Miracle-dz/UniFAR-FTUs huggingface dataset:
Age influences aggressive behaviour: an RNA-seq analysis in bovines

Abstract Aggressiveness is one of our most basic behaviors, characterized by targeted intentional actions oriented to cause harm or damage. The reactive type of aggression is regulated mainly in the brain prefrontal cortex; however, the molecular changes underlying aggressiveness in adults have not been fully characterized. Here we used a RNA-seq approach to investigate differential gene expression in the prefrontal cortex of bovines from the aggressive Lidia breed at different age stages: young three-year old and adult four-year-old bulls. The number of up and down-regulated genes in the adult group were 50 and 193, respectively. These genes were associated with diverse functions, including neural plasticity and behavior. A cross-species comparative analysis retrieved 29 genes in common with previous studies on aggressive behaviors. Particularly, we detected changes in the regulation of networks such as the synaptogenesis, involved in the synapses maintenance and refinement, and the glutamate receptor pathway, which acts as excitatory driver in aggression responses. Furthermore, the Wnt//β-catenin signaling pathway was present in both up and down-regulated genes in the adult group, and has been implicated in adult altered behaviors and cognitive disorders. At the regulatory level, we identified four upstream regulators, all involved in behavioral processes and neuropsychiatric disorders including aggressive demonstrations. Our results on an animal model in which the aging process enhance the intensity of aggressive responses provide, for the first time, insights into candidate genes and networks involved in the molecular mechanisms leading to the maturation of the brain, with a focus on cattle agonistic components.
Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells

DNA replication is well orchestrated in mammalian cells through a tight regulation of the temporal order of replication origin activation, named the replication timing, a robust and conserved process in each cell type. Upon low replication stress, the slowing of replication forks induces delayed replication of fragile regions leading to genetic instability. The impact of low replication stress on the replication timing in different cellular backgrounds has not been explored yet. Here we analysed the whole genome replication timing in a panel of 6 human cell lines under low replication stress. We first demonstrated that cancer cells were more impacted than non-tumour cells. Strikingly, we unveiled an enrichment of specific replication domains undergoing a switch from late to early replication in some cancer cells. We found that advances in replication timing correlate with heterochromatin regions poorly sensitive to DNA damage signalling while being subject to an increase of chromatin accessibility. Finally, our data indicate that, following release from replication stress conditions, replication timing advances can be inherited by the next cellular generation, suggesting a new mechanism by which cancer cells would adapt to cellular or environmental stress.
Minimal Residual Disease Detection in Hairy Cell Leukemia

We studied 86 specimens from 24 patients with hairy cell leukemia (HCL) to determine the sensitivity of routine flow cytometry (FC) and consensus primer PCR (cpPCR) in this disease. FC was more sensitive, detecting HCL in 48 (56%) of 86 specimens, while clonal B-cell populations were detected by cpPCR in only 23 (27%) of 86 specimens. FC and cpPCR were both more sensitive than morphologic examination. A positive cpPCR result is associated with higher tumor cell numbers than a negative cpPCR result, as determined by FC ( P = .0017). We determined cutoff values for number of tumor cells at which cpPCR is consistently positive. At 6.8 tumor cells per microliter, cpPCR would be expected to be positive in at least 90% of the samples. FC was adequate in 86 cases (100%), while cpPCR was adequate in 74 cases (86%). FC is superior to cpPCR for detecting minimal residual HCL. It is more sensitive and more specific and permits quantitation of tumor cell number.
Robot DE NIRO: A Human-Centered, Autonomous, Mobile Research Platform for Cognitively-Enhanced Manipulation

We introduce Robot DE NIRO, an autonomous, collaborative, humanoid robot for mobile manipulation. We built DE NIRO to perform a wide variety of manipulation behaviors, with a focus on pick-and-place tasks. DE NIRO is designed to be used in a domestic environment, especially in support of caregivers working with the elderly. Given this design focus, DE NIRO can interact naturally, reliably, and safely with humans, autonomously navigate through environments on command, intelligently retrieve or move target objects, and avoid collisions efficiently. We describe DE NIRO's hardware and software, including an extensive vision sensor suite of 2D and 3D LIDARs, a depth camera, and a 360-degree camera rig; two types of custom grippers; and a custom-built exoskeleton called DE VITO. We demonstrate DE NIRO's manipulation capabilities in three illustrative challenges: First, we have DE NIRO perform a fetch-an-object challenge. Next, we add more cognition to DE NIRO's object recognition and grasping abilities, confronting it with small objects of unknown shape. Finally, we extend DE NIRO's capabilities into dual-arm manipulation of larger objects. We put particular emphasis on the features that enable DE NIRO to interact safely and naturally with humans. Our contribution is in sharing how a humanoid robot with complex capabilities can be designed and built quickly with off-the-shelf hardware and open-source software. Supplementary Material including our code, a documentation, videos and the CAD models of several hardware parts are openly available at https://www.imperial. ac.uk/robot-intelligence/software/.
Text Entry on Circular Smart Watches: The C-QWERTY Layout

We present a study aimed at comparing diﬀerent circular layouts for entering text on smartwatches. In particular, we measured the extent through which the use of a QWERTY layout increases user performance in the earliest sessions of use. To this aim, we designed C-QWERTY, a soft keyboard designed for circular smartwatches in which the keys are arranged along the edge of the screen in a circular layout. In order to make the keyboard more familiar to users, the order of the keys is similar to the one of traditional rectangular QWERTY keyboards. The method supports two interaction modes: tapping and gesture, in which a whole word can be written with a single gesture. As an evaluation, we compared the C-QWERTY layout with Cirrin, another circular layout in witch the order of the characters has been optimized to minimize the distance between successive keys during writing. The experimental results showed that the C-QWERTY layout outperformed the Cirrin one with respect to the text entry speed with an average increase of 27 percent.
A COMPARISON OF DISTANCE-BASED AND CLASSIFICATION-BASED ANALYSES OF HABITAT USE

Quantifying habitat use is vital to understanding animal ecology. Herein, we contrast classification-based (i.e., animal locations are placed into habitat categories for subsequent analyses) and distance-based (i.e., distance between animal locations and habitat features are used in subsequent analyses) approaches for analyzing habitat use data. Compositional analysis (CA) and a distance-based analysis (DA) were used to quantify habitat selection of Northern Bobwhite (Colinus virginianus). We qualitatively compared the outcome of these different procedures to illustrate advantages of the DA approach. The DA approach identified edges as an important habitat feature, and location error did not alter conclusions from DA. In contrast, CA did not detect the importance of edge, and presence of location errors altered conclusions. Moreover, modeling the distribution of location error did not effectively reduce sensitivity to error within CA. Distance-based approaches to habitat analyses are not restricted to lin.
A second-order semidigital clock recovery circuit based on injection locking

A compact (1 mm /spl times/ 160 /spl mu/m) and low-power (80-mW) 0.18-/spl mu/m CMOS 3.125-Gb/s clock and data recovery circuit is described. The circuit utilizes injection locking to filter out high-frequency reference clock jitter and multiplying delay-locked loop duty-cycle distortions. The injection-locked slave oscillator output can have its output clocks interpolated by current steering the injecting clocks. A second-order clock and data recovery is introduced to perform the interpolation and is capable of tracking frequency offsets while exhibiting low phase wander.
Aster Imagery And Aeromagnetic Data - Powerful Tools To Aid Reconnaissance Geologic Mapping Of The Sierra San José Mountain Range, Northern Sonora State, Mexico

Aeromagnetic and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data are currently being used to assist in geologic mapping of the Sierra San Jose region in the Sonoran San Pedro River basin. Lithologic contacts have also been mapped using Euler deconvolution of aeromagnetic data. A lithologic classification map consisting of quartzfeldspar, clay-muscovite-sericite, and carbonate was produced using thresholded match filter ASTER data and relative band depth absorption analysis (RBD). A minimum noise transform (MNF) false color composite image was used to map lithologic units. A false color composite image of ASTER bands 1 (blue), 2 (green) and 3 (red) was also used to determine the extent of vegetation and assist in mapping structural features, although most of the structural features could be mapped using high altitude stereo pair imagery. To date, field studies indicate that ASTER data have successfully mapped carbonates, sericite, and muscovite and with lesser success have also helped characterize quartz-rich rocks. In addition, our field studies, along with ASTER and Landsat data, have confirmed lithologic contacts at the surface mapped by Euler deconvolution of the aeromag.
CORRELATING DIFFERENTIAL EXPRESSION, PEPTIDE AFFINITIES, CRYSTAL STRUCTURES, AND THERMAL STABILITIES*

Previous studies of HLA-E allelic polymorphism have indicated that balancing selection may be acting to maintain two major alleles in most populations, indicating that a functional difference may exist between the alleles. The alleles differ at only one amino acid position, where an arginine at position 107 in HLA-E*0101 (E R )i s replaced by a glycine in HLA-E*0103 (E G ). To investigate possible functional differences, we have undertaken a study of the physical and biochemical properties of these two proteins. By comparing expression levels, we found that whereas steady-state protein levels were similar, the two alleles did in fact differ with respect to cell surface levels. To help explain this difference, we undertook studies of the relative differences in peptide affinity, complex stability, and three-dimensional structure between the alleles. The crystal structures for HLA-E G complexed with two distinct peptides were determined, and both were compared with the HLA-E R structure. No significant differences in the structure of HLA-E were induced as a result of binding different peptides or by the allelic substitution at position 107. However, there were clear differences in the relative affinity for peptide of each heavy chain, which correlated with and may be explained by differences between their thermal stabilities. These differences were completely consistent with the relative levels of the HLA-E alleles on the cell surface and may indeed correlate with functional differences. This in turn may help explain the apparent balancing selection acting on this locus.
Coccidioidomycosis : an unusual cause of acute respiratory distress syndrome *

A male farmer, 20 years old, from the countryside of the State of Piauí, developed acute respiratory infection. Despite adequate antimicrobial therapy, his conditions worsened, requiring mechanical ventilation. His X-rays showed diffuse pulmonary infiltrates. His PaO2/FiO2 ratio was 58. Direct microscopy and culture of tracheal aspirates showed the presence of Coccidioides immitis. Autochthonous cases of coccidioidomycosis have only recently been described in Brazil, most of them from the State of Piauí. C. immitis has been isolated from humans, dogs and armadillos (Dasypus novemcinctus), and also from soil samples of armadillo’s burrows. Failure to respond to antimicrobial therapy and a patient’s origin from recognized endemic areas should alert to the possibility of acute pulmonary coccidioidomycosis. (J Pneumol 2003;29(1):45-8)
Comparação entre diferentes escores de risco de mortalidade em unidade de tratamento intensivo neonatal Comparison between different mortality risk scores in a neonatal intensive care unit

Objetivo Avaliar peso de nascimento e os escores como preditores de mortalidade neonatal em unidade de terapia intensiva neonatal, comparando os seus resultados. Metodos Foram avaliados 494 recem-nascidos admitidos em uma unidade de terapia intensiva neonatal (UTIN) de um hospital geral de Porto Alegre, RS, logo apos o nascimento, entre marco de 1997 e junho de 1998. Foram avaliados o peso de nascimento e os escores considerando a variavel obito durante a internacao na UTI. Os criterios de exclusao foram: alta ou obito da UTIN com menos de 24 horas de internacao, recemnascidos cuja internacao nao ocorreu logo apos o nascimento, protocolo de estudo incompleto e malformacoes congenitas incompativeis com a vida. Para avaliacao do CRIB (Clinical Risk Index for Babies) foram considerados somente os pacientes com peso de nascimento inferior a 1.500 g. Foram calculadas as curvas ROC (Receiver Operating Characteristics Curve) para SNAP (Score for Neonatal Acute), SNAP-PE (Score for Neonatal Acute Physiology Perinatal Extension), SNAP II, SNAP-PE II, CRIB e peso de nascimento. Resultados Dos 494 pacientes, 44 faleceram (8,9% de mortalidade). Dos 102 recem-nascidos com peso de ate 1.500 g, 32 (31,3%) faleceram. As areas abaixo da curva ROC variaram de 0,81 a 0,94. Todos os escores avaliados mostraram areas abaixo da curva ROC sem diferencas estatisticamente significativas. Os escores de risco de mortalidade estudados apresentaram um melhor desempenho que o peso de nascimento, especialmente em recem-nascidos com peso de nascimento igual ou menor que 1.500 g. Conclusoes Todos os escores de mortalidade neonatal apresentaram melhor desempenho e foram superiores ao peso de nascimento como medidores de risco de obito hospitalar para recem-nascidos internados em UTIN.
Accelerated Failure Time Survival Model to Analyze Morris Water Maze Latency Data

Traumatic brain injury (TBI) induces cognitive deficits clinically and in animal models. Learning and memory testing is critical when evaluating potential therapeutic strategies and treatments to manage the effects of TBI. We evaluated three data analysis methods for the Morris water maze (MWM), a learning and memory assessment widely used in the neurotrauma field, to determine which statistical tool is optimal for MWM data. Hidden platform spatial MWM data aggregated from three separate experiments from the same laboratory were analyzed using 1) a logistic regression model, 2) an analysis of variance (ANOVA) model, and 3) an accelerated failure time (AFT) time-to-event model. The logistic regression model showed no significant evidence of differences between treatments among any swims over all days of the study, p > 0.11. Although the ANOVA model found significant evidence of differences between sham and TBI groups on three out of four swims on the third day, results are potentially biased due to the failure of this model to account for censoring. The time-to-event AFT model showed significant differences between sham and TBI over all swims on the third day, p < 0.045, taking censoring into account. We suggest AFT models should be the preferred analytical methodology for latency to platform associated with MWM studies.
Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation.

BACKGROUND & AIMS Countries endemic for parasitic infestations have a lower incidence of Crohn's disease (CD) than non-endemic countries, and there have been anecdotal reports of the beneficial effects of helminths in CD patients. Tuft cells in the small intestine sense and direct the immune response against eukaryotic parasites. We investigated the activities of tuft cells in patients with CD and mouse models of intestinal inflammation. METHODS We used microscopy to quantify tuft cells in intestinal specimens from patients with ileal CD (n = 19), healthy individuals (n = 14), and TNFΔARE/+ mice, which develop Crohn's-like ileitis. We performed single-cell RNA-sequencing, mass spectrometry, and microbiome profiling of intestinal tissues from wildtype and ATOH1-knockout mice, which have expansion of tuft cells, to study interactions between microbes and tuft cell populations. We assessed microbe dependence on these populations using microbiome depletion, organoids, and microbe transplant experiments. We used multiplex imaging and cytokine assays to assess alterations in inflammatory response following expansion of tuft cells with succinate administration in TNFΔARE/+ and anti-CD3E CD mouse models. RESULTS Inflamed ileal tissues from patients and mice had reduced numbers of tuft cells, compared with healthy individuals or wild-type mice. Expansion of tuft cells was associated with increased expression of genes that regulate the tricarboxylic acid cycle, which resulted from microbe production of the succinate. Experiments in which we manipulated the intestinal microbiota of mice revealed the existence of an ATOH1-independent population of tuft cells that was sensitive to metabolites produced by microbes. Administration of succinate to mice expanded tuft cells and reduced intestinal inflammation in TNFΔARE/+ mice and anti-CD3E-treated mice, increased GATA3+ cells and type 2 cytokines (IL22, IL25, IL13), and decreased RORGT+ cells and type 17 cytokines (IL23) in a tuft cell-dependent manner. CONCLUSIONS We found that tuft cell expansion reduced chronic intestinal inflammation in mice. Strategies to support tuft cells might be developed for treatment of CD.
Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β‐glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene‐deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild‐type strain as well as in β‐glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non‐diauxic growth and metabolite consumptions of the wild‐type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially‐useful strains. Importantly, the model is able to explain the role of the different β‐glucosidases and their behavior under genetic perturbations. This integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.
New insights into the structural properties of κ-(BEDT-TTF)2Ag2(CN)3 spin liquid.

Here, the first accurate study is presented of the room-temperature and 100 K structures of one of the first organic spin liquids, κ-(BEDT-TTF)2Ag2(CN)3. It is shown that the monoclinic structure determined previously is only the average one. It is shown that the exact structure presents triclinic symmetry with two non-equivalent dimers in the unit cell. But surprisingly this does not lead to a sizeable charge disproportionation between dimers. The difference from the analogue compound κ-(BEDT-TTF)2Cu2(CN)3 which also presents a spin liquid phase is discussed in detail. The data provided here show the importance of the anionic layer and in particular the transition metal position in the process of symmetry breaking. The possible impact of the symmetry breaking, albeit weak, on the spin-liquid mechanism and the influence of various disorders on the physical properties of this system is also discussed.
Assessing the Magnitude of Risk for ADHD in Offspring of Parents with ADHD: A Systematic Literature Review and Meta-Analysis

The main aim of this study was to examine the body of knowledge on the prevalence of Attention Deficit Hyperactivity Disorder (ADHD) in “high-risk” children whose parents are diagnosed with ADHD. This knowledge could aid early identification for children presenting with ADHD symptoms at a young age. We conducted a systematic search of the literature assessing high-risk children. Included were original articles published in English with the main aim to assess prevalence of ADHD in high risk children. In addition, a meta-analysis was conducted to examine this prevalence. Four articles met our inclusion and exclusion criteria all suggesting an increased prevalence of ADHD in children of parents with ADHD. The meta-analysis also confirmed the increased prevalence of ADHD in high-risk children. The literature indicates that children of ADHD parents have an increased risk of developing ADHD compared to control children.
Gender Differences in the Use of Engagement and Disengagement Coping Strategies in Patients With Cancer Receiving Chemotherapy.

OBJECTIVES To evaluate the relationship between gender and coping strategies in patients with cancer undergoing chemotherapy in outpatient settings. SAMPLE & SETTING Women (N = 277) and men (N = 293) were recruited from two comprehensive cancer centers, one Veterans Affairs hospital, and four community-based oncology programs. METHODS & VARIABLES Coping data were obtained from patients with gastrointestinal (n = 412) or lung (n = 158) cancer through the Brief COPE scale. RESULTS In terms of engagement coping strategies, women reported higher scores for positive reframing, religion, and using instrumental support. Men reported higher scores for humor. In terms of disengagement coping strategies, women reported higher scores for denial, venting, and self-distraction. Men reported higher scores for substance use. IMPLICATIONS FOR NURSING Gender-based stereotypes of emotional expectations may affect how patients express themselves and the ways in which support is offered. Clinicians should be aware of their own preconceived notions about sex and gender and reflect on how these may influence the psychosocial care they provide.