Miracle-dz/UniFAR-FTUs huggingface dataset:
IL-17C contributes to NTHi-induced inflammation and lung damage in experimental COPD and is present in sputum during acute exacerbations

Neutrophilic inflammation results in loss of lung function in chronic obstructive pulmonary disease (COPD). Gram-negative bacteria, such as nontypeable Haemophilus influenzae (NTHi), trigger acute exacerbations of COPD (AECOPD) and contribute to chronic lung inflammation. The pro-inflammatory cytokine interleukin-17C (IL-17C) is expressed by airway epithelial cells and regulates neutrophilic chemotaxis. Here, we explored the function of IL-17C in NTHi- and cigarette smoke (CS)-induced models of COPD. Neutrophilic inflammation and tissue destruction were decreased in lungs of IL-17C-deficient mice (Il-17c-/-) chronically exposed to NTHi. Numbers of pulmonary neutrophils were decreased in Il-17c-/- mice after acute exposure to the combination of NTHi and CS. However, Il-17c-/- mice were not protected from CS-induced lung inflammation. In a preliminary patient study, we show that IL-17C is present in sputum samples obtained during AECOPD and associates with disease severity. Concentrations of IL-17C were significantly increased during advanced COPD (GOLD III/IV) compared to moderate COPD (GOLD I/II). Concentrations of IL-17A and IL-17E did not associate with disease severity. Our data suggest that IL-17C promotes harmful pulmonary inflammation triggered by bacteria in COPD.
Maximum power of an endoreversible intercooled Brayton cycle

This paper describes an application of finite-time thermodynamics to optimize the power output of endoreversible intercooled Brayton cycles coupled to two heat reservoirs with infinite thermal capacitance rates. The effects of intercooling on the maximum power and maximum-power efficiency of an endoreversible Brayton cycle are examined. With appropriate temperature ratios of turbines and compressors being used, the maximum power output of an endoreversible intercooled Brayton cycle can be higher than that of an endoreversible simple Brayton cycle without lowering the thermal efficiency. New diagrams for maximum power, maximum-power thermal efficiency, and optimum temperature ratios of turbines and compressors are reported. Copyright © 2000 John Wiley & Sons, Ltd.
Very low prevalence of Opisthorchis viverrini s.l. cercariae in Bithynia siamensis siamensis snails from the canal network system in the Bangkok Metropolitan Region, Thailand

The liver fluke Opisthorchis viverrini s.l. is associated with a long-term public health problem in Thailand. However, O. viverrini s.l. infection in Bithynia snails in the canal network system (CNS) in the Bangkok Metropolitan Region (BMR) has never been assessed. This study aimed to investigate the occurrence of B. siamensis siamensis and the prevalence of O. viverrini s.l. infection in this snail in the CNS in BMR along with morphological examination and molecular analyses on O. viverrini s.l. cercariae. The snails were randomly sampled from the CNS in all BMR areas from January 2018 to July 2019. Snail specimens were identified and examined for digenean infection by shedding and dissection. The cercariae were identified using morphology and molecular methods, including PCR with a species-specific primer and a Bayesian phylogenetic analysis of ITS2 sequences. Bithynia siamensis siamensis was found in almost all sampling localities, with different quantities and detected frequencies. From a total of 7473 B. s. siamensis specimens, O. viverrini s.l. infections were detected in the Northern Bangkok, Muang Nakhon Pathom, Krathum Baen, and Lam Luk Ka areas with an overall prevalence of 0.05% (4/7473) and prevalence of 0.22% (1/455), 0.21% (1/469), 0.40% (1/253), and 0.16% (1/614) in individual localities with positive snails, respectively. This study is the first investigation of digenean infection in the canal network system-type habitat in Thailand and revealed extremely low O. viverrini s.l. prevalence.
Asia and Europe: So Distant So Close? The Case of Lipoptena fortisetosa in Italy

In Europe, 5 Lipoptena species have been recorded, including Lipoptena fortisetosa. This species, native to Asian countries, was described as a parasite of sika deer and its appearance in Europe dates back to more than 50 years ago. Lipoptena fortisetosa has been recently reported in Italy, sharing its hosts with Lipoptena cervi. A morpho-molecular approach was developed to determine the phylogenetic interrelationship of Italian and Asian CO1 haplotypes sequenced from Lipoptena fly individuals collected in Italy, and their DNA sequences were compared with conspecifics available in GenBank; morphological key-characters (terminalia) of L. fortisetosa were compared with the original description. Two haplotypes were recorded from Italy and assigned to L. cervi and L. fortisetosa, respectively. The latter was part of the monophyletic clade L. fortisetosa, along with 2 Central European and 2 Korean haplotypes (100% identical to one of the Korean haplotypes); moreover, Italian L. fortisetosa female terminalia were consistent with the original description of Asian individuals. Pending more in-depth investigations, this study provides a first answer to the hypothesis of the recent colonization of Italy by L. fortisetosa from Asia as we did not detect any obvious and stable morphological and molecular differences in specimens from the 2 geographical areas. The presence of the sika deer in Europe was retraced and the possible route traveled by the parasite from Asia and the eco-biological factors that may have enhanced its settlement are discussed.
BERT-GT: Cross-sentence n-ary relation extraction with BERT and Graph Transformer

MOTIVATION A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical text-mining approaches typically formulate the problem as a cross-sentence n-ary relation-extraction task that detects relations among n entities across multiple sentences, and use either a graph neural network (GNN) with long short-term memory (LSTM) or an attention mechanism. Recently, Transformer has been shown to outperform LSTM on many natural language processing (NLP) tasks. RESULTS In this work, we propose a novel architecture that combines Bidirectional Encoder Representations from Transformers with Graph Transformer (BERT-GT), through integrating a neighbor-attention mechanism into the BERT architecture. Unlike the original Transformer architecture, which utilizes the whole sentence(s) to calculate the attention of the current token, the neighbor-attention mechanism in our method calculates its attention utilizing only its neighbor tokens. Thus, each token can pay attention to its neighbor information with little noise. We show that this is critically important when the text is very long, as in cross-sentence or abstract-level relation-extraction tasks. Our benchmarking results show improvements of 5.44% and 3.89% in accuracy and F1-measure over the state-of-the-art on n-ary and chemical-protein relation datasets, suggesting BERT-GT is a robust approach that is applicable to other biomedical relation extraction tasks or datasets. AVAILABILITY AND IMPLEMENTATION the source code of BERT-GT will be made freely available at https://github.com/ncbi-nlp/bert_gt upon publication.
Evaluation of a flow cytometric test for G6PD‐deficient erythrocytes

Glucose‐6‐phosphate dehydrogenase (G6PD) deficiency, an X‐linked recessive disorder, is the commonest erythrocytic enzymopathy worldwide. Reliable diagnosis and severity prediction in G6PD‐deficient/heterozygous females remain challenging. A recently developed flow cytometric test for G6PD deficiency has shown promise in precisely identifying deficient females. This paper presents our experiences with this test in a subtropical setting and presents a modification in flow cytometric data acquisition strategy.
Acute caffeine supplementation improves jumping, sprinting, and change-of-direction performance in basketball players when ingested in the morning but not evening

ABSTRACT This study compared the effects of acute caffeine supplementation (3 mg/kg) administered in the morning and evening on performance-related variables in basketball players. Eleven, national-level, adolescent male basketball players underwent field-based fitness testing on four occasions: morning (10:00) with caffeine ingestion (AMCAFF), morning (10:00) with placebo ingestion (AMPLAC), evening (21:00) with caffeine ingestion (PMCAFF), and evening (21:00) with placebo ingestion (PMPLAC). Fitness testing included of a countermovement jump without arm swing (CMJ), CMJ with arm swing (CMJAS), squat jump (SJ), Lane Agility Drill (LAD), 20-m linear sprint, and Suicide Run with (SRD) and without dribbling (SR). Data were analysed using two-way repeated measures analyses of variance and paired t-tests, with effect sizes (ES) also determined for all pairwise comparisons. Follow-up t-test comparisons revealed that AMCAFF produced small-moderate, significant (p<0.001), improvements in CMJ (ES = 0.51), CMJAS (ES = 0.40), SJ (ES = 0.51), and SR (ES = −0.45) compared to AMPLAC. AMCAFF also produced a moderate, significantly (p<0.001) faster LAD (ES = −0.61) compared to PMCAFF. PMPLAC demonstrated small-moderate, significant (p<0.05) improvements in CMJ (ES = 0.43), CMJAS (ES = 0.48), and 20-m sprint (ES = −0.63) compared to AMPLAC. In contrast, AMPLAC resulted in large, significantly (p<0.001), faster SRD (ES = −1.46) and SR (ES = −1.59) compared to PMPLAC. Given the ergogenic effects of caffeine during basketball-specific fitness tests appear to be influenced by time of ingestion, basketball practitioners should consider administering caffeine only to players in the morning to improve vertical jump, sprinting, and change-of-direction performance, with no beneficial effects observed with caffeine ingestion in the evening. Highlights The effect of caffeine supplementation on basketball-specific performance related variables were mediated by ingestion time in elite, adolescent basketball players. AMCAFF produced small-moderate improvements in vertical jump, change-of-direction, 20-m linear sprint, and repeated-sprint performance compared to AMPLAC while PMCAFF produced trivial differences in each performance-related variable compared to PMPLAC. Comparisons between ingestion times in the placebo condition revealed vertical jump height and 20-m sprint speed were impaired in the morning compared to the evening, but these time-dependent differences were eliminated when caffeine was consumed in the morning. Basketball practitioners should consider administering caffeine only to players in the morning to improve vertical jump, sprinting, and change-of-direction performance, with no beneficial effects observed with caffeine ingestion in the evening.
An integrative look at SARS-CoV-2 (Review)

SARS-CoV-2 is a newly discovered member of the betacoronaviruses and the etiological agent of the disease COVID-19. SARS-CoV-2 is responsible for the worldwide pandemic which has been taking place in 2020, and is causing a markedly higher number of infections and deaths compared to previous coronaviruses, such as SARS-CoV or MERS-CoV. Based on updated scientific literature, the present review compiles the most relevant knowledge of SARS-CoV-2, COVID-19 and the clinical and typical responses that patients have exhibited against this virus, discussing current and future therapies, and proposing strategies with which to combat the disease and prevent a further global threat. The aggressiveness of SARS-CoV-2 arises from its capacity to infect, and spread easily and rapidly through its tight interaction with the human angiotensin-converting enzyme 2 (ACE-2) receptor. While not all patients respond in a similar manner and may even be asymptomatic, a wide range of manifestations associated with COVID-19 have been described, particularly in vulnerable population groups, such as the elderly or individuals with other underlying conditions. The proper function of the immune system plays a key role in an individual's favorable response to SARS-CoV-2 infection. A hyperactivated response, on the contrary, could account for the more severe cases of COVID-19, and this may finally lead to respiratory insufficiency and other complications, such as thrombotic or thromboembolic events. The development of novel therapies and vaccines designed to control and regulate a proper immune system response will be key to clinical management, prevention measures and effective population screening to attenuate the transmission of this novel RNA virus.
Temporal patterns of hospitalizations for diabetic ketoacidosis in children and adolescents

Objectives To examine the temporal patterns of hospitalizations with diabetic ketoacidosis (DKA) in the pediatric population and their associated fiscal impact. Methods The Texas Inpatient Public Use Data File was used to identify hospitalizations of state residents aged 1month-19 years with a primary diagnosis of DKA during 2005–2014. Temporal changes of population-adjusted hospitalization rates and hospitalization volumes were examined for the whole cohort and on stratified analyses of sociodemographic attributes. Changes in the aggregate and per-hospitalization charges were assessed overall and on stratified analyses. Results There were 24,072 DKA hospitalizations during the study period. The population-adjusted hospitalization rate for the whole cohort increased from 31.3 to 35.9 per 100,000 between 2005–2006 and 2013–2014. Hospitalization volume increased by 30.2% over the same period, driven mainly by males, ethnic minorities, those with Medicaid insurance and uninsured patients. The aggregate hospital charges increased from approximately $69 million to $130 million between 2005–2006 and 2013–2014, with 66% of the rise being due to increased per-hospitalization charges. Conclusions There was progressive rise in pediatric DKA hospitalizations over the last decade, with concurrent near-doubling of the associated fiscal footprint. Marked disparities were noted in the increasing hospitalization burden of DKA, born predominantly by racial and ethnic minorities, as well as by the underinsured and the uninsured. Further studies are needed to identify scalable preventive measures to achieve an equitable reduction of pediatric DKA events.
Extracellular vesicles released from the filarial parasite Brugia malayi downregulate the host mTOR pathway

We have previously shown that the microfilarial (mf) stage of Brugia malayi can inhibit the mammalian target of rapamycin (mTOR; a conserved serine/threonine kinase critical for immune regulation and cellular growth) in human dendritic cells (DC) and we have proposed that this mTOR inhibition is associated with the DC dysfunction seen in filarial infections. Extracellular vesicles (EVs) contain many proteins and nucleic acids including microRNAs (miRNAs) that might affect a variety of intracellular pathways. Thus, EVs secreted from mf may elucidate the mechanism by which the parasite is able to modulate the host immune response during infection. EVs, purified from mf of Brugia malayi and confirmed by size through nanoparticle tracking analysis, were assessed by miRNA microarrays (accession number GSE157226) and shown to be enriched (>2-fold, p-value<0.05, FDR = 0.05) for miR100, miR71, miR34, and miR7. The microarray analysis compared mf-derived EVs and mf supernatant. After confirming their presence in EVs using qPCR for these miRNA targets, web-based target predictions (using MIRPathv3, TarBAse and MicroT-CD) predicted that miR100 targeted mTOR and its downstream regulatory protein 4E-BP1. Our previous data with live parasites demonstrated that mf downregulate the phosphorylation of mTOR and its downstream effectors. Additionally, our proteomic analysis of the mf-derived EVs revealed the presence of proteins commonly found in these vesicles (data are available via ProteomeXchange with identifier PXD021844). We confirmed internalization of mf-derived EVs by human DCs and monocytes using confocal microscopy and flow cytometry, and further demonstrated through flow cytometry, that mf-derived EVs downregulate the phosphorylation of mTOR in human monocytes (THP-1 cells) to the same degree that rapamycin (a known mTOR inhibitor) does. Our data collectively suggest that mf release EVs that interact with host cells, such as DC, to modulate host responses.
Residential Proximity to Greenness Mitigates the Hemodynamic Effects of Ambient Air Pollution.

BACKGROUND Residential proximity to greenness is associated with a lower risk of cardiovascular disease (CVD) and all-cause mortality. However, it is unclear whether the beneficial effects of greenness are linked to a reduction in the effects of ambient air pollutants. METHODS AND RESULTS We measured arterial stiffness in 73 participants with moderate to high CVD risk. Average levels of ambient PM2.5 and ozone were calculated from local monitoring stations. Residential greenness was estimated using satellite-derived normalized difference vegetation index (NDVI) for a 200m and 1km radius around each participant's home. Participants were 51% female; average age of 52 years; and, 79% had diagnosed hypertension. In multiple linear regression models, residential NDVI was negatively associated with augmentation index (-3.8% per 0.1 NDVI). Ambient levels of PM2.5 (per interquartile range (IQR) of 6.9 μg/m3)were positively associated with augmentation pressure (3.1 mmHg), pulse pressure (5.9 mmHg), and aortic systolic pressure (8.1 mmHg). Ozone (per IQR of 0.03 ppm) was positively associated with augmentation index (5.5%), augmentation pressure (3.1 mmHg), and aortic systolic pressure (10 mmHg). In areas of low greenness, both PM2.5 and ozone were positively associated with pulse pressure. Additionally, ozone was positively associated with augmentation pressure and systolic blood pressure. However, in areas of high greenness, there was no significant association between indices of arterial stiffness with either PM2.5 or ozone. CONCLUSIONS Residential proximity to greenness is associated with lower values of arterial stiffness. Residential greenness may mitigate the adverse effects of PM2.5 and ozone on arterial stiffness.
Neubestimmung von Struktur und Eigenschaften isotyper Natriumtetraamidometallate des Aluminiums und Galliums

Fur rontgenographische Strukturbestimmungen geeignete Kristalle von NaAl(NH2)4 und NaGa(NH2)4 wurden durch Umsetzung der Metalle mit NH3 in Autoklaven bei 100°C und P(NH3) = 60 bar in 7d erhalten. Die Verbindungen kristallisieren isotyp in der Raumgruppe P21/c mit Z = 4 NaAl(NH2)4 a = 7,328(2) A, b = 6,047(2) A, c = 13,151(3) A, β = 94,04(1)° NaGa(NH2)4 a = 7,4087(8) A, b = 6,0917(5) A, c = 12,855(2) A, β = 92,10(1)° Die Strukturen wurden einschlieslich aller H-Lagen der NH2−-Ionen bestimmt. Die ternaren Amide werden auserdem IR-spektroskopisch und bezuglich ihres thermischen Verhaltens charakterisiert. Redetermination of Structure and Properties of the Isotypic Sodium Tetraamido Metallates of Aluminium and Gallium Crystals for x-ray structure determination of NaAl(NH2)4 and NaGa(NH2)4 were obtained by the reaction of the metals with ammonia in autoclaves at 100°C and P(NH3) = 60 bar within 7 days. The compounds crystallize isotypic in the space group P21/c with Z = 4 NaAl(NH2)4 a = 7.328(2) A, b = 6.047(2) A, c = 13.151(3) A, β = 94.04(1)° NaGa(NH2)4 a = 7.4087(8) A, b = 6.0917(5) A, c = 12.855(2) A, β = 92.10(1)° The structures were refined inclusively all H-positions of the amide ions. The ternay amides are furthermore characterized by their IR spectra and their thermal behaviour.
Quorum sensing across bacterial and viral domains

Quorum sensing (QS) is a process of cell-to-cell communication that bacteria use to orchestrate collective behaviors in response to changes in cell population density and species composition of the community [1]. QS relies on the production, release, and group-wide detection of and response to extracellular signaling molecules called autoinducers (AIs) [1]. Recent studies demonstrate that bacteria-infecting viruses, called phages, also employ chemical communication to regulate collective activities. Phages can encode exclusive phage QS-like systems, or they can tune into and manipulate their host bacterial QS-mediated communication pathways to optimize the timing of the lysis–lysogeny switch. These research advances suggest that phage-mediated QS signaling and phage eavesdropping on bacterial QS signaling drive bacteria–phage interactions, possibly contributing to mechanisms that shape both phage and bacterial biology [2–6]. Here, we briefly review QS in bacteria, and we summarize recent highlights in chemical communication among phages and across the bacterial and phage domains.
Predicting the spatio-temporal spread of West Nile virus in Europe

West Nile virus is a widely spread arthropod-born virus, which has mosquitoes as vectors and birds as reservoirs. Humans, as dead-end hosts of the virus, may suffer West Nile Fever (WNF), which sometimes leads to death. In Europe, the first large-scale epidemic of WNF occurred in 1996 in Romania. Since then, human cases have increased in the continent, where the highest number of cases occurred in 2018. Using the location of WNF cases in 2017 and favorability models, we developed two risk models, one environmental and the other spatio-environmental, and tested their capacity to predict in 2018: 1) the location of WNF; 2) the intensity of the outbreaks (i.e. the number of confirmed human cases); and 3) the imminence of the cases (i.e. the Julian week in which the first case occurred). We found that climatic variables (the maximum temperature of the warmest month and the annual temperature range), human-related variables (rain-fed agriculture, the density of poultry and horses), and topo-hydrographic variables (the presence of rivers and altitude) were the best environmental predictors of WNF outbreaks in Europe. The spatio-environmental model was the most useful in predicting the location of WNF outbreaks, which suggests that a spatial structure, probably related to bird migration routes, has a role in the geographical pattern of WNF in Europe. Both the intensity of cases and their imminence were best predicted using the environmental model, suggesting that these features of the disease are linked to the environmental characteristics of the areas. We highlight the relevance of river basins in the propagation dynamics of the disease, as outbreaks started in the lower parts of the river basins, from where WNF spread towards the upper parts. Therefore, river basins should be considered as operational geographic units for the public health management of the disease.
Brain folding shapes the branching pattern of the middle cerebral artery

The folds of the brain offer a particular challenge for the subarachnoid vascular grid. The primitive blood vessels that occupy this space, when the brain is flat, have to adapt to an everchanging geometry while constructing an efficient network. Surprisingly, the result is a non-redundant arterial system easily challenged by acute occlusions. Here, we generalize the optimal network building principles of a flat surface growing into a folded configuration and generate an ideal middle cerebral artery (MCA) configuration that can be directly compared with the normal brain anatomy. We then describe how the Sylvian fissure (the fold in which the MCA is buried) is formed during development and use our findings to account for the differences between the ideal and the actual shaping pattern of the MCA. Our results reveal that folding dynamics condition the development of arterial anastomosis yielding a network without loops and poor response to acute occlusions.