Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical activity attenuates neuropsychiatric disturbances and caregiver burden in patients with dementia

INTRODUCTION: A significant benefit from physical activity has recently been described in some patients who suffer from neurodegenerative diseases. OBJECTIVE: To assess the effects of physical activity on neuropsychiatric disturbances in demented patients and on the mental burden of their caregivers. METHODS: Assisted by a public geriatric psychiatry clinical unit, we studied 59 patients with dementia. Patients were divided into three groups according to their diagnosis and level of physical activity. Data were assessed through a semi-structured interview. Patients were evaluated with the Neuropsychiatric Inventory, the Mini-Sleep Questionnaire and the Baecke Questionnaire. The data were statistically analyzed using the Mann-Whitney U test and linear regression, with the level of significance set at 5%. RESULTS: Patients with Alzheimer's or vascular dementia who engaged in physical activity had fewer neuropsychiatric symptoms than those who did not. When compared to the control group, the caregivers of patients with vascular dementia who engaged in physical activity had a reduced burden. CONCLUSION: The regular practice of physical activity seems to contribute to a reduction in neuropsychiatric symptoms in dementia patients and to attenuate the burden of the caregivers of those patients.
Enhancing lifetime and security of PCM-based Main Memory with Start-Gap Wear Leveling

Phase Change Memory (PCM) is an emerging memory technology that can increase main memory capacity in a cost-effective and power-efficient manner. However, PCM cells can endure only a maximum of 107-108 writes, making a PCM based system have a lifetime of only a few years under ideal conditions. Furthermore, we show that non-uniformity in writes to different cells reduces the achievable lifetime of PCM system by 20×. Writes to PCM cells can be made uniform with Wear-Leveling. Unfortunately, existing wear-leveling techniques require large storage tables and indirection, resulting in significant area and latency overheads. We propose Start-Gap, a simple, novel, and effective wear-leveling technique that uses only two registers. By combining Start-Gap with simple address-space randomization techniques we show that the achievable lifetime of the baseline 16 GB PCM-based system is boosted from 5% (with no wear-leveling) to 97% of the theoretical maximum, while incurring a total storage overhead of less than 13 bytes and obviating the latency overhead of accessing large tables. We also analyze the security vulnerabilities for memory systems that have limited write endurance, showing that under adversarial settings, a PCM-based system can fail in less than one minute. We provide a simple extension to Start-Gap that makes PCM-based systems robust to such malicious attacks.
FQR 1 , a Novel Primary Auxin-Response Gene , Encodes a Flavin Mononucleotide-Binding Quinone Reductase 1

FQR1 is a novel primary auxin-response gene that codes for a flavin mononucleotide-binding flavodoxin-like quinone reductase. Accumulation of FQR1 mRNA begins within 10 min of indole-3-acetic acid application and reaches a maximum of approximately 10-fold induction 30 min after treatment. This increase in FQR1 mRNA abundance is not diminished by the protein synthesis inhibitor cycloheximide, demonstrating that FQR1 is a primary auxin-response gene. Sequence analysis reveals that FQR1 belongs to a family of flavin mononucleotide-binding quinone reductases. Partially purified His-tagged FQR1 isolated from Escherichia coli catalyzes the transfer of electrons from NADH and NADPH to several substrates and exhibits in vitro quinone reductase activity. Overexpression of FQR1 in plants leads to increased levels of FQR1 protein and quinone reductase activity, indicating that FQR1 functions as a quinone reductase in vivo. In mammalian systems, glutathione S-transferases and quinone reductases are classified as phase II detoxification enzymes. We hypothesize that the auxin-inducible glutathione S-transferases and quinone reductases found in plants also act as detoxification enzymes, possibly to protect against auxin-induced oxidative stress.
A modelling approach to genotype x environment interaction: genetic analysis of the response of maize growth to environmental conditions

Expansive growth of organs has a very large genotype × environment (G×E) interaction. Maximum leaf expansion rate observed in the absence of stress and of evaporative demand has a genetic variability which is usually smaller than environmental effects. The mechanisms driving the reduction in leaf growth rate under stress, namely changes in cell division rate, in cell-wall mechanical properties and in turgor, and their signalling pathways, interact in such a way that a bottom-up approach from genes to the G×E interaction cannot be envisaged. We propose an approach combining modelling and genetic dissection of model parameters. Three genotype-dependent parameters are considered for analysing the G×E interaction for leaf elongation rate of maize. The maximum leaf elongation rate per unit thermal time is stable during the night and over several nights, and it is repeatable for each genotype over several experiments. The responses of leaf elongation rate to evaporative demand and soil water status are linear and their slopes are reproducible over several experiments. Maximum elongation rate and slopes of the responses to evaporative demand and to soil water potential have been analysed genetically in three mapping populations. QTLs of maximum leaf elongation rate tended to co-localize with QTLs of leaf length under well-watered conditions, but also under water deficit. They also co-localized with QTLs of the Anthesis Silking Interval (ASI). In contrast, QTLs of response parameters did not co-localize with QTLs of length under water deficit. They are therefore ‘adaptive’ traits which cannot be identified otherwise. Each parameter of the ecophysiological model was computed as the sum of QTL effects, allowing calculation of parameters of new RILs known by their allelic values only. Leaf elongation rates of these new RILs were simulated and were similar to measurements in a growth-chamber experiment. This opens the way to the simulation of virtual genotypes, known only by their alleles, in any climatic scenario
High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation[OPEN]

A frequently sampled diurnal transcriptome from a synchronous culture of Chlamydomonas provides insights into diverse biological processes and is a new resource for functional genomics. The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
The role of dominant striatum in language: a study using intraoperative electrical stimulations

Background: The role of the striatum in language remains poorly understood. Intraoperative electrical stimulation during surgery for tumours involving the caudate nucleus or putamen in the dominant hemisphere might be illuminating. Objectives: To study the role of these structures in language, with the aim of avoiding postoperative definitive aphasia. Methods: 11 patients with cortico-subcortical low grade gliomas were operated on while awake, and striatal functional mapping was done. Intraoperative direct electrical stimulation was used while the patients carried out motor and naming tasks during the resection. Results: In five cases of glioma involving the dominant putamen, stimulations induced anarthria, while in six cases of glioma involving the dominant caudate, stimulations elicited perseveration. There was no motor effect. The striatum was systematically preserved. Postoperatively, all patients except one had transient dysphasia which resolved within three months. Conclusions: There appear to be two separate basal ganglia systems in language, one mediated by the putamen which might have a motor role, and one by the caudate which might have a role in cognitive control. These findings could have implications for surgical strategy in lesions involving the dominant striatum.
Formation, molecular structure, and morphology of humins in biomass conversion: influence of feedstock and processing conditions.

Neither the routes through which humin byproducts are formed, nor their molecular structure have yet been unequivocally established. A better understanding of the formation and physicochemical properties of humins, however, would aid in making biomass conversion processes more efficient. Here, an extensive multiple-technique-based study of the formation, molecular structure, and morphology of humins is presented as a function of sugar feed, the presence of additives (e.g., 1,2,4-trihydroxybenzene), and the applied processing conditions. Elemental analyses indicate that humins are formed through a dehydration pathway, with humin formation and levulinic acid yields strongly depending on the processing parameters. The addition of implied intermediates to the feedstocks showed that furan and phenol compounds formed during the acid-catalyzed dehydration of sugars are indeed included in the humin structure. IR spectra, sheared sum projections of solid-state 2DPASS (13) C NMR spectra, and pyrolysis GC-MS data indicate that humins consist of a furan-rich polymer network containing different oxygen functional groups. The structure is furthermore found to strongly depend on the type of feedstock. A model for the molecular structure of humins is proposed based on the data presented.
Functional antagonism with formoterol and salmeterol in asthmatic patients expressing the homozygous glycine-16 beta(2)-adrenoceptor polymorphism.

BACKGROUND Formoterol and salmeterol differ in their relative intrinsic activity at airway beta(2)-adrenoceptors, with formoterol being a full agonist. The homozygous glycine-16 polymorphism of the beta(2)-adrenoceptor occurs in approximately 40% of patients and is known to predispose to agonist-induced downregulation and desensitization. OBJECTIVES To evaluate possible differences in intrinsic beta(2)-adrenoceptor agonist activity between salmeterol and formoterol in terms of their functional antagonism against methacholine-induced bronchoconstriction (the primary end point) in genetically susceptible patients who exhibited the homozygous glycine-16 polymorphism. METHODS Eighteen patients with mild-to-moderate persistent asthma receiving inhaled corticosteroid who expressed the homozygous glycine-16 genotype were randomized to completion (mean [SEM] age, 35.8 [3.2] years; mean FEV(1), 76.9 [2. 5]% predicted). Patients received three different treatments for 1 week in randomized, double-blind, crossover fashion, with a 1-week washout period between treatments: formoterol, 12 microg bid; salmeterol, 50 microg bid; and placebo. For each of the randomized treatment periods, there were three separate methacholine challenges: baseline after washout, 12 h after the first dose, and 12 h after the last dose. RESULTS Both salmeterol and formoterol exhibited significantly (p < 0.05) greater bronchoprotection than placebo for their effects after single or repeated dosing, although there was no significant difference between the two drugs. The geometric mean fold protection vs placebo (95% confidence interval [CI]) for the first dose was 1.6-fold (95% CI, 1.1 to 2.2) for salmeterol and 1.9-fold (95% CI, 1.1 to 3.2) for formoterol, and for last dose was 1.6-fold (95% CI, 1.2 to 2.3) for salmeterol and 1. 9-fold (95% CI, 1.2 to 2.8) for formoterol. Salmeterol and formoterol produced significant (p < 0.05) increases in FEV(1) and forced expiratory flow after 25 to 75% of vital capacity has been expelled, after the first but not the last dose compared to placebo, while there were significant (p < 0.05) improvements in domiciliary peak flows during treatment with both drugs. CONCLUSION Our results showed no difference between formoterol and salmeterol in the degree of functional antagonism against methacholine-induced bronchoconstriction at the end of a 12-h dosing interval in patients who expressed the homozygous glycine-16 genotype. There was a significant residual degree of bronchoprotection after 1 week of treatment, which was not significantly different compared to the first-dose effect.
Advanced imaging improves prediction of hemorrhage after stroke thrombolysis

Very low cerebral blood volume (VLCBV), diffusion, and hypoperfusion lesion volumes have been proposed as predictors of hemorrhagic transformation following stroke thrombolysis. We aimed to compare these parameters, validate VLCBV in an independent cohort using DEFUSE study data, and investigate the interaction of VLCBV with regional reperfusion.
Alterations in muscle mass and contractile phenotype in response to unloading models: role of transcriptional/pretranslational mechanisms

Skeletal muscle is the largest organ system in mammalian organisms providing postural control and movement patterns of varying intensity. Through evolution, skeletal muscle fibers have evolved into three phenotype clusters defined as a motor unit which consists of all muscle fibers innervated by a single motoneuron linking varying numbers of fibers of similar phenotype. This fundamental organization of the motor unit reflects the fact that there is a remarkable interdependence of gene regulation between the motoneurons and the muscle mainly via activity-dependent mechanisms. These fiber types can be classified via the primary type of myosin heavy chain (MHC) gene expressed in the motor unit. Four MHC gene encoded proteins have been identified in striated muscle: slow type I MHC and three fast MHC types, IIa, IIx, and IIb. These MHCs dictate the intrinsic contraction speed of the myofiber with the type I generating the slowest and IIb the fastest contractile speed. Over the last ~35 years, a large body of knowledge suggests that altered loading state cause both fiber atrophy/wasting and a slow to fast shift in the contractile phenotype in the target muscle(s). Hence, this review will examine findings from three different animal models of unloading: (1) space flight (SF), i.e., microgravity; (2) hindlimb suspension (HS), a procedure that chronically eliminates weight bearing of the lower limbs; and (3) spinal cord isolation (SI), a surgical procedure that eliminates neural activation of the motoneurons and associated muscles while maintaining neurotrophic motoneuron-muscle connectivity. The collective findings demonstrate: (1) all three models show a similar pattern of fiber atrophy with differences mainly in the magnitude and kinetics of alteration; (2) transcriptional/pretranslational processes play a major role in both the atrophy process and phenotype shifts; and (3) signaling pathways impacting these alterations appear to be similar in each of the models investigated.
Strategic Voting in Sequential Committees

We consider strategic voting with incomplete information and partially common values in sequential committees. A proposal is considered against the status quo in one committee, and only upon its approval advances for consideration in a second committee. Committee members (i) are privately and imperfectly informed about an unobservable state of nature which is relevant to their payoffs, and (ii) have a publicly observable bias with which they evaluate information. We show that the tally of votes in the originating committee can aggregate and transmit relevant information for members of the second committee in equilibrium, provide conditions for the composition and size of committees under which this occurs, and characterize all three classes of voting equilibria with relevant informative voting.
Imaging Informational Conflict: A Functional Magnetic Resonance Imaging Study of Numerical Stroop

We employed a parametric version of the comparison Stroop paradigm to investigate the processing of numerical magnitude and physical size under task-relevant and -irrelevant conditions to investigate two theoretical issues: (1) What is the neural fate of task-irrelevant information? (2) What is the neural basis of the resolution of the conflict between task-relevant and -irrelevant information? We show in 18 healthy adults that numerical magnitudes of numbers call for higher processing requirements than physical sizes. The enhanced activation elicited by numerical magnitudes is not modulated by task relevance, indicating autonomous processing. Moreover, the normal behavioral distance effect when the numerical dimension is task relevant and reversed distance effect when it is not show that autonomous processing fully encodes numerical magnitudes. Conflict trials elicited greater activation in bilateral inferior frontal gyri, right middle frontal gyri, and right superior frontal gyri. We postulate two sources to the conflict, namely, at cognitive and response levels.
Thromboxane Biosynthesis, Neutrophil and Coagulative Activation in Type IIa Hypercholesterolemia

Summary Thromboxane (Tx) A2 biosynthesis is enhanced in the majority of patients with type IIa hypercholesterolemia. Because blood clotting activation is an important component of the inflammatory response, involved in the initiation and progression of atherosclerotic plaques, we have investigated TxA2 biosynthesis, neutrophil activation and thrombin generation in 24 patients with type IIa hypercholesterolemia. Urinary 11-dehydro-TxB2, was significantly higher (p =0.0001) in patients than in 24 sex- and age matched healthy subjects. Similarly, prothrombin fragment 1+2 (F1+2), thrombin-antithrombin III complexes and plasma elastase were significantly higher in patients than incontrols. Urinary 11-dehydro-TxB2 excretion was correlated with plasma elastase (r = 0.758; p =0.000I), and prothrombin fragment 1+2 (r = 0.804; p = 0.001). The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor simvastatin (20 mg/day for 2 months) significantly reduced cholesterol levels, urinary 11-dehydro-TxB2 excretion, plasma elastase and plasma Fl+2 in 8 patients. We conclude that type IIa hypercholesterolemia is associated with biochemical evidence of platelet, neutrophil and blood clotting activation. The relationship between these events remains to be investigated.
Immune Analysis Using Vitreous Optical Coherence Tomography Imaging in Rats with Steroid-Induced Glaucoma

Glaucoma is a multifactorial pathology involving the immune system. The subclinical immune response plays a homeostatic role in healthy situations, but in pathological situations, it produces imbalances. Optical coherence tomography detects immune cells in the vitreous as hyperreflective opacities and these are subsequently characterised by computational analysis. This study monitors the changes in immunity in the vitreous in two steroid-induced glaucoma (SIG) animal models created with drug delivery systems (microspheres loaded with dexamethasone and dexamethasone/fibronectin), comparing both sexes and healthy controls over six months. SIG eyes tended to present greater intensity and a higher number of vitreous opacities (p < 0.05), with dynamic fluctuations in the percentage of isolated cells (10 µm2), non-activated cells (10–50 µm2), activated cells (50–250 µm2) and cell complexes (>250 µm2). Both SIG models presented an anti-inflammatory profile, with non-activated cells being the largest population in this study. However, smaller opacities (isolated cells) seemed to be the first responder to noxa since they were the most rounded (recruitment), coinciding with peak intraocular pressure increase, and showed the highest mean Intensity (intracellular machinery), even in the contralateral eye, and a major change in orientation (motility). Studying the features of hyperreflective opacities in the vitreous using OCT could be a useful biomarker of glaucoma.
Sorting out symptoms: design and evaluation of the 'babylon check' automated triage system

Prior to seeking professional medical care it is increasingly common for patients to use online resources such as automated symptom checkers. Many such systems attempt to provide a differential diagnosis based on the symptoms elucidated from the user, which may lead to anxiety if life or limb-threatening conditions are part of the list, a phenomenon termed 'cyberchondria' [1]. Systems that provide advice on where to seek help, rather than a diagnosis, are equally popular, and in our view provide the most useful information. In this technical report we describe how such a triage system can be modelled computationally, how medical insights can be translated into triage flows, and how such systems can be validated and tested. We present babylon check, our commercially deployed automated triage system, as a case study, and illustrate its performance in a large, semi-naturalistic deployment study.
CONSTRUCTING THE TREEFAM DATABASE

TreeFam is a database of phylogenetic trees of gene families. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable orthologs and paralog assignment. In developing TreeFam, four novel algorithms were designed to improve the accuracy of tree building or to serve special needs for development. The first is a constrained neighbour-joining that efficiently adds new sequences to an existing tree while maintaining the original topology at the same time. This method is used to expand a seed tree to a full tree without losing any information added by manual curation. The second algorithm is a leaf reordering that orders the leaves of a tree according to the weights of leaves. When it is drawn as a picture, one tree can be displayed in different ways, depending on the order of leaves. This algorithm helps to display trees in a consistent algorithm and facilitates visual examination of trees, which is particularly helpful when comparing two trees. Thirdly, duplication and loss inference is fit into a more general theoretical framework and extended to allow for a multifurcated species tree. A fourth algorithm has also been developed, which is a new algorithm for merging trees. The tree merge algorithm itself is not a tree building algorithm, but it reconstructs an optimal tree from several trees that are built from an identical sequence set with different tree building methods. The resultant tree should combine the advantages of, and so outperform, all the candidates. This is shown to occur successfully in a large-scale benchmark presented in the last chapter. This benchmark is one of the few evaluations that are based on real data in the phylogenetics literature. It also highlights the fact that each tree-building algorithm has its own strength, although ML and parsimonious methods are slightly better in general.