bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multicenter study of genotype variation/demographic patterns in 2475 individuals inluding with 1444 cases with breast cancer in Turkey Short Title: BRCA profiling of breast-cancer patients in Turkey
Authors: Bisgin Atil , Sag Sebnem Ozemri , Duman Nilgun , Ozdemir Sevda Yesim , Ergoren Mahmut Cerkez , Boga Ibrahim , Dalci Kubilay , Hanta Abdullah , Mujde Cem , Parsak Cem Kaan , Rencuzogullari Çagla , Sonmezler Ozge , Yalav Orcun , Alemdar Adem , Aliyeva Lamiya , Bozkurt Ozlem , Cetintas Sibel , Cubukcu Erdem , Deligonul Adem , Dogan Berkcan , Erguzeloglu Cemre Ornek , Evrensel Turkkan , Gokgoz Sehsuvar , Tolunay Sahsine , Akyurek Esra , Basgoz Neslihan , Coşkun Nuriye , Dundar Bilge , Ozturk Figen , Taskin Duygu , Demirtas Mercan , Cag Murat , Diker Omer , Olgun Polat , Bozdogan Sevcan , Dundar Munis , Temel Sehime Gulsun 
Published: August 2022

Abstract
BACKGROUND
Breast Cancer is the most common cancer type in women, second among the all cancers, and inherited with autosomal dominant pattern. The clinical diagnosis of BC relies on the published diagnostic criteria, and two genes have been identified as the main causative for breast cancer which are BRCA1 and BRCA2.
OBJECTIVE
We aimed to compare the index cases with the diagnostic features to describe the genotype/demographic information association in breast cancer.
METHODS
We performed mutational analyses for the BRCA1 and BRCA2 genes on 2475 individuals from collobrative centers across Turkey, whom 1444 of them were ascertained index cases.
RESULTS
We identified mutations in 17% (421/2475) of all individuals while its almost the same 16.6% (239/1444) in 1444 index cases. Mutations in BRCA1/BRCA2 genes were detected in 17.8% (131/737) of familial cases and 12% (78/549) of sporadic breast cancer, with 4.9% of mutations in the BRCA1 and 12% in the BRCA2.
CONCLUSIONS
Genotype variation and demographic information patterns were analyzed of all observed breast cancer findings in probands. We showed that patients with BRCA2 mutations have significantly been identified more than BRCA1 mutations. We also observed that sporadic breast cancer cases without familial history have less mutation positivity in BRCA1/BRCA2 genes, and the results were consistent with other studies in the Mediterranean region. On performing meta-analyses of our data and the other limited studies of the Mediterranean region in the literature, we found significant correlations that individual studies did not have sufficient power to conclude. Correlating genotypes with demographic information should facilitate the disease management of BC both the familial and non-familial cases.
PSMD13 is a prognostic biomarker and correlated with immune infiltrates in hepatocellular carcinoma
Authors: Wei kexuan , Lin Chunxiang , Li Jie , Zhang Huaying , Song Qiulu , Zhao Wei 
Published: August 2022

Abstract
Background
The Ubiquitin-Proteasome system (UPS) pathway plays a crucial role in the degradation of protein. PSMD13 is a crucial subunit of proteasome S11 regulatory granules and plays an indispensable role in the UPS. However, its role in tumors was still sealed. Our research mainly to study its expression level and effect on the prognosis of LIHC, what pathways PSMD13 works through and how it relates to the level of immune cells.
Methods
Our exploration mainly used GEPIA, Kaplan-Meier Plotter to discover the differentially expressed level of PSMD13 in multiple cancers and surrounding tissue. In the further study of LIHC, we also downloaded the data from the TCGA database. We used R software for multivariate analysis to explore the value of PSMD13 in the prognosis of LIHC. In studying its pathway, we used GSEA to analyze. We also used TISIDB, TIMER to observe its relationship and immune molecules in LIHC.
Results
PSMD13 is differentially expressed in many cancers including LIHC. In LIHC, PSMD13 was an independent prognostic factor. The PSMD13 is likely to take effect upon the regulation of oxidative phosphorylation and proteasome pathway. Besides, the high-level expression of PSMD13 is also relevant to the infiltration of CD8 + T cells and macrophages.
Conclusions
In LIHC, PSMD13 may play an important role in regulating cell cycle and recruitment of immune cells. In addition, PSMD13 may be a reliable biomarker to judge the response to immunotherapy and prognosis of patients with LIHC.
Dependency-Aware Task Offloading for Vehicular Edge Computing with End-Edge-Cloud Collaborative Computing
Authors: Liu Guozhi , Dai Fei , Huang Bi , Qiang Zhenping , Wang Shuai , Li Lecheng 
Published: August 2022

Abstract
Vehicular edge computing (VEC) is emerging as a new computing paradigm to improve the quality of vehicular services and enhance the capabilities of vehicles. It aids vehicles execution tasks with low latency by deploying computing and storage resources close to the vehicle side. However, the traditional task offloading schemes waste the fine-grained offloading opportunities for subtasks by neglecting the decomposability and dependency of tasks. Furthermore, the continuous control problem caused by the learning-based offloading schemes should be taken into account. In this paper, we proposed an efficient dependency-aware task offloading scheme, which minimizes the average processing delay of tasks by fully utilizing the end-edge-cloud collaborative computing. Specifically, first, the directed acyclic graph (DAG) technique is utilized to model the inter-subtask dependency, which establishes the priority of subtask execution. Second, a task offloading algorithm based on Deep Deterministic Policy Gradient (DDPG) in Reinforcement Learning (RL) was proposed to obtain the optimal offloading strategy in a dynamic environment, which efficiently solves continuous control problems and helps reach fast convergence. Finally, we conduct extensive simulation experiments, and the experimental results show that the proposed dependency-aware task offloading scheme can achieve a good performance.
Primary testicular lymphoma demonstrates an over-expression of Wilms tumor 1 gene and different mRNA and miRNA expression profiles compared to nodal diffuse large B-cell lymphoma
Authors: Mansoor Adnan , Akhter Ariz , Shabani-Rad Meer-Taher , Deschenes Jean , Yilmaz Asli , Trpkov Kiril , Stewart Douglas 
Published: August 2022

Abstract
Diffuse large B-cell lymphoma (DLBCL) shows a high degree of clinical and biological heterogeneity. Primary testicular lymphoma (PTL) is an extra nodal variant of DLBCL associated with higher risk of recurrence including contralateral testicle and central nervous system sanctuary sites. Several molecular aberrations including somatic mutation of MyD88, CD79B and upregulation of NF-Kb, PDL-1 and PDL-2 are thought to contribute to the pathogenesis and poor prognosis of PTL. However, additional biomarkers are needed that may improve the prognosis and help understand the PTL biology and possibly lead to new therapeutic targets. RNA from diagnostic tissue biopsies of PTL (n=31) and matched nodal DLBCLs (n=27) patients, were evaluated by mRNA and miRNA expression. Expression of 770 key genes were screened, utilizing nCounter Human miRNA and PAN-cancer pathway mRNA assays utilizing nCounter analysis System (Nanostring technologies). PTL and nodal DLBCL patients were comparable in age, gender, stage, and putative cell of origin (P>0.05). WT1 expression was higher in PTL compared to nodal DLBCL (> 3-fold; P= 0.0001). In addition, we found that WT1 associated pathway genes THBS4, PTPN5, PLA2G2A and IFNA17 were upregulated in PTL (>2.0-fold, P<0.005). The miRNAs targeting WT1 (hsa15a-5p, hsa-miR-16-5p, hsa-miR-361-5p, hsa-miR-27b-3p, hsa-miR-199a-5p, hsa-miR-199b-5p, hsa-miR-132-3p, hsa-miR-128-3p) were upregulated in PTL compared to nodal DLBCL (≥2.0-fold; FDR 0.01). We also found lower expression of BMP7, LAMB3, GAS1, MMP7 and LAMC2 (>2.0- fold, P<0.01) in PTL compared to nodal DLBCL. Our study demonstrated an overexpression of WT1 in PTL compared to nodal DLBCL. We hypothesize that a select miRNA subset targets the WT1 expression and influences the PI3k/Akt pathway in PTL. Additional studies are needed to further investigate the biological role of WT1 in PTL and its potential as a therapeutic target.
Laparoscopic reduction of sigmoidorectal intussusception by a modified Hutchinson’s maneuver: A case report
Authors: Onoyama Haruna , Nakamura Takashi , Ahiko Yuka , Sakuyama Naoki , Aikou Susumu , Shida Dai 
Published: August 2022

Abstract
Background: Traditionally, adult intestinal intussusception is treated using Hutchinson’s maneuver, i.e., manual proximal bowel compression and reduction of intussusception. However, the lack of manual contact in laparoscopic surgery limits the application of Hutchinson’s maneuver. Moreover, when the lead point is located distal to the peritoneal refection, and the intussusception cannot be reduced prior to bowel resection, stoma construction (e.g., Hartmann surgery or abdominoperineal resection) becomes necessary. Here we report a case of sigmoidorectal intussusception treated laparoscopically using a modified Hutchinson’s maneuver.Case presentation: A 74-year-old man was diagnosed with sigmoidorectal intussusception caused by sigmoid colon cancer. Colonoscopy revealed a malignant-appearing obstructing mass telescoping into the rectum, with the lead point at 3 cm from the anal verge. During endoscopic examination, the lead point did not move. A biopsy of the mass showed adenocarcinoma, leading to a diagnosis of sigmoid cancer with sigmoidorectal intussusception. Since the patient had no symptoms of intestinal ischemia, and defecations were observed, elective laparoscopic surgery was planned. Intraoperatively, an attempt was made to pull out the intussuscepted segment proximally, but the presence of fibrous adhesions made the intussusception irreducible. Therefore, the rectum and mesorectum were mobilized completely up to the level of the levator ani so that the lower rectum could be wrapped with gauze on the anal side of the lead point of the intussusception. The gauze was then pulled up to the oral side and simultaneously, a surgeon pushed the distal end of the intussuscepted segment up using a laparoscopic bowel grasper, with another surgeon pushing the lead point through the anus with fingers. Thereby the intussusception was reduced to some extent, allowing for low anterior resection. The resected specimen contained an ulcerated moderately differentiated adenocarcinoma of the sigmoid colon measuring 3.5 cm × 3.0 cm, combined with circumferential ischemia with mucosal loss and necrosis over an 8-cm length on the distal side of the tumor. The tumor was stage III (T3 N1).Conclusion: We provide a laparoscopic approach for treating intussusception using a modified Hutchinson’s maneuver. This method will be useful in reducing the intussuscepted segment while avoiding stoma construction.
Solvation Structure and Dynamics of Aqueous Solutions of Au + Ions: A Molecular Dynamics Simulation Study
Authors: Saha Sudeshna , Bhadyopadhyay Dibyendu , Choudhury Niharendu 
Published: August 2022

Abstract
Although gold (Au) as an element is precious and noble, its ionic form is of huge scientific importance in view of its applications in electrochemistry, nano-electronics and other related fields. We have studied structure and dynamics of aqueous solutions of gold ions (Au+) using molecular dynamics simulations. Using a modified LJ parameter set for the Au+ ions in water in our molecular dynamics simulations, we have established the hydration structure and dynamics of Au+ ions in terms radial distributions, orientations and residence time of the nearest neighbours. Our results on peak position, height and coordination numbers are in much better agreement with those from the recent CPMD simulations. Relative orientation of the neighbours as obtained from the angular distributions suggests octahedral or trigonal bi-pyramidal structure of the solvation shell. Orientational distributions of dipoles and other molecular orientational vectors indicate that the hydrogen atoms of the water molecules are away from the central Au+ ion. The residence time calculated from the corresponding time correlation function is found to reasonably high, indicating less exchange of water molecules between the first and second solvation shells of the Au+ ion. In essence, the present results are in much better agreement with the CPMD results as compared to other QM/MM and classical force-field based simulations.
Neonatal invasive disease caused by Streptococcus agalactiae in Europe: the DEVANI multi-center study
Authors: Lohrmann Florens , Hufnagel Markus , Kunze Mirjam , Afshar Baharak , Creti Roberta , Detcheva Antoaneta , Kazakova Jana , Rodriguez-Granger Javier , Sørensen Uffe B. Skov , Margarit Immaculada , Maione Domenico , Rinaudo Daniela , Orefici Graziella , Kilian Mogens , Efstratiou Androulla , Berner Reinhard , Melin Pierrette 
Published: August 2022

Abstract

Purpose
Group B streptococcus (GBS) remains a leading cause of invasive disease, mainly sepsis and meningitis, in infants < 3 months of age and of mortality among neonates. This study, a major component of the European DEVANI project (Design of a Vaccine Against Neonatal Infections) describes clinical and important microbiological characteristics of neonatal GBS diseases. It quantifies the rate of antenatal screening and intrapartum antibiotic prophylaxis among cases and identifies risk factors associated with an adverse outcome.
Methods
Clinical and microbiological data from 153 invasive neonatal cases (82 early-onset[EOD], 71 late-onset disease [LOD] cases) were collected in eight European countries from mid-2008 to end-2010.
Results
Respiratory distress was the most frequent clinical sign at onset of EOD, while meningitis is found in > 30% of LOD. The study revealed that 59% of mothers of EOD cases had not received antenatal screening, whilst GBS was detected in 48.5% of screened cases. Meningitis was associated with an adverse outcome in LOD cases, while prematurity and the presence of cardiocirculatory symptoms were associated with an adverse outcome in EOD cases. Capsular-polysaccharide type III was the most frequent in both EOD and LOD cases with regional differences in the clonal complex distribution.
Conclusions
Standardizing recommendations related to neonatal GBS disease and increasing compliance might improve clinical care and the prevention of GBS EOD. But even full adherence to antenatal screening would miss a relevant number of EOD cases, thus, the most promising prophylactic approach against GBS EOD and LOD would be a vaccine for maternal immunization.
Immunohistochemical Analysis of the Distribution of RANKL - A Case of Disseminated Carcinomatosis of Bone Marrow as the First Presentation of Relapse in Curatively Resected Colorectal Cancer
Authors: Shimada Yoshitaka , Nagaba Yasushi , Okawa Hiroyuki , Ehara Kaori , Okada Shinya , Naito Masanori , Yokomori Hiroaki 
Published: August 2022

Abstract
Poorly differentiated adenocarcinoma of colorectal carcinoma (CRC) is a rare condition with poor prognosis. Here, we describe the case of a 69-year-old man who underwent laparoscopic low anterior resection and was pathologically diagnosed with stage IIIA CRC. At 10 months post-operation, he developed fever and loss of appetite. Laboratory examination revealed fibrin degradation products > 120.0 µg/dL and D-dimer > 60.0 µg/dL. Bone marrow (BM) examination showed malignant epithelioid infiltrate with CK20 and CDX2 expression, leading to a diagnosis of disseminated carcinomatosis of bone marrow, which is rare in CRC and indicates widespread disease is throughout the body. Furthermore, immunohistochemistry indicated the predominant expression of receptor activator of nuclear factor κB ligand (RANKL) in CRC and BM tissues. Thus, RANKL expression, which is known to indicate metastatic behavior of cancer cells, in CRC may play a critical role in promoting osteoclast formation, which has been associated with the pathogenesis of BM lesions.
Effects of Buffer Substitution on Rapid Diagnostic Tests for Malaria Diagnosis
Authors: Ofosu David Ntiamoah , Akowuah Emmanuel , Amoateng George , Owusu Emmanuel , Sarfo Michael , Mensah Michael , Marfo-Debrekyei Yeboah , Addai-Mensah Otchere 
Published: August 2022

Abstract
Background: Malaria rapid diagnostic tests (mRDTs) detect Plasmodium antigens by antibody-antigen interactions on a nitrocellulose test strip/cassette. While this has proven useful and can detect Plasmodium spp. in about 15-20 mins, false positives and negatives are known limitations of any diagnostic test and mRDTs are no exception. Buffer substitution in RDTs is one phenomenon known to cause such incorrect results even though its extent in practice on the field is unknown. Aim: This study sought to examine the effects of substituting a designated buffer with other liquids on malaria RDTs.Methods: The study was a cross-sectional analytical study that recruited 125 suspected malaria patients from Tafo Government Hospital in Kumasi, Ghana from February to March, 2022. 5ul of blood was taken using a lancet and a thick smear was prepared, stained and examined under light microscopy for malaria parasites. Part of the blood samples were also used concurrently to perform RDTs (using SD Bioline malaria RDT test kit) but with four different buffers separately (designated RDT buffer, 0.9% saline, distilled water and Hightop HBsAg test buffer). Results: Majority of the participants were in their 20s (21.6%) or 30s (20.8%). The least age group recorded were from 40-49 years (9.6%). More than two-thirds of the participants were females (69.6%). The common symptoms recorded were fever (29.6%), headache (28.0%), general body pain (28.0%) and malaise (23.2%). When the RDTs with the different buffers were compared to microscopy, SD Bioline buffer was 90.6% sensitive, 95.7% specific. When distilled water was used as a substitute buffer, it gave a 100% specificity but was less sensitive (68.8%). Similarly, 0.9% saline and HBsAg buffer were specific but less sensitive. Cohen’s Kappa (k) for using SD Bioline RDT buffer, 0.9% saline, distilled buffer and HBsAg were significantly in agreement at 85.4%, 61.7%, 76.6%, and 73.1% with light microscopy respectively (p < 0.0001). Conclusion: Buffer substitution in malaria rapid diagnostic testing reduces the test sensitivity of the kit.
Analgesia and spread of Erector Spinae Plane Block in breast cancer surgeries: a randomized controlled trial
Authors: Abdella Ahmed , Arida Emad Eldin , Megahed Nagwa , El-Amrawy Wessam , Mohamed Walid 
Published: August 2022

Abstract
Background: The goal of this study was to evaluate varying volumes of ESPB on analgesia, LA spread, sedation, and patient satisfaction.Methods: 60 patients aged between 18 and 50 years with an ASA I-II and scheduled for breast cancer surgery were randomized to receive either ESPB with 20 ml 0.25% bupivacaine (Standard volume ESPB), or with 40 ml 0.125% bupivacaine (High volume ESPB), or no ESPB (GA only group). The primary outcome was pain intensity evaluated by the VAS, 12 hours after surgery. P-values < 0.05 were considered the cutoff point for statistical significance. The secondary outcomes were pain at rest and pain on movement evaluated by the VAS, craniocaudal injectate spread, to PV space and epidural space assessed by CT, clinical dermatomal spread, level of sedation assessed by RASS, and patient satisfaction with anaesthesia and analgesia.Results: VAS at rest 12 h after surgery was less in both intervention groups compared with the control (1.75 ± 0.79 vs. 1.6 ± 0.88 vs. 3.4 ± 1.96, p = 0.001). In other time points, VAS was less in each ESPB group compared to GA only during rest and movement and the volume injected made no difference. The LA had extended further in the high volume group than the standard volume group (11.20 ± 3.07 vs. 9.15 ± 2.54 vertebral levels, p = 0.027). No difference of the spread to PV space or epidural space between the 2 intervention groups. More dermatomes were covered in the high volume group (7.20 ± 2.12 vs. 5.75 ± 1.37 dermatomes, p = 0.014). Agitation was higher in GA only group than both ESPB groups in the first 8 postoperative hours. Patient satisfaction was higher in both ESPB groups compared to GA only group.Conclusions: Preoperative ESPB is an excellent analgesic modality that should be considered in breast cancer surgeries. Apart from analgesia it attenuates postoperative agitation and enhances patient satisfaction. Volume injected has no effect on analgesia or patient satisfaction but it results in more LA spread.Trial registration: NCT04796363 (12/3/2021)
A high-quality blue whale genome, segmental duplications, and historical demography
Authors: Bukhman Yury V , Morin Phillip A. , Meyer Susanne , Chu Li-Fang (Jack) , Jacobsen Jeff K. , Antosiewicz-Bourget Jessica , Mamott Daniel , Gonzales Maylie , Argus Cara , Bolin Jennifer , Berres Mark E. , Fedrigo Olivier , Steill John , Swanson Scott Allen , Jiang Peng , Rhie Arang , Formenti Giulio , Phillippy Adam M. , Harris Robert S. , Wood Jonathan M. D. , Howe Kerstin , Kirilenko Bogdan , Munegowda Chetan , Hiller Michael , Jain Aashish , Kihara Daisuke , Johnston J. Spencer , Ionkov Alexander , Raja Kalpana , Toh Huishi , Lang Aimee , Wolf Magnus , Jarvis Erich , Thomson James A. , Chaisson Mark J.P. , Stewart Ron 
Published: August 2022

Abstract

BackgroundThe blue whale, Balaenoptera musculus , is the largest animal known to have ever existed. Body size is tightly coupled to cell metabolism and environmental adaptations. A high-quality genome assembly of this magnificent animal will aid our understanding of body size regulation and related biological processes.ResultsWe report a reference-quality, long read based assembly of the blue whale genome. We sequenced genomic DNA using PacBio long-read, Illumina short-read, and 10X Genomics synthetic long-read technologies. We also obtained long-range mapping information using Bionano optical mapping and Dovetail Hi-C. Additionally, we sequenced the transcriptome of blue whale fibroblasts using Illumina RNA-seq and PacBio Iso-seq technologies. We also measured genome size using a flow cytometry technique. We report on: (1) comparison of alternative long-read and short-read-based assemblies; (2) segmental duplications within the blue whale genome, which have resulted in dramatic amplifications of several genes; (3) sites in IGF1 gene correlated to body size in cetaceans; and (4) heterozygosity and historical demography of Pacific and Atlantic blue whale populations.ConclusionsThis is one of the first high-quality reference genomes of a cetacean and the first baleen whale sequenced using a long-read technology. A high quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.