Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear fitting of multi-compartmental data using Hooke and Jeeves direct search method

Abstract Compartmental modelling refers to modelling the transport of substances in a system consisting of multiple compartments, which is characterized by the transfer rates among the relevant compartments. In a generalized compartmental system, recycling of substances among the compartments is allowed. Compartmental modelling is a generic technique which is needed in many branches of applied physics. The most challenging task is to determine the transfer rates. The present work described the use of the Hooke and Jeeves (HJ) derivative free direct search method in determining the transfer rates to construct a multi-compartmental model with recycling among the compartments. The use of a direct search method ensures the applicability of the model to functions which are not continuous or differentiable. The present model was successfully validated using previously reported experimental data for distribution of trace elements in four compartments in an animal.
Experiences and attitudes towards mental health problems in first year German university students

Abstract Objectives The study should show how familiar German first year university students are with mental health issues and what their attitudes are regarding mental illness. Methods The study sample consisted of 293 first year German university students (20.37 years ± 1.88), most of them women (82.9%). The majority (77.6%) was studying a social type subject. An additive focus group consisted of four experts. The participants of the quantitative part were recruited at prevention workshops that were offered during the induction week at the beginning of the semester at 15 German universities. Experts of the focus group were recruited by telephone call. In addition to quantitative analysis, we realized a focus group with experts of our target group concerns and university system. For statistical analysis, we used statistic software programme “SPSS” 24 to conduct t-tests. We used content-analytical evaluation to build a category system. Results Every fourth participant reported having had a mental health problem. Male participants had a slightly greater desire for social distance (p=0.008; df=288) and slightly stronger stereotypes (p<0.001; df=289). Conclusions The present study shows that first year university students in Germany have substantial experience with mental health problems. Highlights Every fourth young student reported having had a mental health problem. There is a lack of an overall mental health goal at university. Low-threshold offerings at university are necessary. Networking between offerings and external centers can be a beneficial factor in developing mentally healthy university strategies.
A protein-trap allele reveals roles for Drosophila ATF4 in photoreceptor degeneration, oocyte maturation and wing development

Metazoans have evolved various stress response mechanisms to cope with cellular stress inflicted by external and physiological conditions. The Integrated Stress Response (ISR) is an evolutionarily conserved pathway that mediates adaptation to cellular stress via the transcription factor, ATF4. Loss of function of Drosophila ATF4, encoded by the gene cryptocephal (crc), results in lethality during pupal development. The roles of crc in Drosophila disease models and adult tissue homeostasis thus remain poorly understood. Here, we report that a protein-trap MiMIC insertion in the crc locus generates a crc-GFP fusion protein that allows visualization of crc activity in vivo, and acts as a hypomorphic mutant that uncovers previously unknown roles for crc. Specifically, the crc protein-trap line shows crc-GFP induction in a Drosophila model for Retinitis Pigmentosa (RP). This crc allele renders photoreceptors more vulnerable to age-dependent retinal degeneration. crc mutant adult animals also show greater susceptibility to amino acid deprivation and reduced levels of known crc transcriptional targets. Furthermore, this mutant allele shows defects in wing veins and oocyte maturation, uncovering previously unknown roles for crc in the development of these tissues. Together, our data establish physiological and pathological functions of crc-mediated ISR in adult Drosophila tissues.
A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection

We use first principles of population genetics to model the evolution of proteins under persistent positive selection (PPS). PPS may occur when organisms are subjected to persistent environmental change, during adaptive radiations, or in host-pathogen interactions. Our mutation-selection model indicates protein evolution under PPS is an irreversible Markov process, and thus proteins under PPS show a strongly asymmetrical distribution of selection coefficients among amino acid substitutions. Our model shows the criteria ω > 1 (where ω is the ratio of non-synonymous over synonymous codon substitution rates) to detect positive selection is conservative and indeed arbitrary, because in real proteins many mutations are highly deleterious and are removed by selection even at positively-selected sites. We use a penalized-likelihood implementation of our model to successfully detect PPS in plant RuBisCO and influenza HA proteins. By directly estimating selection coefficients at protein sites, our inference procedure bypasses the need for using ω as a surrogate measure of selection and improves our ability to detect molecular adaptation in proteins. Significance Statement Understanding how natural selection acts on proteins is important as it can inform studies from adaptive radiations to host-pathogen co-evolution. Traditionally, selection on proteins is inferred indirectly by measuring the non-synonymous to synonymous rate ratio, ω, with ω > 1, = 1, and < 1 indicating positive (adaptive) selection, neutral evolution, and negative (purifying) selection respectively. However, the theoretical underpinnings of this ratio are not well understood. Here we use first-principles of population genetics to work out how persistent changes in selection affect protein evolution and we use our new model to detect adaptive sites in plant and influenza proteins. We show measuring selection directly improves detection of adaptation in proteins.
A systematic comparison of fibroblasts derived from postmortem human dura mater versus dermal epithelium for neurodegenerative disease modeling

Patient-derived cells hold great promise for precision medicine approaches in human health. Fibroblast cells have been a major source of human cells for reprogramming and differentiating into specific cell types for disease modeling. Such cells can be isolated at various stages during life (presymptomatic, symptomatic, and postmortem) and thus can potentially be used to model different phases of disease progression. In certain circumstances, however, tissues are not collected during life and only postmortem tissues are the only available source of fibroblasts. Fibroblasts cultured from postmortem human dura mater of individuals with neurodegenerative diseases have been suggested as a primary source of cells for in vitro modeling of neurodegenerative diseases. Although fibroblast-like cells from human and mouse dura mater have been previously described, their utility for reprogramming and direct differentiation protocols requires further characterization. In this study, cells derived from dermal biopsies performed in living subjects were compared to cells derived from postmortem dura mater. In two instances, we have isolated and compared dermal and dural cell lines from the same subject. Notably, striking differences between the dermis and dura mater-derived cell lines were found. Compared to dermal fibroblasts, postmortem dura mater-derived cells demonstrated different morphology, exhibited slower growth rates, failed to express fibroblast protein markers, and exhibited significant differences in gene expression profiles. In addition, dura mater-derived cells were found to exhibit a high rate of chromosomal abnormalities, particularly in the loss of the Y chromosome. Our study highlights potential limitations of postmortem human dura mater-derived cells for disease modeling, argues for rigorous karyotyping prior to reprograming, and brings into question the identity of dura mater-derived cells as belonging to a fibroblast lineage.
Encoding of inflammatory hyperalgesia in mice spinal cord

Inflammation modifies the input-output properties of peripheral nociceptive neurons, thus leading to hyperalgesia, a condition in which the perception of noxious heat stimuli is altered such that the same stimulus produces enhanced pain. The increased nociceptive output enters the superficial dorsal spinal cord (SDH), which comprises the first CNS network integrating the noxious information. Here we used in vivo calcium imaging and a computational approach to investigate how the SDH network in mice encodes the injury-mediated abnormal input from peripheral nociceptive neurons. We show that the application of noxious heat stimuli to the hind paw in naïve mice before induction of injury affects the activity of 70% of recorded neurons by either increasing or suppressing it. Application of the same noxious heat stimuli to hyperalgesic skin following injury leads to activation of previously non-responded cells and de-suppression of the “suppressed” neurons. We further demonstrate that reduction in synaptic inhibition mimics the response to the noxious stimuli in hyperalgesic conditions. Using a computational model of the SDH network, we predict that the “disinhibitory” effect of hyperalgesic stimuli results from the inflammation-mediated increased afferent input to the SDH network and a decrease in SDH inhibition. Both of these processes synergistically contribute to the injury-mediated increase in SDH output towards higher brain centers.
Synaptic Plasticity in the Agranular Insular Cortex Predicts Escalated Ethanol Consumption

The Agranular Insular Cortex (AIC) is implicated in alcohol use disorder and pharmacologically relevant concentrations of acute ethanol inhibit N-methyl-D-aspartate receptor (NMDAR)-mediated glutamatergic synaptic transmission and plasticity onto layer 2/3 AIC pyramidal neurons. However, it is not known whether the actions of ethanol on glutamatergic synapses are means by which chronic ethanol alters mechanisms of learning and memory in AIC as alcohol drinking transitions from controlled to problematic. We utilized the chronic intermittent ethanol (CIE) vapor model of ethanol exposure in adult male mice, alone or in combination with voluntary ethanol consumption, to determine whether glutamatergic synapses on layer 2/3 AIC pyramidal neurons are differentially regulated by different durations and intensities of chronic ethanol exposure. We observed evidence of both ethanol- and age-related metaplasticity of AIC layer 2/3 glutamatergic synapses, as only young adult, ethanol-naïve mice exhibited NMDAR-dependent long term depression ex vivo. Our findings also indicated that voluntary ethanol consumption alone can elicit glutamatergic plasticity in vivo. We found that the ratio of NMDAR- to AMPAR-mediated postsynaptic currents was reduced not only in CIE-treated, but also in air-treated, chronically drinking mice relative to ethanol-naïve controls. Furthermore, lower NMDA/AMPA ratios were predictive of greater escalation of ethanol consumption. These findings suggest that even moderate exposure to ethanol may elicit plasticity in the agranular insular cortex that contributes to the progression toward uncontrolled drinking.
Watching dynamics and assembly of spliceosomal complexes at single molecule resolution

23 CHAPTER 1: Introduction . 25 1.1: Gene expression . 25 1.2: Pre-mRNA splicing . 25 1.2. 1: Alternative splicing . 27 1.3: Discovery and evolution of introns . 27 1.4: Different types of Introns . 28 1.4. 1: Group I introns . 30 1.4. 2: Group II introns . 31 1.4. 2: Nuclear Introns (or spliceosomal introns) . 33
Peripheral neuropathy linked mRNA export factor GANP reshapes gene regulation in human motor neurons

Loss-of-function of the mRNA export protein GANP (MCM3AP gene) cause early-onset sensorimotor neuropathy, characterised by axonal degeneration in long peripheral nerves. GANP functions as a scaffold at nuclear pore complexes, contributing to selective nuclear export of mRNAs. Here, we aimed to identify motor neuron specific transcripts that are regulated by GANP and may be limiting for local protein synthesis in motor neuron axons. We compared motor neurons with a gene edited mutation in the Sac3 mRNA binding domain of GANP to isogenic controls. We also examined patient-derived motor neurons. RNA sequencing of motor neurons as well as nuclear and axonal subcompartments showed that mutant GANP had a profound effect on motor neuron transcriptomes, with alterations in nearly 40 percent of all expressed genes and broad changes in splicing. Expression changes in multiple genes critical for neuronal functions, combined with compensatory upregulation of protein synthesis and early-stage metabolic stress genes, indicated that RNA metabolism was abnormal in GANP-deficient motor neurons. Surprisingly, limited evidence was found for large-scale nuclear retention of mRNA. This first study of neuropathy-linked GANP defects in human motor neurons shows that GANP has a wide gene regulatory role in a disease-relevant cell type that requires long-distance mRNA transport.
Contactless recordings of retinal activity using optically pumped magnetometers

Optically pumped magnetometers (OPMs) have been adopted for the recording of brain activity. Without the need to be cooled to cryogenic temperatures, an array of these sensors can be placed more flexibly, which allows for the recording of neuronal structures other than neocortex. Here we use eight OPM sensors to record human retinal activity following flash stimulation. We compare this magnetoretinographic (MRG) activity to the simultaneously recorded electroretinogram of the eight participants. The MRG shows the familiar flash-evoked potentials (a-wave and b-wave) and shares a highly significant amount of information with the electroretinogram recording (both in a simultaneous and separate recording). We conclude that OPM sensors have the potential to become a contactless alternative to fiber electrodes for the recording of retinal activity. Such a contactless solution can benefit both clinical and neuroscientific settings.
Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GCCV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding)per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and New World vultures). Eliminating high GCCV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.
The Association of Human Astrovirus with Extracellular Vesicles Facilitates Cell Infection and Protects the Virus from Neutralizing Antibodies

Astroviruses are an important cause of diarrhea in vulnerable population, particularly children; recently some reports have found these viruses in extra-intestinal organs, including the central nervous system, causing unexpected clinical disease. In this work, we found that human astrovirus strain Yuc8 associates with extracellular vesicles, possibly during or after their cell egress. ABSTRACT Viral gastroenteritis has a global distribution and represents a high risk for vulnerable population and children under 5 years due to acute diarrhea, fever and dehydration. Human astroviruses (HAstV) have been identified as the third most important cause of viral gastroenteritis in pediatric and immunocompromised patients. Furthermore, HAstV has been reported in biopsies taken from patients with encephalitis, meningitis and acute respiratory infection, yet it is not clear how the virus reaches these organs. In this work we have tested the possibility that the released astrovirus particles could be associated with extracellular vesicles. Comparison between vesicles purified from HAstV Yuc8 infected and mock-infected cells showed that infection enhances production of vesicles larger than 150 nm. These vesicles contain CD63 and Alix, two markers of vesicular structures. Almost 70% of the extracellular virus present in clarified supernatant at 18 h postinfection was found associated with vesicular membranes, and this association facilitates cell infection in the absence of trypsin activation and protects virions from neutralizing antibodies. Our findings suggest a new pathway for HAstV spread and might represent an explanation for the extra-intestinal presence of some astrovirus strains. IMPORTANCE Astroviruses are an important cause of diarrhea in vulnerable population, particularly children; recently some reports have found these viruses in extra-intestinal organs, including the central nervous system, causing unexpected clinical disease. In this work, we found that human astrovirus strain Yuc8 associates with extracellular vesicles, possibly during or after their cell egress. The association with vesicles doubled astrovirus infectivity in less susceptible cells and rendered virus particles insensitive to neutralization by antibodies. These data suggest that extracellular vesicles could represent a novel pathway for astrovirus to disseminate outside the gastrointestinal tract.
How do students develop computational thinking? Assessing early programmers in a maze-based online game

ABSTRACT Background and Context: Despite many initiatives to develop Computational Thinking (CT), not much is known about how early programmers develop CT and how we can assess their learning. Objective: Determine if the analysis of students’ interactions with an online platform allows understanding the development of CT, how we can convert data collected into valuable insights, and the aspects that should be considered in platforms design. Method: We developed an online platform with a fine-grained log–recording system. We analysed the data collected from 1004 students (ages 8-14) to understand the difficulties they face. We explain our platform and the tools to process and filter the interaction logs. We calculate additional indicators that provide useful information about student’s behaviour. Findings: Age and gender have shown to influence on CT learning. Generating additional indicators from basic interaction data provide valuable insights. We provide a list of recommendations for developing more effective programming learning platforms.
Altered Resting-State Brain Activity in Schizophrenia and Obsessive-Compulsive Disorder Compared With Non-psychiatric Controls: Commonalities and Distinctions Across Disorders

Backgrounds: Schizophrenia (SCZ) and obsessive-compulsive disorder (OCD) are classified as two chronic psychiatric disorders with high comorbidity rate and shared clinical symptoms. Abnormal spontaneous brain activity within the cortical–striatal neural circuits has been observed in both disorders. However, it is unclear if the common or distinct neural abnormalities underlie the neurobiological substrates in the resting state. Methods: Resting-state fMRI data were collected from 88 patients with SCZ, 58 patients with OCD, and 72 healthy control subjects. First, we examined differences in amplitude of low-frequency fluctuations (ALFF) among three groups. Resting-state functional connectivity (rsFC) analysis with the brain region that showed different ALFF as the seed was then conducted to identify the changes in brain networks. Finally, we examined the correlation between the altered activities and clinical symptoms. Results: Both the patients with SCZ and OCD showed increased ALFF in the right hippocampus and decreased ALFF in the left posterior cingulate cortex (PCC). SCZ patients exhibited increased ALFF in the left caudate [voxel-level family-wise error (FWE) P < 0.05] and decreased rsFC between the left caudate and right cerebellum, which correlated with positive symptoms. The left caudate showed increased rsFC with the right thalamus and bilateral supplementary motor complex (SMC) in OCD patients (cluster-level FWE P < 0.05). Conclusions: The hippocampus and PCC are common regions presenting abnormal local spontaneous neuronal activities in both SCZ and OCD, while the abnormality of the striatum can reflect the differences. Increased ALFF in the striatum and symptom-related weakened rsFC between the caudate and cerebellum showed SCZ specificity. Enhanced rsFC between the caudate and SMC may be a key characteristic in OCD. Our research shows the similarities and differences between the two diseases from the perspective of resting-state fMRI, which provides clues to understand the disease and find methods for treatment.