient to handle network covert timing channels.
Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: Evolution across a continuum of indicator mechanisms

The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality influences the evolution of female choosiness and male displays. We use a continuum framework that incorporates indicator mechanisms that are traditionally modeled separately. Counter to intuition, we find that intermediate levels of direct detection of male quality can facilitate, rather than impede, the evolution of female choosiness and male displays in broad regions of this continuum. We examine how this evolution is driven by selective forces on genetic quality and on the display, and find that direct detection of male quality results in stronger indirect selection favoring female choosiness. Our results imply that displays maybe more likely to evolve when female choosiness has already evolved to discriminate perceptible forms of male quality. They also highlight the importance of considering general female choosiness, as well as preference, in studies of “good genes. ”
Measuring VLDL1-Triglyceride and VLDL2-Triglyceride Kinetics in Men: Effects of Dietary Control on Day-to-Day Variability

Abstract The aim of this study was to assess the impact of dietary control on VLDL1- and VLDL2-TG kinetics and associated metabolic parameters. Twelve overweight/obese men were randomized to a provided 3 day isocaloric diet with fixed macronutrient composition (diet group, n=6) or to their regular unrestricted diet (non-diet group, n=6). VLDL1- and VLDL2-TG turnovers were measured twice 2–4 weeks apart, using primed-constant infusion of ex vivo labeled [1-14C]VLDL1-TG and [9,10-3H]VLDL2-TG. Isocaloric diet intervention lowered the difference in the mean of both VLDL2-TG secretion and clearance rate (p<0.01), and the coefficient of variation (CV) of VLDL2-TG clearance rate (p<0.05). The difference in mean and CV of the other kinetic estimates (VLDL1-TG secretion, clearance and oxidation rate) were lowered, but not significantly. The CV’s of total triglyceride, VLDL1-TG, and VLDL2-TG concentrations were significantly lowered by diet intervention compared to regular diet; total triglyceride (31%–5%, p<0.01), VLDL1-TG (42%–9%, p<0.01), and VLDL2-TG (36%–10%, p<0.01). In conclusion, VLDL1- and VLDL2-TG kinetics show great day-to-day variability, which may be diminished by diet intervention. Therefore, standardized macronutrient intake prior to study days improves the probability of demonstrating significant outcomes of cross-sectional and intervention studies of VLDL1-TG and VLDL2-TG kinetics and metabolism.
Image biomarker standardisation initiative - feature definitions

The image biomarker standardisation initiative (IBSI) is an independent international collaboration which works towards standardising the extraction of image biomarkers from acquired imaging for the purpose of high-throughput quantitative image analysis (radiomics). Lack of reproducibility and validation of high-throughput quantitative image analysis studies is considered to be a major challenge for the field. Part of this challenge lies in the scantiness of consensus-based guidelines and definitions for the process of translating acquired imaging into high-throughput image biomarkers. The IBSI therefore seeks to provide image biomarker nomenclature and definitions, benchmark data sets, and benchmark values to verify image processing and image biomarker calculations, as well as reporting guidelines, for high-throughput image analysis.