Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards understanding the antagonistic activity of phytic acid against common foodborne bacterial pathogens using a general linear model

The increasing challenge of antibiotic resistance requires not only the discovery of new antibiotics, but also the development of new alternative approaches. Therefore, in the present study, we investigated for the first time the antibacterial potential of phytic acid (myo-inositol hexakisphosphate, IP6), a natural molecule that is ‘generally recognized as safe’ (FDA classification), against the proliferation of common foodborne bacterial pathogens such as Listeria monocytogenes, Staphylococcus aureus and Salmonella Typhimurium. Interestingly, compared to citric acid, IP6 was found to exhibit significantly greater inhibitory activity (P<0.05) against these pathogenic bacteria. The minimum inhibitory concentration of IP6 varied from 0.488 to 0.97 mg/ml for the Gram-positive bacteria that were tested, and was 0.244 mg/ml for the Gram-negative bacteria. Linear and general models were used to further explore the antibacterial effects of IP6. The developed models were validated using experimental growth data for L. monocytogenes, S. aureus and S. Typhimurium. Overall, the models were able to accurately predict the growth of L. monocytogenes, S. aureus, and S. Typhimuriumin Polymyxin acriflavine lithium chloride ceftazidime aesculin mannitol (PALCAM), Chapman broth, and xylose lysine xeoxycholate (XLD) broth, respectively. Remarkably, the early logarithmic growth phase of S. Typhimurium showed a rapid and severe decrease in a period of less than one hour, illustrating the bactericidal effect of IP6. These results suggest that IP6 is an efficient antibacterial agent and can be used to control the proliferation of foodborne pathogens. It has promising potential for environmentally friendly applications in the food industry, such as for food preservation, food safety, and for prolonging shelf life.
Health Communication Through News Media During the Early Stage of the COVID-19 Outbreak in China: Digital Topic Modeling Approach

Background : In December 2019, some COVID-19 cases were first reported and soon the disease broke out. As this dreadful disease spreads rapidly, the mass media has been active in community education on COVID-19 by delivering health information about this novel coronavirus. | Methods: We adopted the Huike database to extract news articles about coronavirus from major press media, between January 1st, 2020, to February 20th, 2020. The data were sorted and analyzed by Python software and Python package Jieba. We sought a suitable topic number using the coherence number. We operated Latent Dirichlet Allocation (LDA) topic modeling with the suitable topic number and generated corresponding keywords and topic names. We divided these topics into different themes by plotting them into two-dimensional plane via multidimensional scaling. | Findings: After removing duplicates, 7791 relevant news reports were identified. We listed the number of articles published per day. According to the coherence value, we chose 20 as our number of topics and obtained their names and keywords. These topics were categorized into nine primary themes based on the topic visualization figure. The top three popular themes were prevention and control procedures, medical treatment and research, global/local social/economic influences, accounting for 32.6%, 16.6%, 11.8% of the collected reports respectively. | Interpretation: The Chinese mass media news reports lag behind the COVID-19 outbreak development. The major themes accounted for around half the content and tended to focus on the larger society than on individuals. The COVID-19 crisis has become a global issue, and society has also become concerned about donation and support as well as mental health. We recommend that future work should address the mass media's actual impact on readers during the COVID-19 crisis through sentiment analysis of news data.
Celecoxib versus mefenamic acid in the treatment of primary dysmenorrhea

Abstract Background The objective was to compare the effectiveness and tolerability of mefenamic acid and celecoxib in women with primary dysmenorrhea (PD) and to compare the quality of life of study participants pre- and post-treatment. Materials and methods This was a randomized crossover clinical trial conducted among sexually inactive female adults aged 18–25 years with PD. Participants were asked to rate their pain score and answer a validated quality of life questionnaire (EQ-5D-3L) before and after consumption of each medication in two menstrual cycles. The effectiveness of celecoxib and mefenamic acid in treating PD was compared with regard to reduction in pain score and the need for medical leave and rescue therapy. Drug tolerability was determined by comparing the occurrence of side effects of both drugs. Quality of life scores pre- and post-intervention were measured and compared. Results Mefenamic acid had a comparable effect to celecoxib in relieving symptoms of PD. Both drugs were equally tolerable and showed similar impacts on quality of life. Conclusions This study demonstrated that mefenamic acid and celecoxib had similar effectiveness in improving pain score and quality of life in women with PD.
Characterization of the structure and interactions of P450 BM3 using hybrid mass spectrometry approaches

The cytochrome P450 monooxygenase P450 BM3 (BM3) is a biotechnologically important and versatile enzyme capable of producing important compounds such as the medical drugs pravastatin and artemether, and the steroid hormone testosterone. BM3 is a natural fusion enzyme comprising two major domains: a cytochrome P450 (heme-binding) catalytic domain and a NADPH-cytochrome P450 reductase (CPR) domain containing FAD and FMN cofactors in distinct domains of the CPR. A crystal structure of full-length BM3 enzyme is not available in its monomeric or catalytically active dimeric state. In this study, we provide detailed insights into the protein-protein interactions that occur between domains in the BM3 enzyme and characterize molecular interactions within the BM3 dimer by using several hybrid mass spectrometry (MS) techniques, namely native ion mobility MS (IM-MS), collision-induced unfolding (CIU), and hydrogen-deuterium exchange MS (HDX-MS). These methods enable us to probe the structure, stoichiometry, and domain interactions in the ∼240 kDa BM3 dimeric complex. We obtained high-sequence coverage (88–99%) in the HDX-MS experiments for full-length BM3 and its component domains in both the ligand-free and ligand-bound states. We identified important protein interaction sites, in addition to sites corresponding to heme-CPR domain interactions at the dimeric interface. These findings bring us closer to understanding the structure and catalytic mechanism of P450 BM3.
Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.
Male phenotypes in a female framework: Evidence for degeneration in sperm produced by male snails from asexual lineages.

How changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species, Potamopyrgus antipodarum, to address how evolution in an asexual content- including the potential for relaxed selection on male-specific traits- influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual P. antipodarum lineages affords a unique and powerful opportunity to assess the fate of sperm traits in a context where males are exceedingly rare. These comparisons revealed that the sperm produced by "asexual" males are markedly distinct from sexual counterparts. We also found that the asexual male sperm harbored markedly higher phenotypic variation and was much more likely to be morphologically abnormal. Together, these data suggest that transitions to asexual reproduction might be irreversible, at least in part because male function is likely to be compromised. These results are also consistent with a scenario where relaxed selection and/or mutation accumulation in the absence of sex translates into rapid trait degeneration.
ABCG2 Deficiency Does Not Alter Dolutegravir Metabolism and Pharmacokinetics

Dolutegravir (DTG) is a potent integrase inhibitor of human immunodeficiency virus. Because DTG is a substrate of the efflux transporter ABCG2 and ABCG2 is highly polymorphic, we asked whether dose adjustment of DTG is needed for ABCG2-deficient individuals. Using Abcg2-null mice, the current work investigated the impact of ABCG2 deficiency on DTG metabolism and pharmacokinetics. Compared with wild-type mice, no statistically significant difference was found in the systemic and tissue-specific (liver, kidney, and brain) pharmacokinetics of DTG in Abcg2-null mice. In addition, ABCG2 deficiency had no statistically significant impact on the production and excretion of DTG metabolites. In summary, this study demonstrated that deficiency of ABCG2 does not alter DTG metabolism and pharmacokinetics, suggesting that dose adjustment of DTG is not needed for individuals with ABCG2 deficiency. SIGNIFICANCE STATEMENT The current work demonstrated that deficiency of ATP-binding cassette subfamily G member 2 (ABCG2) does not alter Dolutegravir (DTG) metabolism and pharmacokinetics, suggesting that dose adjustment of DTG is not needed for individuals with ABCG2 deficiency.
Excellent Outcome of Young Children with Nodular Desmoplastic Medulloblastoma Treated on "Head Start" III: A Multi-Institutional, Prospective Clinical Trial.

BACKGROUND "Head Start" III, was a prospective clinical trial using intensive induction followed by myeloablative chemotherapy and autologous hematopoietic cell rescue (AuHCR) to either avoid or reduce the dose/volume of irradiation in young children with medulloblastoma. METHODS Following surgery, patients received five cycles of induction followed by myeloablative chemotherapy using carboplatin, thiotepa, and etoposide with AuHCR. Irradiation was reserved for children >6 years old at diagnosis or with residual tumor post-induction. RESULTS Between 2003 and 2009, 92 children <10 years old with medulloblastoma were enrolled. 5-year event-free survival (EFS) and overall-survival (OS) rates (±SE) were 46±5% and 62±5% for all patients, 61±8% and 77±7% for localized medulloblastoma, and 35±7% and 52±7% for disseminated patients. Nodular/desmoplastic (ND) medulloblastoma patients had 5-year EFS and OS (±SE) rates of 89±6% and 89±6% compared to 26±6% and 53±7% for classic and 38±13% and 46±14% for large-cell/anaplastic (LCA) medulloblastoma, respectively. In multivariate Cox regression analysis, histology was the only significant independent predictor of EFS after adjusting for stage, extent of resection, regimen, age and sex (p<0.0001). 5-year irradiation-free EFS was 78±8% for ND and 21±5% for classic/LCA medulloblastoma patients. Myelosuppression was the most common toxicity with two toxic deaths. Twenty-four survivors completed neurocognitive evaluation at a mean of 4.9 years post-diagnosis.IQ and memory scores were within average range overall whereas processing speed and adaptive functioning were low-average. CONCLUSION We report excellent survival and preservation of mean IQ and memory for young children with ND medulloblastoma using high-dose chemotherapy with most patients surviving without irradiation.
Analysis of Phonetic Balance in Standard English Passages.

Purpose A common way of eliciting speech from individuals is by using passages of written language that are intended to be read aloud. Read passages afford the opportunity for increased control over the phonetic properties of elicited speech, of which phonetic balance is an often-noted example. No comprehensive analysis of the phonetic balance of read passages has been reported in the literature. The present article provides a quantitative comparison of the phonetic balance of widely used passages in English. Method Assessment of phonetic balance is carried out by comparing the distribution of phonemes in several passages to distributions consistent with typical spoken English. Data regarding the distribution of phonemes in spoken American English are aggregated from the published literature and large speech corpora. Phoneme distributions are compared using Spearman rank order correlation coefficient to quantify similarities of phoneme counts in those sources. Results Correlations between phoneme distributions in read passages and aggregated material representative of spoken American English ranged from . 70 to . 89. Correlations between phoneme counts from all passages, literature sources, and corpus sources ranged from . 55 to . 99. All correlations were statistically significant at the Bonferroni-adjusted level. Conclusions Passages considered in the present work provide high, but not ideal, phonetic balance. Space exists for the creation of new passages that more closely match the phoneme distributions observed in spoken American English. The Caterpillar provided the best phonetic balance, but phoneme distributions in all considered materials were highly similar to each other.
Genetic variability in Danish polecats Mustela putorius as assessed by microsatellites

Genetic variability and population structure was investigated in 83 European polecats Mustela putorius by means of six microsatellite markers. The samples came from two areas in Denmark, Østjylland and Thy, which are separated by the Limfjord. The genetic diversity (He = 0.583) found in the total sample was similar to those found in other mustelid species and carnivores in general. A heterozygote deficiency, probably due to a Wahlund effect, suggested a further substructuring of the Danish sample. Population genetic substructuring was investigated in three different ways: by means of the program STRUCTURE, Wright's F-statistics and by an assignment test. All the tests indicate a subdivision of the sample into two distinct groups, which is concordant with the two sampling locations, with an average genetic divergence of FST = 0.126 and RST = 0.1692. The higher genetic diversity found in the Thy population (He = 0.578), as compared to the Østjylland population (He = 0.420), could be explained by assuming two ancient waves of colonisation of the Danish peninsula. Tests for recent bottlenecks were conducted, and the results suggest no evidence of neither population decline nor expansion. Our study is the first one in which microsatellite markers are used on polecat samples, and one locus (mv54) was found to be diagnostic in distinguishing between American mink Mustela vison and European polecat.
Effectiveness of the Common Elements Treatment Approach (CETA) in reducing intimate partner violence and hazardous alcohol use in Zambia (VATU): A randomized controlled trial

Background Both intimate partner violence (IPV) and alcohol misuse are highly prevalent, and partner alcohol misuse is a significant contributor to women’s risk for IPV. There are few evidence-based interventions to address these problems in low- and middle-income countries (LMICs). We evaluated the effectiveness of an evidence-based, multi-problem, flexible, transdiagnostic intervention, the Common Elements Treatment Approach (CETA) in reducing (a) women’s experience of IPV and (b) their male partner’s alcohol misuse among couples in urban Zambia. Methods and findings This was a single-blind, parallel-assignment randomized controlled trial in Lusaka, Zambia. Women who reported moderate or higher levels of IPV and their male partners with hazardous alcohol use were enrolled as a couple and randomized to CETA or treatment as usual plus safety checks (TAU-Plus). The primary outcome, IPV, was assessed by the Severity of Violence Against Women Scale (SVAWS) physical/sexual violence subscale, and the secondary outcome, male alcohol misuse, by the Alcohol Use Disorders Identification Test (AUDIT). Assessors were blinded. Analyses were intent-to-treat. Primary outcome assessments were planned at post-treatment, 12 months post-baseline, and 24 months post-baseline. Enrollment was conducted between May 23, 2016, and December 17, 2016. In total, 123 couples were randomized to CETA, 125 to TAU-Plus. The majority of female (66%) and a plurality of male (48%) participants were between 18 and 35 years of age. Mean reduction in IPV (via SVAWS subscale score) at 12 months post-baseline was statistically significantly greater among women who received CETA compared to women who received TAU-Plus (−8.2, 95% CI −14.9 to −1.5, p = 0.02, Cohen’s d effect size = 0.49). Similarly, mean reduction in AUDIT score at 12 months post-baseline was statistically significantly greater among men who received CETA compared to men who received TAU (−4.5, 95% CI −6.9 to −2.2, p < 0.001, Cohen’s d effect size = 0.43). The Data and Safety Monitoring Board recommended the trial be stopped early due to treatment effectiveness following the 12-month post-baseline assessment, and CETA was offered to control participants. Limitations of the trial included the lack of a true control condition (i.e., that received no intervention), self-reported outcomes that may be subject to social desirability bias, and low statistical power for secondary IPV outcomes. Conclusions Results showed that CETA was more effective than TAU-Plus in reducing IPV and hazardous alcohol use among high-risk couples in Zambia. Future research and programming should include tertiary prevention approaches to IPV, such as CETA, rather than offering only community mobilization and primary prevention. Trial registration The trial was registered on ClinicalTrials.gov (NCT02790827).
Diseases in a moose population subjected to low predation.

Well-publicized studies on two moose diseases, elaphostrongylosis and moose wasting syndrome, conducted across Sweden from 1985 to 1994 resulted in an increased number of reports of sick and dead moose. A sample of 724 moose were investigated, including 426 females, 208 males, and 90 of unknown sex with an average age of 3.7 years (SD = 4.9, range 0-20). Prominent diagnoses were elaphostrongylosis (18%), moose wasting syndrome (11%), and accidental death (11%). Other important diagnoses were neoplasm (5%), parasitic (6%), nervous system (5%), infectious (4%), eye and ear diseases (4%), and predation (3%). From the beginning to the middle of the 20th century approximately 10 wolves, 130 bears, 175 lynx, and 100 wolverines were present in Sweden (449,000 km2). Currently, the scene is quite different with wolf, bear, lynx, and wolverine populations all increasing. The total number of large predators and scavengers is estimated at 2,500-3,000. We believe that the diversity of moose diseases seen in the future will differ from that observed during the 1980s and 1990s by being less visible due to increasing predation. ALCES VOL. 41: 37-48 (2005)
Estimation of the prevalence of idiopathic epilepsy and structural epilepsy in a general population of 900 dogs undergoing MRI for epileptic seizures

Due to variation in study designs the prevalence of idiopathic epilepsy (IE) and structural epilepsy (SE) in dogs is largely unknown. The objective was to provide estimates of the prevalence of IE and SE in a large population of dogs undergoing MRI for epileptic seizures. A retrospective study on 900 dogs undergoing MRI for seizures was performed. MRI scans, summary clinical history and neurological examination from the VetCT database were reviewed and a diagnosis assigned by board-certified radiologists. Structural lesions were identified as a cause of seizures in 45.1 per cent (n=406) of cases. No structural lesions were identified in 54.9 per cent (n=494) of cases with presumed IE diagnosed in 53.8 per cent (n=484) of dogs. Dogs between six months and six years were more often associated with IE (P<0.001), small breeds were overrepresented with suspected inflammatory brain disease (P=0.001) and large entire dogs more often diagnosed with extra-axial neoplasms (P=0.001). Over 31.0 per cent of dogs with suspected IE were six years or older. This study is the largest of its kind in dogs and provides accurate estimates of underlying causes of epilepsy. MRI findings should be considered in the context of a detailed clinical history and neurological examination.
Stable establishment of wMel Wolbachia in Aedes aegypti populations in Yogyakarta, Indonesia

The successful establishment of the wMel strain of Wolbachia for the control of arbovirus transmission by Aedes aegypti has been proposed and is being implemented in a number of countries. Here we describe the successful establishment of the wMel strain of Wolbachia in four sites in Yogyakarta, Indonesia. We demonstrate that Wolbachia can be successfully introgressed after transient releases of wMel-infected eggs or adult mosquitoes. We demonstrate that the approach is acceptable to communities and that Wolbachia maintains itself in the mosquito population once deployed. Finally, our data show that spreading rates of Wolbachia in the Indonesian setting are slow which may reflect more limited dispersal of Aedes aegypti than seen in other sites such as Cairns, Australia.
Managing COVID-19 in Patients With Cancer: A Double Blow for Oncologists.

Currently, the world is facing a medical emergency because of the current outbreak of the novel coronavirus (2019-nCoV, or COVID-19). Within the past few months, the outbreak has turned rapidly from an epidemic to a pandemic. Researchers, scientists, and treating physicians are trying best to provide their patients with the best available treatment. Given the severe immunosuppression caused by cancer and its therapy, patients with cancer are at a higher risk of COVID-19 infection.