Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental Effects on Relative Use of PEPCK and NADP-ME Pathways of C4 Photosynthesis in Maize

C4 photosynthesis is an adaptive photosynthetic pathway which concentrates CO2 around Rubisco in specialized bundle sheath cells to reduce photorespiration. Historically, the pathway has been characterized into three different subtypes based on the decarboxylase involved, although recent work has provided evidence that some plants can use multiple decarboxylases, with maize in particular using both the NADP-malic enzyme (NADP-ME) pathway and phosphoenolpyruvate carboxykinase (PEPCK) pathway. Parallel C4 pathways could be advantageous in balancing energy and reducing equivalents between bundle sheath and mesophyll cells, in decreasing the size of the metabolite gradients between cells and may better accommodate changing environmental conditions or source to sink demands on growth. The enzyme activity of C4 decarboxylases can fluctuate with different stages of leaf development, but it remains unclear if the pathway flexibility is an innate aspect of leaf development or an adaptation to the leaf microenvironment that is regulated by the plant. In this study, variation in the two C4 pathways in maize were characterized at nine plant ages throughout the life cycle. Two positions in the canopy were examined for variation in physiology, gene expression, metabolite concentration, and enzyme activity, with particular interest in asparagine as a potential regulator of C4 decarboxylase activity. Variation in C4 and C3 metabolism was observed for both leaf age and canopy position, reflecting the ability of C4 pathways to adapt to changing microenvironments. One Sentence Summary The proportion of the two C4 pathways in maize plants is dependent on canopy position and not the age of the leaf.
Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Cranberry (Vaccinium macrocarpon) is a member of the Heath family (Ericaceae) and is a temperate low-growing woody perennial native to North America that is both economically important and has significant health benefits. While some native varieties are still grown today, breeding programs over the past 50 years have made significant contributions to improving disease resistance, fruit quality and yield. An initial genome sequence of an inbred line of the wild selection ‘Ben Lear,’ which is parent to multiple breeding programs, provided insight into the gene repertoire as well as a platform for molecular breeding. Recent breeding efforts have focused on leveraging the circumboreal V. oxycoccos, which forms interspecific hybrids with V. macrocarpon, offering to bring in novel fruit chemistry and other desirable traits. Here we present an updated, chromosome-resolved V. macrocarpon reference genome, and compare it to a high-quality draft genome of V. oxycoccos. Leveraging the chromosome resolved cranberry reference genome, we confirmed that the Ericaceae has undergone two whole genome duplications that are shared with blueberry and rhododendron. Leveraging resequencing data for ‘Ben Lear’ inbred lines, as well as several wild and elite selections, we identified common regions that are targets of improvement. These same syntenic regions in V. oxycoccos, were identified and represent environmental response and plant architecture genes. These data provide insight into early genomic selection in the domestication of a native North American berry crop.
Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1

Organisms are inherently equipped with buffering systems against genetic perturbations. Upregulation of homologous genes responding to gene loss, termed genetic compensation, is one such buffering mechanism. Recently, a well-conserved compensatory mechanism was proposed: transcriptional adaptation of homologs under the nonsense-mediated mRNA decay pathways. However, this model cannot explain the onset of all compensatory events. We report a novel genetic compensation mechanism operating over the Mesp gene locus. Mesp1 and Mesp2 are homologs located adjacently in the genome. Mesp2 loss is partially rescued by Mesp1 upregulation in the presomitic mesoderm (PSM). Using a cultured PSM induction system, we reproduced the compensatory response in vitro and found that the Mesp2-enhancer is required to promote Mesp1. We revealed that the Mesp2-enhancer directly interacts with the Mesp1 promoter, thereby upregulating Mesp1 expression upon the loss of Mesp2. Of note, this interaction is established by genomic arrangement upon PSM development independently of Mesp2 disruption. We propose that the repurposing of this established enhancer-promoter communication is the mechanism underlying this compensatory response for the upregulation of the adjacent homolog.
Contraction-dependent intracortical inhibition supports gravity-efficient motor control

Efficient control of voluntary movements along the gravity axis requires adapted shifts in muscular contraction modes. In daily life, rising the arm up involves shortening (i.e., concentric) contractions of arm flexors, while the reverse movement can rely on lengthening (i.e., eccentric) contractions of the same muscles with the help of gravity force. Although this muscular-control mode is universal, the neuromuscular mechanisms that subserve the control of such gravity-oriented movements remain unknown. In this study, we designed two neurophysiological experiments that allowed tracking modulations of cortical, spinal, and muscular outputs of arm flexors while healthy humans carried out vertical pointing movements. In conditions where upward and downward movements revealed kinematic features reminiscent of optimal motor commands (i.e., directional asymmetries), we report fine contraction-dependent modulations of the corticospinal output. The overall corticospinal excitability dropped during lengthening contractions (downward movements) compared with shortening contractions (upward movements). Specifically, we did not observe any change in spinal motoneuron responsiveness from cervicomedullary stimulations but a specific increase in intracortical inhibition during lengthening vs. shortening contractions. We discuss these fine contraction-dependent modulations of the supraspinal motor output in the light of feedforward mechanisms that may support gravity-tuned motor control. Generally, these results shed a new perspective on the neural policy that optimize movement control along the gravity axis.
Circadian modulation of human sleep spindle frequency

Circadian modulation of human sleep spindle frequency Róbert Bódizs, Csenge G. Horváth, Orsolya Szalárdy, Péter P. Ujma, Péter Simor, Ferenc Gombos, Ilona Kovács, Lisa Genzel, Martin Dresler Institute of Behavioural Sciences, Semmelweis University, Budapest, Hungary National Institute of Clinical Neurosciences, Budapest, Hungary Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
Population structure and environmental niches of Rimicaris shrimps from the Mid Atlantic Ridge

Among the endemic and specialized fauna from hydrothermal vents, Rimicaris shrimp surely constitutes one of the most important and emblematic components of these ecosystems. In the Mid Atlantic Ridge, two species affiliated to this genus co-occur: Rimicaris exoculata and Rimicaris chacei that differ by their morphology, their trophic regime as well as by their abundance. The first forms large and dense aggregations on active vent chimney walls in close proximity to vent fluid emissions, whereas the second is recognized as much less conspicuous, living mostly in scattered groups or solitary further away from the fluids. However, the recent revision of Rimicaris juvenile stages from the Mid Atlantic Ridge show that R. chacei abundance would be higher than expected at these early life stages. Here, we describe and compare the population structures of R. exoculata and R. chacei at the Snake Pit and TAG vent fields. We show distinct population demographics between the two co-occurring shrimps with a large post settlement collapse in R. chacei population suggesting a large juvenile mortality for this species. We also observe important spatial segregation patterns between the two species and their different life stages. Additionally, our results highlight distinct niches for the earliest juvenile stages of both R. exoculata and R. chacei, compared to all the other life stages. Finally, we discuss the potential factors - predation and competitive interactions among others - that could explain the differences we observe in the population structure of these two species.
Revisiting the Examination of Sharp/Dull Discrimination as Clinical Measure of Spinothalamic Tract Integrity

Objective: Revisiting the sharp/dull discrimination as clinical measure of spinothalamic tract function considering the International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI). Three clinically relevant factors were evaluated as to their impact on reliability: (1) the localization of dermatomes in relation to the sensory level, (2) the examination tool, and (3) the threshold of correct answers for grading of a preserved sharp/dull discrimination. Design: Prospective monocentric psychometric study. Setting: Spinal Cord Injury Center, Heidelberg University Hospital, Germany. Participants: Convenient sample of 21 individuals with subacute spinal cord injury (age: 31–82 years) and 20 individuals without spinal cord injury (age: 24–63 years). Assessment: All participants underwent three assessments for sharp/dull discrimination, applying five commonly used examination tools in seven dermatomes, performed by three trained examiners under conditions in accordance with ISNCSCI. Main Outcome Measures: Assessment of interrater reliability by determining both the Fleiss kappa (κ) coefficient and the percentage agreement between raters. Data were dichotomized regarding the ISNCSCI threshold. Results: Interrater reliability in individuals with SCI was overall substantial (κ = 0.68; CI 0.679–0.681) and moderate (κ = 0.54; CI 0.539–0.543) in dermatomes below the sensory level. All applied tools led to at least moderate reliability below the sensory level (lowest κ = 0.44; CI 0.432–0.440), with the officially endorsed safety pin achieving the highest (substantial) reliability (κ = 0.64; CI 0.638–0.646). Percentage agreement differed between non-SCI (97.3%) and formally intact above level dermatomes in SCI (89.2%). Conclusions: Sharp/dull discrimination as a common clinical examination technique for spinothalamic tract function is a reliable assessment. Independent from the used examination tools, reliability was substantial, with the medium-sized safety pin delivering the most favorable results. Notwithstanding this, all other tools could be considered if a safety pin is not available. Regarding interrater reliability and guessing probability, a threshold of 80% correct responses for preserved sharp/dull discrimination appears to be most suitable, which is in line with current clinical approaches and ISNCSCI. The causal attribution of the identified differences in sharp/dull discrimination between clinically intact dermatomes of individuals with SCI and unaffected dermatomes of individuals without SCI requires future work. Clinical Trial Registration Number (German Clinical Trials Register): DRKS00015334 (https://www.drks.de).
Decision Making and Impulsivity in Young Adult Cannabis Users

Aims: Chronic cannabis users show impairments on laboratory measures of decision making which reflect risk factors for initiation and continued use of cannabis. However, the differential sensitivity of these tasks to cannabis use has not been established. Moreover, studies to date have often lacked assessment of psychiatric histories and use of other illicit substances, both of which may influence decision making outcomes. The current study aimed to address these limitations by (1) including multiple types of decision making tasks, (2) implementing the Probabilistic Reversal Learning Task, a measure of decision making under uncertainty, for the first time in cannabis users, (3) including young adult cannabis users with no other psychiatric disorders, and (4) conducting urinalysis to exclude users of other illicit drugs. Methods: Thirty-three current cannabis users without comorbid psychiatric disorders and 35 cannabis non-users completed behavioral measures of decision-making (Iowa Gambling Task), reward discounting (Delay Discounting Task), choice-outcome learning (the Probabilistic Reversal Learning Task) and a questionnaire assessment of impulsivity (Barratt Impulsiveness Scale). Results: Relative to non-users, cannabis users demonstrated greater preference for immediate vs. delayed rewards on the Delay Discounting Task, made fewer advantageous decisions on the Iowa Gambling Task, and endorsed greater impulsivity on the Barratt Impulsiveness Scale scales. Cannabis users and non-users showed comparable performance on the Probabilistic Reversal Learning Task. Frequency of past-month cannabis use and total years of use did not predict decision making or impulsivity. Conclusions: Young adult cannabis users demonstrated higher discounting rates and impairments in learning cost-benefit contingencies, while reversal learning was unaffected. Self-reported impulsivity was elevated as well. None of these measures correlated with current or lifetime estimates of cannabis use, arguing against a dose-relationship. Interventions that target improvement in affected components of decision making may be helpful in reducing cannabis use and relapse.
Determination of Diffusion Kinetics of Ketamine in Brain Tissue: Implications for in vitro Mechanistic Studies of Drug Actions

Ketamine has been in use for over 50 years as a general anesthetic, acting primarily through blockade of N-methyl-D-aspartate receptors in the brain. Recent studies have demonstrated that ketamine also acts as a potent and rapid-acting antidepressant when administered at sub-anesthetic doses. However, the precise mechanism behind this effect remains unclear. We examined the diffusion properties of ketamine in brain tissue to determine their effects in in vitro studies related to the antidepressant action of ketamine. Brain slices from adult mice were exposed to artificial cerebrospinal fluid (aCSF) containing ∼17 μM ketamine HCl for varying amounts of time. The amount of ketamine within each slice was then measured by tandem high-performance liquid chromatography – mass spectrometry to characterize the diffusion of ketamine into brain tissue over time. We successfully modeled the diffusion of ketamine into brain tissue using a mono-exponential function with a time constant of τ = 6.59 min. This curve was then compared to a one-dimensional model of diffusion yielding a diffusion coefficient of approximately 0.12 cm2⋅s–1 for ketamine diffusing into brain tissue. The brain:aCSF partition coefficient for ketamine was determined to be approximately 2.76. Our results suggest that the diffusion properties of ketamine have a significant effect on drug concentrations achieved within brain tissue during in vitro experiments. This information is vital to determine the ketamine concentration necessary for in vitro slice preparation to accurately reflect in vivo doses responsible for its antidepressant actions.
A Comparison Between Body Weight-Supported Treadmill Training and Conventional Over-Ground Training in Dogs With Incomplete Spinal Cord Injury

In human medicine there was no evidence registered of a significant difference in recovery between body weight-supported treadmill training (BWSTT) and conventional over-ground (COGI). There isn't any similar study in veterinary medicine. Thus, this study aimed to compare the locomotor recovery obtained in incomplete SCI (T11–L3 Hansen type I) post-surgical dogs following BWSTT or COGI protocols, describing their evolution during 7 weeks in regard to OFS classifications. At admission, dogs were blindly randomized in two groups but all were subjected to the same protocol (underwater treadmill training) for the first 2 weeks. After, they were divided in the BWSTT group (n = 10) and the COGI group (n = 10) for the next 2 weeks, where they performed different training. In both groups locomotor training was accompanied by functional electrical stimulation (FES) protocols. Results reported statistically significant differences between all OFS evaluations time-points (p < 0.001) and between the two groups (p < 0.001). In particular with focus on T1 to T3 a two-way repeated measures ANOVA was performed and similar results were obtained (p = 0.007). Functional recovery was achieved in 90% (17/19) of all dogs and 100% recovered bladder function. The BWSTT group showed 100% (10/10) recovery within a mean time of 4.6 weeks, while the COGI group had 78% (7/9) within 6.1 weeks. Therefore, BWSTT leads to a faster recovery with a better outcome in general.
Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer

Long non-coding RNAs are diverse class of non-coding RNA molecules >200 base pairs of length having various functions like gene regulation, dosage compensation, epigenetic regulation. Dysregulation and genomic variations of several lncRNAs have been implicated in several diseases. Their tissue and developmental specific expression are contributing factors for them to be viable indicators of physiological states of the cells. Here we present an comprehensive review the molecular mechanisms and functions, state of the art experimental and computational pipelines and challenges involved in the identification and functional annotation of lncRNAs and their prospects as biomarkers. We also illustrate the application of co-expression networks on the TCGA-LIHC dataset for putative functional predictions of lncRNAs having a therapeutic potential in Hepatocellular carcinoma (HCC).
CT-Based Risk Factors for Mortality of Patients With COVID-19 Pneumonia in Wuhan, China: A Retrospective Study

Purpose: Computed tomography (CT) characteristics associated with critical outcomes of patients with coronavirus disease 2019 (COVID-19) have been reported. However, CT risk factors for mortality have not been directly reported. We aim to determine the CT-based quantitative predictors for COVID-19 mortality. Methods: In this retrospective study, laboratory-confirmed COVID-19 patients at Wuhan Central Hospital between December 9, 2019, and March 19, 2020, were included. A novel prognostic biomarker, V-HU score, depicting the volume (V) of total pneumonia infection and the average Hounsfield unit (HU) of consolidation areas was automatically quantified from CT by an artificial intelligence (AI) system. Cox proportional hazards models were used to investigate risk factors for mortality. Results: The study included 238 patients (women 136/238, 57%; median age, 65 years, IQR 51–74 years), 126 of whom were survivors. The V-HU score was an independent predictor (hazard ratio [HR] 2.78, 95% confidence interval [CI] 1.50–5.17; p = 0.001) after adjusting for several COVID-19 prognostic indicators significant in univariable analysis. The prognostic performance of the model containing clinical and outpatient laboratory factors was improved by integrating the V-HU score (c-index: 0.695 vs. 0.728; p < 0.001). Older patients (age ≥ 65 years; HR 3.56, 95% CI 1.64–7.71; p < 0.001) and younger patients (age < 65 years; HR 4.60, 95% CI 1.92–10.99; p < 0.001) could be further risk-stratified by the V-HU score. Conclusions: A combination of an increased volume of total pneumonia infection and high HU value of consolidation areas showed a strong correlation to COVID-19 mortality, as determined by AI quantified CT.
Validation of the Lifetime Incidence of Traumatic Events (LITE-S/P) Questionnaires in Children and Adolescents in Slovenia

Introduction: A traumatic event is an extremely threatening and frightening experience in an individual's life. Children who are exposed to traumatic events are twice as likely to develop a mental disorder. Screening can provide insight into the traumatic experience of children, identifying those eligible for further evaluation, and support. With this aim, we evaluated the psychometric properties of the Lifetime Incidence of Traumatic Events questionnaire (LITE) in Slovene by calculating retest reliabilty, construct validity (cross-informant agreement) and external validity, where we calculated the correlation of the number of differenet traumatic events with psychopathological symptoms. Methods: 280 child-parent pairs (children aged 11.3 ± 2.2 years) from various Slovenian primary schools participated in the study. They were divided into two groups: 180 healthy primary school students and 100 children with Type 1 Diabetes (our study was a part of a larger study The Influence of Psychobiological Adversity on Children and Adolescents with Type 1 Diabetes Study). Two versions of the LITE questionnaire were used. Children completed the child report (LITE-S) and parents the parent report (LITE-P) version. After 4 weeks, 117 children, and 114 parents filled out the LITEs again. External validity was assessed using the Youth Self Report and Child Behaviour Checklist syndrome-oriented scales. Results: Retest reliability for individual scales was r = 0.469–0.639 (ρ = 0.443–0.636; p < 0.001), but higher for individual items (κ = 0.263–0.821; p < 0.001). Correlations between reports from parents and children were r = 0.313–0.345 (ρ = 0.317–0.348; p < 0.001). The number of different events experienced by children correlated significantly with the measured depressive—anxiety, and posttraumatic stress disorder symptoms. Conclusions: Based on our results, the LITE-S and LITE-P “All events” scale have acceptable psychometric properties for use in research and in clinical practise screening. We recommend looking at single items, taking into consideration the responses from both the child and the parent for more precise information. To improve the precision of the psychodiagnostic capacity of the questionnaire, further research on various populations should be performed.
Impacts of Social and Emotional Learning Interventions for Teachers on Teachers' Outcomes: A Systematic Review With Meta-Analysis

Teaching is among the most emotionally demanding jobs, impacting teachers' personal lives and job performance. Since teaching-specific stressors are mainly socio-emotional related, social and emotional learning (SEL) interventions targeting teachers have increased rapidly in recent years. This study conducted a systematic review with meta-analysis of 43 empirical studies which evaluated the efficacy of school-based SEL interventions involving 3,004 in-service preK-12 teachers. The initial systematic review showed that these interventions were very heterogeneous and the research on their efficacy assessed widely distinct outcome variables. Concerning the meta-analysis, results showed statistically significant small to medium effect sizes favoring the experimental group, with SEL interventions impacting teachers' social and emotional competence [g = 0.59, 95% CI (0.29, 0.90)], well-being [g = 0.35, 95% CI (0.16, 0.54)], and psychological distress [g = −0.34, 95% CI (−0.57, −0.10)]. Meta-regressions did not reveal significant values of the explanatory variables, and publication bias was found for social and emotional competence and well-being domains. Findings add to growing empirical evidence regarding the impact of these interventions and contribute to the development of guidelines for the design of effective SEL interventions for teachers.