Miracle-dz/UniFAR-FTUs huggingface dataset:
The genomics of rapid climatic adaptation and parallel evolution in North American house mice

Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.
The Effectiveness of an Acceptance and Commitment Therapy and Mindfulness Group Intervention for Enhancing the Psychological and Physical Well-Being of Adults with Overweight or Obesity Seeking Treatment: The Mind&Life Randomized Control Trial Study Protocol

Although several interventions that target obesity have been examined, the success of these interventions in generating and maintaining positive results has yet to be confirmed. This study protocol therefore presents a trial aimed at analyzing the effectiveness of a well-being-centered acceptance and commitment therapy (ACT)- and mindfulness-based group intervention following the valued-based healthy living (VHL) approach (Mind&Life intervention) for individuals experiencing overweight-related distress. A randomized controlled trial with two parallel groups will be conducted in 110 adults attending primary care units with overweight or obesity. Participants will be randomly allocated to one of the two study conditions. Interventions will either be the treatment as usual (TAU) or the Mind&Life intervention—an ACT- and mindfulness-based intervention—plus the TAU intervention. Quality of life, weight self-stigma, general health status, eating habits, physical activity, eating behavior, anthropometric, body composition, cardiovascular, and physiological variables, as well as process variables, will be examined at baseline, posttreatment, 6-month follow-up, and 1-year follow-up. This trial aims to offer a novel psychological approach for addressing the psychological and physical impairments suffered by people with overweight or obesity in the current environment. ClinicalTrials.gov identifier: NCT03718728.
Biomarkers in Prostate Cancer Diagnosis: From Current Knowledge to the Role of Metabolomics and Exosomes

Early detection of prostate cancer (PC) is largely carried out using assessment of prostate-specific antigen (PSA) level; yet it cannot reliably discriminate between benign pathologies and clinically significant forms of PC. To overcome the current limitations of PSA, new urinary and serum biomarkers have been developed in recent years. Although several biomarkers have been explored in various scenarios and patient settings, to date, specific guidelines with a high level of evidence on the use of these markers are lacking. Recent advances in metabolomic, genomics, and proteomics have made new potential biomarkers available. A number of studies focused on the characterization of the specific PC metabolic phenotype using different experimental approaches has been recently reported; yet, to date, research on metabolomic application for PC has focused on a small group of metabolites that have been known to be related to the prostate gland. Exosomes are extracellular vesicles that are secreted from all mammalian cells and virtually detected in all bio-fluids, thus allowing their use as tumor biomarkers. Thanks to a general improvement of the technical equipment to analyze exosomes, we are able to obtain reliable quantitative and qualitative information useful for clinical application. Although some pilot clinical investigations have proposed potential PC biomarkers, data are still preliminary and non-conclusive.
Design and Evaluation of a Flexible Dual-Band Meander Line Monopole Antenna for On- and Off-Body Healthcare Applications

The human body is an extremely challenging environment for wearable antennas due to the complex antenna-body coupling effects. In this article, a compact flexible dual-band planar meander line monopole antenna (MMA) with a truncated ground plane made of multiple layers of standard off-the-shelf materials is evaluated to validate its performance when worn by different subjects to help the designers who are shaping future complex on-/off-body wireless devices. The antenna was fabricated, and the measured results agreed well with those from the simulations. As a reference, in free-space, the antenna provided omnidirectional radiation patterns (ORP), with a wide impedance bandwidth of 1282.4 (450.5) MHz with a maximum gain of 3.03 dBi (4.85 dBi) in the lower (upper) bands. The impedance bandwidth could reach up to 688.9 MHz (500.9 MHz) and 1261.7 MHz (524.2 MHz) with the gain of 3.80 dBi (4.67 dBi) and 3.00 dBi (4.55 dBi), respectively, on the human chest and arm. The stability in results shows that this flexible antenna is sufficiently robust against the variations introduced by the human body. A maximum measured shift of 0.5 and 100 MHz in the wide impedance matching and resonance frequency was observed in both bands, respectively, while an optimal gap between the antenna and human body was maintained. This stability of the working frequency provides robustness against various conditions including bending, movement, and relatively large fabrication tolerances.
Genetic Determinants in a Critical Domain of NS5A Correlate with Hepatocellular Carcinoma in Cirrhotic Patients Infected with HCV Genotype 1b

HCV is an important cause of hepatocellular carcinoma (HCC). HCV NS5A domain-1 interacts with cellular proteins inducing pro-oncogenic pathways. Thus, we explore genetic variations in NS5A domain-1 and their association with HCC, by analyzing 188 NS5A sequences from HCV genotype-1b infected DAA-naïve cirrhotic patients: 34 with HCC and 154 without HCC. Specific NS5A mutations significantly correlate with HCC: S3T (8.8% vs. 1.3%, p = 0.01), T122M (8.8% vs. 0.0%, p < 0.001), M133I (20.6% vs. 3.9%, p < 0.001), and Q181E (11.8% vs. 0.6%, p < 0.001). By multivariable analysis, the presence of ≥1 of them independently correlates with HCC (OR (95%CI): 21.8 (5.7–82.3); p < 0.001). Focusing on HCC-group, the presence of these mutations correlates with higher viremia (median (IQR): 5.7 (5.4–6.2) log IU/mL vs. 5.3 (4.4–5.6) log IU/mL, p = 0.02) and lower ALT (35 (30–71) vs. 83 (48–108) U/L, p = 0.004), suggesting a role in enhancing viral fitness without affecting necroinflammation. Notably, these mutations reside in NS5A regions known to interact with cellular proteins crucial for cell-cycle regulation (p53, p85-PIK3, and β-catenin), and introduce additional phosphorylation sites, a phenomenon known to ameliorate NS5A interaction with cellular proteins. Overall, these results provide a focus for further investigations on molecular bases of HCV-mediated oncogenesis. The role of these NS5A domain-1 mutations in triggering pro-oncogenic stimuli that can persist also despite achievement of sustained virological response deserves further investigation.
Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction

We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 to about 60% and ~500 ns for ALA21, and folding free energies decreasing linearly with the increasing number of residues. The helix folding was analyzed with the Optimal Dimensionality Reduction method, yielding coarse-grained kinetic models that provided a detailed representation of the folding process. The shorter peptides, ALA5 and ALA8, tended to convert directly from coil to helix, while ALA15 and ALA21 traveled through several intermediates. Coarse-grained aggregate states representing the helix, coil, and intermediates were heterogeneous, encompassing multiple peptide conformations. The folding involved multiple pathways and interesting intermediate states were present on the folding paths, with partially formed helices, turns, and compact coils. Statistically, helix initiation was favored at both termini, and the helix was most stable in the central region. Importantly, we found the presence of underlying universal local dynamics in helical peptides with correlated transitions for neighboring hydrogen bonds. Overall, the structural and dynamical parameters extracted from the trajectories are in good agreement with experimental observables, providing microscopic insights into the complex helix folding kinetics.
A Temperature Independent Inclinometer Based on a Tapered Fiber Bragg Grating in a Fiber Ring Laser

We demonstrate a new concept for an all-fiber inclinometer based on a tapered fiber Bragg grating (tFBG) in a fiber ring laser (FRL) with the capability of measuring the tilt angle and temperature simultaneously. The sensor performance is analyzed theoretically and investigated experimentally. The dependence of tilt angle on the spectral response in variable temperature conditions was measured. Two inclinometers with different lengths have been fabricated and characterized in FRL. The sensitivity is 0.583 dB/° and 0.849 dB/°, respectively, in the range of 0° to 90°. Thanks to the FRL system, narrow 3-dB bandwidth (<0.1 nm) and high optical signal-to-noise ratio (~60 dB) are achieved. The tFBG in the FRL system can be used for working as a temperature insensitive inclinometer. The results suggested that the proposed inclinometer has the advantages of compact size and convenient manufacture, enhancing its potential for application prospect.
In Situ LSPR Sensing of Secreted Insulin in Organ-on-Chip

Organ-on-a-chip (OOC) devices offer new approaches for metabolic disease modeling and drug discovery by providing biologically relevant models of tissues and organs in vitro with a high degree of control over experimental variables for high-content screening applications. Yet, to fully exploit the potential of these platforms, there is a need to interface them with integrated non-labeled sensing modules, capable of monitoring, in situ, their biochemical response to external stimuli, such as stress or drugs. In order to meet this need, we aim here to develop an integrated technology based on coupling a localized surface plasmon resonance (LSPR) sensing module to an OOC device to monitor the insulin in situ secretion in pancreatic islets, a key physiological event that is usually perturbed in metabolic diseases such as type 2 diabetes (T2D). As a proof of concept, we developed a biomimetic islet-on-a-chip (IOC) device composed of mouse pancreatic islets hosted in a cellulose-based scaffold as a novel approach. The IOC was interfaced with a state-of-the-art on-chip LSPR sensing platform to monitor the in situ insulin secretion. The developed platform offers a powerful tool to enable the in situ response study of microtissues to external stimuli for applications such as a drug-screening platform for human models, bypassing animal testing.
Translational Attenuation by an Intron Retention in the 5′ UTR of ENAM Causes Amelogenesis Imperfecta

Amelogenesis imperfecta (AI) is a collection of rare genetic conditions affecting tooth enamel. The affected enamel can be of insufficient quantity and/or altered quality, impacting structural content, surface integrity and coloration. Heterozygous mutations in ENAM result in hypoplastic AI without other syndromic phenotypes, with variable expressivity and reduced penetrance, unlike other AI-associated genes. In this study, we recruited a Caucasian family with hypoplastic AI. Mutational analysis (using whole exome sequencing) revealed a splicing donor site mutation (NM_031889.3: c. −61 + 1G > A). Mutational effects caused by this variant were investigated with a minigene splicing assay and in vitro expression analysis. The mutation resulted in a retention of intron 1 and exon 2 (a normally skipped exon), and this elongated 5′ UTR sequence attenuated the translation from the mutant mRNA. Structure and translation predictions raised the possibility that the long complex structures—especially a hairpin structure located right before the translation initiation codon of the mutant mRNA—caused reduced protein expression. However, there could be additional contributing factors, including additional uORFs. For the first time, we determined that a mutation altered the ENAM 5′ UTR, but maintained the normal coding amino acid sequence, causing hypoplastic AI.
Two-Staged Revision Total Ankle Arthroplasty Surgery with Primary Total Ankle Arthroplasty System: A Case Report.

CASE Case of a 2-staged revision surgical technique for the treatment of an aseptic total ankle arthroplasty (TAA) loosening: first surgery: removal of the loosened and painful TAA Scandinavian Total Ankle Replacement, with exclusion of infection, and reconstruction of the large bone defect (bone-defect downsizing surgery); proof of successful ankle bone reconstruction by CT-scan imaging; second surgery: implantation of a primary VANTAGE TAA (ankle reconstruction with new primary TAA). CONCLUSION The present case shows the management of a failed TAA with bone defect by performing a 2-step surgical approach: removal of loosened TAA with simultaneous bone stock restoration and then implantation of a new primary TAA. This concept is a possible alternative to a post-TAA ankle arthrodesis or to the use of a TAA revision system.
Comparative Neurodevelopment Effects of Bisphenol A and Bisphenol F on Rat Fetal Neural Stem Cell Models

Bisphenol A (BPA) is considered as one of the most extensively synthesized and used chemicals for industrial and consumer products. Previous investigations have established that exposure to BPA has been linked to developmental, reproductive, cardiovascular, immune, and metabolic effects. Several jurisdictions have imposed restrictions and/or have banned the use of BPA in packaging material and other consumer goods. Hence, manufacturers have replaced BPA with its analogues that have a similar chemical structure. Some of these analogues have shown similar endocrine effects as BPA, while others have not been assessed. In this investigation, we compared the neurodevelopmental effects of BPA and its major replacement Bisphenol F (BPF) on rat fetal neural stem cells (rNSCs). rNSCs were exposed to cell-specific differentiation media with non-cytotoxic doses of BPA or BPF at the range of 0.05 µM to 100 µM concentrations and measured the degree of cell proliferation, differentiation, and morphometric parameters. Both of these compounds increased cell proliferation and impacted the differentiation rates of oligodendrocytes and neurons, in a concentration-dependent manner. Further, there were concentration-dependent decreases in the maturation of oligodendrocytes and neurons, with a concomitant increase in immature oligodendrocytes and neurons. In contrast, neither BPA nor BPF had any overall effect on cellular proliferation or the cytotoxicity of astrocytes. However, there was a concentration-dependent increase in astrocyte differentiation and morphological changes. Morphometric analysis for the astrocytes, oligodendrocytes, and neurons showed a reduction in the arborization. These data show that fetal rNSCs exposed to either BPA or BPF lead to comparable changes in the cellular differentiation, proliferation, and arborization processes.
Animal Harms and Food Production: Informing Ethical Choices

Simple Summary Consideration of animal welfare in food choices has become an influential contemporary theme. Traditional animal welfare views about food have been largely restricted to direct and intentional harms to livestock in intensive animal agriculture settings. However, many harms to animals arising from diverse food production practices in the world are exerted indirectly and unintentionally and often affect wildlife. Here we apply a qualitative analysis of food production by considering the breadth of harms caused by different food production systems to wild as well as domestic animals. Production systems are identified that produce relatively few and relatively many harms. The ethical implications of these findings are discussed for consumers concerned with the broad animal welfare impacts of their food choices. Abstract Ethical food choices have become an important societal theme in post-industrial countries. Many consumers are particularly interested in the animal welfare implications of the various foods they may choose to consume. However, concepts in animal welfare are rapidly evolving towards consideration of all animals (including wildlife) in contemporary approaches such as “One Welfare”. This approach requires recognition that negative impacts (harms) may be intentional and obvious (e.g., slaughter of livestock) but also include the under-appreciated indirect or unintentional harms that often impact wildlife (e.g., land clearing). This is especially true in the Anthropocene, where impacts on non-human life are almost ubiquitous across all human activities. We applied the “harms” model of animal welfare assessment to several common food production systems and provide a framework for assessing the breadth (not intensity) of harms imposed. We considered all harms caused to wild as well as domestic animals, both direct effects and indirect effects. We described 21 forms of harm and considered how they applied to 16 forms of food production. Our analysis suggests that all food production systems harm animals to some degree and that the majority of these harms affect wildlife, not livestock. We conclude that the food production systems likely to impose the greatest overall breadth of harms to animals are intensive animal agriculture industries (e.g., dairy) that rely on a secondary food production system (e.g., cropping), while harvesting of locally available wild plants, mushrooms or seaweed is likely to impose the least harms. We present this conceptual analysis as a resource for those who want to begin considering the complex animal welfare trade-offs involved in their food choices.
Dielectric Relaxation Behavior of BTO/LSMO Heterojunction

The BaTiO3 (BTO)/La0.7Sr0. 3MnO3 (LSMO) magnetoelectric composite films were prepared by sol-gel method on STO (001) substrates. The heterojunction has highly preferred orientation and exhibits well ferroelectric properties with perfect hysteresis loops and microscopic polarization switch behaviors. The most interesting thing is the abnormal dielectric relaxation phenomenon in the dielectric spectra at high frequency range and around the phase transition temperature of LSMO. By analyzing the resistance properties of LSMO films, it is indicated that charge-based interfacial coupling, Maxwell-Wagner effect due to the JT polaron and fast resistivity rise in LSMO layer is the main reason. This work emphasizes the crucial role of resistivity exchanges and of carrier accumulation at interfaces for the application of magnetoelectric heterojunction.
Risk factors for COVID-19 mortality: The effect of convalescent plasma administration

Background Convalescent plasma, widely utilized in viral infections that induce neutralizing antibodies, has been proposed for COVID-19, and preliminary evidence shows that it might have beneficial effect. Our objective was to determine the risk factors for 28-days mortality in patients who received convalescent plasma for COVID-19 compared to those who did not, who were admitted to hospitals in Buenos Aires Province, Argentina, throughout the pandemic. Methods This is a multicenter, retrospective cohort study of 2-month duration beginning on June 1, 2020, including unselected, consecutive adult patients with diagnosed COVID-19, admitted to 215 hospitals with pneumonia. Epidemiological and clinical variables were registered in the Provincial Hospital Bed Management System. Convalescent plasma was supplied as part of a centralized, expanded access program. Results We analyzed 3,529 patients with pneumonia, predominantly male, aged 62±17, with arterial hypertension and diabetes as main comorbidities; 51.4% were admitted to the ward, 27.1% to the Intensive Care Unit (ICU), and 21.7% to the ICU with mechanical ventilation requirement (ICU-MV). 28-day mortality was 34.9%; and was 26.3%, 30.1% and 61.4% for ward, ICU and ICU-MV patients. Convalescent plasma was administered to 868 patients (24.6%); their 28-day mortality was significantly lower (25.5% vs. 38.0%, p<0.001). No major adverse effects occurred. Logistic regression analysis identified age, ICU admission with and without MV requirement, diabetes, and preexistent cardiovascular disease as independent predictors of 28-day mortality, whereas convalescent plasma administration acted as a protective factor. Conclusions Our study suggests that the administration of convalescent plasma in COVID-19 pneumonia admitted to the hospital might be associated with improved outcomes.