Miracle-dz/UniFAR-FTUs huggingface dataset:
A Procedure to Select Meteorological Data for Air Dispersion Modeling of Pesticide Applications in California

This study developed a procedure to select a set of 5‐y meteorological data with the potential to estimate the highest concentrations (“worst‐case scenario”) in air dispersion modeling of pesticide applications with American Meteorological Society/Environmental Protection Agency Regulatory Model (AERMOD). The study analyzed the relationship between the 95th percentile maximum concentrations estimated by AERMOD and the percentages of low wind speed (LWS, 0.5–2 m/s) in the meteorological data used for the modeling. Statistical analysis showed that they were positively correlated within various distances to different types of emission sources. In addition, the LWS percentages of 1‐y data could be used to predict the LWS percentages of 5‐y data for the same station. Based on these results, the selection procedure for meteorological data began with the evaluation of 1‐y data quality and LWS percentages for all the available stations in California, USA, counties with high use of a pesticide of interest. Five‐year meteorological data were then processed for the top 5 stations with the highest LWS percentages to perform AERMOD modeling. Finally, the air concentration estimates of the modeled meteorological data were compared to determine the worst‐case scenario data. This procedure provided a strategic plan for selecting meteorological data for AERMOD modeling of pesticide applications in California. The procedure was applied to the modeling of residential structural fumigations and determined that the 5‐y (2011–2015) data of the weather station WBAN 93134 (downtown Los Angeles, University of Southern California campus) was the worst‐case scenario meteorological data for this modeling case. Integr Environ Assess Manag 2019;15:648–658. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

Significance Given the large genetic redundancy of transfer RNA (tRNA) genes, the physiological relevance of variations in expression levels of individual tRNA genes is unclear. This is particularly true for variations within isodecoder gene sets (tRNAs having the same anticodon sequence), where no influence over codon usage during translation can be invoked. Here we show that differences in isodecoder tRNA gene expression between different human samples most often do not result in changes in the levels of mature tRNAs, but rather in changes in the abundance of alternative products of the genes, such as immature tRNA sequences, or tRNA fragments that are linked to noncanonical biological functions unrelated to protein synthesis. The human genome encodes hundreds of transfer RNA (tRNA) genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and posttranscriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons), but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to noncanonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate noncanonical tRNA functions performed by tRFs.
Drivers of recovery and reassembly of coral reef communities

Understanding processes that drive community recovery are needed to predict ecosystem trajectories and manage for impacts under increasing global threats. Yet, the quantification of community recovery in coral reefs has been challenging owing to a paucity of long-term ecological data and high frequency of disturbances. Here we investigate community re-assembly and the bio-physical drivers that determine the capacity of coral reefs to recover following the 1998 bleaching event, using long-term monitoring data across four habitats in Palau. Our study documents that the time needed for coral reefs to recover from bleaching disturbance to coral-dominated state in disturbance-free regimes is at least 9–12 years. Importantly, we show that reefs in two habitats achieve relative stability to a climax community state within that time frame. We then investigated the direct and indirect effects of drivers on the rate of recovery of four dominant coral groups using a structural equation modelling approach. While the rates of recovery differed among coral groups, we found that larval connectivity and juvenile coral density were prominent drivers of recovery for fast growing Acropora but not for the other three groups. Competitive algae and parrotfish had negative and positive effects on coral recovery in general, whereas wave exposure had variable effects related to coral morphology. Overall, the time needed for community re-assembly is habitat specific and drivers of recovery are taxa specific, considerations that require incorporation into planning for ecosystem management under climate change.
Mucociliary Clearance in Former Tobacco Smokers with Both Chronic Obstructive Pulmonary Disease and Chronic Bronchitis and the Effect of Roflumilast.

BACKGROUND Little is known of the repeatability and reliability of mucociliary clearance (MCC) in former tobacco smokers who have both chronic obstructive pulmonary disease (COPD) and chronic bronchitis (CB). Less is known of the effect of roflumilast, a selective inhibitor of PDE4, on MCC in these patients. METHODS Former tobacco smokers with COPD and CB were treated for 4 weeks with either roflumilast, or placebo, in a randomized, crossover trial. The following were measured on two baseline and two posttreatment visits: MCC values through 90 minutes, following inhalation of 99mtechnetium sulfur colloid and gamma camera imaging; outer:inner (O:I) deposition ratio; forced expiratory volume in 1 second (FEV1); and symptom scores. Comparisons included: MCC measures through 30 minutes (MCC30), 60 minutes (MCC60), and 90 minutes (MCC90) on the two baseline visits (n = 9) and mean change [(roflumilast - baseline)-(placebo - baseline)] for MCC30, MCC60, MCC90, and FEV1 (n = 8). Associations between MCC measurements, FEV1 and O:I ratio with symptom scores were also examined. RESULTS Pearson correlation tests indicated good repeatability for baseline measures of MCC30, MCC60, and MCC90 and intraclass correlation coefficients indicated good reliability. Only FEV1 (percent predicted) improved significantly following roflumilast treatment. There were no statistically significant correlations between MCC measures and symptom scores. Lower FEV1 values were significantly associated with increased shortness of breath (dyspnea), and lower O:I ratios (more inner region deposition) were significantly associated with increased cough and sputum. CONCLUSIONS Measurements of MCC30, MCC60, and MCC90 are repeatable and reliable in former tobacco smokers with both COPD and CB. One month of treatment with roflumilast did not improve MCC in this limited study. Airway narrowing in the larger, central airways of these subjects could lead to decreased FEV1, increased inner region deposition of the radiolabeled particles, and the associated increase in symptoms of dyspnea, cough, and sputum.
Assessment of cerebrovascular reserve impairment using the breath-holding index in patients with leukoaraiosis

Many studies have demonstrated that leukoaraiosis is associated with impaired cerebrovascular reserve function. However, the definitive hemodynamic changes that occur in leukoaraiosis are not clear, and there are many controversies. This study aimed to investigate hemodynamic changes in symptomatic leukoaraiosis using transcranial Doppler ultrasonography and the breath-holding test in a Chinese Han population, from northern China. A total of 203 patients who were diagnosed with ischemic stroke or clinical chronic progressive ischemic symptoms were enrolled in this study, including 97 males and 106 females, with an age range of 43–93 years. The severity of leukoaraiosis was evaluated according to the Fazekas grading scale, and patients were divided into four groups accordingly. Grade 0 was no leukoaraiosis, and grades I, II, and III were mild, moderate, and severe leukoaraiosis, respectively, with 44, 79, 44, and 36 cases in each group. Transcranial Doppler ultrasonography and the breath-holding test were performed. The mean blood flow velocity of the bilateral middle cerebral artery was measured and the breath-holding index was calculated. The breath holding index was correlated with leukoaraiosis severity and cognitive impairment. Patients with a low breath holding index presented poor performance in the Montreal Cognitive Assessment (MoCA) and executive function tests. That is, the lower the breath holding index, the lower the scores for the MoCA and the higher for the trail-making test Parts A and B. These results indicate that the breath-holding index is a useful parameter for the evaluation of cerebrovascular reserve impairment in patients with leukoaraiosis. In addition, the breath-holding index can reflect cognitive dysfunction, providing a new insight into the pathophysiology of leukoaraiosis. This study was approved by the Ethics Committee of the Fifth People’s Hospital of Shenyang, China (approval No. 20160301) and registered in the Chinese Clinical Trial Registry (registration number: ChiCTR1800014421).
Relationship between components of metabolic syndrome and arterial stiffness in Chinese hypertensives

ABSTRACT Background: Subjects with metabolic syndrome showed increased risk of cardiovascular events. We investigated the relationship between components of metabolic syndrome and arterial stiffness in Chinese hypertensives. Method: 680 subjects (aged 58.44 ± 11.67 years, male 63.53%, hypertension 65.00%) were divided into five groups based on the number of known components of metabolic syndrome (MSCs) according to the criteria of 2010 Chinses Guidelines for Prevention and Management of Hypertension (0MSCs: n= 86; 1MSCs: n= 153; 2MSCs: n= 201; 3MSCs: n= 148; 4/5MSCs: n= 92.). Body weight, height, waist circumference, blood pressure and clinical biochemical tests were measured. Carotid-femoral pulse wave velocity (cfPWV) was measured using a non-invasive automatic device (Complior Analysis, France). Results: The level of cfPWV was significantly increased with the increasing number of MSCs (8.20 ± 1.54 vs 8.72 ± 1.48 vs 9.34 ± 1.77 vs 9.64 ± 1.86 vs 9.91 ± 2.19 m/s, P<0.05). In subjects with hypertension (n= 442), cfPWV was higher than those without hypertension (n= 238) (9.59 ± 1.90 vs 8.49 ± 1.50 m/s, P<0.05) . Stepwise multiple regression analysis revealed that age, gender, the number of MSCs, heart rate as well as serum uric acid level were determinants for cfPWV (P<0.05). In the subgroups stratified by age, systolic blood pressure correlated with cfPWV in hypertensives under 55 years old, while in non-hypertensives the correlation was found after 60 years old. Conclusion: The arterial stiffness became significant with the increasing of the metabolic components numbers, which was independent of age, gender and blood pressure. And the presence of hypertension played the most important role in the progress of arterial stiffness even compared with age.
Effect of roscovitine on developmental competence of small follicle-derived buffalo oocytes

Background & objectives: The lower recovery of competent oocytes in buffalo species limits the commercialization of in vitro embryo production technology in field condition. In this context, pre-maturation of small follicle (SF)-derived oocytes with meiotic inhibition may be a promising alternative to obtain more number of competent oocytes. Thus, the present study was conducted with an objective to enhance the developmental potential of less competent SF-derived buffalo oocytes. Methods: All the visible follicles (used for aspiration) from buffalo ovaries were divided into two categories: large follicle (LF) (follicles having diameter ≥6 mm) and SF (follicles of diameter <6 mm). The competence of LF and SF oocytes was observed in terms of brilliant cresyl blue (BCB) staining, cleavage rate, blastocyst rate and relative gene expression of oocyte and blastocyst competence markers. Thereafter, less competent SF oocytes were treated with 0, 12.5, 25, 50 and 100 mM doses of roscovitine (cyclin-dependent kinase inhibitor) to enhance their developmental potential. Results: Based on parameters studied, LF oocytes were found to be more competent than SF oocytes. Pre-maturation incubation of SF oocytes with roscovitine reversibly arrested oocyte maturation for 24 h to ensure the proper maturation of less competent oocytes. A significantly higher number of BCB-positive oocytes were noted in roscovitine-treated group than SF group. Cleavage and blastocyst rates were also higher in roscovitine-treated group. The relative messenger RNA expression of oocyte (GDF9, BMP15, GREM1, EGFR, PTGS2 and HAS2) as well as blastocyst (INF-τ, GLUT1 and POU5F1) competence markers was significantly greater in roscovitine-treated group relative to SF group. Again, on comparison with LF group, these parameters depicted a lower value in the treatment group. Interpretation & conclusions: The findings of this study has revealed that pre-maturation incubation of SF-derived oocytes with 25 μM roscovitine can improve its developmental competence and thus can be utilized to get maximum number of competent oocytes for better commercialization of in vitro embryo production technology in buffalo.
Colonoscopy quality assessment and accuracy: analysis of the influencing factors and surgical sequelae on 216 colonoscopies.

OBJECTIVE Colonoscopy is recognized as the primary screening test for colorectal cancer. However, its inaccuracy in identifying the exact tumor localization is still high. As a consequence, repeated colonoscopies and changes in the surgical management have been reported. This study aims to evaluate the quality of 216 colonoscopies, to define colonoscopy accuracy and to investigate the surgical sequelae of an incorrect localization. PATIENTS AND METHODS A retrospective analysis of 216 colonoscopies has been conducted. Colonoscopy quality was assessed on: quality of bowel preparation, completeness of the examination, video and/or photographic documentation, and reported the distance of the lesion from the anal verge. Colonoscopy accuracy was evaluated in terms of correspondence between the endoscopic and intra-operative tumor localization. RESULTS Bowel preparation adequateness was reported in 121 out of 216 (56%) colonoscopies, with an adequate grade in 68.6% of cases. A complete colonoscopy was accomplished in 86.9% of cases with photo documentation in only 59 colonoscopies (27.3%). The lesion distance from the anal verge was documented only in 93 out of 216 colonoscopies. Of the 157 lesions described at the colonoscopy, 117 matched with the intra-operative localization (accuracy 74.5%). Fifteen of the 40 incorrectly localized lesions (37.5%) required changes in the surgical management. At multivariate analysis, the colonoscopy completeness was the only influencing factor on the concordance between endoscopic and intra-operative localization. CONCLUSIONS Colonoscopy demonstrated adequate accuracy in localizing lesions. However, the incorrect tumor localization leads to a high rate of changes in surgical management. Increase in.
Integration of elicited expert information via a power prior in Bayesian variable selection: Application to colon cancer data

Background Building tools to support personalized medicine needs to model medical decision-making. For this purpose, both expert and real world data provide a rich source of information. Currently, machine learning techniques are developing to select relevant variables for decision-making. Rather than using data-driven analysis alone, eliciting prior information from physicians related to their medical decision-making processes can be useful in variable selection. Our framework is electronic health records data on repeated dose adjustment of Irinotecan for the treatment of metastatic colorectal cancer. We propose a method that incorporates elicited expert weights associated with variables involved in dose reduction decisions into the Stochastic Search Variable Selection (SSVS), a Bayesian variable selection method, by using a power prior. Methods Clinician experts were first asked to provide numerical clinical relevance weights to express their beliefs about the importance of each variable in their medical decision making. Then, we modeled the link between repeated dose reduction, patient characteristics, and toxicities by assuming a logistic mixed-effects model. Simulated data were generated based on the elicited weights and combined with the observed dose reduction data via a power prior. We compared the Bayesian power prior-based SSVS performance to the usual SSVS in our case study, including a sensitivity analysis using the power prior parameter. Results The selected variables differ when using only expert knowledge, only the usual SSVS, or combining both. Our method enables one to select rare variables that may be missed using only the observed data and to discard variables that appear to be relevant based on the data but not relevant from the expert perspective. Conclusion We introduce an innovative Bayesian variable selection method that adaptively combines elicited expert information and real world data. The method selects a set of variables relevant to model medical decision process.
Adsorption studies on the treatment of battery wastewater by purified carbon nanotubes (P-CNTs) and polyethylene glycol carbon nanotubes (PEG-CNTs)

Abstract Fe–Ni/kaolin catalyst was used for the production of carbon nanotubes (CNTs) via catalytic chemical vapour deposition followed by acid purification treatment and functionalization with polyethylene glycol to give purified carbon nanotubes (P-CNTs) and polyethylene glycol carbon nanotubes (PEG-CNTs), respectively. The as-synthesized CNTs, P-CNTs and PEG-CNTs were characterized by high-resolution transmission electron microscopy (HRTEM), high-resolution scanning electron microscopy (HRSEM), Fourier transform infrared and Brunauer Emmett Teller (BET). The adsorption behaviour P-CNTs and PEG-CNTs to remove specifically Cr and Zn from battery wastewater were examined by the batch adsorption process as a function of different contact time, adsorbent dosage and temperature. The HRSEM/HRTEM/BET analysis confirmed that both nano-adsorbents were tube-like in nature, high porosity and crystalline, with PEG-CNTs possessing high surface area (970.81 m2/g) than P-CNTs (781.88 m2/g). The optimum contact time and adsorbent dosage to remove Cr and Zn by P-CNTs and PEG-CNTs were 90 and 50 min and 0.3 g, respectively. Under the applied conditions, PEG-CNTs exhibited high adsorption capacity than P-CNTs for the selected heavy metals. The adsorption equilibrium data were better fitted to the Freundlich model while the kinetic data conformed to the pseudo-second-order model. Thermodynamic studies demonstrated the feasibility and endothermic nature of the system. This study demonstrated that both nano-adsorbents purify battery wastewater and with better performance by PEG-CNTs.
Compartmentalized necroptosis activation in excitotoxicity-induced axonal degeneration: a novel mechanism implicated in neurodegenerative disease pathology

Excitotoxicity and neuronal cell death: Glutamate is the main excitatory neurotransmitter of the central nervous system and functionally involved in most brain activities, including brain development, synaptic plasticity, learning and memory. Excitatory synaptic transmission is primarily mediated by ligand-gated ion channels, including α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA), N-methyl-D-aspartate (NMDA) and kainate receptors. Activation of glutamate receptors, particularly NMDA receptors, usually leads to calcium influx, which can act as a second messenger for several processes to mediate synaptic activity and brain function. Nevertheless, excessive release of glutamate neurotransmitter may produce intracellular calcium overload, leading to a cascade of events mediating cytoskeleton damage accompanied with reactive oxygen species (ROS) generation, mitochondrial dysfunction and ultimately neuronal cell death. These toxic effects of glutamate are known as excitotoxicity. Neuronal excitotoxicity has been linked to several acute and chronic brain diseases, such as stroke/ischemia, epilepsy and a range of neurodegenerative disorders, including Alzheimer’s disease (AD), Huntington’s disease, amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD), contributing to the neuronal lost in different brain regions. Unfortunately, treating nervous system disorders with general glutamate receptor blockers has been associated with undesirable side effects, becoming increasingly necessary to unravel downstream effectors in the excitotoxicity-dependent cell death pathway in order to develop novel therapeutic strategies. As glutamate receptors are expressed in the neuronal soma, dendrites, axons and synaptic terminals, excitotoxicity could affect different neuronal compartments. In fact, glutamate excitotoxicity leads to neuronal apoptosis, as well as degeneration of axons and dendrites. Central myelinated axons express functional AMPA and GluR5 kainate receptors, and can directly respond to glutamate receptor agonists. These glutamate receptor-dependent signaling pathways promote an increase in intra-axonal Ca levels potentially contributing to axonal degeneration. Here, we discuss whether the compartmentalized destruction induced by excitotoxicity in neurons comprises different cell death mechanisms.