Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and evaluation of a point‐of‐care test with a combination of EZ‐Fast DNA extraction and real‐time PCR and LAMP detection: evaluation using blood samples containing the bovine leukaemia DNA

Along with progress in globalization of society, the spread of infectious diseases has accelerated worldwide. The deployment of highly sensitive genetic tests is essential for early diagnosis and early containment of potential outbreaks and epidemics, as well as routine surveillance, although tedious and expensive nucleic acid extraction steps represent a major drawback. Here we developed a simple and rapid DNA extraction method, named as an EZ‐Fast kit, applicable to the field setting. The kit does not require advanced laboratory equipment or expensive DNA extraction kits and achieves crude DNA extraction within 10 min at extremely low cost and can easily be performed in field settings. When combined with real‐time PCR and LAMP analyses, the performance of the POCT, using 183 bovine blood samples, was similar to that of the existing DNA extraction method: 92·5% (135/146) (real‐time PCR) and 93·7% (133/142) (LAMP) diagnostic sensitivities, and 100% diagnostic specificities. The developed POCT provides a powerful tool to facilitate on‐site diagnosis in a field setting.
Effects of mortality awareness on attitudes toward dying and death and meaning in life—a randomized controlled trial

Abstract A randomized controlled trial was carried out to investigate effects of heightened mortality awareness on meaning in life and attitudes toward dying and death. An intervention group (n = 51) completed questionnaires and participated in interventions to increase mortality awareness; a control group (n = 47) only completed the questionnaires. Longitudinal analyses revealed a decrease in the intervention group’s fear of dying and an increase in their acceptance of dying, but no effects on attitudes toward death. Changes in meaningfulness were contingent on participants’ religiousness. Unexpected cross-sectional results and the study’s implications for theory and further empirical work are discussed.
Protein elongation variant of PUF60: Milder phenotypic end of the Verheij syndrome

The PUF60 gene encodes a ubiquitously expressed essential splicing factor that is recruited to the U2snRNA complex. The complex binds to the 3′ splice site of exons in specific target genes and regulates the inclusion or exclusion of such exons. Recently, pathogenic variants of PUF60 have been shown to cause a relatively specific and potentially recognizable pattern of malformation referred to as Verheij syndrome. Here, we report a 12‐year‐old female patient with a de novo mutation in PUF60 whose phenotype was representative of the milder end of the phenotypic spectrum of Verheij syndrome; the de novo mutation was a frameshift mutation p.(Ser558Cysfs*21) that resulted in the addition of 21 extra amino acids at the carboxy end of the protein. Among the frequent features of Verheij syndrome, the patient exhibited coloboma, cervical spinal segmentation defects, and borderline intellectual functioning, but lacked cardiac abnormalities, deafness, and urogenital abnormalities. The results of RNA analysis using peripheral blood showed the escape of the mutant allele from nonsense‐mediated mRNA decay, possibly accounting for the mild phenotype in the presently reported patient. Based on our clinical observations, we inferred that two embryologic processes, closure of the ocular plate and cervical spinal segmentation, are particularly susceptible to deficient PUF60‐mediated splicing regulation, compared with other embryogenetic processes leading to the central nervous system, heart, ear, and kidney.
Nanotherapeutics in Neuropathologies: Obstacles, Challenges and Recent Advancements in CNS Targeted Drug Delivery Systems

Neurology and associated nanotherapeutics are a complex field in terms of therapeutics and neurological disorder complexity. The brain is an intricate appendage and requires more precise embattled treatment for the particular diseases and hence it is a broad scale for developing more targeted drug deliveries. The brain is one of the most inaccessible tissues of the body due to the existence of the blood-brain barrier (BBB), thus delivery of drugs inside the brain is a striking dare and it is also tricky to treat central nervous system (CNS) complications pharmacologically. The therapeutic aspiration is to accomplish the lowest drug meditation in the brain tissues so as to gain favoured therapeutic results. To devastate this obstacle, nanotechnology is engaged in the field of targeted brain drug delivery and neuropathology targeting. These carriers hold myriad abilities as they may augment the drug delivery into the brain by shielding them from degradation and prolonging their transmission in the blood, as well as promoting their transport through the BBB. Nanopharmaceuticals are quickly sprouting as a new avenue that is engaged with the drug-loaded nanocarriers to demonstrate unique physicochemical properties and tiny size range for penetrating the central nervous system. The enchantment behind their therapeutic achievement is the condensed drug dose and inferior toxicity, whereby restricting the therapeutic compound to the specific site. Therefore, in this article, we have tried to recapitulate the advances of the novel scopes for the brain targeted drug delivery for complex neurological disorders.
Weakly-supervised deep learning of interstitial lung disease types on CT images

Accurate classification and precise quantification of interstitial lung disease (ILD) types on CT images remain important challenges in clinical diagnosis. Multi-modality image information is required to assist diagnosing diseases. To build scalable deep-learning solutions for this problem, how to take full advantage of existing large-scale datasets in modern hospitals has become a critical task. In this paper, we present DeepILD, as a novel computer-aided diagnostic framework to address the ILD classification task only from single modality (CT image) using a deep neural network. More specifically, we propose integrating spherical semi-supervised K- means clustering and convolutional neural networks for ILD classification and disease quantification. We firstly use semi-supervised spherical K-means to divide the CT lung area into normal and abnormal sub-regions. A convolutional neural network (CNN) is subsequently invoked to perform training using image patches extracted from the abnormal regions. Here, we focus on the classification of three chronic fibrosing ILD types: idiopathic pulmonary fibrosis (IPF), idiopathic non-specific interstitial pneumonia (iNSIP), and chronic hypersensitivity pneumonia (CHP). Excellent classification accuracy has been achieved using a dataset of 188 CT scans; in particular, our IPF classification reached about 88% accuracy.
The Spheres & Shield Maze Task: A Virtual Reality Serious Game for the Assessment of Risk Taking in Decision Making

Risk taking (RT) is an essential component in decision-making process that depicts the propensity to make risky decisions. RT assessment has traditionally focused on self-report questionnaires. These classical tools have shown clear distance from real-life responses. Behavioral tasks assess human behavior with more fidelity, but still show some limitations related to transferability. A way to overcome these constraints is to take advantage from virtual reality (VR), to recreate real-simulated situations that might arise from performance-based assessments, supporting RT research. This article presents results of a pilot study in which 41 individuals explored a gamified VR environment: the Spheres & Shield Maze Task (SSMT). By eliciting implicit behavioral measures, we found relationships between scores obtained in the SSMT and self-reported risk-related constructs, as engagement in risky behaviors and marijuana consumption. We conclude that decontextualized Virtual Reality Serious Games are appropriate to assess RT, since they could be used as a cross-disciplinary tool to assess individuals' capabilities under the stealth assessment paradigm.
Evaluation of propensity score used in cardiovascular research: a cross-sectional survey and guidance document

Background Propensity score (PS) methods are frequently used in cardiovascular clinical research. Previous evaluations revealed poor reporting of PS methods, however a comprehensive and current evaluation of PS use and reporting is lacking. The objectives of the present survey were to (1) evaluate the quality of PS methods in cardiovascular publications, (2) summarise PS methods and (3) propose key reporting elements for PS publications. Methods A PubMed search for cardiovascular PS articles published between 2010 and 2017 in high-impact general medical (top five by impact factor) and cardiovascular (top three by impact factor) journals was performed. Articles were evaluated for the reporting of PS techniques and methods. Data extraction elements were identified from the PS literature and extraction forms were pilot tested. Results Of the 306 PS articles identified, most were published in Journal of the American College of Cardiology (29%; n=88), and Circulation (27%, n=81), followed by European Heart Journal (15%; n=47). PS matching was performed most often, followed by direct adjustment, inverse probability of treatment weighting and stratification. Most studies (77%; n=193) selected variables to include in the PS model a priori. A total of 38% (n=116) of studies did not report standardised mean differences, but instead relied on hypothesis testing. For matching, 92% (n=193) of articles presented the balance of covariates. Overall, interpretations of the effect estimates corresponded to the PS method conducted or described in 49% (n=150) of the reviewed articles. Discussion Although PS methods are frequently used in high-impact medical journals, reporting of methodological details has been inconsistent. Improved reporting of PS results is warranted and these proposals should aid both researchers and consumers in the presentation and interpretation of PS methods.
Baseline Vitamin D Status, Sleep Patterns, and the Risk of Incident Type 2 Diabetes in Data From the UK Biobank Study

OBJECTIVE Circulating vitamin D concentrations have been associated with the risk of type 2 diabetes (T2D), but the results are inconsistent. Emerging evidence suggests that vitamin D metabolism is linked to sleep behaviors. We investigated the prospective association between serum 25-hydroxyvitamin D (25OHD) and the risk of incident T2D and whether such association was modified by sleep behaviors. RESEARCH DESIGN AND METHODS The study included 350,211 individuals free of diabetes in the UK Biobank. Serum 25OHD (nmol/L) concentrations were measured. Five sleep behaviors including sleep duration, insomnia, snoring, chronotype, and daytime sleepiness were included to generate overall sleep patterns, defined by healthy sleep scores. We also calculated genetic risk scores of sleep patterns. RESULTS During a median follow-up of 8.1 years, we documented 6,940 case subjects with incident T2D. We found that serum 25OHD was significantly associated with a lower risk of incident T2D, and the multivariate adjusted hazard ratio (HR) (95% CI) per 10 nmol/L increase was 0.88 (0.87–0.90). We found a significant interaction between 25OHD and overall sleep patterns on the risk of incident T2D (P for interaction = 0.002). The inverse association between high 25OHD and T2D was more prominent among participants with healthier sleep patterns. Among the individual sleep behaviors, daytime sleepiness showed the strongest interaction with 25OHD (P for interaction = 0.0006). The reduced HR of T2D associated with high 25OHD appeared to be more evident among participants with no frequent daytime sleepiness compared with those with excessive daytime sleepiness. The genetic variations of the sleep patterns did not modify the relation between 25OHD and T2D. CONCLUSIONS Our study indicates that higher serum 25OHD concentrations are associated with a lower risk of incident T2D, and such relations are modified by overall sleep patterns, with daytime sleepiness being the major contributor.
A broad mutational target explains a fast rate of phenotypic evolution

The rapid evolution of a trait in a clade of organisms can be explained by the sustained action of natural selection or by a high mutational variance, that is the propensity to change under spontaneous mutation. The causes for a high mutational variance are still elusive. In some cases, fast evolution depends on the high mutation rate of one or few loci with short tandem repeats. Here, we report on the fastest evolving cell fate among vulva precursor cells in Caenorhabditis nematodes, that of P3.p. We identify and validate causal mutations underlying P3.p's high mutational variance. We find that these positions do not present any characteristics of a high mutation rate, are scattered across the genome and the corresponding genes belong to distinct biological pathways. Our data indicate that a broad mutational target size is the cause of the high mutational variance and of the corresponding fast phenotypic evolutionary rate.
Assessing the format and content of journal published and non-journal published rapid review reports: A comparative study

Background As production of rapid reviews (RRs) increases in healthcare, knowing how to efficiently convey RR evidence to various end-users is important given they are often intended to directly inform decision-making. Little is known about how often RRs are produced in the published or unpublished domains, and what and how information is structured. Objectives To compare and contrast report format and content features of journal-published (JP) and non-journal published (NJP) RRs. Methods JP RRs were identified from key databases, and NJP RRs were identified from a grey literature search of 148 RR producing organizations and were sampled proportionate to cluster size by organization and product type to match the JP RR group. We extracted and formally compared ‘how’ (i.e., visual arrangement) and ‘what’ information was presented. Results We identified 103 RRs (52 JP and 51 NJP) from 2016. A higher percentage of certain features were observed in JP RRs compared to NJP RRs (e.g., reporting authors; use of a traditional journal article structure; section headers including abstract, methods, discussion, conclusions, acknowledgments, conflict of interests, and author contributions; and use of figures (e.g., Study Flow Diagram) in the main document). For NJP RRs, a higher percentage of features were observed (e.g., use non-traditional report structures; bannering of executive summary sections and appendices; use of typographic cues; and including outcome tables). NJP RRs were more than double in length versus JP RRs. Including key messages was uncommon in both groups. Conclusions This comparative study highlights differences between JP and NJP RRs. Both groups may benefit from better use of plain language, and more clear and concise design. Alternative innovative formats and end-user preferences for content and layout should be studied further with thought given to other considerations to ensure better packaging of RR results to facilitate uptake into policy and practice. Study registration The full protocol is available at: https://osf.io/29xvk/.
Development of Crystallinity of Triclinic Polymorph of Tricalcium Silicate

Tricalcium silicate phase is one of the main components of modern Portland cements. One of the major industrial challenges in the field of cement production is mapping the influence of individual clinker minerals and their polymorphs on the properties of industrially produced clinkers. The primary goal of this work is to improve the fundamental knowledge of understanding the process of alite formation and development from a crystallographic point of view. This study focuses on the observation of the crystallization process of triclinic alite during the firing process, which to date has not been thoroughly described. The effects of a wide range of temperatures and sintering periods on crystallinity were assessed on samples fired in platinum crucibles in a laboratory furnace. X-ray analysis—together with calculation of crystallinity using Scherrer’s equation—was used for observing the crystallite size changes of T1 alite polymorph. According to the acquired results, among the most technologically and economically advantageous regimes of production of a high-quality triclinic alite is the temperature of 1450 °C and sintering time of two hours. The most significant changes in the crystallite size occurred within the first hour of sintering for the whole investigated temperature range.
A new era in electroencephalographic monitoring? Subscalp devices for ultra–long‐term recordings

Inaccurate subjective seizure counting poses treatment and diagnostic challenges and thus suboptimal quality in epilepsy management. The limitations of existing hospital‐ and home‐based monitoring solutions are motivating the development of minimally invasive, subscalp, implantable electroencephalography (EEG) systems with accompanying cloud‐based software. This new generation of ultra–long‐term brain monitoring systems is setting expectations for a sea change in the field of clinical epilepsy. From definitive diagnoses and reliable seizure logs to treatment optimization and presurgical seizure foci localization, the clinical need for continuous monitoring of brain electrophysiological activity in epilepsy patients is evident. This paper presents the converging solutions developed independently by researchers and organizations working at the forefront of next generation EEG monitoring. The immediate value of these devices is discussed as well as the potential drivers and hurdles to adoption. Additionally, this paper discusses what the expected value of ultra–long‐term EEG data might be in the future with respect to alarms for especially focal seizures, seizure forecasting, and treatment personalization.
A new method for assessing the performance of signal processing filters in suppressing the side lobe level

Purpose This study aimed to propose a new ground truth ultrasound imaging method and to confirm its efficacy when applied to side lobe suppression filtering. Methods Using a computer simulation, we synthesized a side lobe-free image (i.e., with no side lobe whatsoever) by separating the main and side lobe signals in the construction of point target, speckled cyst, and pseudo-kidney images. During signal processing, we assessed the quality of the filtered image by comparing it with a ground truth image (i.e., the main lobe image). Results We examined the effect of reducing the side lobe by applying aperture apodization, side lobe estimation and reduction filtering, and minimum variance beamforming, which are widely used as side lobe suppression techniques. Despite the drawback of decreased resolution, the commonly used apodization method increases the contrast, which improves ultrasound image quality and enables a better diagnosis. Although side lobe estimation and reduction filtering and minimum variance beamforming are demanding in terms of computational resources, they can considerably improve ultrasound images. Compounding of ultrasound images processed by various signal processing methods increases the resolution and contrast, while reducing the speckle noise. Conclusion Although it appears that the proposed method can only be used for computer-generated radiofrequency data, this method can improve ultrasound image quality by identifying the characteristics of signal processing filters for side lobe suppression and applying appropriately adjusted filters to in vivo human imaging data.
The use of 3D ultrasound in comparing surgical techniques for posterior wall prolapse repair: a pilot randomised controlled trial

Abstract The most appropriate method for repairing posterior vaginal wall prolapse is still debatable. Women with symptomatic prolapse scheduled to undergo surgical repair in the posterior compartment were randomised to standard posterior colporrhaphy (SPC) or fascial and vaginal epithelial plication (FEP). Participants were assessed with the Prolapse Quality of Life (P-QOL) questionnaire, pelvic organ prolapse quantification (POP-Q) examination and three-dimensional ultrasound (3D US) prior to surgery and 6 months postoperatively. The research hypothesis is that 3D US of the pelvic floor is a reliable tool in comparing the anatomical outcomes of the two different surgical techniques. Differences in anatomical outcomes, assessed clinically and by ultrasonographic evaluation, were compared between the two groups using the Independent Mann–Whitney U-test and the Wilcoxon signed-rank sum test. Twenty-two women were included in the analysis. Six months postoperatively, women in the FEP arm had better anatomical outcomes compared to those who had undergone SPC (p = .02). Repeatability of the ultrasound technique was confirmed, showing moderate to very good agreement in all parameters and the 3D US evaluation was corroborated with the clinical examination, showing a greater reduction in the urogenital size in the FEP group. Impact statement What is already known on this subject? The low cost and universal availability of the ultrasound (US) makes it the most commonly used diagnostic modality. The ability to see beyond surface anatomy is important and useful in the assessment of the posterior vaginal wall prolapse and the obstructed defaecation, where this method may replace the defaecation proctography (Dietz 2019). Recent advances in pelvic floor ultrasonography (3D US) have achieved repeatability in the measurement of the levator hiatal (LH) dimensions, introducing a valid and readily available tool for researchers and clinicians (Dietz et al. 2005). Ultrasound may distinguish a true rectocele due to the weakening of the rectovaginal fascia from an enterocele, a rectal intussusception, or just a deficient perineum (Guzman Rojas et al. 2016). What do the results of this study add? Our study demonstrates that 3D translabial pelvic floor ultrasound is a useful and reliable tool in assessing the anatomical outcome of prolapse surgery. What are the implications of these findings for clinical practice and/or further research? Our study demonstrates that 3D translabial ultrasound of the pelvic floor is a useful and reproducible method in evaluating the anatomical outcomes of surgical repair for posterior wall prolapse. Genital hiatus (GH) and levator hiatus (LH) dimensions measured by ultrasound can be used as surrogate anatomical markers in comparing the efficacy of different surgical techniques.