Miracle-dz/UniFAR-FTUs huggingface dataset:
Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

Abstract There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.
Functional foods for dyslipidaemia and cardiovascular risk prevention

A food can be regarded as ‘functional’ if it can demonstrate a beneficial efficacy on one or more target functions in the body in a convincing way. Beyond adequate nutritional qualities, functional foods should either improve the state of health and wellbeing and/or reduce the risk of disease. Functional foods that are marketed with claims of heart disease reduction focus primarily on the major risk factors, i.e. cholesterol, diabetes and hypertension. Some of the most innovative products are designed to be enriched with ‘protective’ ingredients, believed to reduce risk. They may contain, for example, soluble fibre (from oat and psyllium), useful both for lowering cholesterol and blood pressure, or fructans, effective in diabetes. Phytosterols and stanols lower LDL-cholesterol in a dose-dependent manner. Soya protein is more hypocholesterolaemic in subjects with very high initial cholesterol and recent data indicate also favourable activities in the metabolic syndrome. n-3 Fatty acids appear to exert significant hypotriacylglycerolaemic effects, possibly partly responsible for their preventive activity. Dark chocolate is gaining much attention for its multifunctional activities, useful both for the prevention of dyslipidaemia as well as hypertension. Finally, consensus opinions about tea and coffee have not emerged yet, and the benefits of vitamin E, garlic, fenugreek and policosanols in the management of dyslipidaemia and prevention of arterial disease are still controversial.
Intake of Marine-Derived Omega-3 Polyunsaturated Fatty Acids and Mortality in Renal Transplant Recipients

The effect of marine-derived omega-3 polyunsaturated fatty acids (n-3 PUFA) on long-term outcome in renal transplant recipients (RTR) remains unclear. We investigated whether marine-derived n-3 PUFA intake is associated with all-cause and cardiovascular (CV) mortality in RTR. Intake of eicosapentaenoic acid plus docosahexaenoic acid (EPA-DHA) was assessed using a validated Food Frequency Questionnaire. Cox regression analyses were performed to evaluate the associations of EPA-DHA intake with all-cause and CV mortality. We included 627 RTR (age 53 ± 13 years). EPA-DHA intake was 102 (42–215) mg/day. During median follow-up of 5.4 years, 130 (21%) RTR died, with 52 (8.3%) due to CV causes. EPA-DHA intake was associated with lower risk of all-cause mortality (Hazard Ratio (HR) 0.85; 95% confidence interval (95% CI) 0.75–0.97). Age (p = 0.03) and smoking status (p = 0.01) significantly modified this association, with lower risk of all-cause and CV mortality particularly in older (HR 0.75, 95% CI 0.61–0.92; HR 0.68, 95% CI 0.48–0.95) and non-smoking RTR (HR 0.80, 95% CI 0.68–0.93; HR 0.74, 95% CI 0.56–0.98). In conclusion, marine-derived n-3 PUFA intake is inversely associated with risk of all-cause and CV mortality in RTR. The strongest associations were present in subgroups of patients, which adds further evidence to the plea for EPA-DHA supplementation, particularly in elderly and non-smoking RTR.
Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms

Collagens are the most abundant extracellular matrix proteins in vertebrates and have a characteristic triple-helix structure. Hydroxylation of proline residues is critical for helix stability, and diminished prolyl hydroxylase activity causes wide-spread defects in connective tissues. Still, the role of proline hydroxylation in the binding of collagen receptors such as integrins is unclear. Here, we isolated skin collagen from genetically modified mice having reduced prolyl 4-hydroxylase activity. At room temperature, the reduced proline hydroxylation did not affect interactions with the recombinant integrin α2I domain, but at 37 °C, collagen hydroxylation correlated with the avidity of α2I domain binding. Of note, LC–MS/MS analysis of isolated skin collagens revealed no major changes in the hydroxyproline content of the main integrin-binding sites. Thus, the disrupted α2I domain binding at physiological temperatures was most likely due to structural destabilization of the collagenous helix. Integrin α2I binding to the triple-helical GFPGER motif was slightly weaker than to GFOGER (O = hydroxyproline). This phenomenon was more prominent when α1 integrin was tested. Integrin α1β1 expressed on CHO cells and recombinant α1I domain showed remarkably slower binding velocity and weaker avidity to GFPGER when compared with GFOGER. Structural modeling revealed the critical interaction between Arg-218 in α1I and the hydroxyproline residue in the integrin-binding motif. The role of Arg-218 was further validated by testing a variant R218D α1I domain in solid-phase binding assays. Thus, our results show that the lack of proline hydroxylation in collagen can affect integrin binding by a direct mechanism and via structural destabilization of the triple helix.
A platform for quantifying atrial structural remodelling

Cross sectional imaging tools are increasingly used prior to cardiac electrophysiology procedures. Cardiac Magnetic Resonance (CMR) imaging provides detailed anatomic information that can quantify structural remodelling of the atrial chambers. Atrial Late Gadolinium Enhanced (LGE) CMR may be used to identify fibrotic change in the atrium. A standardised and transparent approach to the analysis of CMR imaging would facilitate a broader applicability of such tools for complex image analysis. Furthermore, an assessment of the utility of such tools beyond highly specialised centres would be possible. In this paper, we introduce an open source platform, provide standardised solutions for extracting information from clinical images, and propose standard definitions of the atrial anatomy for comparing clinical indices.
Electronically tunable generalized impedance converter structures

New generalized impedance converter (GIC) structures realizable with four and six active components (operational amplifiers (OA) and operational tansconductance amplifers (OTA)) in the grounded and floating configurations, respectively, only three passive elements are derived. The resulting circuits enable a wide range linear tuning of impedance through the control voltage or current of the ()TA and are expected to find applications in tunable circuits (filter and oscillator for instance). The viability of the proposed structures has been confirmed by SPICE simulation results.
Design of Dual-Mode Local Oscillators Using CMOS Technology for Motion Detection Sensors

Recently, studies have been actively carried out to implement motion detecting sensors by applying radar techniques. Doppler radar or frequency-modulated continuous wave (FMCW) radar are mainly used, but each type has drawbacks. In Doppler radar, no signal is detected when the movement is stopped. Also, FMCW radar cannot function when the detection object is near the sensor. Therefore, by implementing a single continuous wave (CW) radar for operating in dual-mode, the disadvantages in each mode can be compensated for. In this paper, a dual mode local oscillator (LO) is proposed that makes a CW radar operate as a Doppler or FMCW radar. To make the dual-mode LO, a method that controls the division ratio of the phase locked loop (PLL) is used. To support both radar mode easily, the proposed LO is implemented by adding a frequency sweep generator (FSG) block to a fractional-N PLL. The operation mode of the LO is determined by according to whether this block is operating or not. Since most radar sensors are used in conjunction with microcontroller units (MCUs), the proposed architecture is capable of dual-mode operation by changing only the input control code. In addition, all components such as VCO, LDO, and loop filter are integrated into the chip, so complexity and interface issues can be solved when implementing radar sensors. Thus, the proposed dual-mode LO is suitable as a radar sensor.
Evaluation of PBS Treatment and PEI Coating Effects on Surface Morphology and Cellular Response of 3D-Printed Alginate Scaffolds

Three-dimensional (3D) printing is an emerging technology for the fabrication of scaffolds to repair/replace damaged tissue/organs in tissue engineering. This paper presents our study on 3D printed alginate scaffolds treated with phosphate buffered saline (PBS) and polyethyleneimine (PEI) coating and their impacts on the surface morphology and cellular response of the printed scaffolds. In our study, sterile alginate was prepared by means of the freeze-drying method and then, used to prepare the hydrogel for 3D printing into calcium chloride, forming 3D scaffolds. Scaffolds were treated with PBS for a time period of two days and seven days, respectively, and PEI coating; then they were seeded with Schwann cells (RSC96) for the examination of cellular response (proliferation and differentiation). In addition, swelling and stiffness (Young’s modulus) of the treated scaffolds was evaluated, while their surface morphology was assessed using scanning electron microscopy (SEM). SEM images revealed significant changes in scaffold surface morphology due to degradation caused by the PBS treatment over time. Our cell proliferation assessment over seven days showed that a two-day PBS treatment could be more effective than seven-day PBS treatment for improving cell attachment and elongation. While PEI coating of alginate scaffolds seemed to contribute to cell growth, Schwann cells stayed round on the surface of alginate over the period of cell culture. In conclusion, PBS-treatment may offer the potential to induce surface physical cues due to degradation of alginate, which could improve cell attachment post cell-seeding of 3D-printed alginate scaffolds.
ATRA attenuate proteinuria via downregulation of TRPC6 in glomerulosclerosis rats induced by adriamycin

Abstract Objective: In this research, we explored the molecular mechanism of proteinuria in glomerulosclerosis rats and the protective effects of ATRA. Methods: This research set up three groups: SHO group, GS group, and ATRA group (15 mg/(kg d), Sigma, St. Louis, MO). The serum creatinine (Scr), urea nitrogen (BUN), and 24-h proteinuria were detected 12 weeks after administration of ATRA. The pathological and ultrastructure changes were observed under light microscope and transmission electron microscope. The protein expression of TGF-β1 and Col-IV in glomerulus was detected by immunohitochemistry method. The mRNA and the protein expression of glomerular TRPC6 were detected by RT-PCR and Western blot. Results: In the rat model of GS, the expressions of TRPC6 were significantly elevated compared with the normal rat group; however, the use of ATRA down-regulated the expression of TRPC6 in the glomeruli and attenuated glomerulosclerosis and proteinuria. Scr and BUN were also improved by the treatment of ATRA. Conclusions: Our results demonstrated that ATRA could ameliorate glomerulosclerosis and proteinuria in GS, which may be related to suppressed expression of TRPC6.
Nonalcoholic fatty liver disease contributes to subclinical atherosclerosis: A systematic review and meta‐analysis

Nonalcoholic fatty liver disease (NAFLD) is associated with an increased risk of atherosclerotic cardiovascular disease. In our meta‐analysis, we aimed to assess the correlation of NAFLD and four surrogate markers of subclinical atherosclerosis. PubMed, Embase, and the Cochrane Library were searched up until April 2017. Original studies investigating the association between NAFLD and subclinical atherosclerosis were included. The outcome data were extracted and pooled for the effect estimate by using a random‐effects model. We used the Newcastle‐Ottawa Quality Assessment Scale to assess the quality of the included studies. Of the 434 initially retrieved studies, 26 studies involving a total of 85,395 participants (including 29,493 patients with NAFLD) were included in this meta‐analysis. The Newcastle‐Ottawa Quality Assessment Scale scores suggested the included studies were of high quality. The pooled effects estimate showed that subjects with NAFLD exhibited a significant independent association with subclinical atherosclerosis compared to the non‐NAFLD group (odds ratio, 1.60; 95% confidence interval, 1.45‐1.78). Subgroup analysis suggested that the presence of NAFLD yielded a remarkable higher risk of increased carotid artery intima‐media thickness/plaques, arterial stiffness, coronary artery calcification, and endothelial dysfunction with odds ratios (95% confidence interval) of 1.74 (1.47‐2.06), 1.56 (1.24‐1.96), 1.40 (1.22‐1.60), and 3.73 (0.99‐14.09), respectively. Conclusion: Our meta‐analysis revealed a close link between NAFLD and subclinical atherosclerosis in light of four different indices. Patients with NAFLD might benefit from screening and surveillance of early atherosclerosis, which would facilitate the prediction of potential cardiovascular disease burden, risk stratification, and appropriate intervention in the long term. (Hepatology Communications 2018;2:376‐392)
Identification and removal of defects on silicon wafer processed with a rinse with/without megasonics in DI water

Watermark generation during wafer cleaning, which is the most repeated step in IC manufacturing, was investigated. Watermark formed during the HF last cleaning was monitored by KLA and SEM. It was found that megasonics at the final rinse (F/R) stage was the source of the defects. Megasonics in F/R step can generate a damage on the hydrophobic wafer surface. This damage may be a cause of watermark. Under the same rinse condition, which generate watermark on bare wafer, watermark density of patterned wafer is much less than that of bare wafer. A geometrical combination of hydrophilic and hydrophobic wafer surface can prevent the watermark on a part of the hydrophobic wafer surface. It was confirmed that micro watermark did not affect the quality of gate oxide of 58 /spl Aring/ thickness.
Urinary RKIP/p-RKIP is a potential diagnostic and prognostic marker of clear cell renal cell carcinoma

Clear cell Renal Cell Carcinoma (ccRCC) causes over 13,000 deaths each year, and about 20,000 new cases/year in Europe. In most cases, the causes are unknown and, most importantly, there are no reliable biomarkers for the diagnosis and prognosis of this disease. The search for sensitive biomarkers for early diagnosis and prognosis of clear cell Renal Cell Carcinoma (ccRCC) is currently a fast growing field. We carried out proteomics analysis of 93 urinary samples of healthy subjects (HS) and patients affected by ccRCC, prostate cancer (PCa) and chronic kidney disease (CKD), that was able to successfully distinguish each group. The most significant candidate biomarker was identified by mass spectrometry as Raf Kinase Inhibitor Protein (RKIP), a key regulator of cell signaling, already described in several cancer types as a metastasis suppressor. By combining ELISA, immunoblotting and tissue microarray, we demonstrated that, in ccRCC, urinary excretion of RKIP and its phosphorylated form (p-RKIP) reflected the tissue expression of these putative biomarkers. Baseline urinary RKIP, evaluated in an independent cohort of 56 ccRCC patients and 28 HS, successfully distinguished both groups and, most importantly, a cut-off value of 10 ng/mg/g Pr/uCr enabled a highly accurate prediction of Cancer-specific survival and Progression-free survival. Furthermore, p-RKIP was totally undetectable in both tissue and urine samples of ccRCC, showing a great potential for diagnostics purposes. Our data indicate that urinary RKIP encompasses both the unphosphorylated and the phosphorylated form and that their combined evaluation can help in the diagnosis and prognosis of ccRCC.
What are judgment skills in health literacy? A psycho-cognitive perspective of judgment and decision-making research

Objective The aim of this review is to summarize current research relating to psychological processes involved in judgment and decision-making (JDM) and identify which processes can be incorporated and used in the construct of health literacy (HL) in order to enrich its conceptualization and to provide more information about people’s preferences. Methods The literature review was aimed at identifying comprehensive research in the field; therefore appropriate databases were searched for English language articles dated from 1998 to 2015. Results Several psychological processes have been found to be constituents of JDM and potentially incorporated in the definition of HL: cognition, self-regulation, emotion, reasoning-thinking, and social perception. Conclusion HL research can benefit from this JDM literature overview, first, by elaborating on the idea that judgment is multidimensional and constituted by several specific processes, and second, by using the results to implement the definition of “judgment skills”. Moreover, this review can favor the development of new instruments that can measure HL. Practical implications Future researchers in HL should work together with researchers in psychological sciences not only to investigate the processes behind JDM in-depth but also to create effective opportunities to improve HL in all patients, to promote good decisions, and orient patients’ preferences in all health contexts.
The relationship between search based software engineering and predictive modeling

Search Based Software Engineering (SBSE) is an approach to software engineering in which search based optimization algorithms are used to identify optimal or near optimal solutions and to yield insight. SBSE techniques can cater for multiple, possibly competing objectives and/ or constraints and applications where the potential solution space is large and complex. This paper will provide a brief overview of SBSE, explaining some of the ways in which it has already been applied to construction of predictive models. There is a mutually beneficial relationship between predictive models and SBSE. The paper sets out eleven open problem areas for Search Based Predictive Modeling and describes how predictive models also have role to play in improving SBSE.
Select Skeletal Muscle mRNAs Related to Exercise Adaptation Are Minimally Affected by Different Pre-exercise Meals that Differ in Macronutrient Profile

Background: Substantial research has been done on the impact of carbohydrate and fat availability on endurance exercise adaptation, though its role in the acute adaptive response to resistance exercise has yet to be fully characterized. Purpose: We aimed to assess the effects of a pre-resistance exercise isocaloric mixed meal containing different amounts of carbohydrates and fat, on post-resistance exercise gene expression associated with muscle adaptation. Methods: Thirteen young (age 21.2 ± 1.6 year), recreationally trained (VO2max 51.3 ± 4.8 ml/kg/min) men undertook an aerobic exercise session of 90-min continuous cycling (70% VO2max) in the morning with pre- and post-exercise protein ingestion (10 and 15 g casein in a 500 ml beverage pre- and post-exercise, respectively). Subjects then rested for 2 h and were provided with a meal consisting of either 3207 kJ; 52 g protein; 51 g fat; and 23 g carbohydrate (FAT) or 3124 kJ; 53 g protein; 9 g fat; and 109 g carbohydrate (CHO). Two hours after the meal, subjects completed 5 × 8 repetitions (80% 1-RM) for both bilateral leg press and leg extension directly followed by 25 g of whey protein (500 ml beverage). Muscle biopsies were obtained from the vastus lateralis at baseline (morning) and 1 and 3 h post-resistance exercise (afternoon) to determine intramuscular mRNA response. Results: Muscle glycogen levels were significantly decreased post-resistance exercise, without any differences between conditions. Plasma free fatty acids increased significantly after the mixed meal in the FAT condition, while glucose and insulin were higher in the CHO condition. However, PDK4 mRNA quantity was significantly higher in the FAT condition at 3 h post-resistance exercise compared to CHO. HBEGF, INSIG1, MAFbx, MURF1, SIRT1, and myostatin responded solely as a result of exercise without any differences between the CHO and FAT group. FOXO3A, IGF-1, PGC-1α, and VCP expression levels remained unchanged over the course of the day. Conclusion: We conclude that mRNA quantity associated with muscle adaptation after resistance exercise is not affected by a difference in pre-exercise nutrient availability. PDK4 was differentially expressed between CHO and FAT groups, suggesting a potential shift toward fat oxidation and reduced glucose oxidation in the FAT group.
Examining Public Perceptions about Lead in School Drinking Water: A Mixed-Methods Analysis of Twitter Response to an Environmental Health Hazard

Exposure to lead has long been a community health concern in St. Louis, Missouri. The objective of this study was to examine public response to reports of elevated lead levels in school drinking water in St. Louis, Missouri via Twitter, a microblogging platform with over 320 million active users. We used a mixed-methods design to examine Twitter user status updates, known as “tweets,” from 18 August to 31 December 2016. The number of tweets each day was recorded, and Twitter users were classified into five user types (General Public, Journalist/News, Health Professional/Academic, Politician/Government Official, and Non-Governmental Organization). A total of 492 tweets were identified during the study period. The majority of discourse on Twitter occurred during the two-week period after initial media reports and was driven by members of the General Public. Thematic analysis of tweets revealed four themes: Information Sharing, Health Concerns, Sociodemographic Disparities, and Outrage. Twitter users characterized lead in school drinking water as an issue of environmental inequity. The findings of this study provide evidence that social media platforms can be utilized as valuable tools for public health researchers and practitioners to gauge public sentiment about environmental health issues, identify emerging community concerns, and inform future communication and research strategies regarding environmental health hazards.