Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of B-Cell Compartment Hyperactivation in European Adolescents Living With Perinatally Acquired HIV-1 After Over 10 Years of Suppressive Therapy

Background Despite a successful antiretroviral therapy (ART), adolescents living with perinatally acquired HIV (PHIV) experience signs of B-cell hyperactivation with expansion of ‘namely’ atypical B-cell phenotypes, including double negative (CD27-IgD-) and termed age associated (ABCs) B-cells (T-bet+CD11c+), which may result in reduced cell functionality, including loss of vaccine-induced immunological memory and higher risk of developing B-cells associated tumors. In this context, perinatally HIV infected children (PHIV) deserve particular attention, given their life-long exposure to chronic immune activation. Methods We studied 40 PHIV who started treatment by the 2nd year of life and maintained virological suppression for 13.5 years, with 5/40 patients experiencing transient elevation of the HIV-1 load in the plasma (Spike). We applied a multi-disciplinary approach including immunological B and T cell phenotype, plasma proteomics analysis, and serum level of anti-measles antibodies as functional correlates of vaccine-induced immunity. Results Phenotypic signs of B cell hyperactivation were elevated in subjects starting ART later (%DN T-bet+CD11c+ p=0.03; %AM T-bet+CD11c+ p=0.02) and were associated with detectable cell-associated HIV-1 RNA (%AM T-bet+CD11c+ p=0.0003) and transient elevation of the plasma viral load (spike). Furthermore, B-cell hyperactivation appeared to be present in individuals with higher frequency of exhausted T-cells, in particular: %CD4 TIGIT+ were associated with %DN (p=0.008), %DN T-bet+CD11c+ (p=0.0002) and %AM T-bet+CD11c+ (p=0.002) and %CD4 PD-1 were associated with %DN (p=0.048), %DN T-bet+CD11c+ (p=0.039) and %AM T-bet+CD11c+ (p=0.006). The proteomic analysis revealed that subjects with expansion of these atypical B-cells and exhausted T-cells had enrichment of proteins involved in immune inflammation and complement activation pathways. Furthermore, we observed that higher levels of ABCs were associated a reduced capacity to maintain vaccine-induced antibody immunity against measles (%B-cells CD19+CD10- T-bet+, p=0.035). Conclusion We identified that the levels of hyperactivated B cell subsets were strongly affected by time of ART start and associated with clinical, viral, cellular and plasma soluble markers. Furthermore, the expansion of ABCs also had a direct impact on the capacity to develop antibodies response following routine vaccination.
High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters

Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 104 cells mL−1) and heterotrophic bacteria (1.6–4.3 × 105 cells mL−1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.
Temperature-Induced Environmental Chain Reaction in Marine Sedimentation and Its Impact on Manila Clam Ruditapes philippinarum

Marine Heatwaves (MHWs) events have been increasing, causing severe impacts on marine ecosystems and aquaculture. In this study, the effects of temperature on changes in sediment dissolved oxygen (DO) and hydrogen sulfide (H2S) concentrations and their effects on the behavioral and physiological responses of a bivalve were investigated by simulating different sudden summer temperature change conditions. The results showed that temperature was an important factor affecting DO consumption and H2S release in sediments, and sediment type also played a key role. At higher temperatures, DO was consumed more rapidly and H2S release increased in sediments, and the DO was consumed and H2S released in sandy sediments was less than in silty sand sediments. The response of Manila clam’s exercise behavior under environmental pressure was also rapid. The excavation index of the Manila clam decreased with the DO consumption, indicating that the Manila clam could alter its burial depth and move toward the sediment-water interface when stressed. Compared with phenol oxidases (PO) activity being activated under experimental conditions, succinate concentrations only increased slightly at 32°C, and did not surpass the threshold indicative of anaerobic metabolism. However, when toxic substances such as H2S start to accumulate, they may damage the immune system and tissues of the Manila clam, thereby affecting its future survival. Therefore, when temperatures are high for long periods in summer, it is necessary to take timely action to prevent and guard against harm caused by DO and H2S to aquaculture organisms.
Characterisation of the Introgression of Brassica villosa Genome Into Broccoli to Enhance Methionine-Derived Glucosinolates and Associated Health Benefits

Broccoli cultivars that have enhanced accumulation of methionine-derived glucosinolates have been developed through the introgression of a novel allele of the MYB28 transcription factor from the wild species Brassica villosa. Through a novel k-mer approach, we characterised the extent of the introgression of unique B. villosa genome sequences into high glucosinolate broccoli genotypes. RNAseq analyses indicated that the introgression of the B. villosa MYB28 C2 allele resulted in the enhanced expression of the MYB28 transcription factor, and modified expression of genes associated with sulphate absorption and reduction, and methionine and glucosinolate biosynthesis when compared to standard broccoli. A adenine-thymine (AT) short tandem repeat (STR) was identified within the 5′ untranslated region (UTR) B. villosa MYB28 allele that was absent from two divergent cultivated forms of Brassica oleracea, which may underpin the enhanced expression of B. villosa MYB28.
Novel Advances in the Evaluation and Treatment of Children With Symptoms of Gastroesophageal Reflux Disease

Gastroesophageal reflux disease has long been implicated as a cause for multiple pediatric symptoms ranging from abdominal pain and regurgitation to cough and dental erosions. Diagnostic testing has evolved greatly over the last 20 years; initial testing with pH-metry to measure esophageal acid reflux burden has evolved into measurement of both acid and non-acid reflux and liquid and gas reflux. However, measuring reflux burden alone only tells a small part of the GERD story and many symptoms originally thought to be reflux related are, in fact, related to other disorder which mimic reflux. The current paradigm which involves empiric treatment of symptoms with acid suppression has been replaced with early testing for not only gastroesophageal reflux but also for other diagnostic masqueraders. The focus for interventions has shifted away from acid suppression toward motility interventions and includes a greater recognition of both functional and motility disorders which present with reflux symptoms.
Big Data in Cardiology: State-of-Art and Future Prospects

Cardiological disorders contribute to a significant portion of the global burden of disease. Cardiology can benefit from Big Data, which are generated and released by different sources and channels, like epidemiological surveys, national registries, electronic clinical records, claims-based databases (epidemiological Big Data), wet-lab, and next-generation sequencing (molecular Big Data), smartphones, smartwatches, and other mobile devices, sensors and wearable technologies, imaging techniques (computational Big Data), non-conventional data streams such as social networks, and web queries (digital Big Data), among others. Big Data is increasingly having a more and more relevant role, being highly ubiquitous and pervasive in contemporary society and paving the way for new, unprecedented perspectives in biomedicine, including cardiology. Big Data can be a real paradigm shift that revolutionizes cardiological practice and clinical research. However, some methodological issues should be properly addressed (like recording and association biases) and some ethical issues should be considered (such as privacy). Therefore, further research in the field is warranted.
Development and Validation of a Nomogram for Predicting the Unresolved Risk of Parents of Adolescents With Psychiatric Diagnoses

Evaluating the resolution of parents of ill children can help in taking measures to alleviate their distress in a timely manner and promote children's rehabilitation. This study aims to develop and validate a nomogram for predicting the unresolved risk of parents of adolescents with psychiatric diagnoses. The data for 130 parents (modeling dataset = 90; validation dataset = 40) were collected. A nomogram was first developed to predict the unresolved risk for parents based on the logistic regression analysis in the modeling dataset. The internal and external validation then were conducted through quantifying the performance of the nomogram with respect to discrimination and calibration, respectively, in the modeling and validation datasets. Finally, the clinical use was evaluated through decision curve analyses (DCA) in the overall dataset. In the results, the nomogram consisted of six risk factors and provided a good discrimination with areas under the curve of 0.920 (95% CI, 0.862–0.978) in internal validation and 0.886 (95% CI, 0.786–0.986) in external validation. The calibration with good consistency between the observed probability and predicted probability was also found in both internal and external validation. DCA showed that the nomogram had a good clinical utility. In conclusion, the proposed nomogram exhibited a favorable performance with regard to its predictive accuracy, discrimination capability, and clinical utility, and, thus, can be used as a convenient and reliable tool for predicting the unresolved risk of parents of children with psychiatric diagnoses.
AI-2 Induces Urease Expression Through Downregulation of Orphan Response Regulator HP1021 in Helicobacter pylori

Helicobacter pylori causes gastric infections in more than half of the world's population. The bacterium's survival in the stomach is mediated by the abundant production of urease to enable acid acclimation. In this study, our transcriptomic analysis demonstrated that the expression of urease structural proteins, UreA and UreB, is induced by the autoinducer AI-2 in H. pylori. We also found that the orphan response regulator HP1021 is downregulated by AI-2, resulting in the induction of urease expression. HP1021 represses the expression of urease by directly binding to the promoter region of ureAB, ranging from −47 to +3 with respect to the transcriptional start site. The study findings suggest that quorum sensing via AI-2 enhances acid acclimation when bacterial density increases, and might enable bacterial dispersal to other sites when entering gastric acid.
Effective social planning for mine closure

Most Australian resource companies recognise that effective community engagement enhances their corporate reputation and underpins their social licence to operate. Industry-leading companies also understand that the socio-economic impacts of their operations need to be assessed and managed with the same rigour as environmental, health and safety impacts. Some companies, however, fail to see the value of robust community engagement or socio-economic impact assessment during mine closure planning. A robust approach to mine closure planning considers community impacts and relevant mitigation strategies in both the lead-up to mine closure and during mine closure – in fact, some would advocate that consideration of the social aspects of closure should be undertaken from the inception of a project or operation. This paper will demonstrate a best-practice approach to assessing the socio-economic impacts of mine closure, and will outline how to engage with communities during this time of uncertainty. Through discussion of a range of practical case studies, a suite of tools will be highlighted that can be used at an operational level to assess the status of key community assets and capitals and in determining a community’s sustainability when facing closure of a nearby mine. Such tools include: Community Sensitivity Analysis (Coakes and Sadler, 2011), Town Resource Cluster Analysis (Fenton et al., 2003) Stakeholder Mapping and Community Needs Assessment. In addition, effective management strategies to prepare communities for mine closure will be explored and recommended approaches to community engagement during each phase of mine closure discussed. Mine closures can afford genuine opportunities for communities when companies are proactive, diligent, and comprehensive in their planning approach. This paper will demonstrate how companies can work with communities to leave a positive legacy and genuinely support a community’s sustainability long after a mining operation is gone.
SATE V Ockham Sound Analysis Criteria

Static analyzers examine the source or executable code of programs to ﬁnd problems. Many static analyzers use heuristics or approximations to handle programs up to millions of lines of code. We established the Ockham Sound Analysis Criteria to recognize static analyzers whose ﬁndings are always correct. In brief the criteria are (1) the analyzer’s ﬁndings are claimed to always be correct, (2) it produces ﬁndings for most of a program, and (3) even one incorrect ﬁnding disqualiﬁes an analyzer. This document begins by explaining the background and requirements of the Ockham Criteria. In Static Analysis Tool Exposition (SATE) V, only one tool was submitted to be reviewed. Pascal Cuoq and Florent Kirchner ran the August 2013 development version of Frama-C on pertinent parts of the Juliet 1.2 test suite. We divided the warnings into eight classes, including improper buffer access, NULL pointer dereference, integer overﬂow, and use of uninitialized variable. This document details the many technical and theoretical challenges we addressed to classify and review the warnings against the Criteria. It also describes anomalies, our observations, and interpretations. Frama-C reports led us to discover three unintentional, systematic ﬂaws in the Juliet test suite involving 416 test cases. Our conclusion is that Frama-C satisﬁed the SATE V Ockham Sound Analysis Criteria.
Children With a Soft Scalp Hematoma Presenting to the Emergency Department More Than 24 Hours After a Head Injury

Objectives The soft scalp hematoma is one of the clinical markers used as a predictor for the presence of intracranial injury in children with a head trauma. We evaluated the significance of time presentation in the management of these patients. Methods We conducted a retrospective study of children and adolescents aged 0 to <18 years by comparing the clinical, radiological, and epidemiological features in those presenting within 24 hours with those presenting greater than 24 hours after a head injury. Results We identified 188 and 98 patients with early presentation and late presentation, respectively. The percentage of children aged 0 to <6 months was lower in those with late presentation (6.12%) than those with early presentation (20.21%) with a significant difference (P < .001). Likewise, the percentage of children aged ≥24 months was lower in children with late presentation (7.14%) than those with early presentation (34.04%) with a significant difference (P < .001). The severe mechanism rate was more elevated in early presentation (38.83%) with a significant difference (−14.34%; 95% confidence interval [CI], −25.34% to −3.34%; P = .015). The symptom rate resulted higher in early presentation (14.36%) with a significant difference (−11.30%; 95% CI, −17.36% to 5.22%; P = .003). The parietal scalp hematoma occurred mostly in children with late presentation (85.71%) with a significant difference (19.76%; 95% CI, 10.07% to 29.45%; P < .001). The occipital scalp hematoma rate was higher in early presentation with a significant difference (−17.50%; 95% CI, −22.99% to −12.12%; P < .001). There was no significant difference in the prevalence of different types of intracranial injury, and the only 5 patients needing a neurosurgical intervention were exclusively children with an early presentation. Conclusion Although children with soft scalp hematoma presenting to the emergency department greater than 24 hours after a head injury may have pathological findings on computed tomography, all of them had a good short- and long-term outcomes, and no neurological deterioration aroused the medical attention on follow-up. For this subset of patients that does not experience red flags (neurological symptoms, focal signs on examination, or severe injury mechanism), a wait-and-see approach might be more appropriate rather than neuroimaging.
Parameters to develop a knowledge management computerized tool

Para que la informacion en accion genere productividad en las empresas debe ser un elemento diferenciador. Para lograrlo requiere de una aplicacion sistematica y organizada que facilite un ambiente colaborativo en el que varios participantes conduzcan deliberaciones encaminadas hacia las decisiones del conocimiento en su contexto dentro del ambiente de trabajo, al relacionar los artefactos con los procesos de conocimiento que lo generan y modifican, por medio de la aplicacion de parametros que influyen en las herramientas TIC que ayudan en la toma de decisiones de la Gestion del Conocimiento.
Diseño, desarrollo y test de un prototipo de pulsera para adquirir el electrocardiograma y la onda de pulso

The project is focused on the design of a wristband and the associated signal conditioning circuitry that enables to measure simultaneously the pulse arrival and the QRS complexes of the user. The prototype consists of a wristband that let to acquire this two signals in the same wrist. In this project, electrodes and photoplethysmographic techniques are proposed to measure this signals overcoming the disadvantages of using dry electrodes. The project is part of a larger project that aims to develop a wristband to record daily activity, heart rate, pulse transit time, heart rate variability and other physiological variables in order to track how healthy is the lifestyle of the user. Heart rate variability (HRV) and pulse transit time variability (PTT) are key physiological signals that can stratify the level of psychological and physiological stress as well as the fitness, attention and wellness of the subject under measurement. So these indicators are ideal candidates to be incorporated in any system for tracking changes in lifestyle.
Unsupervised Graph-based Entity Resolution for Accurate and Efficient Family Pedigree Search

Tremendous progress has been made in medical research in recent years to detect, treat, and prevent a variety of commonly occurring cancers. There is now a shift towards better identifying and understanding cancers and other diseases that occur very rarely in a population. One approach to investigate such rare diseases is to look at a patient’s family history through genealogical as well as genetic research. The Genetics Genealogy Team, part of Public Health Scotland, has been providing a unique service exploring family pedigrees (family trees) using birth, death, and marriage certificates going back to 1855. Thus far searches have been manually exploring each digitised record individually which can be time consuming and labour intensive. Here we present a prototype application for automated family pedigree search that is based on unsupervised graph-based entity resolution techniques combined with approximate query matching and ranking methods to efficiently and accurately extract and visualise family pedigrees from searched birth or death certificates. We describe the steps of our application, and how we anonymise sensitive personal data to allow it being used for training and educational purposes. Our prototype application and an anonymised data set are available at: https://dmm.anu. edu.au/SNAPS/
Validation of lameness nociception tools Evaluation of mechanical and thermal nociception as objective tools to measure painful and non-painful lameness phases in multiparous sows

The objective of this study was to quantify pain sensitivity differences using mechanical nociception threshold (MNT) and thermal (TNT) tests when sows were in painful and non-painful transient lameness phases. A total of 24 mixed parity crossbred sows (220.15 ± 21.23 kg) were utilized for the mechanical nociception threshold test and a total of 12 sows (211.41 ± 20.21 kg) were utilized for the thermal nociception threshold test. On induction day (D0), all sows were anesthetized and injected with Amphotericin B (10mg/mL) in the distal interphalangeal joint space in both claws of one randomly selected hind limb to induce transient lameness. Three days were compared (1) D-1 (Sound phase, defined as 1 d before induction), (2) D+1 (Most lame phase, defined as 1 d after induction) and (3) D+6 (Resolution phase, defined as 6 d after induction). After completion of the first round, sows were given a 7-d rest period and then the procedures were repeated with lameness induced in the contralateral hind limb. During the MNT test, pressure was applied perpendicularly to three landmarks in a randomized sequence for each sow: 1) middle of cannon on the hind limb (Cannon), 2) 1 cm above the coronary band on the medial hind claw (Medial claw), and 3) 1 cm above the coronary band on the lateral hind claw (Lateral claw). During the TNT test, a radiant heat stimulus was directed 1 cm above the coronary band. The data were analyzed using the MIXED procedure in SAS with sow as the experimental unit. Differences were analyzed between sound and lame limbs on each day. For the MNT test, pressure tolerated by the lame limb decreased for every landmark (P < 0.05) when comparing D-1 and D+1. The sound limb tolerated more pressure on D+1 and D+6 than on baseline D-1 (P < 0.05). Thermal stimulation tolerated by the sound limb did not change over the compared to D-1 levels (P < 0.05). Both mechanical and thermal tests indicated greater pain sensitivity thresholds when sows were acutely lame.