Miracle-dz/UniFAR-FTUs huggingface dataset:
SparkFlow: Towards High-Performance Data Analytics for Spark-based Genome Analysis

The recent advances in DNA sequencing technology triggered next-generation sequencing (NGS) research in full scale. Big Data (BD) is becoming the main driver in analyzing these large-scale bioinformatics data. However, this complicated process has become the system bottleneck, requiring an amal-gamation of scalable approaches to deliver the needed performance and hide the deployment complexity. Utilizing cutting-edge scientific workflows can robustly address these challenges. This paper presents a Spark-based alignment workflow called SparkFlow for massive NGS analysis over singularity containers. SparkFlow is highly scalable, reproducible, and capable of parallelizing computation by utilizing data-level parallelism and load balancing techniques in HPC and Cloud environments. The proposed workflow capitalizes on benchmarking two state-of-art NGS workflows, i.e., Base Recalibrator and ApplyBQSR. SparkFlow realizes the ability to accelerate large-scale cancer genomic analysis by scaling vertically (HyperThreading) and horizontally (provisions on-demand). Our result demonstrates a trade-off inevitably between the targeted applications and proces-sor architecture. SparkFlow achieves a decisive improvement in NGS computation performance, throughput, and scalability while maintaining deployment complexity. The paper's findings aim to pave the way for a wide range of revolutionary enhancements and future trends within the High-performance Data Analytics (HPDA) genome analysis realm.
Phylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of Streptococcus dysgalactiae

Streptococcus dysgalactiae (SD) is capable of infecting both humans and animals and causing a wide range of invasive and non-invasive infections. With two subspecies, the taxonomic status of subspecies of SD remains controversial. Subspecies equisimilis (SDSE) is an important human pathogen, while subspecies dysgalactiae (SDSD) has been considered a strictly animal pathogen; however, occasional human infections by this subspecies have been reported in the last few years. Moreover, the differences between the adaptation of SDSD within humans and other animals are still unknown. In this work, we provide a phylogenomic analysis based on the single-copy core genome of 106 isolates from both the subspecies and different infected hosts (animal and human hosts). The accessory genome of this species was also analyzed for screening of genes that could be specifically involved with adaptation to different hosts. Additionally, we searched putatively adaptive traits among prophage regions to infer the importance of transduction in the adaptation of SD to different hosts. Core genome phylogenetic relationships segregate all human SDSE in a single cluster separated from animal SD isolates. The subgroup of bovine SDSD evolved from this later clade and harbors a specialized accessory genome characterized by the presence of specific virulence determinants (e.g., cspZ) and carbohydrate metabolic functions (e.g., fructose operon). Together, our results indicate a host-specific SD and the existence of an SDSD group that causes human–animal cluster infections may be due to opportunistic infections, and that the exact incidence of SDSD human infections may be underestimated due to failures in identification based on the hemolytic patterns. However, more detailed research into the isolation of human SD is needed to assess whether it is a carrier phenomenon or whether the species can be permanently integrated into the human microbiome, making it ready to cause opportunistic infections.
Episodic Memory, Hippocampal Volume, and Function for Classification of Mild Cognitive Impairment Patients Regarding Amyloid Pathology

Background: Previous studies of hippocampal function and volume related to episodic memory deficits in patients with amnestic mild cognitive impairment (aMCI) have produced mixed results including increased or decreased activity and volume. However, most of them have not included biomarkers, such as amyloid-β (Aβ) deposition which is the hallmark for early identification of the Alzheimer’s disease continuum. Objective: We investigated the role of Aβ deposition, functional hippocampal activity and structural volume in aMCI patients and healthy elderly controls (HC) using a new functional MRI (fMRI) ecological episodic memory task. Methods: Forty-six older adults were included, among them Aβ PET PIB positive (PIB+) aMCI (N = 17), Aβ PET PIB negative (PIB–) aMCI (N = 15), and HC (N = 14). Hippocampal volume and function were analyzed using Freesurfer v6.0 and FSL for news headlines episodic memory fMRI task, and logistic regression for group classification in conjunction with episodic memory task and traditional neuropsychological tests. Results: The aMCI PIB+ and PIB–patients showed significantly worse performance in relation to HC in most traditional neuropsychological tests and within group difference only on story recall and the ecological episodic memory fMRI task delayed recall. The classification model reached a significant accuracy (78%) and the classification pattern characterizing the PIB+ included decreased left hippocampal function and volume, increased right hippocampal function and volume, and worse episodic memory performance differing from PIB–which showed increased left hippocampus volume. Conclusion: The main findings showed differential neural correlates, hippocampal volume and function during episodic memory in aMCI patients with the presence of Aβ deposition.
Mitochondrial Homeostasis and Mast Cells in Experimental Hepatic Ischemia-Reperfusion Injury of Rats

Background: Ischemia-reperfusion injury is a histopathological event and is an important cause of morbidity and mortality after hepatobiliary surgery. We aimed to investigate the protective effect of uridine on hepatic ischemia-reperfusion injury in rats. Methods: he animals were divided into 4 groups (n = 8): group I (control), group II: ischemia-reperfusion (30 minutes ischemia and 120 minutes reperfusion), group III: ischemia-reperfusion + uridine (at the beginning of reperfusion), and group IV: ischemia-reperfusion + uridine (5 minutes before ischemia-reperfusion). Uridine was administered a single dose of 30 mg/kg IV. The 3 elements of the hepatoduodenal ligament (hepatic artery, portal vein, and biliary tract) were obliterated for 30 minutes. Then hepatic reperfusion was achieved for 120 minutes. Results: In the ischemia-reperfusion group, both liver tissues and serum chymase activity and high-temperature requirement A2 levels were higher. Severe central vein dilatation and congestion, widening sinusoidal range, diffuse necrotic hepatocytes and dense erythrocyte accumulation in sinusoids, and strongly inducible nitric oxide synthase expression were seen in the ischemia-reperfusion group. A clear improvement was seen in both uridine co-administration and pretreatment groups. Conclusion: Our results revealed that uridine limits the development of liver damage under conditions of ischemia-reperfusion, thus contributing to an increase in hepatocyte viability.
Canopy Height and Climate Dryness Parsimoniously Explain Spatial Variation of Unstressed Stomatal Conductance

The spatio‐temporal variation of stomatal conductance directly regulates photosynthesis, water partitioning, and biosphere‐atmosphere interactions. While many studies have focused on stomatal response to stresses, the spatial variation of unstressed stomatal conductance remains poorly determined, and is usually characterized in land surface models (LSMs) simply based on plant functional type (PFT). Here, we derived unstressed stomatal conductance at the ecosystem‐scale using observations from 115 global FLUXNET sites. When aggregated by PFTs, the across‐PFT pattern was highly consistent with the parameterizations of LSMs. However, PFTs alone captured only 17% of the variation in unstressed stomatal conductance across sites. Within the same PFT, unstressed stomatal conductance was negatively related to climate dryness and canopy height, which explained 45% of the total spatial variation. Our results highlight the importance of plant‐environment interactions in shaping stomatal traits. The trait‐environment relationship established here provides an empirical approach for improved parameterizations of stomatal conductance in LSMs.
Exposição ocupacional à vibração de corpo inteiro e repercussões sobre a saúde de pilotos agrícolas

Agricultural pilots work in conditions that can affect them and contribute to the occurrence of work-related accidents. In this context, earlier studies have focused their efforts on the understanding of the effects of many factors on pilot performance, health and/or flight safety. Typical examples include exposure to pesticides, exposure to environmental noise and unfavorable thermal conditions, as well as the distribution of responsibilities among the professionals involved with the aerial application. Other problems related to the work of agricultural pilots, such as operation on improvised runways and the effect of this working condition on exposure to vibrations is not explored. In addition, it is noted that complaints of pain in the spine are common among professionals and, depending on working conditions, they may have an increased risk of spinal problems. The objective of this thesis is to explore the exposure of agricultural pilots to Whole-Body Vibrations (WBV) and to identify the effects of this on health, especially regarding to musculoskeletal symptoms of the spine. The methodology consisted of three stages: a field research aimed at understanding the working conditions of agricultural pilots, mainly on the factors capable of influencing the occupational exposure to WBV and the occurrence of musculoskeletal disorders; The data collection and analysis about occupational exposure of agricultural pilots to WBV; and, the data collection and analysis about musculoskeletal symptoms of the spine. As results of the field research, data are presented on surface roughness of landing fields, exposure to WBV and prevalence of musculoskeletal symptoms in agricultural pilots. The significant factors identified as in the exposure of the agricultural pilots to the WBV were the aircraft model used, the surface roughness conditions of the landing areas, as well as the flight stages. Regarding the health of the spine of the pilots, only the occupational exposure to the WBV was presented as significant. Given the complexity of labor relations in the context of agricultural aviation with the involvement of different types of workers, three types of solutions are included to prevent the occurrence of musculoskeletal disorders in agricultural pilots: frequent maintenance of landing areas, farmers; The management of the daily exposure time, the responsibility of the operational managers and operational safety; And changes in aircraft design, either at the interface with the pilot, to mitigate the transmissibility of vibrations from the aircraft, or, in damping systems, capable of isolating the source from vibrations, preventing their propagation.
Wheat grain proteins: Past, present, and future

Abstract Background and Objectives Research on wheat grain proteins is reviewed, including achievements over the past century and priorities for future research. The focus is on three groups of proteins that have major impacts on wheat quality and utilization: the gluten proteins which determine dough viscoelasticity but also trigger celiac disease in susceptible individuals, the puroindolines which are major determinants of grain texture and the amylase/trypsin inhibitors which are food and respiratory allergens and are implicated in triggering celiac disease and nonceliac wheat sensitivity. Findings Although earlier work focused on protein structure and properties, the development of genomics and high‐sensitivity proteomics has resulted in the availability of a vast amount of information on the amino acid sequences of individual wheat proteins, including allelic variants of gluten proteins which are associated with good processing quality and of puroindolines, which are associated with a hard or soft grain texture, and on protein expression and polymorphism. Conclusions However, our ability to exploit this knowledge is limited by a lack of detailed understanding of the structure:function relationships of wheat proteins. In particular, we need to understand how the three‐dimensional structures of the individual proteins determine their interactions with other grain components (to determine functional properties) and with the immune systems of susceptible consumers (to trigger adverse responses), how these interactions are affected by allelic variation, and how they can be manipulated. Significance and Novelty The article, therefore, identifies priorities for future research which should enable the adoption of a more rational approach to improving the quality of wheat grain proteins.
Internal migration, children’s schooling and gender gaps in education

ABSTRACT In many sub-Saharan African countries, a large number of people migrate internally due to economic, demographic and political factors. We ask whether household mobility affects child educational outcomes and in what direction. Because girls and boys face different challenges in achieving education, and families often underinvest in girls’ human capital, we focus on gender differentials. We study the case of Uganda, a country where universal basic education and gender equality are still complicated goals. We use the National Panel Survey of 2005, 2009, 2010 and 2011 to develop fixed effects models of the relationship between mobility and children’s educational outcomes: school delay and attendance. We find that moving with the family during primary or lower secondary school decreases delay in schooling and increases school attendance for boys, while we do not find any significant effect for girls. We argue that our results confirm pro-male preferences of families, where girls do not benefit equally from the opportunities offered by internal migration. Expanding girls’ opportunities, as well as providing adequate services, are crucial steps in achieving gender equality in education.
Deconstructing and reconstructing turn-taking in caregiver-infant interactions: a platform for embodied models of early cooperation

ABSTRACT Despite recent advances in AI, building systems that can engage in natural and realistic cooperative interactions with human partners remains a challenge. In this article, we argue that as a precursor to modelling sophisticated cooperation in adults, it’s useful to build a model of how cooperation develops in infants. We present a simple initial model of infant cooperation, embodied in BabyX – a hyperrealistic virtual simulation of an 18-month-old infant that can interact with human partners in real time. Our focus in this paper is on cooperative behaviours in the nonverbal domain. The framework for our model of these behaviours is a cognitive model of events and event processing. We detail how cognitive and motor mechanisms in BabyX lead to rudimentary cooperation manifested in nonverbal turn-taking. We introduce a novel empirical paradigm for testing BabyX’s model of cooperation, by comparing her interactions with users with ‘real’ interactions between human infants and their caregivers, which we observed in a detailed empirical study. In this study, we find nonverbal turn-taking in human infant-caregiver interactions, consistent with our BabyX model. This initial model provides the foundation for a comprehensive, and developmentally consistent, model of human cooperation.
In-depth characterization of a mouse model of postoperative atrial fibrillation

Introduction: Postoperative atrial fibrillation (POAF), characterized as AF that arises 1-3 days after surgery, occurs after 30%-40% of cardiac and 10%-20% of non-cardiac surgeries, and is thought to arise due to transient surgery-induced triggers acting on a preexisting vulnerable atrial substrate often associated with inflammation and autonomic nervous system dysfunction. Current experimental studies often rely on human atrial tissue samples, collected during surgery prior to arrhythmia development, or animal models such as sterile pericarditis and atriotomy, which have not been robustly characterized. Aim: To characterize the demographic, electrophysiologic, and inflammatory properties of a POAF mouse model. Methods and Results: A total of 131 wild-type C57BL/6J mice were included in this study. A total of 86 (65.6%) mice underwent cardiothoracic surgery (THOR), which consisted of bi-atrial pericardiectomy with 20 s of aortic cross-clamping; 45 (34.3%) mice underwent a sham procedure consisting of dissection down to but not into the thoracic cavity. Intracardiac pacing, performed 72 h after surgery, was used to assess AF inducibility. THOR mice showed greater AF inducibility (38.4%) compared to Sham mice (17.8%, P = 0.027). Stratifying the cohort by tertiles of age showed that the greatest risk of POAF after THOR compared to Sham occurred in the 12-19-week age group. Stratifying by sex showed that cardiothoracic (CT) surgery increased POAF risk in females but had no significant effect in males. Quantitative polymerase chain reaction of atrial samples revealed upregulation of transforming growth factor beta 1 (TGF-β1) and interleukin 6 (IL6) and 18 (IL18) expression in THOR compared to Sham mice. Conclusion: Here, we demonstrate that the increased POAF risk associated with CT surgery is most pronounced in female and 12-19-week-old mice, and that the expression of inflammatory cytokines is upregulated in the atria of THOR mice prone to inducible AF.
An Efficient Text Summarization Using Term and Inverse Frequency With Key Phrase Identification in Malayalam Language

Malayalam is a morphologically rich language. Indian languages have several language genres like Indo-Aryan, Sino-Tibetan, and Dravidian languages, where Malayalam comes under the Dravidian language genres. Text summarization in Indian languages is hard because of their rich content and lack of easy availability of annotated data. Here we propose a summarization system for Malayalam language documents based on the Term Frequency – Inverse Document Frequency (TF-IDF) scheme. Our summarizer will accept a single Malayalam text document as input, then by using the TF-IDF measurement scheme with keyword identification a summary document is generated. The proposed method successfully summarized Malayalam literature documents with 90.6% accuracy.
Exploring the Impact of COVID‐19 on Employees’ Boundary Management and Work–Life Balance

Abstract The COVID‐19 pandemic altered the ways academics work and live by creating a context during the spring of 2020 when working from home was largely mandatory and where, for cohabiting workers, the home as workplace was simultaneously occupied by all household members during working hours (and beyond). Using a multi‐method qualitative approach, we examine how academics experienced working from home during the unprecedented circumstances imposed by the first UK lockdown and social distancing measures. Our findings show that a working arrangement commonly termed ‘flexible’ – working from home – can actually reduce flexibility in a context of mandatory implementation, accompanied by the removal of instrumental and emotional support structures such as childcare and face‐to‐face (physical) social gatherings. Intensified workloads, increased employer monitoring, social disconnection and blurred boundaries between work and personal life collectively generate the reduction of employees’ perceived flexibility‐ability. Experiences may be particularly negative for those with low flexibility‐willingness, whose pre‐pandemic preference was to separate work and home as much as possible. Employee efforts to assert agency in this context include establishing ‘micro‐borders’ and using time‐based strategies to create ‘controlled integration’. We discuss implications for border theory and outline directions for future research.
Students on board: designing a board game for 1000+ students

This session will explore the challenges of designing a game for a large-scale course. ‘Capture the Market’ is a deconstructed board game designed to be played by 1590 LSE100 students in 137 classes, taught by a team of 43 teachers, over a condensed period of 4 days. We will look at how some of the theory on games based learning applied to the ‘Capture the Market’ game and the lessons learnt from the experience of both designing and playing the game in class.
Going 'beyond the mean' in analysing immigrant health disparities

BACKGROUND On arrival, immigrants are on average healthier than Italian natives, but their health advantage tends to dissipate over time. This constitutes a relevant public health issue for the hosting societies, as it implies higher health care costs, lower labor market participation among immigrants, and lower tax revenues. OBJECTIVE This study is the ﬁrst to take a “beyond the mean” perspective in analyzing health differences between Italians and short-say immigrants, as well as between short- and long-stay immigrants. It highlights whether health differences are concentrated in speciﬁc parts of the distributions and which observed or unobserved factors contribute to these differences. We use unconditional quantile regressions combined with Oaxaca-Blinder decompositions on data from the Italian Health Condition Survey. We ﬁnd that the health advantage of short-stay immigrants over both Italians and long-stay immigrants is concentrated in the lower part of the health distributions. In both cases, this is mainly due to unobserved factors. Observed economic characteristics are actually associated with better health for long-stay immigrants compared to short-stay immigrants. Our results reveal the need of monitoring immigrants’ health, particularly of those with poorer initial health conditions.
Stem cell therapy for the treatment of severe tissue damage after radiation exposure

I recent years, the application of attenuated strains of Salmonella spp. has been widely investigated for the development of various biotechnological products, especially vaccines. However, the industrial production of these compounds is hampered by metabolic constraints presented by Salmonella cells, which naturally produce high amounts of growth inhibitor metabolites, mainly acetate. To deal with this problem, two different approaches were evaluated in the present work: Changing culture conditions (carbon source evaluation) and implementing genetic modifications (enhancement of cell’s acetate scavenging capabilities by overexpression of acetyl-CoA synthetase (ACS)). Wild type and recombinant cells were cultured in minimal medium with glucose or glycerol as carbon source in Erlenmeyer flasks agitated at 200 rpm and 37 oC. Samples were collected during cultivation and analyzed by HPLC to quantify organic acids production and the carbon source consumption. Cellular growth was assessed by optical density readings (OD 600 nm) of the culture broth. The results showed that the carbon source plays an important role on byproducts excretion by S. typhimurium cells, indicating that for both strains acetate production is greatly reduced using glycerol. The overexpression of ACS also reduced the acetate accumulation as this enzyme acted assimilating the excreted acetate. From all the conditions studied, the best results were obtained by the recombinant cells cultured in glycerol. An increase of 40% of biomass production was achieved, while the acetate accumulation was reduced by more than 50% in comparison to the average values registered in the other experiments.