Miracle-dz/UniFAR-FTUs huggingface dataset:
Bias and standard deviation due to Weibull parameter estimation for small data sets

Weibull statistics have become the most popular statistics to describe breakdown events in solid dielectrics. The version most applied is probably the Weibull 2-parameter model. The present paper briefly reviews the development of the Weibull distribution while paying most attention to the 2-parameter version. Subsequently, the performance of two types of analysis methods, i.e. maximum likelihood and linear regression methods, are investigated. Particularly, the performance with small data sets were of interest. The reason for this interest are common events that do not allow the collection of larger data sets. Rather than fall into pure gambling, it is attempted to describe both the bias, i.e. systematic error, and the standard deviation under these conditions. As a practical tool, a recently introduced asymptotic difference function is utilized to cast bias and standard deviation in simple formulas, even for small data sets. The unbiased maximum likelihood method is also compared to an alternative so-called 'generalized' or 'relative' maximum likelihood method. For ten cases, a selection of formulas is tabulated which can be added to current programs. Among this set is a formula to unbias the Weibull shape parameter for censored data sets.
Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells

RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face.
Neuronal activation and performance changes in working memory induced by chronic sleep restriction in adolescents

Most adolescents get less than the recommended 8–10 hr of sleep per night. Functional deficits from lack of sleep include disruption of working memory. Adult neuroimaging studies of sleep deprivation suggest diminished responses in task‐related brain networks if performance degrades, but compensatory increased responses with maintained performance. This study utilized functional magnetic resonance imaging to examine compensatory and diminished brain responses in adolescents during working memory performance, comparing chronic sleep restriction and healthy sleep duration. Thirty‐six healthy adolescents, 14–17 years old, experienced a 3‐week protocol: (a) sleep phase stabilization; (b) sleep restriction (~6.5 hr nightly); and (c) healthy sleep duration (~9 hr nightly). After each sleep manipulation, we acquired functional magnetic resonance imaging with an NBack working memory task with four difficulty levels (0 to 3‐back). NBack performance degraded with higher task difficulty, but without a detectable effect of sleep duration. ANOVA revealed main effects of both NBack difficulty and sleep in widespread brain networks. Planned contrasts showed that, compared with healthy sleep, sleep restriction resulted in greater medial prefrontal activation and weaker activation in the precuneus for the most difficult task condition. During sleep restriction, we found compensatory functional responses in brain regions that process sensory input and vigilance. However, adolescents also showed impaired performance and diminished brain responses during the hardest task level under a week of chronic sleep restriction. Chronic sleep restriction during adolescence is common. Understanding the impact of ongoing functional compensation and performance breakdown during this developmental period can have important implications for learning and educational strategies.
A functional model of soil porosity used to interpret measurements of gas diffusion

Summary A simple model was employed to interpret the results of a series of measurements of gas diffusion in soil cores. The model divides air-filled porosity into three functional categories: arterial, marginal and remote. Diffusion along the axis of the core occurs through arterial pores; marginal pores do not contribute to axial diffusion; remote pores are isolated from gas transport. Simulations based on the model closely resembled data acquired from real cores. Optimizing the fit between real and simulated data gave estimates of the three functional pore fractions which generally made sense (compaction or wetting of cores resulted in reduced arterial and increased marginal porosities, for example). Dividing the pores into the different classes specified by the model was functionally equivalent (i.e. observable results were identical) to the introduction of a tortuosity factor to represent pore convolution. In order to account for observed diffusion rates in terms of pore convolution alone it is sometimes necessary to invoke implausibly high tortuosities; the introduction of marginal porosity renders this unnecessary without in any way compromising the ability of the model to simulate real diffusion data.
The role of dietary diversity in preventing metabolic‐related outcomes: Findings from a systematic review

Dietary diversity has been linked to insulin resistance; however, studies are inconsistent on whether dietary diversity protects against metabolic‐related outcomes. We aimed to comprehensively assess metabolic‐related outcomes of greater diversity across the diet and within major food groups. A systematic search of peer‐reviewed literature was done in bibliographic databases (Medline, Scopus, and Web of Science) for longitudinal studies that reported on original research. Data extraction and quality appraisal used predefined criteria; reported findings were synthesized through a narrative approach. Fourteen studies were identified as eligible. Greater dietary diversity across major food groups, and diversity within fruits and/or vegetables, was associated with reduced risk of type 2 diabetes (T2D). Effects varied based on exposure definition and adjustment for known confounders. While diversity of less healthy foods was associated with greater adiposity, diversity of all foods and healthy foods was associated with reduced incidence of depression and cognitive decline. Evidence supports the protective effect of dietary diversity against cognitive decline and T2D. The association between dietary diversity and adiposity may be dependent on the healthiness of foods. Public health efforts to prevent metabolic‐related diseases should include an emphasis on a varied diet as a healthy eating strategy.
Comparison of different scoring methods based on latent variable models of the PHQ-9: an individual participant data meta-analysis

Abstract Background Previous research on the depression scale of the Patient Health Questionnaire (PHQ-9) has found that different latent factor models have maximized empirical measures of goodness-of-fit. The clinical relevance of these differences is unclear. We aimed to investigate whether depression screening accuracy may be improved by employing latent factor model-based scoring rather than sum scores. Methods We used an individual participant data meta-analysis (IPDMA) database compiled to assess the screening accuracy of the PHQ-9. We included studies that used the Structured Clinical Interview for DSM (SCID) as a reference standard and split those into calibration and validation datasets. In the calibration dataset, we estimated unidimensional, two-dimensional (separating cognitive/affective and somatic symptoms of depression), and bi-factor models, and the respective cut-offs to maximize combined sensitivity and specificity. In the validation dataset, we assessed the differences in (combined) sensitivity and specificity between the latent variable approaches and the optimal sum score (⩾10), using bootstrapping to estimate 95% confidence intervals for the differences. Results The calibration dataset included 24 studies (4378 participants, 652 major depression cases); the validation dataset 17 studies (4252 participants, 568 cases). In the validation dataset, optimal cut-offs of the unidimensional, two-dimensional, and bi-factor models had higher sensitivity (by 0.036, 0.050, 0.049 points, respectively) but lower specificity (0.017, 0.026, 0.019, respectively) compared to the sum score cut-off of ⩾10. Conclusions In a comprehensive dataset of diagnostic studies, scoring using complex latent variable models do not improve screening accuracy of the PHQ-9 meaningfully as compared to the simple sum score approach.
Protective effect of melatonin against herbicides-induced hepatotoxicity in rats.

Exposure to the herbicides Paraquat and Roundup® may cause cell lesions due to an increase in oxidative stress levels in different biological systems, even in the liver. The aim of this study was to analyze the effect of melatonin on liver of rats exposed to herbicides. A total of 35 rats were randomly divided into seven equal-sized groups: control, Paraquat, Roundup®, Paraquat + Roundup®, Paraquat + melatonin, Roundup® + melatonin, and Paraquat + Roundup® + melatonin. Samples of blood and hepatic tissue were collected at the end of the seventh day of exposure and treatment with melatonin. Body weight, hematological parameters, and histopathological, biochemical analyses and determination of oxidative stress levels in liver were evaluated. Body weight was compromised (P < 0.01). Alterations of hematologic parameters were significant when compared to control (P < 0.001). Biochemically, serum levels of albumin decreased (P < 0.001), but serum levels of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase increased (P < 0.001). Histopathology revealed necrotic hepatocytes, portal and central-lobular inflammatory infiltrate, congestion of capillaries. Serum levels of thiobarbituric acid reactive substances were found to be significantly elevated (P < 0.05; P < 0.001), and serum level of reduced glutathione was significantly lower (P < 0.05; P < 0.001). The groups treated concomitantly with melatonin revealed results similar to those of the control. However, melatonin acted as a protective agent for the liver against experimentally induced hepatic toxicity, promoting prevention of body weight, oxidative stress, and normalization of hematological and biochemical parameters.
Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus)

Abstract Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai–Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.
The synergistic and antagonistic antioxidant interactions of dietary phytochemical combinations

Abstract The frequent intake of whole foods and dietary food variety is recommended due to their health benefits, such as prevention of multiple chronic diseases, including cancer, Alzheimer’s disease, cardiovascular diseases, and type 2 diabetes mellitus. Often, consuming whole fruits or vegetables showed the enhanced effects than consuming the individual dietary supplement from natural products, which is widely explained by the interactive effects of co-existing phytochemicals in whole foods. Although research relevant to interactive effects among the bioactive compounds mounted up, the mechanism of interaction is still not clear. Especially, biological influence factors such as bioavailability are often neglected. The present review summarizes the progress on the synergistic and antagonistic effects of dietary phytochemicals, the evaluating models for antioxidant interactions, and the possible interaction mechanisms both in vitro and in vivo, and with an emphasis on biological-related molecular mechanisms of phytochemicals. The research on the interaction mechanism is of value for guiding how to take advantage of synergistic effects and avoid antagonistic effects in daily diets or phytochemical-based treatments for preventing chronic diseases.
Weight and body mass index increase after switch from tenofovir disoproxil fumarate to tenofovir alafenamide fumarate-containing treatment in an antiretroviral therapy-experienced group

Tenofovir alafenamide fumarate (TAF) is an alternative to tenofovir disoproxil fumarate (TDF). Currently, TAF is increasingly being used because of its non-inferior antiviral properties, lower risk of nephrotoxicity, and lower decrease in bone mineral density than TDF. There is growing evidence of unfavorable effects of TAF on weight and body mass index (BMI) in antiretroviral therapy (ART)-experienced patients treated with TAF-based ART. The aim of this study was to evaluate whether switching from TDF-containing to TAF-containing ART is associated with an increase in BMI and body weight in ART-experienced patients. Two study groups were established: 32 patients who switched from TDF to TAF only and 68 patients who switched from TDF to TAF along with changes to other components of the ART regimen. Significant weight gain and BMI increase was observed during the first year after initiation of TAF-containing ART regimens in both groups (mean change +1.91 kg and +0.61 kg/m2 in the first group and +1.50 kg and +0.49 kg/m2 in the second group). During the second year of TAF-based treatment, a sustained trend of body weight and BMI increase was noted only in the second group (mean change +1.46 kg, + 0.46 kg/m2). Analysis of body weight changes in certain subpopulations from the second group (selected based on patients’ baseline characteristics) revealed a significant weight gain within two years after the switch in patients over 50 years old and in those whose ART had lasted longer than 10 years. These findings suggest that a possible impact of TAF on weight gain should be taken into account when selecting ART components, especially in older patients or those with a long history of antiretroviral treatment.
A systematic review and meta-analysis on cognitive frailty in community-dwelling older adults: risk and associated factors

Abstract Objectives To identify which factors are associated with cognitive frailty (CF), as well as the impact of CF on the incidence of dementia and mortality. Methods A systematic review with meta-analysis was carried out using papers that enrolled a total of 75,379 participants and were published up to January 2020. Results Of the 558 identified records, 28 studies met the inclusion criteria and were included in the review. The meta-analysis of cross-sectional studies showed that CF has a significant association of having an older age and a history of falls. In longitudinal studies, the analysis showed a significant increase in risk of mortality and dementia for those with CF. Discussion This is the first systematic review and meta-analysis on CF, which addressed a wide variety of factors associated with the theme and which pointed out some as a potential target for prevention or management with different interventions or treatments, showing the clinical importance of its identification in the most vulnerable and susceptible groups.
Improving lives not just saying no to substances: Evaluating outcomes for a young people’s substance use team trained in the AMBIT approach

Adaptive Mentalization Based Integrative Therapy (AMBIT) is a systemic, mentalization based intervention designed for young people with multiple problems including mental health problems. The purpose of this paper is to examine the impact of this approach both on clinical and functional outcomes for young people seen by a specialist young people’s substance use service between 2015 and 2018. About 499 cases were seen by the service during this period. Substance use outcomes were obtained for 383 cases using the Treatment Outcome Profile (TOP). Cannabis and alcohol use were the key substance use problems for 81% and 63% respectively. Functional outcomes using the AMBIT Integrative Measure (AIM) were obtained for 100 cases covering domains of daily living, socio-economic context, peer relationships and mental health. At treatment end, cannabis use reduced significantly (t = 10.78; df = 311; p = .00; Cohen’s d ES.61 as did alcohol use (t = 6.938; df = 242; p = .000; ES 0.44). Functional improvements were shown in five out of seven domains with highly significant total functional improvements on key problems selected by the client (t = 14.01; df = 99; p = .000; ES1.34). Measuring functional as well as clinical outcomes appears to reflect more accurately the overall benefit of the service to clients.
A Solid-Phase Extraction-Thin-Layer Chromatographic-Fiber Optical Scanning Densitometric Method for Determination of Flavonol Aglycones in Extracts of Rose Leaves

A qualitative and quantitative analytical procedure using thin-layer chromatography in combination with fiber optical scanning densit-ometry is presented for identification of, mainly, flavonol aglycones (quercetin and kaempferol) in extracts from rose leaves. Preliminary cleaning of the extracts was necessary to remove matrix components; SPE was used for this purpose. The compounds were identified by automatic measurement and computer-based comparison of in-situ UV spectra with reference spectra using a cross-correlation function. For amounts between 1 and 10 µg spot−1 there were no differences between in-situ UV spectra acquired for kaempferol but some differences were observed for quercetin.
Similarity-Based Unsupervised Spelling Correction Using BioWordVec: Development and Usability Study of Bacterial Culture and Antimicrobial Susceptibility Reports

Background Existing bacterial culture test results for infectious diseases are written in unrefined text, resulting in many problems, including typographical errors and stop words. Effective spelling correction processes are needed to ensure the accuracy and reliability of data for the study of infectious diseases, including medical terminology extraction. If a dictionary is established, spelling algorithms using edit distance are efficient. However, in the absence of a dictionary, traditional spelling correction algorithms that utilize only edit distances have limitations. Objective In this research, we proposed a similarity-based spelling correction algorithm using pretrained word embedding with the BioWordVec technique. This method uses a character-level N-grams–based distributed representation through unsupervised learning rather than the existing rule-based method. In other words, we propose a framework that detects and corrects typographical errors when a dictionary is not in place. Methods For detected typographical errors not mapped to Systematized Nomenclature of Medicine (SNOMED) clinical terms, a correction candidate group with high similarity considering the edit distance was generated using pretrained word embedding from the clinical database. From the embedding matrix in which the vocabulary is arranged in descending order according to frequency, a grid search was used to search for candidate groups of similar words. Thereafter, the correction candidate words were ranked in consideration of the frequency of the words, and the typographical errors were finally corrected according to the ranking. Results Bacterial identification words were extracted from 27,544 bacterial culture and antimicrobial susceptibility reports, and 16 types of spelling errors and 914 misspelled words were found. The similarity-based spelling correction algorithm using BioWordVec proposed in this research corrected 12 types of typographical errors and showed very high performance in correcting 97.48% (based on F1 score) of all spelling errors. Conclusions This tool corrected spelling errors effectively in the absence of a dictionary based on bacterial identification words in bacterial culture and antimicrobial susceptibility reports. This method will help build a high-quality refined database of vast text data for electronic health records.
Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or “captured” by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch‐flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot‐winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations of S. trivirgatus form two paraphyletic clades, one being sister to and presumably introgressed by S. guttula despite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event between S. guttula and Australian S. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies of S. trivirgatus into an island population of S. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction of S. guttula from mainland Australia resulted from range expansion by S. trivirgatus.