Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated DNA methylation analysis reveals a potential role for PTPRN2 in Marfan syndrome scoliosis

Abstract Background Marfan syndrome (MFS) is a rare genetic disorder caused by mutations in the Fibrillin‐1 gene (FBN1) with significant clinical features in the skeletal, cardiopulmonary, and ocular systems. To gain deeper insights into the contribution of epigenetics in the variability of phenotypes observed in MFS, we undertook the first analysis of integrating DNA methylation and gene expression profiles in whole blood from MFS and healthy controls (HCs). Methods The Illumina 850K (EPIC) DNA methylation array was used to detect DNA methylation changes on peripheral blood samples of seven patients with MFS and five HCs. Associations between methylation levels and clinical features of MFS were analyzed. Subsequently, we conducted an integrated analysis of the outcomes of the transcriptome data to analyze the correlation between differentially methylated positions (DMPs) and differentially expressed genes (DEGs) and explore the potential role of methylation‐regulated DEGs (MeDEGs) in MFS scoliosis. The weighted gene co‐expression network analysis was used to find gene modules with the highest correlation coefficient with target MeDEGs to annotate their functions in MFS. Results Our study identified 1253 DMPs annotated to 236 genes that were primarily associated with scoliosis, cardiomyopathy, and vital capacity. These conditions are typically associated with reduced lifespan in untreated MFS. We calculated correlations between DMPs and clinical features, such as cobb angle to evaluate scoliosis and FEV1% to assess pulmonary function. Notably, cg20223687 (PTPRN2) exhibited a positive correlation with cobb angle of scoliosis, potentially playing a role in ERKs inactivation. Conclusions Taken together, our systems‐level approach sheds light on the contribution of epigenetics to MFS and offers a plausible explanation for the complex phenotypes that are linked to reduced lifespan in untreated MFS patients.
Annual Burning Enhances Biomass Production and Nutrient Cycling in Degraded Imperata Grasslands

The invasive species Imperata cylindrica is a dominant grass covering a large part of degraded lands of India. Imperata is managed through traditional annual burning, a practice that is prevalent throughout tropical grasslands. A field experiment was conducted to quantify the effects of burning on aboveground and belowground biomass production and soil organic carbon (SOC), total nitrogen (TN), available phosphorus (Ave P), potassium (K+), calcium (Ca+), and magnesium (Mg+) concentrations in 0‐ to 15‐cm soil depth under Imperata grassland. The burnt site had 44% and 14% higher aboveground and belowground biomass over the un‐burnt control plots after 300 days of the fire event. The concentrations of SOC, TN, and Ave P increased soon after the fire but decreased regressively with time after the fire in both micro and macro soil aggregate size fractions. In contrast, concentrations of K+, Ca+, and Mg+ increased up to 30 days after the fire in both soil aggregate fractions. Burning did not significantly alter the stoichiometric ratios (C : N, C : P, and N : P) in macro aggregates. However, burning significantly reduced the C : N, C : P, and N : P ratios in micro aggregates during the first 0–30 days. Fire increased nutrient stocks (kg ha−1) by 20–35% in the burnt site in comparison to an un‐burnt control site. It is concluded that the conventional practice of annual burning increases soil nutrients in surface soils and supports higher biomass production in Imperata‐covered degraded lands. Copyright © 2017 John Wiley & Sons, Ltd.
Supplement usage and doping attitudes in elite youth sports: The mediating role of dietary supplement acceptance

This study investigated whether dietary supplement acceptance mediated the relationship between supplement use and doping attitudes in youth sports. To this end, we employed a two-wave half-longitudinal design during a sports season (time point one [T1] to time point two [T2]). The sample consisted of 217 elite youth athletes (47% male; mean age = 16.98 years, standard deviation = 0.88) who competed in team sports (43%; N = 93; basketball, floorball, handball, and ice hockey) and individual sports (57%; N = 124; alpine skiing, biathlon, cross-country skiing, swimming, and tennis). The participants were recruited from eight Norwegian sports academy high schools that provide extracurricular, higher-level training and specialization for youth athletes. Results from structural equation modeling analysis indicated that dietary supplement acceptance (T2) mediated the positive relationship between supplement use (T1) and doping attitudes (T2) when accounting for prior levels of the mediator and the outcome variable. These findings suggest that when young athletes used dietary supplements at the start of the season to improve their performance, they were more likely to view the use of supplements as acceptable and to report more favorable attitudes toward doping at the end of the season six months later. For those seeking to prevent doping in youth sports, targeting athletes’ views on the acceptable use of dietary supplements may be important.
Does simultaneous comminuted fracture of both radial ends represent a distinct fracture pattern?

ABSTRACT BACKGROUND: Although isolated distal radius and radial head fractures are common injuries, simultaneous ipsilateral fractures are uncommon. They can range from simple undisplaced fractures at either end to severely comminuted ipsilateral proximal and distal radial fractures. Few cases have been reported with concomitant comminuted distal radius and radial head fractures, and no treatment guidelines are available. Decisions are often based on personal recommendations. The purpose of our study is to increase awareness of this injury pattern and to discuss the mechanism of injury, treatment approach, and functional outcome. METHODS: Skeletally mature patients with comminuted simultaneous ipsilateral fractures of the distal and proximal radius from 2016 to 2021 were identified and studied retrospectively. Demographic information, mechanism of injury, treatment approach, and complication rate were analyzed. Radiographic assessment for inadequacy or loss of reduction and radiographic parameters of the distal radius, including radial inclination, radial length, and palmar inclination, was performed immediately postoperatively and at the final follow-up. Clinical outcomes were determined by calculating the Visual Analog Scale (VAS) score, measuring the range of motion in both joints, and using the Quick Disabilities of the Arm, Shoulder and Hand (QuickDASH) score at the final follow-up. RESULTS: A total of 11 patients met the inclusion criteria. All had ipsilateral Mason III radial head fractures and type C (according to the Arbeitsgemeinschaft für Osteosynthesefragen (AO) classification) intra-articular distal radius fracture. On-table radial head reconstruction and fixation with a proximal radius plate were used for radial head fractures, and osteosynthesis with an anatomic volar locking plate was used for distal radius fractures. The mean follow-up duration was 32 months (range 12-65 months). At the final follow-up, osseous union of both the radial head and distal radius was observed in all patients. The mean VAS score was 1.5 (range 0-7) at rest and 3.9 (range 0-9) with activities, while the mean QuickDASH score was 32 (range 12-65). No significant complications were recorded. CONCLUSION: Simultaneous comminuted fractures of the ipsilateral distal radius and radial head represent a distinct injury pattern, most likely resulting from high-energy trauma, such as falling from a height onto an outstretched hand. Greater emphasis should be placed on clinical examination and radiological imaging of the elbow in cases of wrist injuries and vice versa. Treatment involving on-table reconstruction of the radial head and open reduction and internal fixation with a volar plate can lead to good radiological and functional outcomes.
Analysis of rainfall characteristics in Tanzania for climate change signals

Tanzania as many other countries in Africa depends on rain water for various economic activities in order to achieve its development. The global climate change has not isolated Tanzania, the rainfall climatology of the country has some changes which need to be taken into account while planning for economic activities such as hydro power generation, civil and structural engineering, mining, Agriculture which is the back-borne of the country as it is the main source of employment, foreign currency and revenue. This study aims at aims examining the rainfall characteristics over Tanzania in order to determine the climate change signals in rainfall characteristics in particular. The daily, monthly and seasonal rainfall datasets from all the eleven zones in Tanzania covering a period of 48 years from 1961 to 2008 were used. Tanzania meteorological agency is the source of data used. Arithmetic method was used to estimate the missing data for Loliondo the only station which had missing data. The single line mass curve method was used to test homogeneity of the data for the stations selected to represent each of the eleven zones, results from the mass curve showed all the data from all the seven zones were homogeneous. During analysis, time series and trend / . methods were used. The eleven zones used in this research project were adopted from the ones used by the Tanzania Meteorological Agency. This study revealed that all the zones have some changes in their rainfall characteristics as the amounts of seasonal rainfall were found to show decreasing trends in some stations and increasing trends in the others. The time series for the accumulated seasonal rainfall in pentads showed delays in the onsets and cessations while other zones were found to experience delay of onsets and earlier cessations implying the seasons are becoming short. Rainfall characteristics in Tanzania are changing differently in different parts over the country. , The people in the country especially those who are stakeholders of the meteorological services in particular rainfall must be empowered with updates in changes of rainfall climatology. Agriculture as a long time and term back-born of the country should be adequately performed along the current changes in the rainfall characteristics so as to make it sustainable and profitable and therefore avoiding the demerits which normally arise from poor harvests and hence control for the food security.
Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans

Abstract The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.
LAS-NCS: A Laser-Assisted Spintronic Neuromorphic Computing System

In spintronic-based neuromorphic computing systems (NCSs), the switching of magnetic moment in a magnetic tunnel junction (MTJ) is used to mimic biological neuron firing. However, the high currents required for MTJ switching will lead to a large energy consumption and low speed operation of the MTJ-based NCSs. In this brief, the energy consumption and the delay of the proposed MTJ-based NCS are reduced by thermally assisting the MTJ switching through a microwatt nanosecond laser pulse. Simulation results show 85.7%, 84%, and 97.8% improvements in energy consumption, delay, and energy-delay product, respectively, for the laser-assisted spintronic NCS (LAS-NCS) by heating the MTJs up to 127 °C. The energy consumption of the laser pulse for heating up the MTJ stack is <inline-formula> <tex-math notation="LaTeX">$1.2 {\times }$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">$2.4 {\times }$ </tex-math></inline-formula> lower than Joule heating method. Moreover, in contrast with Joule heating method, the LAS-NCS does not require MTJ with modified structure.
Aqueous chemimemristor based on proton-permeable graphene membranes

Significance We implemented memristive behavior in aqueous electrolytes using monolayer graphene supported on a CaF2 substrate as a model system and probed in situ the ion dynamics of the neuromorphic devices with surface-specific vibrational spectroscopy. Our work demonstrates a unique and simple concept for developing aqueous electrolyte-based neuromorphic iontronics using two-dimensional (2D) materials through manipulating interfacial acid-base equilibrium.
The genome in space and time comes of age

ABSTRACT DNA sequencing is not enough to grasp the complexity of genome organization and function. The four-dimensional (three in space, one in time) configuration of the eukaryotic nucleus varies with cell types, during development and in diseased tissues, and has to be taken into account to decipher genome function. To study, discuss, and advance in such direction, the International Nucleome Consortium COST Action, funded by the European Union, held its concluding symposium ‘The Genome in Space and Time’ at the Ionian University in Corfu, Greece, on September 10–13, 2023.
Permissive epigenetic regulatory mechanisms at the histone level are enhanced in postmortem dorsolateral prefrontal cortex of individuals with schizophrenia

Background: Susceptibility to schizophrenia is determined by interactions between genes and environment, possibly via epigenetic mechanisms. Schizophrenia has been associated with a restrictive epigenome, and histone deacetylase (HDAC) inhibitors have been postulated as coadjuvant agents to potentiate the efficacy of current antipsychotic drugs. We aimed to evaluate global histone posttranslational modifications (HPTMs) and HDAC expression and activity in the dorsolateral prefrontal cortex (DLPFC) of individuals with schizophrenia. Methods: We used postmortem DLPFC samples of individuals with schizophrenia and controls matched for sex, age, and postmortem interval. Schizophrenia samples were classified into antipsychotic-treated or antipsychotic-free subgroups according to blood toxicology. Expression of HPTMs and HDAC was quantified by Western blot. HDAC activity was measured with a fluorometric assay. Results: H3K9ac, H3K27ac, and H3K4me3 were globally enhanced in the DLPFC of individuals with schizophrenia (+24%–42%, p < 0.05). HDAC activity (−17%, p < 0.01) and HDAC4 protein expression (−20%, p < 0.05) were downregulated in individuals with schizophrenia. Analyses of antipsychotic-free and antipsychotic-treated subgroups revealed enhanced H3K4me3 and H3K27ac (+24%–49%, p < 0.05) and reduced HDAC activity in the antipsychotic-treated, but not in the antipsychotic-free subgroup. Limitations: Special care was taken to control the effect of confounding factors: age, sex, postmortem interval, and storage time. However, replication studies in bigger cohorts might strengthen the association between permissive HPTMs and schizophrenia. Conclusion: We found global HPTM alterations consistent with an aberrantly permissive epigenome in schizophrenia. Further studies to elucidate the significance of enhanced permissive HPTMs in schizophrenia and its association with the mechanism of action of antipsychotic drugs are encouraged.
Lumbar degeneration and quality of life in patients with lumbar disc herniation: a case-control long-term follow-up study

Background and purpose Adults treated surgically for lumbar disc herniation in adolescence have a higher degree of lumbar disc degeneration than controls. We aimed to establish whether the degree of lumbar degeneration differs at diagnosis or at follow-up between surgically and non-surgically treated individuals. Methods We identified individuals with a lumbar disc herniation in adolescence diagnosed with magnetic resonance imaging (MRI) and contacted them for follow-up MRI. Lumbar degeneration was assessed according to Pfirrmann, Modic, and total end plate score (TEP score). Patient-reported outcome measures at follow-up comprised the Oswestry Disability Index (ODI), EQ-5D-3-level version, 36-Item Short Form Health Survey (SF-36), and Visual Analogue Scale (VAS) for back and leg pain. Fisher’s exact test, Mann–Whitney U tests, Wilcoxon tests, and logistic regression were used for statistical analysis. Results MRIs were available at diagnosis and after a mean of 11.9 years in 17 surgically treated individuals and 14 non-surgically treated individuals. Lumbar degeneration was similar at diagnosis (P = 0.2) and at follow-up, with the exception of higher TEP scores in surgically treated individuals at levels L4–L5 and L5–S1 at follow-up (P ≤ 0.03), but this difference did not remain after adjustment for age and sex (P ≥ 0.8). There were no significant differences in patient-reported outcome measures between the groups at follow-up (all P ≥ 0.2). Conclusion Adolescents with a lumbar disc herniation have, irrespective of treatment, a similar degree of lumbar degeneration at the time of diagnosis, and similar lumbar degeneration and patient-reported outcomes at long-term follow-up.
Excess natural-cause mortality in US counties and its association with reported COVID-19 deaths

Significance Official COVID-19 mortality statistics have not fully captured deaths attributable to SARS-CoV-2 infection in the United States. While some excess deaths were likely related to pandemic health care interruptions and socioeconomic disruptions, temporal correlations between reported COVID-19 deaths and excess deaths reported to non-COVID-19 natural causes suggest that many of those excess deaths were unrecognized COVID-19 deaths. Efforts to target resources during public health emergencies should consider geographic variation in the quality of mortality surveillance data. Incomplete or delayed cause-of-death reporting may obscure impacts in some areas, leading to ineffective and inequitable responses and evaluations of the pandemic’s effects. To address this, future pandemic preparedness and response efforts should include activities to strengthen the death investigation system.
Optimization-based coordination strategies for connected and autonomous vehicles

Automated vehicles (AV) are expected to reach the consumer market within the next decade. Once AVs become ubiquitous, they could resolve difficult traffic situations through communication-based cooperation. Intersections are of particular interest in this context, as they form bottlenecks in the traffic system and are responsible for a large share of all accidents. Rather than relying on traffic lights, road signs and rules, AVs could employ cooperative strategies to decide how an intersection should be crossed safely and efficiently. However, designing efficient coordination strategies for AVs at intersections is challenging, as computationally hard problems are involved, with a safety-critical dependence on both wireless communication and imprecise sensing. This thesis treats control algorithms for cooperative coordination of CAVs at intersections. The proposed algorithms are based on Optimal Control (OC) formulations of the coordination problem and aim at finding the optimal control commands for each vehicle through a two-stage approximation procedure. In the first stage, the order in which the vehicles cross the intersection is determined using a heuristic based on Mixed-Integer Quadratic Programming (MIQP). In the second stage, the optimal control commands for each vehicle are found under a fixed crossing order. Two algorithms are presented that solves the problem of the second stage in a communication efficient, distributed fashion. In the first algorithm, the problem is decomposed into one master-problem and one sub-problem for each vehicle. The master-problem is solved using a Sequential Quadratic Programming (SQP) algorithm, where most computations are performed in parallel on-board the vehicles. In the second algorithm, the problem is solved using a Primal-Dual Interior Point (PDIP) method. The computations involved are separable so that the largest part can be performed in parallel on-board the vehicles, a lesser part in parallel on lead-vehicles for each lane, and a small part at a central network node. The two-stage approximation procedure is used in a Model Predictive Controller (MPC), and conditions for persistent feasibility and stability are derived. Performance of the MPC-based closed-loop controller is assessed in simulation, and compared to traffic-lights and alternative coordination algorithms. The results demonstrate that the two-stage approach outperforms existing alternatives, with almost zero average travel-time delay and a marginal increase in energy consumption compared to cruising at constant speed. An MPC controller based on the SQP algorithm is verified experimentally at a test-track with three real vehicles. The results demonstrate that efficient coordination is practically realizable through communication-based optimization and MPC. In particular, the experiments show that the MPC algorithm performs well under adverse conditions with significant sensor noise, communication impairments and external perturbations.