bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gastroesophageal Reflux Disease Outcomes After Vertical Sleeve Gastrectomy and Gastric Bypass
Authors: Leslie Daniel , Wise Eric , Sheka Adam , Abdelwahab Hisham , Irey Ryan , Benner Ashley , Ikramuddin Sayeed 
Published: July 2021

Objective:
The objective of this study is to assess whether vertical sleeve gastrectomy (VSG) increases the incidence of gastroesophageal reflux disease (GERD), esophagitis and Barrett esophagus (BE) relative to patients undergoing Roux-en-Y gastric bypass (RYGB) in patients with and without preoperative GERD.

Summary of Background Data:
Concerns for potentiation of GERD, supported by multiple high-quality retrospective studies, have hindered greater adoption of the VSG.

Methods:
From the OptumLabs Data Warehouse, VSG and RYGB patients with ≥2 years enrollment were identified and matched by follow-up time. GERD [reflux esophagitis, prescription for acid reducing medication (Rx) and/or diagnosis of BE], upper endoscopy (UE), and re-admissions were evaluated beyond 90 days.

Results:
A total of 8362 patients undergoing VSG were matched 1:1 to patients undergoing RYGB, on the basis of post-operative follow-up interval. Age, sex, and follow-up time were similar between the 2 groups (P > 0.05). Among all patients, postoperative GERD was more frequently observed in VSG patients relative to RYGB patients (60.2% vs 55.6%, respectively; P < 0.001), whereas BE was more prevalent in RYGB patients (0.7% vs 1.1%; P = 0.007). Postoperatively, de novo esophageal reflux symptomatology was more common in VSG patients (39.3% vs 35.3%; P < 0.001), although there was no difference in development of the histologic diagnoses reflux esophagitis and BE. Furthermore, postoperative re-admission was higher in the RYGB cohort (38.9% vs 28.9%; P < 0.001).

Conclusions:
Compared to RYGB, VSG may not have inferior long-term GERD outcomes, while also leading to fewer re-hospitalizations. These data challenge the prevailing opinion that patients with GERD should undergo RYGB instead of VSG.
Expanding the Donor Pool: First Use of Hepatitis B Virus Nat Positive Solid Organ Allografts Into Seronegative Recipients
Authors: Delman Aaron M. , Turner Kevin M. , Safdar Kamran , Anwar Nadeem , Silski Latifa S. , Lee Tiffany C. , Luckett Keith , Cuffy Madison C. , Quillin Ralph C. , Schoech Michael , Kaiser Tiffany E. , Govil Amit , Bari Khurram , Shah Shimul A. 
Published: July 2021

Objectives:
The aim of this study was to assess the 1-year safety and effectiveness of HBV Nucleic Acid Test positive (HBV NAT+) allografts in seronegative kidney transplant (KT) and liver transplant (LT) recipients.

Summary Background Data:
Despite an ongoing organ shortage, the utilization of HBV NAT+ allografts into seronegative recipients has not been investigated.

Methods:
From January 2017 to October 2020, a prospective cohort study was conducted among consecutive KT and LT recipients at a single institution. Primary endpoints were post-transplant HBV viremia, graft and patient survival.

Results:
With median follow-up of 1-year, there were no HBV-related complications in the 89 HBV NAT+ recipients. Only 9 of 56 KTs (16.1%) and 9 of 33 LTs (27.3%) experienced post-transplant HBV viremia at a median of 185 (KT) and 269 (LT) days postoperatively. Overall, viremic episodes resolved to undetected HBV DNA after a median of 80 days of entecavir therapy in 16 of 18 recipients. Presently, 100% of KT recipients and 93.9% of LT recipients are HBV NAT− with median follow-up of 13 months, whereas 0 KT and 8 LT (24.2%) recipients are HBV surface antigen positive indicating chronic infection. KT and LT patient and allograft survival were not different between HBV NAT+ and HBV NAT− recipients (P > 0.05), whereas HBV NAT+ KT recipients had decreased waitlist time and pretransplant duration on dialysis (P < 0.01).

Conclusions:
This is the largest series describing the transplantation of HBV NAT+ kidney and liver allografts into HBV seronegative recipients without chronic HBV viremia or decreased 1-year patient and graft survival. Increasing the utilization of HBV NAT+ organs in nonviremic recipients can play a role in decreasing the national organ shortage.
Open-source mapping and variant calling for large-scale NGS data from original base-quality scores
Authors: Krasheninina Olga , Hwang Yih-Chii , Bai Xiaodong , Zalcman Aleksandra , Maxwell Evan , Reid Jeffrey G. , Salerno William J. 
Published: July 2021

AbstractStandardized genome informatics protocols minimize reprocessing costs and facilitate harmonization across studies if implemented in a transparent, accessible and reproducible manner. Here we define the OQFE protocol, a lossless read-mapping protocol that retains key features of existing NGS standard methods. We demonstrate that variants can be called directly from NovaSeq OQFE data without the need for base quality score recalibration and describe a large-scale variant calling protocol for OQFE data. The OQFE protocol is open-source and a containerized implementation is provided.
Comparative genomics supports that Brazilian bioethanolSaccharomyces cerevisiaecomprise a unified group of domesticated strains related to cachaça spirit yeasts
Authors: Jacobus Ana Paula , Stephens Timothy G. , Youssef Pierre , González-Pech Raul , Chen Yibi , Basso Luiz Carlos , Frazzon Jeverson , Chan Cheong Xin , Gross Jeferson 
Published: July 2021

AbstractEthanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation areSaccharomyces cerevisiaestrains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of theS. cerevisiaePE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288c and diverseS. cerevisiae. All genomes of bioethanol yeasts have amplifiedSNO2(3)/SNZ2(3)gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence ofSAM-dependent methyl transferases, a gene family rare inS. cerevisiae. Widespread amplifications of quinone oxidoreductasesYCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.
Comparative phytotoxicity and chironomid toxicity assessments of leaf successive extract fractions of Asiatic poison bulb,Crinum asiaticumL
Authors: Goswami Souren , Ray Sanjib 
Published: July 2021

AbstractCrinum asiaticumis an evergreen bulbous perennial shrub of Amaryllidaceae family with ethnomedicinal importance and our earlier study described a comparative account antimicrobial and antioxidant properties of the different solvent-mediated sequential extract fractions. The present study aimed to analyze their comparative account of induced phytotoxicity and chironomid toxicity. For phytotoxicity assessment, germination inhibition and seedling’s root and shoot growth retardation effects onTriticum aestivum and Cicer arietinumwere analyzed and for lethal concentration determination, the freshwater bottom-dwelling first instars chironomid larvae were used. The crude aqueous, petroleum ether and ethyl acetate extracts showed significant toxic effects on both meristematic tissue and aquatic midges. The phytotoxic assays indicate that the ethyl acetate fraction contains the most potent growth inhibitors, followed by the crude aqueous and petroleum ether fractions. The last aqueous fraction was found to be the least toxic, the highest LC50and LT50values and ethyl acetate extract fraction having highest toxicity. Thus the present study supplements to our earlier report, that indicated the last aqueous extract fraction ofC. asiaticumhas potent antioxidant and antibacterial potentials as well as its prospective use in livestock maintenance, as it is least toxic and the ethyl acetate extract, the most toxic fraction identified here, is needed to explore for pharmaceutical importance.
Neural evidence for categorical biases in working memory for location and orientation
Authors: Bae Gi-Yeul 
Published: July 2021

AbstractPrevious research demonstrated that visual working memory exhibits biases with respect to the categorical structure of the stimulus space. However, a majority of those studies used behavioral measures of working memory, and it is not clear whether the working memory representations per se are influenced by the categorical structure or whether the biases arise in decision or response processes during the report. Here, I applied a multivariate decoding technique to EEG data collected during working memory tasks to determine whether neural activity associated with the working memory representation is categorically biased prior to the report. I found that the decoding of spatial working memory was biased away from the nearest cardinal location, consistent with the biases observed in the behavioral responses. In a follow-up experiment which was designed to prevent the use of a response preparation strategy, I found that the decoding still exhibited categorical biases. Together, these results provide neural evidence that working memory representations themselves are categorically biased, imposing important constraints on the computational models of working memory representations.
TranSuite: a software suite for accurate translation and characterization of transcripts
Authors: Entizne Juan C. , Guo Wenbin , Calixto Cristiane P.G. , Spensley Mark , Tzioutziou Nikoleta , Zhang Runxuan , Brown John W.S. 
Published: July 2021

ABSTRACTProtein translation programs often select the longest open reading frame (ORF) in a transcript leading to numerous inaccurate and mis-annotated ORFs in databases. Unproductive transcript isoforms containing premature termination codons (PTCs) are potential substrates for nonsense-mediated decay (NMD). These transcripts often contain truncated ORFs but are incorrectly annotated due to selection of a long ORF beginning at an AUG downstream of the PTC despite the transcript containing the authentic translation start AUG. In gene expression and alternative splicing analyses, it is important to identify transcript isoforms which code for different protein variants and to distinguish these from potential NMD substrates. Here, we present TranSuite, a pipeline of bioinformatics tools that address these challenges by performing accurate translations, characterizing alternative ORFs and identifying NMD and other features of transcripts in newly assembled and existing transcriptomes. Directly comparing ORFs defined by TranSuite and TransDecoder for the Arabidopsis transcriptome AtRTD2 identified ORF mis-calling in over 16k (27%) of transcripts by TransDecoder.
Mechanism through which retrocyclin targets flavivirus multiplication
Authors: Jia Xiaoying , Guo Jiao , Yuan Weirong , Sun Lingling , Liu Yang , Zhou Minmin , Xiao Gengfu , Lu Wuyuan , Garzino-Demo Alfredo , Wang Wei 
Published: July 2021

AbstractCurrently, there are no approved drugs for the treatment of flavivirus infection. Accordingly, we tested the inhibitory effects of the novel θ-defensin retrocyclin-101 (RC-101) against flavivirus infection, and investigated the mechanism underlying the potential inhibitory effects. First, RC-101 robustly inhibited both Japanese encephalitis virus (JEV) and Zika virus (ZIKV) infections. RC-101 exerted inhibitory effects on the entry and replication stages. Results also indicated that the non-structural protein NS2B-NS3 serine protease might serve as a potential viral target. Further, RC-101 inhibited protease activity at the micromolar level. We also demonstrated that with respect to the glycoprotein E protein of flavivirus, the DE loop of domain III, which is the receptor-binding domain of the E protein, might serve as another viral target of RC-101. Moreover, a JEV DE mutant exhibited resistance to RC-101, which was associated with deceased binding affinity of RC-101 to DIII. These findings provide a basis for the development of RC-101 as a potential candidate for the treatment of flavivirus infection.ImportanceRC has been reported to have a broad-spectrum antimicrobial activity. In this study, we firstly report that RC-101 could inhibit ZIKV and JEV infections. Moreover, both the NS2B-NS3 serine protease and the DE loop in the E glycoprotein might serve as the viral targets of RC-101.
Screening, Identification and Growth Promotion Ability of Phosphate Solubilizing Bacteria from Soybean Rhizosphere under Maize-Soybean Intercropping Systems
Authors: Wang Wenjing , Sarpong Clement Kyei , Song Chun , Zhang Xiaofeng , Gan Yuefeng , Wang Xiaochun , Yong Taiwen , Chang Xiaoli , Wang Yu , Yang Wenyu 
Published: July 2021

ABSTRACTThe solubilization and mineralization of phosphorus by phosphate-solubilizing bacteria (PSB) is one of the most important bacterial physiological characteristics in the soil biogeochemical cycle. Through the isolation and screening of microorganisms in the rhizosphere soil of intercropped soybean in Ya’an, Renshou and Chongzhou, 9 PSBs with high phosphorus solubilizing ability were identified. It mainly belongs toBacillusandPseudomonas. The phosphate solubility ofBacillus aryabhattaiB8W22 is as high as 388.62 µg·mL-1. The physiological and biochemical characteristics of each strain showed that it can secrete organic acids such as formic acid, acetic acid lactic acid and pyruvic acid. In addition, all strains can produce indole acetic acid and siderophores that promote plant growth. Seed germination experiments also showed that the phosphorus solubilizing bacteria isolated in this research have a certain ability to promote plant growth.IMPRTANCEBacillus aryabhattaifrom rhizosphere soil of intercropped soybean has high phosphate-solubilizing ability, could produce indole acetic acid and siderophores that promote plant growth, and are of great significance in reducing the application of chemical phosphate fertilizers and promoting sustainable agricultural development.
Evaluation of the effect of life extension of DHEA extract from sweet potato onCaenorhabditis elegans
Authors: Chen Huan , Zou Dan , Wang Lufeng , Huang Junyi 
Published: July 2021

AbstractProducts from natural sources are being used from centuries. This study investigates the potential antiaging activity of DHEA extracts from sweet potato. DHEA was extracted with the assistance of acid hydrolysis-ultrasonic, and theCaenorhabditis elegansmodel was used to investigate the antiaging activity. The results from the current study articulated that DHEA from sweet potato in 50 μmol / L effectively prolonged the life-span ofC. elegansby 13.60%, but the effect was not concentration-dependent. Besides, DHEA had no effect on the growth ofE. coliOP50and the nematode pharyngeal pump rate, indicating that DHEA didn’t delay the aging of the nematode through calorie restriction. Further experiments demonstrated that DHEA would slow the growth of nematode body size, reduce the accumulation of ROS and lipofuscin ofC. elegans. The expression and migration ofdaf-16into the nucleus of nematode were significantly improved as well. The antiaging effect of DHEA onC. elegansmay be achieved by strengthening the nematode’s ability to resist oxidative stress and promoting nuclear expression of thedaf-16gene.Summary StatementThis study proved that DHEA from sweet potato can extended lifespan ofCaenorhabditis elegansinduced by strengthening the antioxidant capacity and promoting the nuclear expression ofdaf-16
Paracrine signalling between intestinal epithelial and tumour cells induces a regenerative programme
Authors: Jacquemin Guillaume , Wurmser Annabelle , Huyghe Mathilde , Sun Wenjie , Homayed Zeinab , Merle Candice , Perkins Meghan , Qasrawi Fairouz , Richon Sophie , Dingli Florent , Arras Guillaume , Loew Damarys , Vignjevic Danijela , Pannequin Julie , Fre Silvia 
Published: July 2021

AbstractTumours are complex ecosystems composed of different types of cells that communicate and influence each other. While the critical role of stromal cells in affecting tumour growth is well established, the impact of mutant cancer cells on healthy surrounding tissues remains poorly defined. Here, we uncovered a paracrine mechanism by which intestinal cancer cells reactivate foetal and regenerative Yap-associated transcriptional programs in neighbouring wildtype epithelial cells, rendering them adapted to thrive in the tumour context. We identified the glycoprotein Thrombospondin-1 (THBS1) as the essential factor that mediates non-cell autonomous morphological and transcriptional responses. Importantly, Thbs1 is associated with bad prognosis in several human cancers. This study reveals the THBS1-YAP axis as the mechanistic link mediating paracrine interactions between epithelial cells in intestinal tumours.
Valproic acid stimulates myogenesis in pluripotent stem cell–derived mesodermal progenitors in a Notch-dependent manner
Authors: Breuls Natacha , Giarratana Nefele , Yedigaryan Laura , Carai Paolo , Heymans Stephane , Ranga Adrian , Deroose Christophe M. , Sampaolesi Maurilio 
Published: July 2021

ABSTRACTMuscular dystrophies are debilitating neuromuscular disorders for which no cure exists. As this disorder affects both cardiac and skeletal muscle, patients would benefit from a cellular therapy that can simultaneously regenerate both tissues. The current protocol to derive bipotent mesodermal progenitors which can differentiate into cardiac and skeletal muscle relies on the spontaneous formation of embryoid bodies, thereby hampering further clinical translation. Additionally, as skeletal muscle is the largest organ in the human body, a high myogenic potential is necessary for successful regeneration. Here, we have optimized a protocol to generate chemically defined induced pluripotent stem cell-derived mesodermal progenitors (cdMiPs). We demonstrate that these cells contribute to myotube formation and differentiate into cardiomyocytes, both in vitro and in vivo. Furthermore, the addition of valproic acid, a clinically approved small molecule, increases the potential of the cdMiPs to contribute to myotube formation without compromising their ability to differentiate towards cardiomyocytes. This effect is mediated through the activation of the Notch signaling pathway. Taken together, these results constitute a novel approach to generate mesodermal progenitors with enhanced myogenic potential using clinically approved reagents, which opens the door to new therapeutic solutions in the treatment of muscular dystrophy.
TetrODrive: An open-source microdrive for combined electrophysiology and optophysiology
Authors: Brosch Marcel , Vlasenko Alisa , Ohl Frank W. , Lippert Michael T. 
Published: July 2021

AbstractObjectiveIn tetrode recordings, the cell types of the recorded units are difficult to determine based on electrophysiological characteristics alone. Optotagging, the use of optogenetic stimulation at the tip of electrodes to elicit spikes from genetically identified cells, is a method to overcome this challenge. However, recording from many different cells requires advancing electrodes and light sources slowly through the brain with a microdrive. Existing designs suffer from a number of drawbacks, such as limited stability and precision, high cost, complex assembly, or excessive size and weight.ApproachWe designed TetrODrive as a microdrive that can be 3D printed on an inexpensive desktop resin printer and has minimal parts, assembly time, and cost. The microdrive can be assembled in 15 minutes and the price for all materials, including the 3D printer, is lower than a single commercial microdrive. To maximize recording stability, we mechanically decoupled the drive mechanism from the electrical and optical connectors.Main resultsThe developed microdrive is small and light enough to be carried effortlessly by a mouse. It provides high signal-to-noise ratio recordings from optotagged units, even across recording sessions. Owing to its moveable optical fiber, our microdrive can also be used for fiber photometry. We evaluated our microdrive by recording single units and calcium signals in the ventral tegmental area (VTA) of mice and confirmed cell identity via optotagging. Thereby we found units not following the classical reward prediction error model.SignificanceTetrODrive is a tiny, lightweight, and affordable microdrive for optophysiology in mice. Its open design, price, and built-in characteristics can significantly expand the use of microdrives in mice.
Complement C5 is not critical for the formation of sub-RPE deposits inEfemp1mutant mice
Authors: Garland Donita L. , Pierce Eric A. , Fernandez-Godino Rosario 
Published: July 2021

ABSTRACTThe complement system plays a role in the formation of sub-retinal pigment epithelial (RPE) deposits in early stages of age-related macular degeneration (AMD). But the specific mechanisms that connect complement activation and deposit formation in AMD patients are unknown, which limits the development of efficient therapies to reduce or stop disease progression. We have previously demonstrated that C3 blockage prevents the formation of sub-RPE deposits in a mouse model ofEFEMP1-associated macular degeneration. In this study, we have used double mutantEfemp1R345W/R345W:C5-/-mice to investigate the role of C5 in the formation of sub-RPE depositsin vivoandin vitro. The data revealed that the genetic ablation of C5 does not eliminate the formation of sub-RPE depositsin vivoorin vitro. Contrarily, the absence of C5 in RPE cultures promotes complement dysregulation that results in increased activation of C3, which likely contributes to deposit formation even in the absence of EFEMP1-R345W mutant protein. The results also suggest that genetic ablation of C5 alters the extracellular matrix turnover through an effect on matrix metalloproteinases in RPE cell cultures. These results confirm that C3 rather than C5 could be an effective therapeutic target to treat early AMD.