Miracle-dz/UniFAR-FTUs huggingface dataset:
Pesticides and total polychlorinated biphenyls in chinook salmon and carp harvested from the great lakes : effects of skin-on and skin-off processing and selected cooking methods

Pesticides and total PCBs were determined in raw skin-on and skin-of chinook salmon harvested from Lakes Huron and Michigan as well as in carp fillets harvested from Lakes Erie and Huron and after baking, charbroiling, and canning salmon as well as pan and deep fat frying carp. Raw skin-off fillets had an average of less than 50% of the residues found in ranq skin-on fillets. Cooked skin-off fillets were also found to have significantly lower residues than the cooked skin-on fillets. Cooking significantly reduced the DDT complex, dieldrin, hexachlorobenzene, the chlordane complex, toxaphene, heptachlor epoxide, and total PCBs contents. Few significant differences were found among cooking methods. Canning did significantly reduce DDE in salmon. Average losses of pesticides and total PCBs from the chinook salmon ranged from 30 to 41%. Similar average percentage losses were found for carp, ranging from 30 to 35% for the DDT complex, chlordane complex, and total PCBs, while the losses of HCB and dieldrin were greater than 40%
Fitness maps to a large-effect locus in introduced stickleback populations

Significance The role of mutations of large effect in adaptive evolution is a question of enduring interest. Large-effect mutations were once seen as unlikely contributors to adaptation, but we now have numerous examples. A major shortcoming of the evidence is the lack of information on fitness effects of mutations. We conducted a quantitative trait locus study that mapped fitness in an experimental field population of stickleback to a large-effect gene, Ectodysplasin (Eda). We compared this result with allele frequency change at the gene in a young lake population, which also revealed strong natural selection and large fitness effects of the Eda gene and/or linked genes. Selection on ancient genetic variants may increase the prevalence of large-effect fitness variants in adaptive evolution. Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
Bioremediation and Bioreduction of Dissolved U(VI) by Microbial Mat Consortium Supported on Silica Gel Particles

The goal of this research was to simulate natural attenuation processes for uranium (U) by constructing a bioremediation system based on microbial mats. Ancient microbial consortia, such as microbial mats, have evolved the capacity to manage hostile environments and potentially bioremediate metal-contaminated water. To facilitate the engineering applications of microbial mats, the constituent microbial groups of the mat consortium were immobilized with required nutrients in silica gel. Resulting silica mat particles (SMP) were tested for efficiency in removing and, subsequently, reducing U(VI) to U(IV). Uranium-containing groundwaters from a Superfund Site (0.2 mg U(VI) L-1, 293 mg HCO3 L-1 at pH 8.2) and synthetic waters (∼0.05−2 mg U(VI) L-1, pH 8−9) were assessed with this system. Over 80% of the dissolved U(VI), present as mostly U(VI)−carbonate (Superfund) or U(VI)−hydrolysis species (synthetic), was removed by the SMP within 15 min of treatment. X-ray absorption near-edge structure spectroscopy stud.
Urosepsis in Older Adults: Epidemiologic Trends in Florida

ABSTRACT The incidence and geographic distribution of urosepsis, a life-threatening condition in older adults, is not well understood. The Florida State Inpatient Databases (2012–2014) showed an increase in the incidence of community-acquired urosepsis (5.37 to 6.16 per 1000), particularly among Hispanic older adults residing in low socioeconomic, urban areas with large numbers of nursing homes. These findings suggest a state policy is needed to address community-based preventative care and education for early detection of urosepsis in low-income urban areas. It is important for local health departments to partner with nursing homes to address disparities in care that disproportionally impact Hispanics.
Mobile App–Based Self-Report Questionnaires for the Assessment and Monitoring of Bipolar Disorder: Systematic Review

Background Bipolar disorder is a chronic, progressive illness characterized by recurrent episodes of mania and depression. Self-report scales have historically played a significant role in the monitoring of bipolar symptoms. However, these tools rely on episodic memory, which can be unreliable and do not allow the clinician to monitor brief episodic symptoms or the course of symptoms over shorter periods of time. Mobile app–based questionnaires have been suggested as a tool to improve monitoring of patients with bipolar disorder. Objective This paper aims to determine the feasibility and validity of mobile app–based self-report questionnaires. Methods We performed a systematic review of the literature according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. The PubMed, PsycInfo, Web of Science, Ovid MEDLINE, and EMBASE databases were searched for papers published in English that assessed adherence to and the validity of mobile app–based self-report questionnaires. Relevant studies published from database creation to May 22, 2020, were identified, and results examining the validity of and rates of adherence to app-based self-report questionnaires are reported. Results A total of 13 records were identified for inclusion in this review. Of these studies, 4 assessed the concurrent validity of mobile app–based self-report tools, with the majority of findings indicating significant associations between data collected using these tools and the Young Mania Rating Scale, Hamilton Depression Rating Scale-17, or Montgomery-Åsberg Depression Rating Scale (P<.001 to P=.24). Three studies comparing the variability or range of symptoms between patients with bipolar disorder and healthy controls suggested that these data are capable of differentiating between known groups. Two studies demonstrated statistically significant associations between data collected via mobile app–based self-report tools and instruments assessing other clinically important factors. Adherence rates varied across the studies examined. However, good adherence rates (>70%) were observed in all but 1 study using a once-daily assessment. There was a wide range of adherence rates observed in studies using twice-daily assessments (42%-95%). Conclusions These findings suggest that mobile app–based self-report tools are valid in the assessment of symptoms of mania and depression in euthymic patients with bipolar disorder. Data collected using these tools appear to differ between patients with bipolar disorder and healthy controls and are significantly associated with other clinically important measures. It is unclear at this time whether these tools can be used to detect acute episodes of mania or depression in patients with bipolar disorder. Adherence data indicate that patients with bipolar disorder show good adherence to self-report assessments administered daily for the duration of the study periods evaluated.
Organoids enabling COVID-19 research and significance of Biomaterial technologies.

Organoids, which are self-organizing 3D culture systems, have greatly expanded our understanding of molecular interactions between cells and their niche, mechanisms underlying development and organ regeneration apart from serving as highly valuable in vitro model systems for drug testing and platforms for personalized therapeutics[1]. Organoids grow in vitro into a complete mimic of an organ of interest containing all the cell types present in that organ in a three-dimensional (3D) biomaterial environment with the source of those cell types derived from the organ of interest itself or pluripotent stem cells[1].
Maternal inheritance of mitochondrial DNA in mice after inter-species hybridization and 138 generations of backcrossing

This study represents a continuation of a backcrossing experiment initiated in 1982 and reported on earlier after seven generations of backcrossing (Gyllensten et al. 1985) and again after 26 generations (Gyllensten et al. 1991). For the better part of 50 years, it has been demonstrated that mitochondrial DNA (mtDNA) has a largely, if not exclusively maternal mode of inheritance among the multicellular organisms studied to date (Dawid and Blackler 1972; Hutchison et al. 1974; Francisco et al. 1979; Giles et al. 1980; Reilly and Thomas 1980 as cited in Gyllensten et al. 1985). Few studies of invertebrates and no studies of vertebrates have examined maternal inheritance of mtDNA over the course of 139 generations as is the case here (Degrugillier and Newman 1993). Our initial results identify 100% conformity of mtDNA with M. spretus suggesting that any potential paternal contribution of mtDNA to this mouse lineage will require more detailed analysis to detect it.
Protein foods from animal sources, incident cardiovascular disease and all-cause mortality: a substitution analysis.

BACKGROUND Protein-rich foods are major parts of the human diet and are highly heterogeneous in nutrient composition and health effects. Designing healthy diets for disease prevention requires careful consideration of substituting unhealthier protein foods with healthier protein foods. METHODS This was a pooled analysis of six prospective cohort studies of 29 682 US participants. Data were collected in 1985-2016. Adjusted hazard ratios (HRs) and 30-year absolute risk differences (ARDs) were calculated for the associations between simultaneous substitution of one or more animal protein foods with other animal or plant protein foods at various amounts, and incident cardiovascular disease (CVD) and all-cause mortality. RESULTS Substituting eggs, processed meat, unprocessed red meat or poultry with nuts, whole grains, legumes or fish was associated with lower risks of incident CVD and all-cause mortality. According to different substitution amounts (varying from one serving per week to one serving per day) and different numbers of protein foods being simultaneously substituted (varying from one to four), estimates ranged between 1%: HR, 0.99 [95% confidence interval (CI), 0.98-1.00], and 54%: HR, 0.46 (0.35-0.60), lower risks on the relative scale and between 0.3%: ARD, -0.29% (-0.48% to -0.05%), and 14.0%: ARD, -13.96% (-17.29% to -9.96%) lower risks on the absolute scale. CONCLUSIONS Nuts, whole grains, legumes and fish appeared to be healthier protein sources than eggs, processed meat, unprocessed red meat and poultry for preventing incident CVD and premature death. The magnitude of lower risk for incident CVD and all-cause mortality was driven by amount and number of animal protein foods substituted.
An Attempt to Minimize the Cost of Extracting Lithium from Boron Clays Through Robust Process Design

In this study a robust design method is developed for extracting Li from boron (B) clays with the aim of minimizing cost and maximizing productivity. Lithium is commercially extracted from brines and certain minerals. Its extraction from clays has previously been found to be expensive, a major part of the extraction cost being attributed to the raw materials used. In this study, raw materials from lower-cost resources are used without applying any standardization to them and this might increase variation in the results. To minimize the variation, and achieve high extraction levels, robust design, statistical design and analysis of experiments, and response surface methodologies are utilized. As a result, consistently higher extraction levels have been achieved compared to previous studies. The experiments were conducted using the Bigadiç boron clay fields in Turkey. However, the method is generally applicable to other cases also.
MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor–1

The oncoprotein transcription factor MYC is a major driver of malignancy and a highly validated but challenging target for the development of anticancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here we interrogate how one MYC co-factor, host cell factor (HCF)–1, contributes to MYC activity in a human Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets and demonstrate how modulation of the MYC–HCF-1 interaction influences cell growth, metabolite profiles, global gene expression patterns, and tumor growth in vivo. This work defines HCF-1 as a critical MYC co-factor, places the MYC–HCF-1 interaction in biological context, and highlights HCF-1 as a focal point for development of novel anti-MYC therapies.
Home-based music therapy for children with developmental disorders during the COVID-19 pandemic

Introduction During the COVID-19 pandemic, children with neurodevelopmental disabilities could not attend their usual rehabilitation therapies, with a consequent reduced support of developmental process and risk of worsening of their clinical conditions. Methods We prospectively enrolled 14 children with developmental delay, who had already tried a personalised music therapy (Euterpe method). We included them in a 12-day programme of home-based music therapy. The children and their parents were investigated using the Sleep Disturbance Scale for Children and the Parent Stress Index-Short Form. Results Fourteen children started the intervention, while only 12 children completed all the planned home sessions and assessments. We observed a significant improvement in children’s sleep quality and a reduction of parental distress. Discussion The significant improvements in parental distress and sleep quality must be considered important achievements for the quality of life of a child and their family. Home-based music therapy can provide a feasible approach to improving sleep and parent’s stress for children with developmental disorders.
Assessment of the quality, oxidative status and dietary energy value of lipids used in non‐ruminant animal nutrition

Abstract BACKGROUND Fats and oils represent the most concentrated source of energy available to animal nutritionists and form an expensive part of the diet. Thorough understanding of lipid quality and composition are required for efficient and precise diet formulation. Therefore, 724 samples of commercially available fats and oils were assessed for fatty acid profile, oxidation status and energetic value as per the Wiseman equation, with consideration of a correction factor K, which is based on the presence of the energy diluting compounds moisture, impurities and unsaponifiables. RESULTS Energy diluting compounds were widespread across fat types and sources. Average MIU (moisture, insoluble impurities and unsaponifiable matter) presence in individual oils was 5.1–28.1 g kg−1. Using the adapted Wiseman equation presented in the current paper, which reflects the energy diluting potential of MIU, the calculated energy values of fats and oils is reduced by up to 46% in extreme cases compared to those predicted by the original equation. From the chemical parameters, it is clear that there is limited correlation between individual measures of oxidation, with only weak negative correlations between 2‐thiobarbituric acid (TBA) and Oxidative Stability Index (OSI) values (Spearman's ρ between −0.20 and −0.39) and a weak to moderate negative correlation between peroxide value (PV) and OSI (Spearman's ρ between −0.20 and −0.59) for certain fats and oils. A moderate to very strong positive correlation between FFA and the energy diluting compounds MIU was observed for all animal fats (Spearman's ρ between 0.40 and 1.00). CONCLUSION The current report highlights the large variation in composition and quality seen in commercially available fats and oils and encourages ongoing analysis and assessment rather than reliance on published values. The results also indicate that the oxidation parameters when interpreted as separate values lack the power of inferring oil and fat quality. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling

MOTIVATION Statistical detection of co-occurring genes across genomes, known as "phylogenetic profiling", is a powerful bioinformatic technique for inferring gene-gene functional associations. However, this can be a challenging task given the size and complexity of phylogenomic databases, difficulty in accounting for phylogenetic structure, inconsistencies in genome annotation, and substantial computational requirements. RESULTS We introduce PhyloCorrelate-a computational framework for gene co-occurrence analysis across large phylogenomic datasets. PhyloCorrelate implements a variety of co-occurrence metrics including standard correlation metrics and model-based metrics that account for phylogenetic history. By combining multiple metrics, we developed an optimized score that exhibits a superior ability to link genes with overlapping GO terms and KEGG pathways, enabling gene function prediction. Using genomic and functional annotation data from the Genome Taxonomy Database and AnnoTree, we performed all-by-all comparisons of gene occurrence profiles across the bacterial tree of life, totaling 154,217,052 comparisons for 28,315 genes across 27,372 bacterial genomes. All predictions are available in an online database, which instantaneously returns the top correlated genes for any PFAM, TIGRFAM, or KEGG query. In total, PhyloCorrelate detected 29,762 high confidence associations between bacterial gene/protein pairs, and generated functional predictions for 834 DUFs and proteins of unknown function. AVAILABILITY PhyloCorrelate is available as a web-server at phylocorrelate.uwaterloo. ca as well as an R package for analysis of custom datasets. We anticipate that PhyloCorrelate will be broadly useful as a tool for predicting function and interactions for gene families. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Improved metabolic fitness, but no cardiovascular health effects, of a low-frequency short-term combined exercise programme in 50–70-year-olds with low fitness: A randomized controlled trial

ABSTRACT We evaluated the cardiometabolic effects of a 15-week combined exercise programme, implemented in sports clubs, for 50–70-year-olds with low aerobic fitness. In a randomized controlled trial, 45 participants (26 women) with low fitness were randomly assigned (2:1-ratio) to a training group (TG, n = 30) or inactive control group (CG, n = 15). TG had 15 weeks with one weekly 90-min supervised group-based session in a recreational sports club with combined aerobic exercise and strength training and were encouraged to perform home-based training 30 min/wk. Evaluations of relative VO2max (mLO2/min/kg), blood pressure, resting heart rate (HR), echocardiography, peripheral arterial tonometry, body composition, lipid profile and HbA1c were performed at 0 and 15 wks. Average HR during supervised training was 113 ± 13 bpm (68.6 ± 7.0%HRmax), with 4.3 ± 6.6% spent >90%HRmax. At 15-wk follow-up, intention-to-treat analyses revealed no between-group difference for VO2max/kg (0.4 mLO2/min/kg, 95%CI −0.8–1.5, P = 0.519; −3 mL/min, 95%CI −123–118, P = 0.966) or other cardiovascular outcomes (all P > 0.05). Compared to CG, total fat mass (−1.9 kg; 95%CI −3.2 to −0.5, P = 0.005), total fat percentage (−1.3%, 95%CI −2.2 to −0.3, P = 0.01) and total/HDL cholesterol ratio (P = 0.032) decreased in TG. Regular adherence to supervised training was high (81%), but 0% for home-based exercise. In conclusion, the group-based supervised training was associated with high adherence and moderate exercise intensity, whereas insufficiently supported home-based training was not feasible. Together, 15 wks of combined exercise training did not improve aerobic fitness or affected cardiovascular function in 50–70-yr-olds with low aerobic fitness, whereas some positive effects were observed in metabolic parameters. Highlights Combined exercise training implemented in a sports club elicited moderate aerobic intensity in 50-70-year-old untrained individuals. Supervised group-based training had high adherence whereas unsupported home-based training had very low adherence. 15 weeks of low-frequency combined moderate intensity exercise training improved lipid profile and fat mass, but had no effect on cardiovascular fitness.
High-Speed Nanomechanical Mapping of the Early Stages of Collagen Growth by Bimodal Force Microscopy

High-speed atomic force microscopy (AFM) enabled the imaging of protein interactions with millisecond time resolutions (10 fps). However, the acquisition of nanomechanical maps of proteins is about 100 times slower. Here, we developed a high-speed bimodal AFM that provided high-spatial resolution maps of the elastic modulus, the loss tangent, and the topography at imaging rates of 5 fps. The microscope was applied to identify the initial stages of the self-assembly of the collagen structures. By following the changes in the physical properties, we identified four stages, nucleation and growth of collagen precursors, formation of tropocollagen molecules, assembly of tropocollagens into microfibrils, and alignment of microfibrils to generate microribbons. Some emerging collagen structures never matured, and after an existence of several seconds, they disappeared into the solution. The elastic modulus of a microfibril (∼4 MPa) implied very small stiffness (∼3 × 10–6 N/m). Those values amplified the amplitude of the collagen thermal fluctuations on the mica plane, which facilitated microribbon build-up.
New kinetic model of ethene polymerization with Cp2Zrcl2/MAO catalyst

The kinetics of ethene polymerization catalyzed by Cp 2 ZrCl 2 /MAO is studied. A detailed look is taken at the different kinetic models used to describe the polymerization process. Also, a new model was developed on the basis of previous work. The new model takes both the active-sites mechanism and the reactivation effect of MAO into account. Better agreement between the experimental data and the fitting profile was achieved by applying the new model, when compared with the results from older models. A plausible mechanism of polymerization is outlined.