Miracle-dz/UniFAR-FTUs huggingface dataset:
Drug Susceptibility and Replication Capacity of a Rare HIV-1 Subtype C Protease Hinge Region Variant

Background Protease inhibitors form the main component of second-line antiretroviral treatment in South Africa. Despite their efficacy, mutations arising within the HIV-1 gag and protease coding regions contribute to the development of resistance against this class of drug. In this paper we investigate a South African HIV-1 subtype C Gag-protease that contains a hinge region mutation and insertion (N37T↑V). Methods In vitro single-cycle drug susceptibility and viral replication capacity assays were performed on W1201i, a wild-type reference isolate (MJ4) and a chimeric construct (MJ4GagN37T↑VPR). Additionally, enzyme assays were performed on the N37T↑V protease and a wild-type reference protease. Results W1201i showed a small (threefold), but significant (P<0.0001) reduction in drug susceptibility to darunavir compared with MJ4. Substitution of W1201i-Gag with MJ4-Gag resulted in an additional small (twofold), but significant (P<0.01) reduction in susceptibility to lopinavir and atazanavir. The W1201i pseudovirus had a significantly (P<0.01) reduced replication capacity (16.4%) compared with the MJ4. However, this was dramatically increased to 164% (P<0.05) when W1201i-Gag was substituted with MJ4-Gag. Furthermore, the N37T↑V protease displayed reduced catalytic processing compared with the SK154 protease. Conclusions Collectively, these data suggest that the N37T↑V mutation and insertion increases viral infectivity and decreases drug susceptibility. These variations are classified as secondary mutations, and indirectly impact inhibitor binding, enzyme fitness and enzyme stability. Additionally, polymorphisms arising in Gag can modify the impact of protease with regards to viral replication and susceptibility to protease inhibitors.
Listening for Young-adult EFL Learners: Metacognitive Intervention through L1

ABSTRACT This study investigates the effects of metacognitive intervention in first language on the listening performance of young-adult English as foreign language (EFL) learners in Iran, and probes the learners’ attitude toward such intervention in English as foreign language classrooms. The participants in the study were 61 young-adult EFL learners divided randomly into two groups: An experimental and a control group. Following Metacognitive Pedagogical Sequence and its importance in listening comprehension, the participants in the experimental group underwent an eight-week intervention delivered in L1 including the linear instruction of metacognitive strategies assisting their metacognitive awareness of the processes in second language listening. The control group, however, followed the conventional pedagogy of the language institute. The data were collected in the learners’ listening performance before, and after the intervention through listening comprehension test. The analysis of the quantitative data shows that metacognitive intervention in first language leads to a significant improvement in the overall listening performance of the learners. Similarly, the results of the interviews show that the Metacognitive Pedagogical Sequence and the presentation of metacognitive strategies in first language lead to learners’ higher listening performance and better mastery of note-taking and word-meaning guessing.
Valspodar-modulated chemotherapy in human ovarian cancer cells SK-OV-3 and MDAH-2774.

Overcoming drug resistance in ovarian cancer is the overarching goal in gynecologic oncology. One way to increase drug cytotoxicity without increasing the drug dose is to simultaneously apply multidrug resistance modulator. Valspodar is the second generation P-glycoprotein 1 modulator capable of reversing multidrug resistance in different cancers. In this study, we evaluated the effect of valspodar and cisplatin co-treatment on cell viability, cell death and oxidative status in ovarian cancer cells. The two cisplatin-resistant human ovarian cancer cell lines SK-OV-3 and MDAH-2774 were treated with cisplatin, valspodar, or cisplatin+valspodar for 24 and 48 hours. Untreated cells were used as control group. Cell viability was evaluated by MTT assay. Cell death was assessed by TUNEL and comet assay. Lipid peroxidation (malondialdehyde) and protein thiol groups were analyzed as oxidative stress markers. The expression of mitochondrial superoxide dismutase (MnSOD) was assessed by immunocytochemistry. Valspodar effectively reduced the resistance of SK-OV-3 cells to cisplatin, as demonstrated by increased oxidative stress, decreased cell viability and increased apoptosis in SK-OV-3 cells co-treated with valspodar and cisplatin compared to other groups. However, valspodar did not affect the resistance of MDAH-2774 cells to cisplatin. Stronger staining for MnSOD in MDAH-2774 vs. SK-OV-3 cells after co-treatment with cisplatin and valspodar may determine the resistance of MDAH-2774 cell line to cisplatin.
Carry-over and contamination of veterinary drugs in feed production lines for poultry and pigs

ABSTRACT The current model of pigs and poultry production has increased stocking density and reduced downtime between lots. This scenario may favour a rise of infection and disease risk in animals. To avoid this problem, routine use of drugs has been made, intensifying the possibility of residues in animal products and antimicrobial resistance. The aim of this study was to measure carry-over and contaminants of veterinary drugs included in the feed production lines for poultry and pigs. Samples were taken from 25 production lines. LC-MS/MS was used for simultaneous analysis of 62 active ingredients. In the medicated feed, 80.4% of the samples had a concentration of active ingredients different from the stated doses. In 70% of the feed samples, there was heterogeneity in the mixture of active ingredients. In subsequent feeds, carry-over was greater than 1% of the stated dose in 63% of cases. Of the 25 analysed lines, only one showed no contamination with other active ingredients. No correlations were found between the nutritional composition of the feed and carry-over. The present study demonstrated that the current production model allows the occurrence of unwanted drugs in feed-in doses that can contaminate animal products and can select antimicrobial-resistant bacteria.
The role of CD44H molecule in the interactions between human monocytes and pancreatic adenocarcinoma-derived microvesicles.

INTRODUCTION CD44H is a transmembrane molecule important for cell-cell and cell-extracellular matrix interactions. In monocytes, CD44H is implicated in phagocytosis of particles coated by hyaluronan (HA). HA fragments were shown to induce chemokine secretion by monocytes. Tumour derived microvesicles (TMVs), which are small membrane fragments derived from tumour cells can carry fragments of HA. The aim of the study was to examine whether monocyte's CD44H is involved in the engulfment of pancreatic adenocarcinoma-derived microvesicles and in the production of chemokines induced by TMVs. MATERIALS AND METHODS TMVs engulfment and chemokines' secretion stimulated with TMVs were determined in control human monocytes and cells incubated with anti-CD44H monoclonal antibody (mAb) by flow cytometry and ELISA, respectively. Phosphorylation of STAT3, transcription factor essential for chemokines' production and CD44 signal transduction, was determined by Western blotting. RESULTS Blocking of CD44H by anti-CD44H mAb on monocytes decreased the engulfment of TMVs and the secretion of CCL4 and CCL5, but had no effect on CCL2, CCL3 and CXCL8. STAT-3 phosphorylation in monocytes incubated with TMVs after CD44 blocking was also reduced. CONCLUSION The results suggest that tumour-derived microvesicles (TMVs) may carry bioactive cargo(s) which induces STAT3 dependent signalling pathway in human monocytes via CD44 molecules.
Functional Connectivity of Cognitive Control and Visual Regions During Verb Generation Is Related to Improved Reading in Children

Reading is a complex cognitive ability, which relies on visual and language processing as well as on executive functions (EFs). Recent studies have demonstrated that increased reading ability in children aged 7-17 years is related to greater activation of cognitive control regions during verb generation, a task which merges linguistic and cognitive control ability. The aim of the current study is to determine the relationships between neural circuits specifically related to EF and reading ability. We focused on functional connectivity between the dorsolateral prefrontal cortex (DLPFC), a region involved in EF and is part of the frontoparietal network during a verb generation task, and reading ability in seventeen 8-12-year-old typical readers. Results show positive functional connectivity between the left and right DLPFCs and regions related to cognitive control and visual processing while generating verbs. Increased reading ability was positively correlated with greater functional connectivity between the left and right DLPFCs and right-lateralized visual processing regions. The current study highlights the importance of neural circuits related to EF during both verb generation and reading and points to the role of the right occipital cortex in generating verbs as well as automatic word recognition in typical readers.
TO STUDY THE SPECTRUM OF NEONATAL CONGENITAL CARDIAC DISORDERS

Background:Congenital heart disease (CHD) is the commonest of all congenital lesions and is the most common type of heart disease among children. Congenital heart disease, in a definition proposed by Mitchell et al is a gross structural abnormality of the heart or intrathoracic great vessels that is actually or potentially of functional significance. It is the most common cause of major congenital anomalies, representing a major global health problem. Twenty-eight percent of all major congenital anomalies consist of cardiac anamolies. In India, 10% of the present infant mortality may be accounted for by Congenital Heart Disease as reported by Saxena et al. Aim: To study the Spectrum of Neonatal Congenital Cardiac Disorders Material and methods:It was an observational prospective study carried out in the Neonatology Section, Department of Pediatrics, GB Panth Childrens hospital Srinagar from November 2017 to August 2019. Results:During the two year study, 471 neonates were diagnosed with congenital heart disease in which 335 (71.1%) were acyanotic and 136 (28.9%) were cyanotic. Males and females comprised of 253 and 218 respectively with a male to female ratio of 1.2:1. The most common cyanotic CHD was d-transposition of great arteries (d-TGA) 39 (8.3%), followed by tetralogy of Fallot (TOF) 23 (4.9%) and single ventricle (double inlet left ventricle [DILV] with pulmonary arterial hypertension/pulmonary stenosis [PAH/PS]) 17 (3.6%). In our study the most common acyanotic CHD was ventricular septal defect (VSD) 103 (32.5%) followed by atrial septal defect (ASD) 98 (20.8%) and PDA 47 (10.0%). Conclusion:Congenital heart disease (CHD) is a common congenital disorder of the neonatal population. Early diagnosis and timely management are key factors for optimal outcome of this problem.
Gamified physics instruction in a reformatory classroom context

Gamification is the use of game elements and game-design techniques in non-game contexts. It has five main elements: points, badges, leaderboards, rules and levels. A classroom that has any or all of these elements can be considered a gamified classroom. This study explored the effects of a gamified environment to the motivation and achievement of high school students in Physics. The framework of the study is anchored on the Self-Determination Theory which claims that humans are inherently active, inquisitive and self-motivated even without external reward. However, extrinsic motivators can be converted to intrinsic motivators if they are meaningful, pleasurable and consistent with a person's worldview. To determine if gamification has a significant effect on the student motivation, the students' responses to the pre-gamification and post-gamification administration of the Physics Motivation Questionnaire were compared using the paired sample t-test on SPSS. Its effects to student achievement in Physics, on the other hand, was identified after calculating the mean normalized gains for all the pretests-posttests administration after each of the 5 modules. Feedback from students, teacher-implementer and external observers were collected and analyzed. Results showed that gamified instruction brings about a significant increase in student achievement in Physics but not in student motivation. However, the feedback coming from students, teacher-implementer and external observers substantiate the influence of gamification to student motivation. Implementation must be done properly so that no unhealthy competition develops, no student becomes extremely grade conscious that he or she ends up resorting to cheating and that an environment conducive to learning is maintained inside the classroom. Consequently, it is recommended that more rigorous studies should be done to further confirm or invalidate the effects of gamification in learning Physics that are exposed in this study.
A maximal correlation embedding method for multilabel human context recognition: poster abstract

Real-time human context recognition is one of the most exciting emerging technologies in sensing nowadays. Compared with most recognition problems in machine learning, the challenge lies in the complexity and incompleteness of labels, in other words, each sample can have several label concepts simultaneously but some of them could be missing. This poster proposes an effective approach for multilabel human context recognition with signals from sensors embedded in the wearable devices. The proposed algorithm demonstrates to be very robust to incomplete labels.
A validated computational framework to evaluate the stiffness of 3D printed ankle foot orthoses

Abstract The purpose of this study was to create and validate a standardized framework for the evaluation of the ankle stiffness of two designs of 3D printed ankle foot orthoses (AFOs). The creation of four finite element (FE) models allowed patient-specific quantification of the stiffness and stress distribution over their specific range of motion during the second rocker of the gait. Validation was performed by comparing the model outputs with the results obtained from a dedicated experimental setup, which showed an overall good agreement with a maximum relative error of 10.38% in plantarflexion and 10.66% in dorsiflexion. The combination of advanced computer modelling algorithms and 3D printing techniques clearly shows potential to further improve the manufacturing process of AFOs.
Security and Safety Co-Engineering of the FlexRay Bus in Vehicular Networks

Recently, researchers have demonstrated how the lack of security features in road vehicles may allow adversaries to take over partial or even full control. Specifically, in-vehicle communication protocols are prone to attacks, because no security mechanisms have been developed for them. For a long time, they have been optimized only towards safety, in order to guarantee a high degree of reliability, robustness and real-time behavior. In this work, we focus on FlexRay, an automotive communication protocol whose core properties are strong determinism and high fault-tolerance for safety-critical applications. We propose to leverage the distinct safety-tailored features of FlexRay for security purposes, such as authentication. In particular, we demonstrate that the optional dualchannel mode can be used to provide authentication for FlexRay in a backward compatible manner. Additionally, we suggest different ways of transmitting the relevant message authentication codes over FlexRay. Finally, we propose a number of techniques for managing cryptographic keys, i.e. we associate these keys with FlexRay time slots and we use hash chains to derive new keys at low cost at runtime. In this way, we offer multiple security solutions for the FlexRay protocol, while trying to keep the overhead low.
XOR-Based Low-Cost Reconfigurable PUFs for IoT Security

With the rapid development of the Internet of Things (IoT), security has attracted considerable interest. Conventional security solutions that have been proposed for the Internet based on classical cryptography cannot be applied to IoT nodes as they are typically resource-constrained. A physical unclonable function (PUF) is a hardware-based security primitive and can be used to generate a key online or uniquely identify an integrated circuit (IC) by extracting its internal random differences using so-called challenge-response pairs (CRPs). It is regarded as a promising low-cost solution for IoT security. A logic reconfigurable PUF (RPUF) is highly efficient in terms of hardware cost. This article first presents a new classification for RPUFs, namely circuit-based RPUF (C-RPUF) and algorithm-based RPUF (A-RPUF); two Exclusive OR (XOR)-based RPUF circuits (an XOR-based reconfigurable bistable ring PUF (XRBR PUF) and an XOR-based reconfigurable ring oscillator PUF (XRRO PUF)) are proposed. Both the XRBR and XRRO PUFs are implemented on Xilinx Spartan-6 field-programmable gate arrays (FPGAs). The implementation results are compared with previous PUF designs and show good uniqueness and reliability. Compared to conventional PUF designs, the most significant advantage of the proposed designs is that they are highly efficient in terms of hardware cost. Moreover, the XRRO PUF is the most efficient design when compared with previous RPUFs. Also, both the proposed XRRO and XRBR PUFs require only 12.5% of the hardware resources of previous bitstable ring PUFs and reconfigurable RO PUFs, respectively, to generate a 1-bit response. This confirms that the proposed XRBR and XRRO PUFs are very efficient designs with good uniqueness and reliability.
Lazy Determinism for Faster Deterministic Multithreading

Deterministic multithreading (DMT) fundamentally requires total, deterministic ordering of synchronization operations on each synchronization variable, i.e. a partial ordering over all synchronization operations. In practice, prior DMT systems totally order all synchronization operations, regardless of synchronization variable; the result is severe performance degradation for highly concurrent applications using fine-grained synchronization. Motivated by this class of programs, we propose lazy determinism as a way to go beyond this total order bottleneck. Lazy determinism executes synchronization operations speculatively, and enforces determinism by subsequently validating the resulting order of operations. If an ordering violation is detected, part of the computation is restarted. By enforcing only the partial ordering required to guarantee determinism, lazy determinism increases the available parallelism during deterministic execution. We implement LazyDet via a pure-software runtime system accelerated by custom Linux kernel support. Our experiments with hash table benchmarks from Synchrobench show roughly an order of magnitude improvement in the performance of lock-based data structures compared to the state of the art in eager determinism. For benchmarks from PARSEC-2, SPLASH-2, and Phoenix, we demonstrate runtime improvements of up to 2× on the programs that challenge deterministic execution environments the most.
Employee Sleep and Workplace Health Promotion: A Systematic Review

Objective: Workplace-based employee health promotion programs often target weight loss or physical activity, yet there is growing attention to sleep as it affects employee health and performance. The goal of this review is to systematically examine workplace-based employee health interventions that measure sleep duration as an outcome. Data Source: We conducted systematic searches in PubMed, Web of Knowledge, EMBASE, Scopus, and PsycINFO (n = 6177 records). Study Inclusion and Exclusion Criteria: To be included in this systematic review, studies must include (1) individuals aged >18 years, (2) a worker health-related intervention, (3) an employee population, and (4) sleep duration as a primary or secondary outcome. Results: Twenty studies met criteria. Mean health promotion program duration was 2.0 months (standard deviation [SD] = 1.3), and mean follow-up was 5.6 months (SD = 6.5). The mean sample size of 395 employees (SD = 700.8) had a mean age of 41.5 years (SD = 5.2). Measures of sleep duration included self-report from a general questionnaire (n = 12, 66.6%), self-report based on Pittsburgh Sleep Quality Index (n = 4, 22.2%), and self-report and actigraphy combined (n = 5, 27.7%). Studies most commonly included sleep hygiene (35.0%), yoga (25.0%), physical activity (10.0%), and cognitive–behavioral therapy for insomnia (10.0%) interventions. Across the interventions, 9 different behavior change techniques (BCTs) were utilized; the majority of interventions used 3 or fewer BCTs, while 1 intervention utilized 4 BCTs. Study quality, on average, was 68.9% (SD = 11.1). Half of the studies found workplace-based health promotion program exposure was associated with a desired increase in mean nightly sleep duration (n = 10, 50.0%). Conclusions: Our study findings suggest health promotion programs may be helpful for increasing employee sleep duration and subsequent daytime performance.
Behavior of Some Egyptian Bread Wheat Genotypes Under Different Natural Photo-thermal Environments

This investigation was conducted during the 2018/2019 and 2019/2020 seasons at Sakha Agricultural Research Station, Egypt to study the influence of four planting dates on earliness and yield of fourteen wheat genotypes. The combined analyses showed highly significant differences due to years, sowing dates, genotypes and their interactions for most studied traits. December 5th was the best sowing date for wheat production. The wheat new genotypes lines 1 and 2 had the lowest days to booting, heading, anthesis and maturity on the other side they had the highest values for grain filling period (GFP) and 1000-kernel weight. Based on the genotype means, the late heading genotype (Giza 163) had short GFP (29.5 days) and possessed a high grain filling rate (233 kg ha-1 days-1). The cultivar Misr 3 was superior overall genotypes for grain yield (10.529 t ha.-1), spikes per square meter (552 spikes), and straw yield (20.164 t ha.-1); and it ranked first under early sowing date (Nov. 5th) with 9% higher grain yield overstudied genotypes. According to stability analyses, Misr 3, Sakha 95 and Giza 171 recorded the highest yield, with the regression coefficient values ˃1. This study recommended release of new wheat genotypes (Lines 1 and 2) as new cultivars and use them to develop early maturing and heat-tolerant bread wheat genotypes in breeding programs.
Exposure‐response modeling of tocilizumab in rheumatoid arthritis using continuous composite measures and their individual components

Tocilizumab has a direct effect on inflammatory markers. Therefore, composite measures for disease activity assessment in rheumatoid arthritis (RA) using these inflammatory markers may not be suitable for tocilizumab treatment. We used a modelling approach to describe the tocilizumab exposure‐response relationship and to investigate the different dynamics of the individual components of the routinely used continuous composite measures.