Miracle-dz/UniFAR-FTUs huggingface dataset:
A Printable Device for Measuring Clarity and Colour in Lake and Nearshore Waters

Two expanding areas of science and technology are citizen science and three-dimensional (3D) printing. Citizen science has a proven capability to generate reliable data and contribute to unexpected scientific discovery. It can put science into the hands of the citizens, increasing understanding, promoting environmental stewardship, and leading to the production of large databases for use in environmental monitoring. 3D printing has the potential to create cheap, bespoke scientific instruments that have formerly required dedicated facilities to assemble. It can put instrument manufacturing into the hands of any citizen who has access to a 3D printer. In this paper, we present a simple hand-held device designed to measure the Secchi depth and water colour (Forel Ule scale) of lake, estuarine and nearshore regions. The device is manufactured with marine resistant materials (mostly biodegradable) using a 3D printer and basic workshop tools. It is inexpensive to manufacture, lightweight, easy to use, and accessible to a wide range of users. It builds on a long tradition in optical limnology and oceanography, but is modified for ease of operation in smaller water bodies, and from small watercraft and platforms. We provide detailed instructions on how to build the device and highlight examples of its use for scientific education, citizen science, satellite validation of ocean colour data, and low-cost monitoring of water clarity, colour and temperature.
Identification of miRNA Reference Genes in Extracellular Vesicles from Adipose Derived Mesenchymal Stem Cells for Studying Osteoarthritis

Osteoarthritis (OA) leads to chronic pain and disability, and traditional conservative treatments are not effective in the long term. The intra-articular injection of mesenchymal stem cells (MSCs) is considered a novel therapy for OA whose efficacy mainly relies on the adaptive release of paracrine molecules which are either soluble or extracellular vesicles (EVs) embedded. The correct quantification of EV-miRNAs using reliable reference genes (RGs) is a crucial step in optimizing this future therapeutic cell-free approach. The purpose of this study is to rate the stabilities of literature-selected proposed RGs for EV-miRNAs in adipose derived-MSCs (ASCs). EVs were isolated by ultracentrifugation from ASCs cultured with or without inflammatory priming mimicking OA synovial fluid condition. Expression of putative RGs (let-7a-5p, miR-16-5p, miR-23a-3p, miR-26a-5p, miR-101-3p, miR-103a-3p, miR-221-3p, miR-423-5p, miR-425-5p, U6 snRNA) was scored by using the algorithms geNorm, NormFinder, BestKeeper and ΔCt method. miR-16a-5p/miR-23a-3p yielded the most stable RGs, whereas let-7a-5p/miR-425-5p performed poorly. Outcomes were validated by qRT-PCR on miR-146a-5p, reported to be ASC-EVs enriched and involved in OA. Incorrect RG selection affected the evaluation of miR-146a-5p abundance and modulation by inflammation, with both values resulting strongly donor-dependent. Our findings demonstrated that an integrated approach of multiple algorithms is necessary to identify reliable, stable RGs for ASC-EVs miRNAs evaluation. A correct approach would increase the accuracy of embedded molecule assessments aimed to develop therapeutic strategies for the treatment of OA based on EVs.
Functional reconstitution of vacuolar H+-ATPase from Vo proton channel and mutant V1-ATPase provides insight into the mechanism of reversible disassembly

The vacuolar H+-ATPase (V-ATPase; V1Vo-ATPase) is an ATP-dependent proton pump that acidifies subcellular compartments in all eukaryotic organisms. V-ATPase activity is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel subcomplexes, a process that is poorly understood on the molecular level. V-ATPase is a rotary motor, and recent structural analyses have revealed different rotary states for disassembled V1 and Vo, a mismatch that is likely responsible for their inability to reconstitute into holo V-ATPase in vitro. Here, using the model organism Saccharomyces cerevisiae, we show that a key impediment for binding of V1 to Vo is the conformation of the inhibitory C-terminal domain of subunit H (HCT). Using biolayer interferometry and biochemical analyses of purified mutant V1-ATPase and Vo proton channel reconstituted into vacuolar lipid-containing nanodiscs, we further demonstrate that disruption of HCT's V1-binding site facilitates assembly of a functionally coupled and stable V1Vo-ATPase. Unlike WT, this mutant enzyme was resistant to MgATP hydrolysis-induced dissociation, further highlighting HCT's role in the mechanism of V-ATPase regulation. Our findings provide key insight into the molecular events underlying regulation of V-ATPase activity by reversible disassembly.
In vitro analysis of RNA polymerase II elongation complex dynamics

RNA polymerase II elongation complexes (ECs) were assembled from nuclear extract on immobilized DNA templates and analyzed by quantitative mass spectrometry. Time course experiments showed that initiation factor TFIIF can remain bound to early ECs, while levels of core elongation factors Spt4-Spt5, Paf1C, Spt6-Spn1, and Elf1 levels remain steady. Importantly, the dynamic phosphorylation patterns of the Rpb1 C-terminal domain (CTD), and the factors that recognize them, change as a function of post-initiation time, rather than distance elongated. Chemical inhibition of Kin28/Cdk7 blocks both Serine 5 and Serine 2 phosphorylation, affects initiation site choice, and inhibits elongation efficiency. EC components dependent on CTD phosphorylation include capping enzyme, Cap Binding Complex, Set2, and the PAF1 complex. By recapitulating many known features of in vivo elongation, this system reveals new details that clarify how EC-associated core elongation factors, chromatin regulators, and RNA processing factors change at each step of transcription.
The complete mitochondrial genome of silver fox (Caniformia: Canidae)

Abstract Silver fox is color variant of Vulpes vulpes. At present, there are few studies on phylogeny of Canidae and Caniformia. In this article, we determined and described the complete mitogenome of silver fox for the first time, which is 16,723 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL) and a putative control region (CR). The overall base composition is 31.4% A, 27.9% T, 26.0% C, 14.7% G, respectively, with a AT bias (59.3%). Ten protein-coding genes use the initiation codon ATG while ND2, ND3 and ND5 use ATA. Most of them have TAA as the stop codon, except ND2 uses TAG, Cytb uses AGA, and COX3, ND3, ND4 use an incomplete stop codon TA. The information is expected to provide useful molecular data for further taxonomic and phylogenetic studies of Canidae and Caniformia.
Editor’s presentation

Non-coding ribonucleic acids (RNAs), such as micro RNAs (miRNAs) or long non-coding RNAs, currently represent one of the leading frontiers in research. In the current issue, 187 target miRNAs in 20 coronary artery disease (CAD) and 20 non-CAD patients before and after a single bout of exercise were measured to assess their diagnostic power. After a logistic regression analysis, four miRNAs, one measured at rest (miR-150-5p) and three in response to exercise (miR-101-3p, miR141-3p and miR-200b-3p), together with maximal oxygen uptake and maximal exercise power, allowed discrimination between healthy subjects and CAD patients with an accuracy of 92.5%. In the conclusion, the authors further speculated that analysing these four miRNAs together with well recognised prognostic parameters obtained from an ergospirometry could identify patients at risk for developing CAD.
Evidence for an Upper Threshold for Resistance Training Volume in Trained Women

Introduction The purpose of the present study was to compare the effects of different volumes of resistance training (RT) on muscle performance and hypertrophy in trained women. Methods The study included 40 volunteers that performed RT for 24 wk divided into groups that performed 5 (G5), 10 (G10), 15 (G15), and 20 (G20) sets per muscle group per session. Ten-repetition maximum (10RM) tests were performed for the bench press, lat pulldown, 45° leg press, and stiff-legged deadlift. Muscle thickness (MT) was measured using ultrasound at biceps brachii, triceps brachii, pectoralis major, quadriceps femoris, and gluteus maximus. Results All groups significantly increased all MT measures and 10RM tests after 24 wk of RT (P < 0.05). Between-group comparisons revealed no differences in any 10RM test between G5 and G10 (P > 0.05). G5 and G10 showed significantly greater 10RM increases than G15 for lat pulldown, leg press, and stiff-legged deadlift. 10RM changes for G20 were lower than all other groups for all exercises (P < 0.05). G5 and G10 showed significantly greater MT increases than G15 and G20 in all sites (P < 0.05). MT increased more in G15 than G20 in all sites (P < 0.05). G5 increases were higher than G10 for pectoralis major MT, whereas G10 showed higher increases in quadriceps MT than G5 (P < 0.05). Conclusions Five to 10 sets per week might be sufficient for attaining gains in muscle size and strength in trained women during a 24-wk RT program. There appears no further benefit by performing higher exercise volumes. Because lack of time is a commonly cited barrier to exercise adoption, our data support RT programs that are less time consuming, which might increase participation and adherence.
Sperm selection methods in the 21st century

Abstract Natural sperm selection in humans is a rigorous process resulting in the highest quality sperm reaching, and having an opportunity to fertilize, the oocyte. Relative to other mammalian species, the human ejaculate consists of a heterogeneous pool of sperm, varying in characteristics such as shape, size, and motility. Semen preparation in assisted reproductive technologies (ART) has long been performed using either a simple swim-up method or density gradients. Both methodologies provide highly motile sperm populations; however neither replicates the complex selection processes seen in nature. A number of methods have now been developed to mimic some of the natural selection processes that exist in the female reproductive tract. These methods attempt to select a better individual, or population of, spermatozoa when compared to classical methods of preparation. Of the approaches already tested, platforms based upon sperm membrane markers, such as hyaluronan or annexin V, have been used to either select or deselect sperm with varied success. One technology that utilizes the size, motility, and other characteristics of sperm to improve both semen analysis and sperm selection is microfluidics. Here, we sought to review the efficacy of both available and emerging techniques that aim to improve the quality of the sperm pool available for use in ART. Summary Sentence This manuscript reviews the efficacy of both available and emerging sperm selection techniques to improve the pool of sperm available for assisted reproductive technologies.
Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate‐accumulating organism, in sediments of the Columbia River estuary

Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments.
A new iridoid diglycoside from Sambucus ebulus L

Abstract The phytochemical examination of the polar constituents of Sambucus ebulus L. leaves led to the identification of patrinoside (1) and of a new diglycoside iridoid, patrinoside-aglycone-11-O-[β-D-glucopyranosyl-(1→6)-2′-deoxy-β-D-glucopyranoside] (trivially named as sambuloside) (2). Both of these structures have been assigned by spectroscopic means (NMR and MS). Graphical Abstract
Transcriptomic Analysis of Vibrio parahaemolyticus Reveals Different Virulence Gene Expression in Response to Benzyl Isothiocyanate

Vibrio parahaemolyticus isolated from seafood is a pathogenic microorganism that leads to several acute diseases that are harmful to our health and is frequently transmitted by food. Therefore, there is an urgent need for the control and suppression of this pathogen. In this paper, transcriptional analysis was used to determine the effect of treatment with benzyl isothiocyanate (BITC) extracted from cruciferous vegetables on V. parahaemolyticus and to elucidate the molecular mechanisms underlying the response to BITC. Treatment with BITC resulted in 332 differentially expressed genes, among which 137 genes were downregulated, while 195 genes were upregulated. Moreover, six differentially expressed genes (DEGs) in RNA sequencing studies were further verified by quantitative real-time polymerase chain reaction (qRT-PCR). Genes found to regulate virulence encoded an l-threonine 3-dehydrogenase, a GGDEF family protein, the outer membrane protein OmpV, a flagellum-specific adenosine triphosphate synthase, TolQ protein and VirK protein. Hence, the results allow us to speculate that BITC may be an effective control strategy for inhibiting microorganisms growing in foods.
Effects of feed intake level on efficiency of microbial protein synthesis and nitrogen balance in Boran steers consuming tropical poor-quality forage

ABSTRACT This study aimed at evaluating the effects of feed intake level on the efficiency of rumen microbial protein synthesis (EMPS), nitrogen (N) excretion, and N balance in twelve 18-months old Boran (Bos indicus) steers with initial average liveweight of 183 kg (standard deviation (SD) 15.2). The experiment followed a 4 × 4 complete Latin Square design with four dietary treatments tested in four periods. Each period ran for 5 weeks with 3 weeks of adaptation and 2 weeks of sample collection; separated by 2 weeks of re-feeding. Steers were fed at 100%, 80%, 60%, and 40% of their metabolisable energy requirement for maintenance (MER, referred to as MER100, MER80, MER60, and MER40, respectively). Steers receiving MER80, MER60, and MER40 were only fed Rhodes grass hay. MER100 steers were offered Rhodes grass hay at 80% of their MER and cottonseed meal and sugarcane molasses at each 10% of MER. Mean daily dry matter intake differed between treatments (p < 0.001) and ranged between 2.1 kg/animal (SD 0.13) in MER40 and 4.5 kg/animal (SD 0.31) in MER100. Urinary N excretion and N balance did not differ between MER80, MER60, and MER40. According to contrast test, declining feed intake level from MER80 to MER40 reduced duodenal microbial crude protein flow (p < 0.001), but did not alter the EMPS (g microbial N/kg digestible organic matter intake). Yet, if scaled to N intake, EMPS increased (p < 0.049), whereas total N and faecal N excretions decreased linearly with declining intake level (p < 0.001 for both variables). At similar grass hay intake, duodenal microbial crude protein flow was 41% higher in MER100 than in MER80 steers (p < 0.001). In cattle offered poor-quality tropical forage below their MER, the very low EMPS and thus microbial protein supply aggravate the negative effects of low dietary nutrient and energy intakes in periods of feed shortage.
Systematic review: economic evaluations of HCV screening in the direct‐acting antivirals era

The World Health Organization estimated that 90% of the infected people need to be diagnosed and 80% need to be treated to reach the aim of hepatitis C virus (HCV) elimination by 2030. For this reason, all possible strategies to detect and treat HCV‐infected people need to be carefully evaluated to implement the best one.
Deep Learning for Segmentation Using an Open Large-Scale Dataset in 2D Echocardiography

Delineation of the cardiac structures from 2D echocardiographic images is a common clinical task to establish a diagnosis. Over the past decades, the automation of this task has been the subject of intense research. In this paper, we evaluate how far the state-of-the-art encoder-decoder deep convolutional neural network methods can go at assessing 2D echocardiographic images, i.e., segmenting cardiac structures and estimating clinical indices, on a dataset, especially, designed to answer this objective. We, therefore, introduce the cardiac acquisitions for multi-structure ultrasound segmentation dataset, the largest publicly-available and fully-annotated dataset for the purpose of echocardiographic assessment. The dataset contains two and four-chamber acquisitions from 500 patients with reference measurements from one cardiologist on the full dataset and from three cardiologists on a fold of 50 patients. Results show that encoder-decoder-based architectures outperform state-of-the-art non-deep learning methods and faithfully reproduce the expert analysis for the end-diastolic and end-systolic left ventricular volumes, with a mean correlation of 0.95 and an absolute mean error of 9.5 ml. Concerning the ejection fraction of the left ventricle, results are more contrasted with a mean correlation coefficient of 0.80 and an absolute mean error of 5.6%. Although these results are below the inter-observer scores, they remain slightly worse than the intra-observer’s ones. Based on this observation, areas for improvement are defined, which open the door for accurate and fully-automatic analysis of 2D echocardiographic images.
Understanding the association between advanced paternal age and schizophrenia and bipolar disorder

Abstract Background Previous studies reported an association between advanced paternal age at birth and increased risk for schizophrenia and bipolar disorder. While some hypothesize that this association is caused by de-novo mutations in paternal spermatozoa, others cite factors associated with psycho-social characteristics of fathers who have children at a late age. This study aims to test these hypotheses. Methods A historical-prospective, population-based cohort study, performed by linking the Israeli Draft Board Registry and the Israeli National Psychiatric Hospitalization Registry (N = 916 439; 4488 with schizophrenia, 883 with bipolar disorder). Odds ratios (OR) and two-sided 95% confidence intervals (CI) were calculated by logistic regression models, using paternal age as predictor and risk for later hospitalizations for schizophrenia or bipolar disorder as outcome measure. Models were first fitted unadjusted, then adjusted for paternal age at birth of the first child. Results In the unadjusted model, offspring of fathers aged 45 and above at birth had increased risk of schizophrenia (OR = 1.71, 95% CI 1.49–1.99) and bipolar disorder (OR = 1.63, 95% CI 1.16–2.24). However, taking into account paternal age at birth of first child, advanced paternal age was no longer associated with increased risk of schizophrenia (OR = 0.60, 95% CI 0.48–0.79) or bipolar disorder (OR = 1.03, 95% CI 0.56–1.90). Conclusions Controlling for paternal age at birth of the first offspring, advanced paternal age does not predict increased risk for schizophrenia or bipolar disorder. These data indicate that the association between advanced paternal age and having an offspring with schizophrenia and bipolar disorder is likely due to psychos-social factors, or common genetic variation associated with delayed initial fatherhood.
Discovery of Stealthin Derivatives and Implication of the Amidotransferase FlsN3 in the Biosynthesis of Nitrogen-Containing Fluostatins

Diazobenzofluorene-containing atypical angucyclines exhibit promising biological activities. Here we report the inactivation of an amidotransferase-encoding gene flsN3 in Micromonospora rosaria SCSIO N160, a producer of fluostatins. Bioinformatics analysis indicated that FlsN3 was involved in the diazo formation. Chemical investigation of the flsN3-inactivation mutant resulted in the isolation of a variety of angucycline aromatic polyketides, including four racemic aminobenzo[b]fluorenes stealthins D–G (9–12) harboring a stealthin C-like core skeleton with an acetone or butanone-like side chain. Their structures were elucidated on the basis of nuclear magnetic resonance (NMR) spectroscopic data and X-ray diffraction analysis. A plausible mechanism for the formation of stealthins D–G (9–12) was proposed. These results suggested a functional role of FlsN3 in the formation/modification of N–N bond-containing fluostatins.
Conservative versus Surgical Therapy in Managing Patients with Facial Nerve Palsy Due to the Temporal Bone Fracture

Facial nerve paralysis is classified into immediate or delayed-onset palsy, and affected patients should be treated through conservative or surgical therapy. Appropriate treatment is somewhat debated as well as proper time for performing surgery. This study aimed to assess treatment outcome between conservatively and surgically treated groups and to determine the appropriate time of surgery in selected patients for surgery. Twenty-four patients from April 2008 to July 2015 were included. Performing decompression surgery within the first 2 months following the trauma accompanies a better prognosis (p-value < 0.05). Eleven patients were managed conservatively, and 4 of them demonstrated immediate onset and 7 indicated delayed onset. Nine patients obtained normal nerve function, one patient had partial palsy, and one of them had complete palsy. There was no significant difference in the rate of recovery between types of the treatment (p-value > 0.05). Decompression surgery is recommended in the first 2 months after the trauma for immediate onset and also complete degeneration on electroneuronography.