Miracle-dz/UniFAR-FTUs huggingface dataset:
An accurate and rapid Real-time PCR approach for human Monkeypox virus diagnosis

Background Human monkeypox (MPX) is an emerging zoonotic disease caused by monkeypox virus (MPXV), which is endemic to Western and Central Africa. Despite being identified in captive monkeys in 1958, and in humans from the Democratic Republic of Congo (DRC) in 1970, a MPXV diagnostic test is not routinely implemented in diagnostic laboratories. Currently, a multi-country outbreak of MPXV has been ongoing in several European and American countries since May 2022. Methods To develop this real-time PCR assay, five MPXV positive DNA samples were tested using MPXV-specific primers. The qPCR amplification was conducted on two different qPCR devices. We also tested samples, collected in May 2022, from pox-like lesions of MPXV-suspected patients in Belgium. Results The performance of our real-time PCR was proved with five MPXV positive DNA from DRC. In addition, five out of ten clinical samples, from the current MPXV-outbreak, tested positive with Ct values ranging from 20.6 to 34.9. Conclusions In this study, we present an accurate and rapid real-time PCR approach, based on conserved regions of both MPXV clades, that can be used to test clinical samples from MPXV-suspected persons. Our real-time qPCR assay can be used for the 2022 multi-country outbreak of human MPXV.
G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C–T base-pair

Abstract The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C–T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.
Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery

Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant’s effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes.
Shear Driven Micro-Fluidic Pump for Cardiovascular Applications

A valveless shear-driven micro-fluidic pump design (SDMFP) for hemodynamic applications is presented in this work. One of the possible medical and biomedical applications is in-vivo hemodynamic (human blood circulation) support/assist. One or more SDMFPs can be inserted/implanted into vascular lumens in a form of a stent/duct in series and/or in parallel (bypass duct) to support blood circulation in-vivo. A comprehensive review of various micro-pump designs up to about mid 2000’s is given in [1,2]. Many of micropump designs considered are not suitable for in-vivo or even in-vitro medical/biomedical applications. Operating principles, design, and SDMFP features are given in [3]. A particular design used in cardiovascular applications has no moving valves. SDMFP with Gourneyflap type valves to support high-pressure applications are developed for other applications. SDMFP could be fully bidirectional and can control its operation on the run using embedded microcontrollers and sensors. Estimated efficiency is high with low leakage resulting in low power consumption. Proprietary “fish-scale” surface coating ShearQ designs are implemented to improve unidirectional flow pumping efficiency. Bi-directional feature may be especially critical when clogging of blood vessels is detected. By automatically and temporarily switching into the reverse-mode operation and retrogressive flow, while inducing suction-head for a short time periods it is hoped that possibly blood conduits can be cleared/unclogged and the normal forward-flow operation resumed. Such may be an important feature if SDMFP is used in-vivo, such as, in coronary arteries which are prone to clogging leading to cardiac-arrest.
The role of resistance exercise training for improving cardiorespiratory fitness in healthy older adults: a systematic review and meta-analysis

Abstract Background Declines in cardiorespiratory fitness (CRF) and muscle mass are both associated with advancing age and each of these declines is associated with worse health outcomes. Resistance exercise training (RET) has previously been shown to improve muscle mass and function in the older population. If RET is also able to improve CRF, as it has been shown to do in younger populations, it has the potential to improve multiple health outcomes in the expanding older population. Methods This systematic review aimed to identify the role of RET for improving CRF in healthy older adults. A search across CINAHL, MEDLINE, EMBASE and EMCARE databases was conducted with meta-analysis performed on eligible papers to identify improvements in established CRF parameters (VO2 peak, aerobic threshold (AT), 6-minute walking distance test (6MWT) following RET intervention. Main eligibility criteria included older adults (aged over 60), healthy cohorts (disease-specific cohorts were excluded) and RET intervention. Results Thirty-seven eligible studies were identified. Meta-analysis revealed a significant improvement in VO2 peak (MD 1.89 ml/kg/min; 95% confidence interval (CI) 1.21–2.57 ml/kg/min), AT (MD 1.27 ml/kg/min; 95% CI 0.44–2.09 ml/kg/min) and 6MWT (MD 30.89; 95% CI 26.7–35.08) in RET interventions less than 24 weeks. There was no difference in VO2 peak or 6MWT in interventions longer than 24 weeks. Discussion This systematic review adds to a growing body of evidence supporting the implementation of RET in the older population for improving whole-body health, particularly in time-limited timeframes.
Instance Shadow Detection With a Single-Stage Detector

This article formulates a new problem, instance shadow detection, which aims to detect shadow instance and the associated object instance that cast each shadow in the input image. To approach this task, we first compile a new dataset with the masks for shadow instances, object instances, and shadow-object associations. We then design an evaluation metric for quantitative evaluation of the performance of instance shadow detection. Further, we design a single-stage detector to perform instance shadow detection in an end-to-end manner, where the bidirectional relation learning module and the deformable maskIoU head are proposed in the detector to directly learn the relation between shadow instances and object instances and to improve the accuracy of the predicted masks. Finally, we quantitatively and qualitatively evaluate our method on the benchmark dataset of instance shadow detection and show the applicability of our method on light direction estimation and photo editing.
PERANCANGAN APLIKASI PENCARIAN LOKASI BENGKEL RESMI NASMOCO DI KOTA SEMARANG DENGAN TEKNOLOGI AUGMENTED REALITY BERBASIS ANDROID

Authorized workshops Nasmoco a formal workshop for Toyota cars are scattered in the city of Semarang and Central Java. There are four authorized workshops in Semarang city. The wide of Semarang city andscattered authorized workshops would make it difficult for owners of Toyota cars and people who want to find workshops in search of the nearest authorized workshop. For ease in searching a place needed an location search application that can display directions directly from the user's location to the destination. The system are built using waterfall method as the design of location search application using Augmented Reality technology.The application development using the Wikitude SDK as the Augmented Reality builder and Global Positioning System (GPS). Location search application using Augmented Reality will facilitate user in finding the location of the nearest service station and obtain other information easily.
Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids

Abstract Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III polyketide synthase (PKS) gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica, respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in P. equestris and two proteins each in D. catenatum and A. shenzhenica clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive cis-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of PKS genes and biotechnological production of polyketides. Communicated by Ramaswamy H. Sarma Highlights Identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica based on genome-wide analysis Presence of characteristic conserved domains (Chal_sti_synt_N, Chal_sti_synt_C) with cytological localisation Phylogenetic clustering into two groups, CHS chalcone synthase (CHS) and non-CHS Expression profiling revealing high expression in reproductive tissues Prediction of stress-responsive cis-regulatory elements like ABRE and CGTCA
[Effect of the VOLANTIN resilience promotion program on children with an alternative residential system].

INTRODUCTION Internationally, there are resilience promotion programs applied to children in residential alterna tive care with favorable results. The application of the resilience promotion program "VOLANTÍN" has shown to be effective in different groups of school-age children, favoring the development of resilience. OBJECTIVE To describe the results of the implementation of the "VOLANTÍN' program on the level of resilience, self-concept, and emotional symptoms in children aged 7-12 years in resi dential alternative care (foster care). SUBJECTS AND METHOD descriptive, longitudinal study. The "VO LANTÍN" program was implemented in a sample of 15 foster children between 7-12 years old. The variables measured were the "Escala de Resiliencia Escolar" (ERE), the Piers-Harris Children's Self Concept Scale, the Anxiety Self-report for Children and Adolescents (AANA), and the Children's Depression Inventory (CDI) at the beginning, at the end, and 3 months after the end of the program, and then were analyzed statistically by nonparametric test. RESULTS At the beginning, the end, and three months after the program implementation, there was a significant increase in the total sco res of ERE (p0.045), subscales "networks-models" (p0.002) and "external resources" (p0.018); and Self-concept (p0.005), subscales "behavior" (p0.045) and "popularity" (p0.03). AANA total scores decreased significantly (p0.004) as well as the subscales "panic/somatic" (p0.025) and "generalized anxiety" (p0.009). CDI scores decreased, but not significantly. CONCLUSION The application of the resilience promotion program "VOLANTÍN' increased resilience and self-concept scores and decrea sed anxious symptoms in children aged 7-12 years.
Value-directed remembering in first-episode schizophrenia.

OBJECTIVE Memory deficits in individuals with schizophrenia are well-established, but less is known about how schizophrenia affects metacognitive processes such as metamemory. We investigated metamemory ability using the value-directed remembering task, which assesses the degree to which participants use value cues to guide their learning of a list of items (i.e., their memory selectivity). METHOD Participants were patients undergoing treatment following a recent first episode of schizophrenia (n = 20) and demographically comparable healthy controls (n = 18). Participants viewed six lists of 24 words where each word was paired with either a low value (1-3 points) or a high value (10-12 points), and they were instructed to maximize their score on free recall tests given after each list. After the final free recall test, participants completed a recognition test where they gave remember/know judgments. RESULTS On tests of free recall, patients showed reduced memory selectivity relative to healthy controls. On the recognition test, patients failed to show an effect of value on recognition of nonrecalled words, in contrast to healthy controls, who showed a significant value effect that was characterized by greater "remember" judgments. Patients initially overestimated their memory capacity but were able to adjust their estimates to be more accurate based on task experience. Patients' self-reports of memory selectivity were unrelated to their actual memory selectivity. CONCLUSIONS Patients with first-episode schizophrenia had substantial impairments on the value-directed remembering task, but areas of preserved metamemory ability were also observed. These findings have potential implications for cognitive training interventions. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
COVID‐19 coagulopathy – what should we treat?

What is the topic of this review? Overview of the coagulation abnormalities, including elevated D‐dimers widely reported with COVID‐19, often labelled as COVID coagulopathy. What advances does it highlight? The review highlights the changes in bronchoalveolar haemostasis due to apoptosis of alveolar cells, which contributes to acute lung injury and acute respiratory distress syndrome; the pathophysiological mechanisms, including endothelial dysfunction and damage responsible for thrombosis of pulmonary microcirculation and potential contribution to the hypoxaemia of COVID‐19 acute lung injury; and changes in coagulation proteins responsible for the hypercoagulability and increased risk of thrombosis in other venous and arterial beds. The rationale for anticoagulation and fibrinolytic therapies is detailed, and potential confounders that might have led to less than expected improvement in the various randomised controlled trials are considered.
On the road again: A cross-sectional survey examining work schedules, commuting time, and driving-related outcomes among U.S. oil and gas extraction workers.

BACKGROUND Oil and gas extraction (OGE) workers in the United States experience high fatality rates, with motor vehicle crashes the leading cause of death. Land-based OGE workers drive frequently to remote and temporary worksites. Limited information is available on factors that may influence crash risk for this workforce. METHODS A cross-sectional survey of 500 land-based OGE workers examined work schedules and hours, commuting, sleep, employer policies, and their relationship to potentially harmful events while driving. RESULTS Over 60% of participants worked 12 or more hours per day. The mean daily roundtrip commuting time was 1.82 h. Longer daily commutes, nonstandard work schedules, less sleep on workdays, and lack of employer policies were associated with one or more risky driving-related outcomes. CONCLUSIONS Implementation and evaluation of OGE employer policies and programs to limit long work hours, reduce long daily commutes, promote sufficient sleep, and reduce drowsy driving among U.S. OGE workers are needed.
A de novo start-loss in EFTUD2 associated with mandibulofacial dysostosis with microcephaly: case report

Mandibulofacial dysostosis with microcephaly (MFDM) is a rare genetic disorder inherited in an autosomal dominant pattern. Major characteristics include developmental delay, craniofacial malformations such as malar and mandibular hypoplasia, and ear anomalies. Here, we report a 4.5-yr-old female patient with symptoms fitting MFDM. Using whole-genome sequencing, we identified a de novo start-codon loss (c.3G > T) in the EFTUD2. We examined EFTUD2 expression in the patient by RNA sequencing and observed a notable functional consequence of the variant on gene expression in the patient. We identified a novel variant for the development of MFDM in humans. To the best of our knowledge, this is the first report of a start-codon loss in EFTUD2 associated with MFDM.
Growth‐rate model predicts in vivo tumor response from in vitro data

A major challenge in oncology drug development is to elucidate why drugs that show promising results in cancer cell lines in vitro fail in mouse studies or human trials. One of the fundamental steps toward solving this problem is to better predict how in vitro potency translates into in vivo efficacy. A common approach to infer whether a model will respond in vivo is based on in vitro half‐maximal inhibitory concentration values (IC50), but yields limited quantitative comparison between cell lines and drugs, potentially because cell division and death rates differ between cell lines and in vivo models. Other methods based either on mechanistic modeling or machine learning require molecular insights or extensive training data, limiting their use for early drug development. To address these challenges, we propose a mathematical model integrating in vitro growth rate inhibition values with pharmacokinetic parameters to estimate in vivo drug response. Upon calibration with a drug‐specific factor, our model yields precise estimates of tumor growth rate inhibition for in vivo studies based on in vitro data. We then demonstrate how our model can be used to study dosing schedules and perform sensitivity analyses. In addition, it provides meaningful metrics to assess association with genotypes and guide clinical trial design. By relying on commonly collected data, our approach shows great promise for optimizing drug development, better characterizing the efficacy of novel molecules targeting proliferation, and identifying more robust biomarkers of sensitivity while limiting the number of in vivo experiments.
Radiotherapy-Induced Cleavage of Quaternary Ammonium Groups Activates Prodrugs in Tumors.

Cleavage chemistry offers a new chance to activate chemotherapeutic prodrugs in a tumor-selective manner, yet developing spatiotemporally controllable cleavage chemistry with deep tissue penetration is still a great challenge. Herein, we present a novel radiotherapy-triggered cleavage chemistry that enables controlled drug release in tumors. Quaternary ammonium groups are identified as masking groups that can be efficiently removed by hydrated electrons (e - aq ) from water radiolysis. The subsequently released tertiary amines can be anti-cancer toxins or readily release functional molecules via 1,6-elimination. This radiotherapy-induced cleavage works successfully in living cells and tumor-bearing mice, showing remarkable treatment efficacy when the mice are given carfilzomib prodrug and radiotherapy. This strategy provides a new perspective for combinational radiochemotherapy, which is the first-line treatment for over 50% of cancer patients.
Salmonella enterica subsp. II serovar 4,5,12:a:- may cause gastroenteritis infections in humans

ABSTRACT Some serovars of Salmonella are not or rare found to cause salmonellosis in human. In our clinic-based surveillance, three rare Salmonella 4,5,12:a:- strains were recovered from three patients with diarrhea. To explore their genetic and epidemiological characteristics and pathogenesis, we conducted whole-genome sequencing, in vitro invasion assays in mammalian cells, and in vivo virulence assays in an animal model. The three isolates had indistinguishable molecular patterns and similar genome sequences, and clustered together with an isolate from edible fish traded among countries. The isolates had biochemical reactions identical with those of Salmonella subspecies enterica but belonged to subspecies salamae according to genome phylogeny, revealing a new serovar, S. enterica subsp. II serovar 4,5,12:a:-. The strains contained multiple virulence genes, elicited temporary bacteremia and enteritidis and caused cell damage in the mouse liver and cecum. This study provides evidence that this new Salmonella salamae serovar can infect humans and cause clusters of cases, and whole-genome sequencing detection and surveillance of Salmonella can help to accurately define Salmonella classification and clonality, improve diagnosis, facilitate outbreak detection and aid in the source tracing of salmonellosis epidemics.
Designing a cyber risk assessment tool for small to medium enterprises

With the extensive use of the internet nowadays, companies are becoming more and more at risk from cyber-attacks. Especially SMEs are vulnerable, as they lack in cybersecurity. This is due to time, resource and knowledge constraints. In the literature no clear solutions can be found in order to help SMEs with their cybersecurity. To overcome these issues, this research aims in developing a method with which a tool can be developed that can help SMEs in getting insights in their cybersecurity status. This tool should be capable of letting an SME do their own risk assessment without investing too much money or time. In order to do this, existing methods are analyzed. After the analysis, the TREsPASS method is used a basis for the tool. This method is slimmed down in order to fit the needs of SMEs. By creating a knowledge based system, the SMEs can use the knowledge of cybersecurity experts without the requirement to have to knowledge in-house.