Miracle-dz/UniFAR-FTUs huggingface dataset:
PE_PGRS3 ensures provision of the vital phospholipids cardiolipin and phosphatidylinositols by promoting the interaction between M. tuberculosis and host cells

ABSTRACT PE_PGRS proteins of Mycobacterium tuberculosis (Mtb) constitute a large family of complex modular proteins whose role is still unclear. Among those, we have previously shown, using the heterologous expression in Mycobacterium smegmatis, that PE_PGRS3 containing a unique arginine-rich C-terminal domain, promotes adhesion to host cells. In this study, we investigate the role of PE_PGRS3 and its C-terminal domain directly in Mtb using functional deletion mutants. The results obtained here show that PE_PGRS3 is localized on the mycobacterial cell wall and its arginine-rich C-terminal region protrudes from the mycobacterial membrane and mediates Mtb entry into epithelial cells. Most importantly, this positively charged helical domain specifically binds phosphorylated phosphatidylinositols and cardiolipin, whereas it is unable to bind other phospholipids. Interestingly, administration of cardiolipin and phosphatidylinositol but no other phospholipids was able to turn-off expression of pe_pgrs3 activated by phosphate starvation conditions. These findings suggest that PE_PGRS3 has the key role to serve as a bridge between mycobacteria and host cells by interacting with specific host phospholipids and extracting them from host cells, for their direct integration or as a source of phosphate, during phases of TB pathogenesis when Mtb is short of phosphate supply.
A multi‐parameter artificial neural network model to estimate macrobenthic invertebrate productivity and production

I developed a new model for estimating annual production‐to‐biomass ratio P/B and production P of macrobenthic populations in marine and freshwater habitats. Self‐learning artificial neural networks (ANN) were used to model the relationships between P/B and twenty easy‐to‐measure abiotic and biotic parameters in 1252 data sets of population production. Based on log‐transformed data, the final predictive model estimates log(P/B) with reasonable accuracy and precision (r2 = 0.801; residual mean square RMS = 0.083). Body mass and water temperature contributed most to the explanatory power of the model. However, as with all least squares models using nonlinearly transformed data, back‐transformation to natural scale introduces a bias in the model predictions, i.e., an underestimation of P/B (and P). When estimating production of assemblages of populations by adding up population estimates, accuracy decreases but precision increases with the number of populations in the assemblage.
Development and Evaluation of a Mobile App Designed to Increase HIV Testing and Pre-exposure Prophylaxis Use Among Young Men Who Have Sex With Men in the United States: Open Pilot Trial

Background HIV disproportionately affects young men who have sex with men (YMSM) in the United States. Uptake of evidence-based prevention strategies, including routine HIV testing and use of pre-exposure prophylaxis (PrEP), is suboptimal in this population. Novel methods for reaching YMSM are required. Objective The aim of this study is to describe the development and evaluate the feasibility and acceptability of the MyChoices app, a mobile app designed to increase HIV testing and PrEP use among YMSM in the United States. Methods Informed by the social cognitive theory, the MyChoices app was developed using an iterative process to increase HIV testing and PrEP uptake among YMSM. In 2017, beta theater testing was conducted in two US cities to garner feedback (n=4 groups; n=28 YMSM). These findings were used to refine MyChoices, which was then tested for initial acceptability and usability in a technical pilot (N=11 YMSM). Baseline and 2-month postbaseline assessments and exit interviews were completed. Transcripts were coded using a deductive approach, and thematic analysis was used to synthesize data; app acceptability and use data were also reported. Results The MyChoices app includes personalized recommendations for HIV testing frequency and PrEP use; information on types of HIV tests and PrEP; ability to search for nearby HIV testing and PrEP care sites; and ability to order free home HIV and sexually transmitted infection test kits, condoms, and lube. In theater testing, YMSM described that MyChoices appears useful and that they would recommend it to peers. Participants liked the look and feel of the app and believed that the ability to search for and be pinged when near an HIV testing site would be beneficial. Some suggested that portions of the app felt repetitive and preferred using casual language rather than formal or medicalized terms. Following theater testing, the MyChoices app was refined, and participants in the technical pilot used the app, on average, 8 (SD 5.0; range 2-18) times over 2 months, with an average duration of 28 (SD 38.9) minutes per session. At the 2-month follow-up, the mean System Usability Scale (0-100) score was 71 (ie, above average; SD 11.8). Over 80% (9/11) of the participants reported that MyChoices was useful and 91% (10/11) said that they would recommend it to a friend. In exit interviews, there was a high level of acceptability for the content, interface, and features. Conclusions These data show the initial acceptability and user engagement of the MyChoices app. If future studies demonstrate efficacy in increasing HIV testing and PrEP uptake, the app is scalable to reach YMSM across the United States. Trial Registration Clinicaltrials.gov NCT03179319; https://clinicaltrials.gov/ct2/show/NCT03179319 International Registered Report Identifier (IRRID) RR2-10.2196/10694
Side-effects of COVID-19 on patient care: An INR story

Abstract Background Numerous studies have documented reduced access to patient care due to the COVID-19 pandemic including access to a diagnostic or screening tests, prescription medications, and treatment for an ongoing condition. In the context of clinical management for venous thromboembolism, this could result in suboptimal therapy with warfarin. We aimed to determine the impact of the pandemic on utilization of International normalized ratio (INR) testing and the percentage of high and low results. Methods INR data from 11 institutions were extracted to compare testing volume and the percentage of INR results ≥3.5 and ≤1.5 between a pre-pandemic period (January-June 2019, period 1) and a portion of the COVID-19 pandemic period (January-June 2020, period 2). The analysis was performed for inpatient and outpatient cohorts. Results Testing volumes showed relatively little change in January and February, followed by a significant decrease in March, April and May, and then returned to baseline in June. Outpatient testing showed a larger percentage decrease in testing volume compared to inpatient testing. At 10 of the 11 study sites we observed an increase in the percentage of abnormal high INR results as test volumes decreased, primarily among outpatients. Conclusion The COVID-19 pandemic impacted INR testing among outpatients which may be attributable to several factors. Increased supratherapeutic INR results during the pandemic period when there was reduced laboratory utilization and access to care is concerning because of the risk of adverse bleeding events in this group of patients. This could be mitigated in the future by offering drive through testing and/or widespread implementation of home INR monitoring.
Agricultural intensification and climate change have increased the threat from weeds

Weeds represent a significant threat to crop yields and global food security. We analysed data on weed competition from the world's longest running agricultural experiment to ask whether potential yield losses from weeds have increased in response to management and environmental change since the advent of the Green Revolution in the 1960s. On plots where inorganic nitrogen fertiliser has been applied, potential yield losses from weeds have consistently increased since 1969. This was explained by a warming climate, measured as air temperature averaged over the growing season for the weeds, and a shift towards shorter crop cultivars. Weeds also reduced yield proportionally more on plots with higher rates of nitrogen which had higher yields when weeds were controlled; the relative benefit of herbicides was, therefore, proportional to potential crop yield. Reducing yield losses from weed competition is increasingly challenging because of the evolution of herbicide resistance. Our results demonstrate that weeds now represent a greater inherent threat to crop production than before the advent of herbicides and integrated, sustainable solutions to weed management are urgently needed to protect the high yield potential of modern crop genotypes.
Fire regimes, fire experiments and alternative stable states in mesic savannas

In their comment on Veenendaal et al, (2018) Laris and Jacobs question the appropriateness of fire experiments to simulate effects of fire on tropical vegetation cover as well as objecting to our use of the word "natural" to describe non-anthropogenic fire regimes. They also challenge some of the conclusions we drew as regards the likelihood of fire-mediated feedbacks causing alternate stable states (ASS) in forest-savanna transitions.
COVID-19 in children in the state of Pernambuco: Spatial analysis of confirmed severe cases and the Human Development Index

Abstract INTRODUCTION: Health planning is required for the control and prevention of severe cases of COVID-19 in children. METHODS: Spatial analysis of severe COVID-19 cases in children of Pernambuco in the first six months of the pandemic and its autocorrelation with the Human Development Index was conducted. RESULTS: A total of 551 severe cases (39.4 cases/100,000 inhabitants) was initially concentrated in the metropolitan area, with later interiorization. The spatial autocorrelation of cases was identified. The bivariate analysis revealed alert regions in less developed municipalities (I=0.341; p=0.001). CONCLUSIONS: Considering the local particularities can assist in directing the priorities for decision making.
Discharge pumped non-chain repetitively pulsed HF laser

The design and performance of a closed cycle, repetitively pulsed HF laser is described. The homogeneous glow discharge is formed with UV pre-ionization and transverse discharge structure. The optimal output parameters of single pulse operation are given by the investigation of discharge characteristics in SF6 /C2H6 gas mixture and output characteristics of laser pulse. The repetitively pulse energy stability of laser device are checked with different conditions of gas flowing velocity, charging voltage and total pressure of gas mixture. It is shown that the maximal output energy of laser pulse of 0.6J, peak power 3MW are obtained. Total efficiency of laser device is about 2.4%. When the gas mixture circulating with 4m/s flowing velocity, the maximal running frequency of 50Hz are obtained and operating stability keep well. Under these conditions, the laser pulse energy keeps stable and the average output power is 18W.
Altered distributions in circulating follicular helper and follicular regulatory T cells accountable for imbalanced cytokine production in multiple sclerosis

Follicular T helper (Tfh) and regulatory (Tfr) cells are distinct subsets of CD4+ T lymphocytes, regulating humoral immune responses in the germinal center. It is widely accepted that dysregulated Tfh and Tfr cells are associated with autoimmunity. In this study, we evaluated the frequencies of circulating chemokine receptor (CXCR)5+ programmed cell death 1 (PD‐1+) Tfh (cTfh) and CXCR5+PD‐1+forkhead box protein 3 (FoxP3+) CD25+ Tfr (cTfr) cells, and their corresponding cytokines from the peripheral blood mononuclear cells of 28 patients with relapsing–remitting multiple sclerosis (MS) and 16 age‐ and sex‐matched healthy controls (HC). Subsets of cTfh cells by Th1‐ and Th17‐related surface markers (CXCR3 and CCR6) were also evaluated. We found that the frequency of cTfh cells was significantly higher in MS patients compared to that of HC. Conversely, the frequency of cTfr cells was lower in MS patients than that of HC. Interleukin (IL)‐21‐producing cTfh cells were significantly increased in MS patients, while IL‐10‐secreting cTfr cells were lower in MS patients compared to levels in HC. Among cTfh cells, cTfh17.1 cells were the major subtypes that were significantly increased in MS patients compared to HC, with the frequency of IL‐21‐secreting cells being the highest. These results suggest that an imbalanced distribution of cTfh and cTfr exist in MS patients, which contributes to the reciprocally altered IL‐21 and IL‐10 production.
Neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios in dogs and cats with acute pancreatitis.

BACKGROUND Neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) have been described as prognostic markers in cancer and inflammatory diseases. The use of these measurements in dogs and cats with acute pancreatitis has not yet been investigated. OBJECTIVE The objective was to evaluate NLR and PLR for usefulness as biomarkers for severity and clinical course of acute pancreatitis in dogs and cats. METHODS In this prospective study, we investigated 67 dogs and 41 cats with acute pancreatitis and 17 healthy dogs and cats as controls. We compared the NLR and PLR of dogs and cats with acute pancreatitis with control animals. The severity of disease was measured using a modified "bedside index of severity in acute pancreatitis" (BISAP) score in humans, and the course of the disease was measured with the time to clinical recovery. RESULTS NLR and PLR were significantly higher in dogs and cats with pancreatitis than in healthy controls. However, no significant relationship between NLR or PLR and disease severity was found, as assessed with the modified BISAP score. Dogs and cats with pancreatitis and prolonged recovery displayed a significantly increased PLR, and those same cats also displayed a significantly increased NLR. CONCLUSIONS We conclude that increased NLR and PLR provide information regarding the course of pancreatitis in dogs and cats.
Neural Responses to Heartbeats Detect Residual Signs of Consciousness during Resting State in Postcomatose Patients

The neural monitoring of visceral inputs might play a role in first-person perspective (i.e., the unified viewpoint of subjective experience). In healthy participants, how the brain responds to heartbeats, measured as the heartbeat-evoked response (HER), correlates with perceptual, bodily, and self-consciousness. Here we show that HERs in resting-state EEG data distinguishes between postcomatose male and female human patients (n = 68, split into training and validation samples) with the unresponsive wakefulness syndrome and in patients in a minimally conscious state with high accuracy (random forest classifier, 87% accuracy, 96% sensitivity, and 50% specificity in the validation sample). Random EEG segments not locked to heartbeats were useful to predict unconsciousness/consciousness, but HERs were more accurate, indicating that HERs provide specific information on consciousness. HERs also led to more accurate classification than heart rate variability. HER-based consciousness scores correlate with glucose metabolism in the default-mode network node located in the right superior temporal sulcus, as well as with the right ventral occipitotemporal cortex. These results were obtained when consciousness was inferred from brain glucose met`abolism measured with positron emission topography. HERs reflected the consciousness diagnosis based on brain metabolism better than the consciousness diagnosis based on behavior (Coma Recovery Scale-Revised, 77% validation accuracy). HERs thus seem to capture a capacity for consciousness that does not necessarily translate into intentional overt behavior. These results confirm the role of HERs in consciousness, offer new leads for future bedside testing, and highlight the importance of defining consciousness and its neural mechanisms independently from behavior.
Particle-free inkjet printing of nanostructured porous indium tin oxide thin films

We report a simple, low-cost, single-step inkjet printing method for the fabrication of nanostructured, highly transparent and conductive ITO films, which completely avoids the use of ITO particles in the fabrication process. In our method, the inks are formed from a liquid solution presenting a properly selected mixture of indium and tin acetates. After jet printing, the ink is decomposed during a subsequent annealing step, in which the released CO2 gas bubbles control the ITO nucleation process to provide a porous film texture. We show that the fabricated ITO films are highly crystalline, stoichiometric, and nanoporous with controlled porosity. Electrical measurements show relatively low resistivity values for the films (down to 0.029 Ω cm) comparable to those of the best ITO thin films fabricated by other methods. Optical ellipsometry tests demonstrate a relatively high refractive index (1.5–1.7) and high transparency of the films over a wide region of the spectrum ranging from 500 to 1700 nm. Since the method does not require any pre-fabricated ITO particles, masks or templates, and enables the deposition of films on substrates of various materials and shapes, it can be employed for fabrication of nanoporous ITO films for a diversity of applications, including solar cell, bio- and chemical sensing, etc.
Efficacy of Versajet hydrosurgery system in chronic wounds: A systematic review

Studies demonstrating the effectiveness of hydrosurgery for chronic wounds are extremely limited. This systematic review aimed to evaluate the efficacy of hydrosurgery compared with conventional debridement in chronic wounds, skin ulcers, and non‐acute wounds. This PROSPERO‐registered review was performed following the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses statement. A systematic search was performed in PubMed, Scopus, and Cochrane Library databases. Abstracts of all studies were screened independently by two reviewers. The bias of prospective randomised controlled studies was assessed using the Cochrane Collaboration's tool for assessing the risk of bias and RevMan 5.4 software, whereas the bias of retrospective comparative studies was evaluated using the Risk of Bias Assessment Tool for Non‐randomised Studies. Two prospective randomised controlled trials, two retrospective comparative studies, and three prospective non‐comparative studies were included. Hydrosurgery enabled rapid debridement. The Versajet Hydrosurgery System saved 8.87 minutes compared with the conventional methods. Similarly, the debridement quality was high with this system. The debridement number needed to achieve adequate wound beds was fewer in the hydrosurgery group than in the conventional group. These superiorities lead to subsequent success and cost‐effectiveness. As there were only two prospective randomised controlled studies, and much information was missing, the risk of bias was unclear. This review confirmed that hydrosurgery is useful for the debridement of chronic wounds, considering the procedural speed and quality.
Geostandards and Geoanalytical Research Bibliographic Review 2007

The bibliographic review has a long tradition in“Geostandards Newsletter” and Geostandards andGeoanalytical Research(GGR). Successive reviewshave complied and classified articles from geochemi-cal, cosmochemical, environmental, analytical andgeological journals in which data for reference mate-rials (RMs) of geological and environmental interestwere published. As discussed in the bibliographicreview for 2006 (Jochum 2007) and in Jochum andNohl (2008), the number of geochemical publicationshas increased significantly during recent years. Thistrend continued in 2007. Figure 1 shows the numberof publications containing data for RMs, which havebeen published in the bibliographic reviews for theyears 2001-2007. The number increased slowly from220 to 340 in the five year period from 2001 to2005, then steeply to 540 in 2006 and 710 in 2007(data for 2006 in this figure were corrected becauseeighty-four papers were not considered in Jochum(2007)). The same trend can be observed for someselected RMs (Figure 1), such as the three well-knownUSGS RMs BCR-1, BCR-2 (the replacement for BCR-1)and BCR-2G (a glass made from BCR-2 and mainlyused for microanalytical purposes). Reasons for thisincrease are that the importance of RMs in analyticalwork has been recognised by geochemists (Goldsteinet al.2003, Jochum and Nohl 2008) and that geoa-nalytical laboratories are being confronted with newfields and applications, such as environmental andbiogeochemical research, “non-traditional stable iso-tope” systems and microanalysis.This review contains 710 papers from the publica-tion year 2007. Literature research was performed on
CNNATT: Deep EEG & fNIRS Real-Time Decoding of bimanual forces

Non-invasive cortical neural interfaces have only achieved modest performance in cortical decoding of limb movements and their forces, compared to invasive brain-computer interfaces (BCIs). While non-invasive methodologies are safer, cheaper and vastly more accessible technologies, signals suffer from either poor resolution in the space domain (EEG) or the temporal domain (BOLD signal of functional Near Infrared Spectroscopy, fNIRS). The non-invasive BCI decoding of bimanual force generation and the continuous force signal has not been realised before and so we introduce an isometric grip force tracking task to evaluate the decoding. We find that combining EEG and fNIRS using deep neural networks works better than linear models to decode continuous grip force modulations produced by the left and the right hand. Our multi-modal deep learning decoder achieves 55.2 FVAF[%] in force reconstruction and improves the decoding performance by at least 15% over each individual modality. Our results show a way to achieve continuous hand force decoding using cortical signals obtained with non-invasive mobile brain imaging has immediate impact for rehabilitation, restoration and consumer applications.
Evidences for Adult Hippocampal Neurogenesis in Humans

The rodent hippocampus generates new neurons throughout life. This process, named adult hippocampal neurogenesis (AHN), is a striking form of neural plasticity that occurs in the brains of numerous mammalian species. Direct evidence of adult neurogenesis in humans has remained elusive, although the occurrence of this phenomenon in the human dentate gyrus has been demonstrated in seminal studies and recent research that have applied distinct approaches to birthdate newly generated neurons and to validate markers of adult-born neurons. Our data point to the persistence of AHN until the 10th decade of human life, as well as to marked impairments in this process in patients with Alzheimer's disease. Moreover, our work demonstrates that the methods used to process and analyze postmortem human brain samples can limit the detection of various markers of AHN to the point of making them undetectable. In this Dual Perspectives article, we highlight the critical methodological aspects that should be strictly controlled in human studies and the robust evidence that supports the occurrence of AHN in humans. We also put forward reasons that may account for current discrepancies on this topic. Finally, the unresolved questions and future challenges awaiting the field are highlighted.