bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Bowel Preparation Acutely Impacts Intestinal Microbiota Composition and Recovery Following Colon and Rectal Surgery
Authors: Nalluri-Butz Harika , Bobel Matthew C , Nugent Julia , Boatman Sonja , Emanuelson Ryan , Melton-Meaux Genevieve , Madoff Robert D , Jahansouz Cyrus , Staley Christopher , Gaertner Wolfgang B 
Published: January 2022

Abstract
The intestinal microbiota has been implicated in the pathogenesis of complications following colorectal surgery, yet perioperative changes in gut microbiome composition are poorly understood. The objective of this study was to characterize the perioperative gut microbiome in patients undergoing colonoscopy and colorectal surgery and determine factors influencing its composition. Using Illumina amplicon sequencing coupled with targeted metabolomics, we characterized the fecal microbiota in: (A) patients (n = 15) undergoing colonoscopy who received mechanical bowel preparation, and (B) patients (n = 15) undergoing colorectal surgery who received surgical bowel preparation, composed of mechanical bowel preparation with oral antibiotics, and perioperative intravenous antibiotics. Microbiome composition was characterized before and up to six months following each intervention. Colonoscopy patients had minor shifts in bacterial community composition that recovered to baseline at a mean of 3 (1-13) days. Surgery patients demonstrated substantial shifts in bacterial composition with greater abundances of Enterococcus, Lactobacillus, and Streptococcus. Compositional changes persisted in the early postoperative period with recovery to baseline beginning at a mean of 31 (16-43) days. Our results support surgical bowel preparation as a factor significantly influencing gut microbial composition following colorectal surgery, while mechanical bowel preparation has little impact.
Estimating Social Contacts in Mass Gatherings for Disease Outbreak Prevention and Management (Case of Hajj Pilgrimage)
Authors: Tofighi Mohammadali , Asgary Ali , Tofighi Ghassem , Najafabadi Mahdi , Arino Julien , Amiche Amine , Rahman Ashrafur , McCarthy Zachary , Bragazzi Nicola Luigi , Thommes Edward , Coudeville Laurent , Grunnill Martin David , Bourouiba Lydia , Wu Jianhong 
Published: January 2022

Abstract
Background: Most mass gathering events have been suspended due to the SARS-CoV-2 pandemic. However, with vaccination rollout, whether and how to organize some of these mass gathering events arises as part of the pandemic recovery discussions, and this calls for decision support tools. The Hajj, one of the world's largest religious gatherings, was substantively scaled down in 2020 and 2021 and it is still unclear how it will take place in 2022 and subsequent years. Simulating disease transmission dynamics during the Hajj season under different conditions can provide some insights for better decision-making. Most disease risk assessment models require data on the number and nature of possible close contacts between individuals.Methods: We sought to use integrated agent-based modeling and discrete events simulation techniques to capture risky contacts among the pilgrims and assess different scenarios in one of the Hajj major sites, namely Masjid-Al-Haram.Results: The simulation results showed that a plethora of risky contacts may occur during the rituals. Also, as the total number of pilgrims increases at each site, the number of risky contacts increases, and physical distancing measures may be challenging to maintain beyond a certain number of pilgrims in the site.Conclusions: This study presented a simulation tool that can be relevant for the risk assessment of a variety of (respiratory) infectious diseases, in addition to COVID-19 in the Hajj season. This tool can be expanded to include other contributing elements of disease transmission to quantify the risk of the mass gathering events.
Identification and Introgression of Bacterial Blight Resistance From African Rice (Oryza Glaberrima Steud.)
Authors: V Ajitha , V Udaya , S Anantha M , S Laha G. , M Sundaram R , P Senguttuvel , B Muralidhara , G Ishwarya Lakshmi V , Dasari Aleena , M Honnappa , Ch Raveendra , Ghazi Irfan Ahmad , V Subbarao L , V Padma , V Ramana J , C Gireesh 
Published: January 2022

Abstract
Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the major diseases affecting rice production. In the present study, 31 accessions of O. glaberrima were screened for BB resistance consecutively for four seasons and identified 28 stable BB resistant accessions with a mean lesion length of < 3cm. Molecular characterization revealed absence of xa5, xa13, Xa21, Xa38, xa41(t) and xa45, indicating the possibility of presence of novel gene(s) conferring BB resistance. In order to transfer BB resistance from O. glaberrima, resistant accession EC861812 was crossed to the susceptible cultivar, IR64 and BC2F2 population developed. Genetic studies in BC2F2 population showed transgressive segregation which indicates that O. glaberrima also harbor beneficial alleles for yield related traits. Six resistant BC2F2 plants with mean lesion length of 0.1-0.8 cm were genotyped with 70 parental polymorphic SSR markers which revealed recurrent parent genome 65.1 to 84.5% with average of 67.5%. The BB resistant introgression lines identified in the present study will serve as pre-breeding lines for mapping of BB resistance derived from O. glaberrima.
Manufacturing technique advances in tool and die production
Authors: Ufomba Emmanuel C. , Gadzama Samuel W. , Seboni Lone 
Published: January 2022

Abstract
Extant research on fabrication of machine parts have contributed to an understanding of manufacturing processes for a tank cover, using conventional methods. However, the gap lies in the need to tap on advanced manufacturing processes in the production of a leak-proof tank cover, to achieve not only precision, dependability, and mass production but also to promote the issue of context in the manufacturing industry. To respond to this gap, we present research that utilizes novel experimental techniques for tool and die production, to demonstrate superiority over existing research in terms of using modern trends in the production line. The contribution lies in buttressing the synergy between conventional ways of fabricating machine parts in the workshop by using current trends to achieve same results as conventional ways of fabricating machine parts by exploiting advantages of using computer numerically controlled machines in the production of the minting ink tank cover. A numerically controlled milling machine was used to achieve better results compared with conventional methods. Engineering design software was used to generate 2-D coordinates of the work piece diagram with which a computer program was written, duly simulated and certified fit to produce the work piece. Results showed an exact replication of the minting ink tank cover that is more importantly, capable of producing 25 pieces per hour and an annual volume of 48000 pieces. These results are significant to the manufacturing industry in achieving four things: time and energy management, mass production, super surface finish, and consistent quality.
Development of a New Hybrid Adsorbent Based on Polyaniline@Chitosan and Its Application to Acetaminophen Removal From Aqueous Solution
Authors: Daikh Samia , Ouis Dalila , Abdelghani Benyoucef , Mouffok Benali 
Published: January 2022

Abstract
The polyaniline (PANI) with chitosan (CS) (PANI@CS) was synthesized using in-situ polymerization process and its preparation was assured by surface area, XPS, TPD, XRD, FTIR, TGA and SEM analysis. PANI@CS, CS and PANI were used for the removal of acetaminophen (AAP). The maximum value of adsorption capacities were found to be 385.25 mg.g−1 for PANI@CS, 359.84 mg.g−1 for CS and 242.49 mg.g−1 for PANI which reveal that the adsorption capacity of hybrid adsorbent is major than CS and PANI respectively. Moreover, H–bonding, π–π bonding, pore-filling and chemisorption have been suggested as probable mechanism for the elimination of AAP by PANI@CS. Furthermore, AAP elimination was preferable at pH 7.0. Pseudo-second-order (PSO) and Langmuir models reported the kinetic and isotherm data acceptably. This shows that the adsorption processes of AAP are a monolayer chemical adsorption, and it was endothermic, spontaneous, and favorable for the three adsorbents. Moreover, when reused, the hybrid adsorbent remains at around 69% of their original capacities after five adsorption cycles.
Tool Life and Surface Integrity Characteristics of SLM and C&amp;W Inconel 718 in Dry and MQL Condition
Authors: Periane Sasidharan , Duchosal Arnaud , Vaudreuil Sébastien , Chibane Hicham , Morandeau Antoine , Xavior Michael Anthony , Cormier Jonathan , Leroy René 
Published: January 2022

Abstract
In this paper, a tool life test was performed using PVD coated insert on Inconel 718 (IN718) samples. The tool life was tested on IN718 workpiece fabricated through conventional (Cast & Wrought) and additive (Selective Laser Melting) process routes. The as-built SLM samples were subjected to two heat treatments such as Hot Isostatic Pressing (HIP) and Aeronautic Heat Treatment (AHT). This study aimed to evaluate the machining behavior of C&W and SLM IN718 from the machining point of view such as tool wear, chip appearance, surface roughness, and residual stresses. The tool life tests were performed under a dry and near dry environment like using Minimum Quantity Lubrication (MQL). Meanwhile, the tool wear propagation under different cutting conditions is also explored. Under both the cutting conditions flank wear and fracture of the cutting edge are the most predominant failure modes minimizing the tool life. The microhardness, surface roughness, and residual stress measurements were analyzed. The result indicates that the microstructural difference between the C&W and SLM has more influence on the tool life compared to the machining environment. On machining, the SLM sample has 80% and 43% more tool life than the C&W in dry and MQL machining. Comparing the dry and MQL machining of SLM, on using MQL the tool life is 30% less compared to the dry machining.
EndoCost Aotearoa New Zealand: a Cross-sectional Survey of Chronic Pelvic Pain and Endometriosis
Authors: Tewhaiti-Smith Jordan , Semprini Alex , Bush Deborah , Anderson Augustus , Eathorne Allie , Johnson Neil , Girling Jane , East Michael , Marriott Joy , Armour Mike 
Published: January 2022

Abstract
Chronic pelvic pain (CPP) causes important negative effects on quality of life. Endometriosis is the most common cause of CPP in females, and diagnostic delay is over six years internationally. Data remain scarce for CPP impact or diagnostic delay in Aotearoa New Zealand. This study used an online survey to explore the impact of CPP on various life domains for those aged over 18. Additionally, for those with an endometriosis diagnosis, diagnostic delay and factors affecting this over time were explored. There were 800 respondent (620 with self-reported endometriosis). CPP symptoms, irrespective of final diagnosis, started prior to age 20 and negatively impacted multiple life domains including employment, education, and relationships. Mean diagnostic delay for those with endometriosis was 8.7 years, including 2.9 years between symptom onset and first presentation and 5.8 years between first presentation and diagnosis. Five doctors on average were seen prior to diagnosis. However, there was a reduction in the interval between first presentation and diagnosis over time, from 8.4 years for those presenting before 2005, to two years for those presenting after 2012. While diagnostic delay is decreasing, CPP, irrespective of aetiology, continues to have a significant negative impact on the lives of those affected.
Receptor for Activated C Kinase 1 promotes cervical cancer lymph node metastasis via glycolysis-dependent AKT/mTOR signaling pathway
Authors: Xu Lixiu , Li Jinqiu , Tursun Mikrban , Hai Yan , Tursun Hatila , Mamtimin Batur , hasimu Ayshamgul 
Published: January 2022

Abstract
Background

Cervical cancer (CC), an aggressive squamous cell carcinoma, is characterized by early lymph node metastasis and extremely poor prognosis. We previously showed aberrant glycolysis in patients with CC. The upregulation of Receptor for Activated C Kinase 1 (RACK1) is associated with CC lymph node metastasis. However, its role in mediating aerobic glycolysis in CC lymph node metastasis remains unclear.
Methods

104 cervical cancer and 31 cervicitis tissue were enrolled. RACK1, insulin-like growth factor 1 receptor (IGF1R), POU class 2 homeobox 2 (POU2F2) and Hexokinase 2 (HK2) expression in cervical cancer patients were detected by Immunohistochemistry analysis. 1H-NMR experiment was used for metabolomics of cell supernatant after RACK1 knockdown. Tube formation assay, Transwell assay, determination of glucose consumption and lactate production assay were performed to detected MS751 and SiHa cells lymphangiogenesis, migration, invasion, glucose consumption and lactate production. Chromatin immunoprecipitation-PCR assay and Dual-Luciferase Reporter Assay was performed to detect the binding among POU2F2 and RACK1. Co-immunoprecipitation and Immunofluorescence staining were performed to detect the binding among RACK1 and GF1R. Xenograft footpad lymph node metastasis was performed using nude mice. Xenograft tumor and metastatic lymph node tissues of mice were experienced immunohistochemistry and hematoxylin–eosin staining.
Results

Here, 1H-NMR analysis revealed significantly correlated RACK1 expression with glycolysis/gluconeogenesis pathway. Additionally, RACK1 knockdown inhibited aerobic glycolysis and lymphangiogenesis in vitro and suppressed CC lymph node metastasis in vivo. Furthermore, AKT/mTOR signaling was identified as a critical RACK1-regulated pathway that led to increased lymphangiogenesis in CC. Co-immunoprecipitation, immunofluorescence, and Western blot showed that RACK1 activated AKT/mTOR signaling by interacting with IGF1R. POU2F2 binds to RACK1 promoter and regulates RACK1 transcription, thus functionally contributing to glycolysis and lymphangiogenesis in CC. Importantly, administration of 2-deoxy-D-glucose, which attenuates glycolysis, inhibited RACK1-induced lymphangiogenesis in CC. The positive correlations between RACK1, IGF1R, POU2F2, and HK2 were further confirmed in CC tissues.
Conclusion

RACK1 plays an important role in CC tumor lymph node metastasis by regulating IGF1R/AKT/mTOR signaling mediated glycolysis pathways. Targeting the POU2F2/ RACK1/IGF1R/AKT/mTOR signaling pathway may provide a novel strategy for CC treatment.
Comparative Analyses of Scylla Olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis
Authors: Lau Nyok-Sean , Ting Seng Yeat , Sam Ka-Kei , M. Janaranjani , Wong Swe Cheng , Wu Xugan , Waiho Khor , Fazhan Hanafiah , Shu-Chien Alexander Chong 
Published: January 2022

Abstract
Multiple studies have linked lipid metabolism with intestinal bacterial structure in aquatic organisms. However, the possibility of the gut microbiota participating in synthesizing beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of mud crab Scylla olivacea fed with either a LC-PUFA rich diet (FO), a LC-PUFA-poor but C18-PUFA substrate rich diet (LOCO), and diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid. Additionally, the microbiota of wild-caught S. olivacea was also analyzed. Compared to diet FO treatment, crabs fed diet LOCO contain a higher proportion of Proteobacteria, represented by Vibrio and Shewanella, two known taxonomy groups with PUFA biosynthesis capacity. Annotation of metagenomic datasets also suggests functional contribution by these two genera in terms of the KEGG pathway of unsaturated fatty acids biosynthesis and the keto-acyl synthase domains in the microbiota of LOCO treatment. Diet LOCOAB impeded the presence of Vibrio and Shewanella within the gut, and concurrently, the abundance of PUFA biosynthesis pathway-related genes. However, there was an increase in the function of short-chain fatty acids production within this diet, which was accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota, represented by Sunxiuqinia and Carboxylicivirga and Sediminispirochaeta, respectively. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of a farmed crustacean species.
Whole-Genome SNP Analysis for Typing the Pandemic Pathogen Fusarium Graminearum Sensu Stricto
Authors: Kulik Tomasz , Molcan Tomasz , Fiedorowicz Grzegorz , Diepeningen Anne van , Stakheev Alexander , Treder Kinga , Olszewski Jacek , Bilska Katarzyna , Beyer Marco , Pasquali Matias , Stenglein Sebastian 
Published: January 2022

Abstract
Recent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, among them a few may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.
In Silico Study for Acyclovir and Its Derivatives Against Mpro of nCoV: Temperature Dependent Molecular Dynamics Simulations
Authors: Babu Madhur Singh , Jain Pallavi , Kumari Kamlesh , Kumar Vinod , Singh Prashant , Bahadur Indra 
Published: January 2022

Abstract
In the present work three molecules acyclovir (A) and ganciclovir (B) are reported to cure the infection from herpes virus and others. We have designed a derivative of hydroxymethyl derivative of ganciclovir (CH2OH of G, that is D) and investigated its potential against the Mpro of nCoV and compared with A & B. Density functional theory (DFT) calculations of A, G and D were performed using Gaussian on applying B3LYP under default condition to investigate the delocalization of electron density in their optimized geometry. Free energy of A, G and D were found to be -810.66964, -925.16575 and -1039.66047 Hartree per particle. It can be clearly seen that D have least free energy. Further, the molecular docking of the A, B and D against the Mpro of nCoV performed using iGemdock and the binding energy for A, B and D are found to be -105.068, -110.605 and -119.226 kcal/mol. It can be clearly seen the D showed effective binding, that is maximum inhibition. For better understanding for the inhibition of the Mpro of nCoV by A, B and D, molecular dynamics simulations were performed at different temperatures, (290, 300, 310 and 320 K). Various trajectories like RMSD, RMSF, Rg and hydrogen bond were extracted and analyzed. The results of molecular docking corroborate the MD simulations that is, a better inhibitor of Mpro of nCoV.
Whole-brain Irradiation With or Without Hippocampal Sparing in Primary Central Nervous System Lymphoma: Impact of Sites of Primary Lesions and Recurrences on Personalized Treatment
Authors: Mazzarella Ciro , Chiesa Silvia , Toppi Lucrezia , Hohaus Stefan , D’Alo Francesco , Dinapoli Nicola , Gaudino Simona , Bartoli Francesco Beghella , Frascino Vincenzo , Davide Resta , Gambacorta Maria Antonietta , Colosimo Cesare , Valentini Vincenzo , Balducci Mario 
Published: January 2022

Abstract
PurposeOne of the main limiting factors of whole-brain radiation therapy (WBRT) for primary central nervous system lymphoma (PCNSL) is the impairment of neurocognitive functions (NCFs), which is mainly caused by radiation-induced injury to the hippocampus. With a view to preventing NCF impairment and personalizing treatment, we explored the feasibility of sparing the hippocampus during WBRT by correlating the sites of PCNSL lesions with the hippocampus. Methods and MaterialsPre-treatment MR images from patients who underwent WBRT between 2010 and January 2020 - and post-radiotherapy images in cases of relapse - were imported into the Varian Eclipse treatment-planning system and registered with the simulation CT. We constructed three 3-dimensional envelopes around the hippocampus at distances of 5, 10 and 15mm and also contoured primary lesions and recurrences.ResultsWe analyzed 43 patients with 66 primary lesions: 9/66 (13.6%) involved the hippocampus and 11/66 (16.7%) were located within 5mm of it. Thirtysix lesions (54.5%) were situated more than 15 mm from the hippocampus, while 10/66 (15.2%) were between 5 and 15 mm from it. The most common location was in deep brain structures (31%). Thirty-five of the 66 lesions relapsed: 14/35 (40%) in the same location and 21/35 (60%) in different sites. Globally, 16/35 recurrences (45.7%) were located in the hippocampus or within 5mm of it.ConclusionThese data show that routinely sparing the hippocampus is not feasible. This approach could be considered in selected patients, when the lesion is more than 15 mm from the hippocampus.