Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic saccade context triggers more stable spatiotopic object-location binding

Our visual systems rapidly perceive and integrate information about object identities and locations. There is long-standing debate about how we achieve world-centered (spatiotopic) object representations across eye movements, with many studies reporting persistent retinotopic (eye-centered) effects even for higher-level object-location binding. But these studies are generally conducted in fairly static experimental contexts. Might spatiotopic object-location binding only emerge in more dynamic saccade contexts? In the present study, we investigated this using the Spatial Congruency Bias paradigm in healthy adults. In the static (single saccade) context, we found purely retinotopic binding, as before. However, robust spatiotopic binding emerged in the dynamic (multiple frequent saccades) context. We further isolated specific factors that modulate retinotopic and spatiotopic binding. Our results provide strong evidence that dynamic saccade context can trigger more stable object-location binding in ecologically-relevant spatiotopic coordinates, perhaps via a more flexible brain state which accommodates improved visual stability in the dynamic world. Significance Statement One of the most fundamental challenges for human behavior is how we integrate and stabilize perceptual information in our ever-changing sensory environments. In particular, we make multiple eye movements every second, constantly displacing and distorting our visual input. Yet despite receiving visual input in these disjointed, eye-centered (retinotopic) coordinates, we perceive the world as stable, based on objects’ world-centered (spatiotopic) locations. Our study provides strong evidence for a previously unstudied cue – dynamic saccade context – in triggering more stable object-location binding, which offers a novel step forward in understanding how we form a stable perception of the dynamic world. More broadly, these findings suggest the importance of considering dynamic saccade context in visual perception and cognitive neuroscience studies.
Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics

Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined with in silico mutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
Affordances and Information Systems Research: Taking Stock and Moving Forward

The term affordance appears with increasing frequency in the Information Systems (IS) literature. Nevertheless, those who study information technologies/information systems (IT/IS) via the affordance lens often have different views about its origin, meaning, and appropriate application in IS research. In turn, not spelling out the related assumptions and boundaries inherent in these diverse views may have hindered a wider and more cumulative adoption of the affordance lens in IS research. This paper offers a potential solution by (1) synthesizing the ecological psychology literature to suggest five key modules of the affordance concept relevant to IS research and (2) taking stock of IS research that has employed the affordance concept and classifying it according to its focus on three key affordance elements: IT artifact, user, and context. Finally, this paper presents a set of challenges, opportunities, and recommendations regarding how IS researchers can advance affordance-based research in the field.
Ecotrophic perspective in fisheries management: a review of Ecopath with Ecosim models in European marine ecosystems

The aim of this work is to present the food web models developed using the Ecopath with Ecosim (EwE) software tool to describe structure and functioning of various European marine ecosystems (eastern, central and western Mediterranean Sea; Black Sea; Bay of Biscay, Celtic Sea and Iberian coast; Baltic Sea; North Sea; English Channel, Irish Sea and west Scottish Sea; and Norwegian and Barents Seas). A total of 195 Ecopath models based on 168 scientific publications, which report original, updated and modified versions, were reviewed. Seventy models included Ecosim temporal simulations while 28 implemented Ecospace spatiotemporal dynamics. Most of the models and publications referred to the western Mediterranean Sea followed by the English Channel, Irish Sea and west Scottish Sea sub-regions. In the Mediterranean Sea, the western region had the largest number of models and publications, followed by the central and eastern regions; similar trends were observed in previous literature reviews. Most models addressed ecosystem functioning and fisheries-related hypotheses while several investigated the impact of climate change, the presence of alien species, aquaculture, chemical pollution, infrastructure, and energy production. Model complexity (i.e., number of functional groups) increased over time. Main forcing factors considered to run spatial and temporal simulations were trophic interactions, fishery, and primary production. Average scores of ecosystem indicators derived from the Ecopath summary statistics were compared. Uncertainty was also investigated based on the use of the Ecosampler plug-in and the Monte Carlo routine; only one third of the reviewed publications incorporated uncertainty analysis. Only a limited number of the models included the use of the ECOIND plug-in which provides the user with quantitative output of ecological indicators. We assert that the EwE modelling approach is a successful tool which provides a quantitative framework to analyse the structure and dynamics of ecosystems, and to evaluate the potential impacts of different management scenarios.
Different iPSC-derived neural stem cells shows various spectrums of spontaneous differentiation during long term cultivation

Introduction Culturing of human neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSC) is a promising area of research, as these cells have the potential to treat a wide range of neurological, neurodegenerative and psychiatric diseases. However, the development of optimal protocols for the production and long-term culturing of NSCs remains a challenge. One of the most important aspects of this problem is to determine the stability of NSCs during long-term in vitro passaging. To address this problem, our study was aimed at investigating the spontaneous differentiation profile in different iPSC-derived human NSCs cultures during long-term cultivation using. Methods Four different IPSC lines were used to generate NSC and spontaneously differentiated neural cultures using DUAL SMAD inhibition. These cells were analyzed at different passages using immunocytochemistry, qPCR, bulk transcriptomes and scRNA-seq. Results We found that various NSC lines generate significantly different spectrums of differentiated neural cells, which can also change significantly during long-term cultivation in vitro. Discussion Our results indicate that both internal (genetic and epigenetic) and external (conditions and duration of cultivation) factors influence the stability of NSCs. These results have important implications for the development of optimal NSCs culturing protocols and highlight the need to further investigate the factors influencing the stability of these cells in vitro.
Lower limbs inter-joint coordination and variability during typical Tai Chi movement in older female adults

Purpose: This study aimed to investigate the lower limb inter-joint coordination and variability during Tai Chi movements compared with normal walking in older adults. Methods: A total of 30 female Tai Chi practitioners (70.9 ± 5.2 years) were recruited in this study. Herein, each participant performed three trials of the normal walking and Tai Chi movements. The lower limb kinematics data were collected with Vicon 3D motion capture system. The continuous relative phase (CRP) includes both spatial and temporal information of two adjacent joints, which was calculated to assess the inter-joint coordination of lower limbs. Coordination amplitude and coordination variability were assessed with mean absolute relative phase (MARP) and deviation phase (DP). MANOVOA was used to analyze inter-joint coordination parameters between different movements. Results: The CRP values of hip-knee and knee-ankle segments in the sagittal plane of the Tai Chi movements changed frequently. The MARP values of the hip-knee (p < 0.001) and knee-ankle segments (p = 0.032) as well as the DP values of the hip-knee segment (p < 0.001) were significantly lower in Tai Chi than in normal walking. Conclusion: More consistent and stable inter-joint coordination patterns of Tai Chi movements found in this study may be one of the critical factors that Tai Chi could be a suitable coordinated exercise for older adults.
DNA repair-related genes are the key for stony coral ancestors to survive under elevated levels of UVR

DNA damage response (DDR) is a complicated network to defend against physical or chemical changes in DNA in all animals. Elevated levels of ultraviolet radiation (UVR) caused DNA damage, which was a reason for the mass extinction that occurred at the Devonian/Carboniferous (D/C) boundary approximately 359 million years ago (Ma). However, the molecular adaptation of the stony coral ancestors that strangely survived the D/C boundary mass extinction is not well understood. In the present study, the molecular clock analysis using fourfold degenerate sites of 1,463 homologous genes of different stony coral species (a representative group of marine organisms with calcareous skeletons) suggested that their common ancestors originated 384.24 Ma, i.e., slightly earlier than the D/C transition. We identified 21 rapidly evolving genes (REGs) and 49 positive selection genes (PSGs) that were significantly enriched in diverse pathways, including the mitotic cell cycle process, intracellular protein transport, and DNA synthesis involved in DNA repair. Interestingly, four REGs and 21 PSGs were significantly enriched in DDR pathways, including the mitotic cell cycle process, DNA synthesis involved in DNA repair, and cellular response to DNA damage stimulus pathways. We hypothesize that enriched DDR genes are likely involved in the enhanced ability of ancient stony corals to detect and repair DNA damage. For example, the DNA polymerase epsilon catalytic subunit (POLE) gene, which encodes the DNA polymerase epsilon catalytic subunit A, mediates interaction with the other three catalytic subunits through its nonenzymatic carboxy-terminal domain. POLE may potentially enhance the binding ability to other subunits to strengthen its function because eight positive selection sites were distributed in the C-terminal of POLE and on the surface of the simulated 3D protein model. Therefore, our results demonstrated for the first time that the precise transfer of DNA information may help stony coral ancestors survive in elevated levels of ultraviolet radiation, suggesting that DDR levels may be critical to the environmental adaptation of calcareous skeletal organisms during climate change.
Hyperinsulinemia: an early biomarker of metabolic dysfunction

Introduction Hyperinsulinemia in the absence of impaired glucose tolerance and normal HbA1c is considered indicative of pre-diabetes. Very few Indian studies have focused on hyperinsulinemia particularly in young adults. The present study aimed to determine whether hyperinsulinemia may be present despite HbA1c being normal. Methods This was a cross–sectional study conducted on adolescents and young adults aged 16-25 years living in Mumbai, India. The participants attended various academic institutions and were those who underwent screening as the first step of a clinical trial for studying the efficacy of almond intake in prediabetes. Results Among this young population (n=1313), 4.2% (n=55) of the participants were found to be prediabetic (ADA criteria) and 19.7% of them had HbA1c levels between 5.7%-6.4%. However, almost, 30.5% had hyperinsulinemia inspite of normal blood glucose levels and normal HbA1c. Among those with HbA1c<5.7 (n=533), 10.5% (n=56) participants had fasting insulin>15 mIU/L and a higher percentage (39.4%, n=260) had stimulated insulin above 80 mIU/L. These participants had higher mean anthropometric markers than those with normal fasting and/or stimulated insulin. Conclusion Hyperinsulinaemia in the absence of impaired glucose tolerance and normal HbA1c may provide a much earlier indicator of detection for risk of metabolic disease and progression to metabolic syndrome and diabetes mellitus.
A systematic review on sex differences in adverse drug reactions related to psychotropic, cardiovascular, and analgesic medications

Background and objective: Adverse drug reactions (ADRs) are the main safety concerns of clinically used medications. Accumulating evidence has shown that ADRs can affect men and women differently, which suggests sex as a biological predictor in the risk of ADRs. This review aims to summarize the current state of knowledge on sex differences in ADRs with the focus on the commonly used psychotropic, cardiovascular, and analgesic medications, and to aid clinical decision making and future mechanistic investigations on this topic. Methods: PubMed search was performed with combinations of the following terms: over 1,800 drugs of interests, sex difference (and its related terms), and side effects (and its related terms), which yielded over 400 unique articles. Articles related to psychotropic, cardiovascular, and analgesic medications were included in the subsequent full-text review. Characteristics and the main findings (male-biased, female-biased, or not sex biased ADRs) of each included article were collected, and the results were summarized by drug class and/or individual drug. Results: Twenty-six articles studying sex differences in ADRs of six psychotropic medications, ten cardiovascular medications, and one analgesic medication were included in this review. The main findings of these articles suggested that more than half of the ADRs being evaluated showed sex difference pattern in occurrence rate. For instance, lithium was found to cause more thyroid dysfunction in women, and amisulpride induced prolactin increase was more pronounced in women than in men. Some serious ADRs were also found to exert sex difference pattern, such as clozapine induced neutropenia was more prevalent in women whereas simvastatin/atorvastatin-related abnormal liver functions were more pronounced in men.
CD25 targeting with the afucosylated human IgG1 antibody RG6292 eliminates regulatory T cells and CD25+ blasts in acute myeloid leukemia

Background Acute Myeloid leukemia is a heterogeneous disease that requires novel targeted treatment options tailored to the patients’ specific microenvironment and blast phenotype. Methods We characterized bone marrow and/or blood samples of 37 AML patients and healthy donors by high dimensional flow cytometry and RNA sequencing using computational analysis. In addition, we performed ex vivo ADCC assays using allogeneic NK cells isolated from healthy donors and AML patient material to test the cytotoxic potential of CD25 Mab (also referred to as RG6292 and RO7296682) or isotype control antibody on regulatory T cells and CD25+ AML cells. Results Bone marrow composition, in particular the abundance of regulatory T cells and CD25 expressing AML cells, correlated strongly with that of the blood in patients with time-matched samples. In addition, we observed a strong enrichment in the prevalence of CD25 expressing AML cells in patients bearing a FLT3-ITD mutation or treated with a hypomethylating agent in combination with venetoclax. We adopted a patient-centric approach to study AML clusters with CD25 expression and found it most highly expressed on immature phenotypes. Ex vivo treatment of primary AML patient samples with CD25 Mab, a human CD25 specific glycoengineered IgG1 antibody led to the specific killing of two different cell types, CD25+ AML cells and regulatory T cells, by allogeneic Natural Killer cells. Conclusion The in-depth characterization of patient samples by proteomic and genomic analyses supported the identification of a patient population that may benefit most by harnessing CD25 Mab’s dual mode of action. In this pre-selected patient population, CD25 Mab could lead to the specific depletion of regulatory T cells, in addition to leukemic stem cells and progenitor-like AML cells that are responsible for disease progression or relapse.
The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

Introduction The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme—and unique—oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described. Methods To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria. Results and discussion This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.
Assistance level quantification-based human-robot interaction space reshaping for rehabilitation training

Stroke has become a major disease that seriously threatens human health due to its high incidence and disability rates. Most patients undergo upper limb motor dysfunction after stroke, which significantly impairs the ability of stroke survivors in their activities of daily living (ADL). Robots provide an optional solution for stroke rehabilitation by attending therapy in the hospital and the community, however, the rehabilitation robot still has difficulty in providing needed assistance interactively like human clinicians in conventional therapy. For safe and rehabilitation training, a human-robot interaction space reshaping method was proposed based on the recovery states of patients. According to different recovery states, we designed seven experimental protocols suitable for distinguishing rehabilitation training sessions. To achieve assist-as-needed (AAN) control, a PSO-SVM classification model and an LSTM-KF regression model were introduced to recognize the motor ability of patients with electromyography (EMG) and kinematic data, and a region controller for interaction space shaping was studied. Ten groups of offline and online experiments and corresponding data processing were conducted, and the machine learning and AAN control results were presented, which ensured the effective and the safe upper limb rehabilitation training. To discuss the human-robot interaction in different training stages and sessions, we defined a quantified assistance level index that characterizes the rehabilitation needs by considering the engagement of the patients and had the potential to apply in clinical upper limb rehabilitation training.
Addressing the spread of health-related misinformation on social networks: an opinion article

This article deals with the spread of misinformation in a general context and specifically in the health sector. It presents a theoretical view of the problem and analyzes its characteristics with a focus on medicine and mainly rheumatology. Finally, conclusions from the previous analysis are formulated as well as suggestions for reducing the dimensions of the problem in the health sector.
Prevalence and characteristics of obesity in patients with type-2 diabetes mellitus in primary care centers in Bahrain: A cross-sectional study

BACKGROUND: Obesity is a complex health problem characterized by abnormal and excessive body weight. Globally, the epidemic of obesity is escalating, and today, around one-third of the world's adult population is overweight or obese. Obesity is a risk factor and a predictor of poor outcomes of diabetes. This study aimed to determine the prevalence and characteristics of obesity in adults with type-2 diabetes mellitus. MATERIALS AND METHODS: This study was conducted at five primary care centers in Bahrain. Obesity was assessed using body mass index, while glycemic control status was assessed using glycated hemoglobin (HbA1c). Informed consent was obtained from all participants. Means and standard deviation were computed for continuous variables, while categorical variables were presented as frequencies and percentages. Student's t-test and Mann-WhitneyU test, as appropriate, were performed to determine statistical significance between two continuous variables. Chi-square or Fisher's Exact test were used to test for statistical significance for categorical variables. RESULTS: A total of 732 participants were included; the mean age was 58.4 ± 11.3 years. Hypertension was the most prevalent comorbidity (63.5%), followed by hyperlipidemia (51.9%). Most participants (59.8%) had HbA1c levels of more than 7%, 20.9% had HbA1c levels between 7% and 8%, and 38.9% had HbA1c levels of more than 8%. Of the cohort, 47.5% were obese and 35.0% were overweight. Obesity was significantly higher in Bahraini patients and females (P < 0.001). Lower obesity rates were observed among patients who exercised regularly (P < 0.001) and patients who followed diet control measures (P = 0.039). In addition, we found higher obesity rates were found in patients with uncontrolled diabetes (P = 0.004), hypertension (P = 0.032), and hyperlipidemia (P = 0.048). CONCLUSION: Obesity is prevalent among type-2 diabetic patients and is associated with poor glycemic outcomes. Thus, more efforts should be taken by physicians to address obesity in diabetic patients as it negatively impacts their glycemic control.