Miracle-dz/UniFAR-FTUs huggingface dataset:
Hardware-based Temporal Logic Checkers for the Debugging of Digital Integrated Circuits

Integrated circuit complexity is ever increasing and the debug process of modern devices pose important technical challenges and cause delays in production. A comprehensive Design-for-Debug methodology is therefore rapidly becoming a necessity. This thesis presents a comprehensive system-level approach to debugging based on insilicon hardware checkers. The proposed approach leverages existing assertion-based verification libraries by translating useful temporal logic statements into efficient hardware circuits. Those checker circuits are then integrated in the device as part of the memory map, so they can provide on-line monitoring and debug assistance in addition to accelerating the integration of performance monitoring counters. The thesis presents a set of enhancements to the translation process from temporal language to hardware targeted such that an eventual debug process is made more efficient. Automating the integration of the checker’s output and control structures is covered along with a practical method that allow transparent access to the resulting registers within a modern (Linux) operating system. Finally, a method of integration of the hardware checkers in future Network-onChip systems is proposed. The use of a quality metric encompassing test, monitoring and debug considerations is defined along with the necessary tool flow required to support the process.
The Genome of the Steller Sea Lion (Eumetopias jubatus)

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.
Latin America and the Caribbean Code Against Cancer: Developing Evidence-Based Recommendations to Reduce the Risk of Cancer in Latin America and the Caribbean

Eduardo Cazap, MD, PhD; Liz Maria de Almeida, PhD; Silvina Arrossi, PhD; Patricia J. Garcı́a, MD, MPH, PhD; Marı́a Luisa Garmendia, PhD; Enrique Gil, MD, MSc; Trevor Hassel, MBBS; Rubén Mayorga, MD; Alejandro Mohar, MD, ScD; Raúl Murillo, MD; Gabriel O. Owen, MD; Diego Paonessa, PhD; Julio Santamarı́a; Guillermo Tortolero-Luna, MD, PhD; Walter Zoss, MBA; Rolando Herrero, MD, PhD; Silvana Luciani, MHSc; Joachim Schüz, PhD; and Carolina Espina, PhD
A Novel Risk-based Approach for Online Community Management

Online communities play a pivotal role in innovation, marketing, corporate expertise management, product support and advertising. Communities in the order of millions of users are becoming the norm. However, this proliferation of demand is not met with intelligent, scalable, easy to use community management approaches. Current methods are based on basic statistical tools that aggregate data for the community owner/moderator to interpret and take appropriate actions. The data reflects only the current state of the community, which does not constitute an effective warning system of future events. Moreover, the community health becomes highly dependent on the owner’s skill, interpretation, intimate knowledge of the community and its evolution path. This paper presents a proactive, extensible, risk-based management framework supporting advanced analytical services for managing online communities. The solution allows community owners to focus on the community objectives and proactively manage favourable/unfavourable events at the user and community level.
Crystal structure of a single-chain protein mimetic of the gp41 NHR trimer in complex with the synthetic CHR peptide C34

Abstract Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation. These molecules bind strongly to peptides derived from the gp41 C-heptad repeat (CHR) and are potent and broad HIV-1 inhibitors. Here, we investigated two covNHR variants differing in two mutations, V10E and Q123R (equivalent to V38E and Q40R in gp41 sequence) that reproduce the effect of HIV-1 mutations associated with resistance to fusion inhibitors, such as T20 (enfuvirtide). A detailed calorimetric analysis of the binding between the covNHR proteins and CHR peptides (C34 and T20) reveals drastic changes in affinity due to the mutations as a result of local changes in interactions at the site of T20 resistance. The crystallographic structure of the covNHR:C34 complex shows a virtually identical CHR–NHR binding interface to that of the post-fusion structure of gp41 and underlines an important role of buried interfacial water molecules in binding affinity and in development of resistance against CHR peptides. Despite the great difference in affinity, both covNHR variants demonstrate strong inhibitory activity for a wide variety of HIV-1 strains. These properties support the high potential of these covNHR proteins as new potent HIV-1 inhibitors. Our results may guide future inhibition approaches.
Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants

Pre‐mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease‐inducing mechanism of synonymous variants, its contribution toward disease phenotype of non‐synonymous variants is underappreciated.
A Technique for Meas

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Branched-chain amino acid and branched-chain ketoacid ingestion increases muscle protein synthesis rates in vivo in older adults: a double-blind, randomized trial

ABSTRACT Background Protein ingestion increases muscle protein synthesis rates. However, limited data are currently available on the effects of branched-chain amino acid (BCAA) and branched-chain ketoacid (BCKA) ingestion on postprandial muscle protein synthesis rates. Objective The aim of this study was to compare the impact of ingesting 6 g BCAA, 6 g BCKA, and 30 g milk protein (MILK) on the postprandial rise in circulating amino acid concentrations and subsequent myofibrillar protein synthesis rates in older males. Methods In a parallel design, 45 older males (age: 71 ± 1 y; BMI: 25.4 ± 0.8 kg/m2) were randomly assigned to ingest a drink containing 6 g BCAA, 6 g BCKA, or 30 g MILK. Basal and postprandial myofibrillar protein synthesis rates were assessed by primed continuous l-[ring-13C6]phenylalanine infusions with the collection of blood samples and muscle biopsies. Results Plasma BCAA concentrations increased following test drink ingestion in all groups, with greater increases in the BCAA and MILK groups compared with the BCKA group (P < 0.05). Plasma BCKA concentrations increased following test drink ingestion in all groups, with greater increases in the BCKA group compared with the BCAA and MILK groups (P < 0.05). Ingestion of MILK, BCAA, and BCKA significantly increased early myofibrillar protein synthesis rates (0–2 h) above basal rates (from 0.020 ± 0.002%/h to 0.042 ± 0.004%/h, 0.022 ± 0.002%/h to 0.044 ± 0.004%/h, and 0.023 ± 0.003%/h to 0.044 ± 0.004%/h, respectively; P < 0.001), with no differences between groups (P > 0.05). Myofibrillar protein synthesis rates during the late postprandial phase (2–5 h) remained elevated in the MILK group (0.039 ± 0.004%/h; P < 0.001), but returned to baseline values following BCAA and BCKA ingestion (0.024 ± 0.005%/h and 0.024 ± 0.005%/h, respectively; P > 0.05). Conclusions Ingestion of 6 g BCAA, 6 g BCKA, and 30 g MILK increases myofibrillar protein synthesis rates during the early postprandial phase (0–2 h) in vivo in healthy older males. The postprandial increase following the ingestion of 6 g BCAA and BCKA is short-lived, with higher myofibrillar protein synthesis rates only being maintained following the ingestion of an equivalent amount of intact milk protein. This trial was registered at Nederlands Trial Register (www.trialregister.nl) as NTR6047.
Characteristics of a First Suicide Attempt that Distinguish Between Adolescents Who Make Single Versus Multiple Attempts

Although a history of a suicide attempt is the strongest predictor of future suicide attempts, not all adolescents who make an attempt engage in repetitive suicidal behavior. The present study sought to determine whether certain characteristics of a first suicide attempt (e.g., age of first attempt, method of attempt used, intent seriousness, medical lethality, and receipt of treatment after attempt) can distinguish between adolescents who make single versus multiple suicide attempts. Adolescents (N = 95) who were psychiatrically hospitalized and their guardian completed a diagnostic interview to gather information on all lifetime suicide attempts. A multivariate hierarchical logistic regression was conducted, predicting single attempt versus multiple attempt status. Of the first-attempt characteristics examined, only age of first attempt, OR = 0.33, 95% CI [0.17–0.63], p = . 001, and receipt of treatment following attempt, OR = 0.28, 95% CI [0.09–0.88], p = . 028, significantly distinguished SA vs. MA status, even after controlling for current age and depression at the time of first attempt. Female and White participants were overrepresented in this sample, which limits generalization to more heterogenous and diverse samples. The cross-sectional nature of data introduces the potential for retrospective recall bias. Younger age of first attempt and lack of receipt of mental health treatment following a first attempt were associated with multiple attempt status. These findings highlight the importance of early mental health screening, parental psychoeducation, and linkage to mental health care after a suicide attempt.
Getaruns: a hybrid system for summarization and question answering

Information Retrieval, Summarization and Question Answering need accurate linguistic information with a much higher coverage than what is being recently offered by currently available parsers, so we assume that the starting point of any interesting application in those fields must necessarily be a good syntactic -semantic parser. The system presented in the paper has undergone extensive testing and the parser has been trained on available testsuites and the Remedia corpus texts, one of which will be commented in some detail.
Battery State-of-Charge Estimation Algorithm Using Dynamic Terminal Voltage Measurement

When a battery is discharging, the battery's current and terminal voltage must both be measured to estimate its state of charge (SOC). If the SOC can be estimated by using only the current or voltage, hardware costs will decrease. This paper proposes an SOC estimation algorithm that needs to measure only the terminal voltage while a battery is discharging. The battery's SOC can be deduced from its open circuit voltage (OCV) through the relationship between SOC and OCV. But when the battery is discharging, it is not possible to measure the OCV due to the voltage drop in the battery's internal resistance (IRdrop). The proposed algorithm calculates OCV by estimating IRdrop using a dynamic terminal voltage measurement. This paper confirms the results of applying the algorithm in a hardware environment via algorithm binarization. To evaluate the algorithm, a Simulink battery model based on actual values was used.
A DIC-Based Study on Compressive Responses of Concrete after Exposure to Elevated Temperatures

This paper provides an experimental investigation on the cracking process and residual mechanical properties of concrete after exposure to elevated temperatures. A total of 36 standard concrete prism specimens were tested after exposure to high temperatures of up to 600 °C. The failure modes, cracking process, residual mechanical properties, deformation characteristics and the strain distribution on the surface during the loading procedure were presented. The influences of exposure temperature and water–cement ratio (w/c) were interpreted. The digital image correlation (DIC) method was applied to quantitatively and visually characterize the development of cracking and relative displacement on the concrete surface. The findings suggest that the residual compressive strength and elastic modulus of the concrete decreases gradually with the increasing temperature, especially in the specimens with lower w/c ratio. The DIC technique provides an effective means to measure very precise and detailed information, including the crack opening and distribution of strain on the concrete surface.
Are We Misdiagnosing Diabetic Foot Osteomyelitis? Is the Gold Standard Gold?

To compare the incidence of osteomyelitis based on different operational definitions using the gold standard of bone biopsy, we prospectively enrolled 35 consecutive patients who met the criteria of ≥21 years of age and a moderate or severe infection based on the Infectious Diseases Society of America classification. Bone samples were obtained from all patients by percutaneous bone biopsy or intraoperative culture if the patient required surgery. Bone samples were analyzed for conventional culture, histology, and 16S ribosomal RNA genetic sequencing. We evaluated 5 definitions for osteomyelitis: 1) traditional culture, 2) histology, 3) genetic sequencing, 4) traditional culture and histology, and 5) genetic sequencing and histology. There was variability in the incidence of osteomyelitis based on the diagnostic criteria. Traditional cultures identified more cases of osteomyelitis than histology (68.6% versus 45.7%, p = .06, odds ratio [OR] 2.59, 95% confidence interval [CI] 0.98 to 6.87), but the difference was not significant. In every case that histology reported osteomyelitis, bone culture was positive using traditional culture or genetic sequencing. The 16S ribosomal RNA testing identified significantly more cases of osteomyelitis compared with histology (82.9% versus 45.7%, p = .002, OR 5.74, 95% CI 1.91 to 17.28) and compared with traditional cultures but not significantly (82.9% versus 68.6%, p = .17, OR 2.22, 95% CI 0.71 to 6.87). When both histology and traditional culture (68.6%) or histology and genetic sequencing cultures (82.9%) were used to define osteomyelitis, the incidence of osteomyelitis did not change. There is variability in the incidence of osteomyelitis based on how the gold standard of bone biopsy is defined in diabetic foot infections.
Dexmedetomidine protects aged rats from postoperative cognitive dysfunction by alleviating hippocampal inflammation

The present study investigated the effect of dexmedetomidine on hippocampal inflammation and cognitive function in rats with postoperative cognitive dysfunction (POCD). A total of 80 healthy male Sprague Dawley rats were used, 72 of which developed POCD. The rats were randomly divided into four groups: The control, model, low-dose and high-dose dexmedetomidine anesthesia groups. A POCD model was established and dexmedetomidine was administered. Cognitive function tests were performed and expression levels of interleukin 1β (IL-1β), tumor necrosis factor-α (TNF-α) and NF-κB biomarkers were evaluated on the first, third and seventh day following modeling. The cognitive function of rats was measured using a Y-maze test. The expression levels of IL-1β and TNF-α in the hippocampus were determined by ELISA. The protein expression levels of NF-κB p65 in the hippocampus were determined by western blotting. It was revealed that at 1, 3 and 7 days after surgery, there were no alterations in the exercise ability of rats in the different groups, as reflected by the number of rats passing the alternative arms in the Y-maze. On the first and third day after surgery, the cognitive dysfunction reflected by the alteration scores of the low-dose and high-dose dexmedetomidine anesthesia groups were significantly higher than those of the model group, and the increase in the high-dose group was more pronounced. Additionally, on the first day after surgery, the expression levels of IL-1β, TNF-α and NF-κB in the hippocampi of rats in the low- and high-dose dexmedetomidine anesthesia groups were significantly lower than those in the model group, and the decrease was more pronounced in the high-dose group. At 7 days after surgery, the differences in expression levels of IL-1β, TNF-α and NF-κB in the hippocampus among groups were not identified to be statistically significantly different. Taken together, the results of the present study indicated that dexmedetomidine may inhibit hippocampal inflammation induced by surgical trauma, and that dexmedetomidine may effectively improve postoperative cognitive function in rats.
Phyllotaxis: is the golden angle optimal for light capture?

Phyllotactic patterns are some of the most conspicuous in nature. To create these patterns plants must control the divergence angle between the appearance of successive organs, sometimes to within a fraction of a degree. The most common angle is the Fibonacci or golden angle, and its prevalence has led to the hypothesis that it has been selected by evolution as optimal for plants with respect to some fitness benefits, such as light capture. We explore arguments for and against this idea with computer models. We have used both idealized and scanned leaves from Arabidopsis thaliana and Cardamine hirsuta to measure the overlapping leaf area of simulated plants after varying parameters such as leaf shape, incident light angles, and other leaf traits. We find that other angles generated by Fibonacci-like series found in nature are equally optimal for light capture, and therefore should be under similar evolutionary pressure. Our findings suggest that the iterative mechanism for organ positioning itself is a more likely target for evolutionary pressure, rather than a specific divergence angle and our model demonstrates that the heteroblastic progression of leaf shape in Arabidopsis thaliana can provide a potential fitness benefit via light capture. This article is protected by copyright. All rights reserved.
Employees’ Environmental Protection and Charitable Donation and Ethical Leadership: An Empirical Study

The sustainable development of the environment and society depends not only on firms' social responsibility initiatives, but also on employees' socially responsible behavior during their daily work life. Hence, it is important to study why and how employees go about the socially responsible behaviors (SRB), such as environmental protection and charitable donations. Although research has been done on the antecedents of employees' SRB from personal, contextual and leadership perspectives, little is known about the mechanism through which they affect these behaviors. Moreover, compared with the other two perspectives, research from the leadership perspective is relatively scarce. In this paper, we aim to fill these research gaps. Based on 936 respondents from 109 corporations, we empirically test the cross-level direct effect of ethical leadership on employees' SRB and the cross-level mediating effect of perceived organizational virtuousness. In our empirical analyses, we adopt statistical methodologies such as hierarchical linear modeling and multilevel mediation analysis. Our results show that perceived organizational virtuousness partly mediates the influence of ethical leadership on employees' environmental protection and charitable donation. In other words, ethical leadership enables employees to form the perception of organizational virtuousness, and therefore employees are more engaged in environmental protection and charitable donations. This research provides important insights for firms and their employees to become more socially and environmentally responsible.
Identification of a thymus microRNA-mRNA regulatory network in Down syndrome

The present bioinformatics analysis was performed using a multi-step approach to identify a microRNA (miR)-mRNA regulatory network in Down syndrome. miR (GSE69210) and mRNA (GSE70573) data was downloaded and collected from the thymic tissues of both Down syndrome and karyotypically normal subjects and placed in a public repository. Then, weighted gene co-expression network analysis (WGCNA) was performed to screen for miRs and mRNAs associated with Down syndrome. Subsequently, differentially expressed miRs (DEmiRs) and mRNAs/differentially expressed genes (DEGs) were identified following screening and mapping to RNA data. Bidirectional hierarchical clustering analysis was then performed to distinguish DEmiRs and DEGs between Down syndrome samples and normal control samples. DEmiR targets were retrieved using the miRanda database and mapped to the mRNA module screen by WGCNA. A gene co-expression network was constructed and subjected to functional enrichment analysis. During WGCNA, a total of 6 miR modules and 20 mRNA modules associated with Down syndrome were identified. Following mapping of these miRs and mRNAs to the miR and mRNA modules screened using WGNCA, a total of 12 DEmiRs and 237 DEGs were collected. Following comparison with DEmiR targets retrieved from the miRanda database, a total of 255 DEmiR-DEG pairs, including 6 DEmiRs and 106 DEGs were obtained. At expression correlation coefficient >0.9, a total of 231 gene pairs were selected. These gene pairs were enriched in response to stress and response to stimuli following functional annotation and module division. An integrated analysis of miR and mRNA expression in the thymus in Down syndrome is reported in the present study. miR-30c, miR-145, miR-183 and their targets may serve important roles in the pathogenesis and development of complications in Down syndrome. However, further experimental studies are required to verify these results.