Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging of renal fibrosis

Purpose of review Fibrosis is an important biomarker of chronic kidney injury, and a powerful predictor of renal outcome. Currently, the only method for measuring fibrotic burden is histologic analysis, which requires a kidney biopsy in humans, or kidney removal in animal models. These requirements have not only hindered our ability to manage patients effectively, but have also prevented a full understanding of renal fibrosis pathogenesis, and slowed the translation of new antifibrotic agents. The development of noninvasive fibrosis imaging tools could thus transform both clinical care and renal fibrosis research. Recent findings Conventional imaging modalities have historically failed to image fibrosis successfully. However, recent exciting technological advances have greatly enhanced their capabilities. New techniques, for example, may allow imaging of the physical consequences of scarring, as surrogate measures of renal fibrosis. Similarly, other groups have developed ways to directly image extracellular matrix, either with the use of contrast-enhanced probes, or using matrix components as endogenous contrast agents. Summary New developments in imaging technology have the potential to transform our ability to visualize renal fibrosis and to monitor its progression. In doing so, these advances could have major implications for kidney disease care, the development of new antiscarring agents, and our understanding of renal fibrosis in general.
Ligand-Controlled Copper-Catalyzed Regiodivergent Carbonylative Synthesis of α-Amino Ketones and α-Boryl Amides from Imines and Alkyl Iodides.

Regioselective transformation is among the long-standing challenges in organic synthesis. In this communication, a copper-catalyzed selectivity controlled regiodivergent borocarbonylation of imines with alkyl iodides has been developed. Various α -amino ketones and α -boryl amides were produced in moderate to good yields from the same substrates. The choosing of the appropriate ligand is the key for the regioselectivity control: α -amino ketones were produced selectively in good yields with ( p -CF 3 C 6 H 4 ) 3 P as the ligand; while the corresponding α -boryl amides were obtained in high regioselectivity with Me IMes as the ligand.
Late Ventilator-Induced Diaphragmatic Dysfunction After Extubation.

OBJECTIVES Mechanical ventilation is associated with primary diaphragmatic dysfunction, also termed ventilator-induced diaphragmatic dysfunction. Studies evaluating diaphragmatic function recovery after extubation are lacking. We evaluated early and late recoveries from ventilator-induced diaphragmatic dysfunction in a mouse model. DESIGN Experimental randomized study. SETTING Research laboratory. SUBJECTS C57/BL6 mice. INTERVENTIONS Six groups of C57/BL6 mice. Mice were ventilated for 6 hours and then euthanatized immediately (n = 18), or 1 (n = 18) or 10 days after extubation with (n = 5) and without S107 (n = 16) treatment. Mice euthanatized immediately after 6 hours of anesthesia (n = 15) or after 6 hours of anesthesia and 10 days of recovery (n = 5) served as controls. MEASUREMENTS AND MAIN RESULTS For each group, diaphragm force production, posttranslational modification of ryanodine receptor, oxidative stress, proteolysis, and cross-sectional areas were evaluated. After 6 hours of mechanical ventilation, diaphragm force production was decreased by 25-30%, restored to the control levels 1 day after extubation, and secondarily decreased by 20% 10 days after extubation compared with controls. Ryanodine receptor was protein kinase A-hyperphosphorylated, S-nitrosylated, oxidized, and depleted of its stabilizing subunit calstabin-1 6 hours after the onset of the mechanical ventilation, 1 and 10 days after extubation. Post extubation treatment with S107, a Rycal drug that stabilizes the ryanodine complex, did reverse the loss of diaphragmatic force associated with mechanical ventilation. Total protein oxidation was restored to the control levels 1 day after extubation. Markers of proteolysis including calpain 1 and calpain 2 remained activated 10 days after extubation without significant changes in cross-sectional areas. CONCLUSIONS We report that mechanical ventilation is associated with a late diaphragmatic dysfunction related to a structural alteration of the ryanodine complex that is reversed with the S107 treatment.
THE EFFECT OF SALINITY TO ACTIVITY AND EFFECTIVITY PHOSPHATE SOLUBILIZING BACTERIA ON GROWTH AND PRODUCTION OF PADDY

This study aimed to determine the extent of phosphate solubilizing bacteria resistant to salinity and still be able to provide P for paddy plant. Research using completely randomized design with fertilizer treatments: (A) Bakteri Aerobacter aerogenes + Azotobacter indicus (B) Bakteri Bacillus thuringiensis + B. megaterium + Pseudomonas fluorescens, (C) Bakteri Nocardia mesentrica + Spirillum lipoferum, (D) Mix bakteri Pseudomonas fluorescens, Bacillus thuringiensis, B. megaterium, Nocardia mesentrica, Aerobacter aerogenes, Spirillum lipoferum, dan Azotobacter indicus, and (E) control (whitout inoculant), and salinity (NaCl): (1) 0% (0 grams / 7 kg soil), (2) 0.1% (7 grams / 7 kg soil), (3) 0.2% (14 g / 7 kg soil), (4) 0.3% (21 g / 7 kg soil), and (5) 0 , 4% (28 g / 7 kg soil). Thirty and one hundred days after transplanting (DAT), and then measured plant height, number of tillers, number and dry weight of whole grain paddy. The results showed that 0,1 % (7 gram/7 kg tanah) salinity is very good for the growth, activity and effectiveness of phosphate solubilizing bacteria and production of paddy, but 0.4% salinity (28 gr/7kg land) is still safe on the growth, activity and effectiveness of phosphate solubilizing bacteria (Pseudomonas fluorescens, Bacillus thuringiensis, B. megaterium, Nocardia mesentrica, Aerobacter aerogenes, spirillum lipoferum and Azotobacter indicus) as biofertilizer or growth promoting rhizobacteria on growth and production of paddy. Keywords : Salinity, Phosphate solubilizing bacteria, Paddy
A COMPLETE HIV-1 Env CODING SEQUENCES FROM HIV ISOLATED IN CENTRAL JAVA, INDONESIA

Background:The HIV envelope glycoprotein ( env ) plays a central role in viral transmission to target cells.The genetic diversity of env gene contributes a great mechanism on how HIV-1 could survive.Aims:To determine the genotype and genetic relationship of our isolate compared to the other HIV-1 isolates, especially from Indonesia based on the env gene. Also, for further use, the molecular properties of our gene had been analyzed. Methods: A complete coding sequence of HIV-1 env gene was cloned from 09IDSKA-6 (HIV isolated in Central Java, Indonesia), inserted into an Escherichia coli expression plasmid, and sequenced. The sequencing results of the env gene then subjected for virus subtyping and genotyping. The phylogenetic analysis was performed to know the relationship between the isolate with all HIV isolates in Indonesia based on the env gene.The sequencing results were also subjected for bioinformatics analysis.Results: Based on the molecular analysis of HIV-1 env complete coding sequences, the 09IDSKA-6 belong to HIV CRF01_AEwhich is quite common in Southeast Asia. The signal peptide, protein charge, transmembrane helix, antigenicity, hydrophobicity, secondary structure, and proteolytic cleavageof our gene also had been discussed. Keywords: HIV-1, env gene, Indonesia.
Dilute Acid Induced Changes on Microscopic and Tomographic Structure of Water Hyacinth [Eichhornia Crassipes (Mart.) Solms] Biomass during Bioconversion Process to Xylitol

Background/Objectives: The present study was conducted on Water Hyacinth Biomass (WHB) to understand its anatomy, physiology, biochemistry, tomography and the response of dilute acid pretreatment under different parametric conditions on these aspects. Methods/Statistical Analysis: Leaves and Stems (petioles) of WHB were grinded to make a fresh paste. 8g of paste is soaked in 1, 3 and 5% of H2SO4 solution for 1, 2, 3 and 4 h under agitation of 130, 160 and 190 rpm at temperature of 30 oC, 40 oC, 50 oC and 60 oC and boiled for 15 and 30 min. Untreated and treated biomass were then dried and preserved. Findings: It has been observed under the microscope that there has been a prominent lysis in the cell wall, vascular bundles and several other tissues when the transverse section of young, middle and old aged root, stem and leaf are soaked in 1-5% acid with agitation of 130-160 rpm for 1-4 h at 30-60 oC. To justify the reason behind obtaining higher yield of xylose sugar by acid hydrolysis, fresh WHB paste was treated with dilute acid with same parametric conditions which gave higher xylose yield. Treated biomass was investigated under Scanning Electron Microscope (SEM) and it was observed that the pretreatment alters the structural and chemical composition of complex structure of lignocellulose in WHB for rapid hydrolysis to fermentable sugars. Applications/Improvements: This paper represents the effect of hydrolysis on the WHB which is clearly evident from the anatomical studies in microscope and SEM. The biomass can be efficiently utilized for bioconversion into value added products after acid hydrolysis.
The ABC transporter Pdr18 is required for yeast thermotolerance due to its role in ergosterol transport and plasma membrane properties

Summary Among the mechanisms by which yeast overcomes multiple stresses is the expression of genes encoding ATP‐binding cassette (ABC) transporters required for resistance to a wide range of toxic compounds. These substrates may include weak acids, alcohols, agricultural pesticides, polyamines, metal cations, as in the case of Pdr18. This pleotropic drug resistance transporter was previously proposed to transport ergosterol at the plasma membrane (PM) level contributing to the maintenance of PM lipid organization and reduced diffusional permeation induced by lipophilic compounds. The present work reports a novel phenotype associated with the putative drug/xenobiotic‐efflux‐pump transporter Pdr18: the resistance to heat shock and to long‐term growth at supra‐optimal temperatures. Cultivation at 40°C was demonstrated to lead to higher PM permeabilization of a pdr18Δ cell population with the PDR18 gene deleted compared with the parental strain population, as indicated by flow cytometry analysis of propidium iodide stained cells. Cells of pdr18Δ grown at 40°C also exhibited increased transcription levels from genes of the ergosterol biosynthetic pathway, compared with parental cells. However, this adaptive response at 40°C was not enough to maintain PM physiological ergosterol levels in the population lacking the Pdr18 transporter and free ergosterol precursors accumulate in the deletion mutant cells.
Postural Control When Using an Industrial Lower Limb Exoskeleton: Impact of Reaching for a Working Tool and External Perturbation

Objective To investigate postural control related to a lower limb exoskeleton (Chairless Chair) when (a) reaching for a working tool, and (b) an external perturbation occurs. Background Lower limb exoskeletons aiming to reduce physical load associated with prolonged standing may impair workers’ postural control and increase the risk of falling. Method Forty-five males were reaching for an object (3-kg dumbbell) at the lateral end of their reaching area without the exoskeleton in upright standing (STAND) and with the exoskeleton at a high (EXOHIGH.SEAT) and low sitting position (EXOLOW.SEAT). The task was performed with the object placed in three different angles (120°, 150°, and 180°) in the transversal plane. The minimum absolute static postural stability (SSABS.MIN) as the shortest distance (mm) of the center of pressure to the base of support border was measured (zero indicates risk of falling). Additionally, eight subjects were standing without the exoskeleton or sitting on it (EXOHIGH.SEAT and EXOLOW.SEAT) while being pulled backward. The tilting moment when subjects lost their balance was assessed. Results SSABS.MIN was lower when using the exoskeleton (p < .05) but still about 17 mm. The location of the object to be reached had no influence. Tilting moments of less than 30 nm were sufficient to let people fall backward when sitting on the exoskeleton (50 nm for STAND). Conclusion Impairments in postural control by the exoskeleton may not be relevant when reaching laterally for objects up to 3 kg. When an external perturbation occurs, the risk of falling may be much higher; irrespective of factors like uneven or slippery flooring. Application The risk of falling using the exoskeleton seems to be low when reaching laterally for an object of up to 3 kg. In situations where, for example, a collision with coworkers is likely, this exoskeleton is not recommended.
Factors associated with Candida auris colonization and transmission in skilled nursing facilities with ventilator units, New York, 2016-2018.

BACKGROUND Candida auris is an emerging, multidrug-resistant yeast that spreads in healthcare settings. People colonized with C. auris can transmit this pathogen and are at risk for invasive infections. New York State (NYS) has the largest U.S. burden (>500 colonized and infected people); many colonized individuals are mechanically ventilated or have tracheostomy and are residents of ventilator-capable skilled nursing facilities (vSNF). We evaluated factors associated with C. auris colonization among vSNF residents to inform prevention interventions. METHODS During 2016-2018, the NYS Department of Health conducted point prevalence surveys (PPS) to detect C. auris colonization among residents of vSNFs. In a case-control investigation, we defined a case as C. auris colonization in a resident and identified up to four residents with negative swabs during the same PPS as controls. We abstracted data from medical records on facility transfers, antimicrobials, and medical history. RESULTS We included 60 cases and 218 controls identified from 6 vSNFs. After controlling for potential confounders, the following characteristics were associated with C. auris colonization: being on a ventilator (aOR: 5.9; CI: 2.3-15.4), receiving carbapenem antibiotics in the prior 90 days (aOR: 3.5; CI: 1.6-7.6), having ≥1 acute care hospital visit in the prior six months (aOR: 4.2; CI: 1.9-9.6), and receiving systemic fluconazole in the prior 90 days (aOR: 6.0; CI: 1.6-22.6). CONCLUSIONS Targeted screening of patients in vSNFs with the above risk factors for C. auris can help identify colonized patients and facilitate implementation of infection control measures. Antimicrobial stewardship may be an important factor in the prevention of C. auris colonization.
Mediation and Moderation of an Educational Intervention for Improving Intention to Practise Pneumoconiosis Prevention amongst South Asian Construction Workers.

OBJECTIVE To examine components of the Health Belief Model (HBM) as mediators and socio-demographic characteristics as moderators of the effects of an educational intervention on intention to practise pneumoconiosis prevention amongst South Asian construction workers. METHODS The study used a one-group pretest and posttest design. Analytic data was from 1001 South Asian construction workers in Hong Kong. RESULTS Changes in the perceived susceptibility, perceived severity, perceived benefits, cues to action and self-efficacy mediated the intervention's efficacy in improving intention to practise pneumoconiosis prevention. The intervention was more effective in reducing perceived barriers in younger workers, enhancing self-efficacy in older workers and relatively new employees and improving the intention in unmarried workers. CONCLUSIONS It provided preliminary support for the efficacy of the intervention based on the HBM in improving intention to practise pneumoconiosis prevention amongst South Asian construction workers.
Does Fungal Biliary Contamination after Preoperative Biliary Drainage Increase Postoperative Complications after Pancreaticoduodenectomy?

Simple Summary Biliary drainage leads to bacterial biliary contamination, but there are few studies on the impact of fungal biliary contamination after pancreaticoduodenectomy (PD). This retrospective multicenter study identified two groups: bacterial contamination only (B+, n = 154; 75%), and bacterial and fungal contamination (BF+, n = 52; 25%). An extended duration of preoperative drainage (62 vs. 49 days; p = 0.08) increased the risk of fungal contamination, but there were no differences between the two groups in relation to specific or infectious postoperative complications. According to this study, there is no argument to recommend the use of anti-fungal treatment as a prophylactic treatment during PD preceded by biliary drainage. Abstract (1) Background: preoperative biliary drainage before pancreaticoduodenectomy (PD) is associated with bacterial biliary contamination (>85%) and a significant increase in global and infectious complications. In view of the lack of published data, the aim of our study was to investigate the impact of fungal biliary contamination after biliary drainage on the complication rate after PD. (2) Methods: a multicentric retrospective study that included 224 patients who underwent PD after biliary drainage with intraoperative biliary culture. (3) Results: the global rate of positive intraoperative biliary sample was 92%. Respectively, the global rate of biliary bacterial contamination and the rate of fungal contamination were 75% and 25%, making it possible to identify two subgroups: bacterial contamination only (B+, n = 154), and bacterial and fungal contamination (BF+, n = 52). An extended duration of preoperative drainage (62 vs. 49 days; p = 0.08) increased the risk of fungal contamination. The overall and infectious complication rates were not different between the two groups. In the event of postoperative infectious or surgical complications, the infectious samples taken did not reveal more fungal infections in the BF+ group. (4) Conclusions: fungal biliary contamination, although frequent, does not seem to increase the rate of global and infectious complications after PD, preceded by preoperative biliary drainage.
EEG signal classification based on SVM with improved squirrel search algorithm

Abstract Electroencephalography (EEG) is a complex bioelectrical signal. Analysis of which can provide researchers with useful physiological information. In order to recognize and classify EEG signals, a pattern recognition method for optimizing the support vector machine (SVM) by using improved squirrel search algorithm (ISSA) is proposed. The EEG signal is preprocessed, with its time domain features being extracted and directed to the SVM as feature vectors for classification and identification. In this paper, the method of good point set is used to initialize the population position, chaos and reverse learning mechanism are introduced into the algorithm. The performance test of the improved squirrel algorithm (ISSA) is carried out by using the benchmark function. As can be seen from the statistical analysis of the results, the exploration ability and convergence speed of the algorithm are improved. This is then used to optimize SVM parameters. ISSA-SVM model is established and built for classification of EEG signals, compared with other common SVM parameter optimization models. For data sets, the average classification accuracy of this method is 85.9%. This result is an improvement of 2–5% over the comparison method.
Performance Evaluation of the uEXPLORER Total-Body PET/CT Scanner Based on NEMA NU 2-2018 with Additional Tests to Characterize PET Scanners with a Long Axial Field of View

Visual Abstract The world’s first total-body PET scanner with an axial field of view (AFOV) of 194 cm is now in clinical and research use at our institution. The uEXPLORER PET/CT system is the first commercially available total-body PET scanner. Here we present a detailed physical characterization of this scanner based on National Electrical Manufacturers Association (NEMA) NU 2-2018 along with a new set of measurements devised to appropriately characterize the total-body AFOV. Methods: Sensitivity, count-rate performance, time-of-flight resolution, spatial resolution, and image quality were evaluated following the NEMA NU 2-2018 protocol. Additional measurements of sensitivity and count-rate capabilities more representative of total-body imaging were performed using extended-geometry phantoms based on the world-average human height (∼165 cm). Lastly, image quality throughout the long AFOV was assessed with the NEMA image quality (IQ) phantom imaged at 5 axial positions and over a range of expected total-body PET imaging conditions (low dose, delayed imaging, short scan duration). Results: Our performance evaluation demonstrated that the scanner provides a very high sensitivity of 174 kcps/MBq, a count-rate performance with a peak noise-equivalent count rate of approximately 2 Mcps for total-body imaging, and good spatial resolution capabilities for human imaging (≤3.0 mm in full width at half maximum near the center of the AFOV). Excellent IQ, excellent contrast recovery, and low noise properties were illustrated across the AFOV in both NEMA IQ phantom evaluations and human imaging examples. Conclusion: In addition to standard NEMA NU 2-2018 characterization, a new set of measurements based on extending NEMA NU 2-2018 phantoms and experiments was devised to characterize the physical performance of the first total-body PET system. The rationale for these extended measurements was evident from differences in sensitivity, count-rate–activity relationships, and noise-equivalent count-rate limits imposed by differences in dead time and randoms fraction between the NEMA NU 2 70-cm phantoms and the more representative total-body imaging phantoms. Overall, the uEXPLORER PET system provides ultra-high sensitivity that supports excellent spatial resolution and IQ throughout the field of view in both phantom and human imaging.
Integrative genomic analysis in African American children with asthma finds three novel loci associated with lung function

Bronchodilator (BD) drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of BD medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken before BD medication have been extensively studied, and the genetics of the BD response itself have received some attention. However, few studies have focused on the genetics of post‐BD lung function. To address this gap, we analyzed lung function phenotypes in 1103 subjects from the Study of African Americans, Asthma, Genes, and Environment, a pediatric asthma case–control cohort, using an integrative genomic analysis approach that combined genotype, locus‐specific genetic ancestry, and functional annotation information. We integrated genome‐wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (forced expiratory volume in 1 s [FEV1], forced vital capacity [FVC], and FEV1/FVC) taken before and after albuterol BD administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and five additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine‐mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre‐ and post‐BD lung function: ADAMTS1, RAD54B, and EGLN3.