bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh
Authors: Rahman Aura , Styczynski Ashley , Khaleque Abdul , Hossain Sakib Abrar , Sadique Abdus , Hossain Arman , Jain Mukesh , Tabassum Syeda Naushin , Khan Fahad , Bhuiyan Mohammad Sami Salman , Alam Jahidul , Khandakar Amith , Kamruzzaman Mohammad , Ahsan Chowdhury Rafiqul , Kashem Saad Bin Abul , Chowdhury Muhammad E. H. , Hossain Maqsud 
Published: June 2022

Abstract
Background:
Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones.
Results:
Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes (CCs): the globally dominant CC1 and CC2, and CC10; one strain had a novel sequence type (ST). AMR phenotype-genotype agreement was observed and the genomes contained various beta-lactamase genes including blaADC-25 (n = 14), blaOXA-23 (n = 12) and blaNDM-1 (n = 3). All genomes displayed roughly similar virulomes, however some virulence genes such as the Acinetobactin bauA and the type IV pilus gene pilA displayed high genetic variability. CC2 strains carried highest levels of plasmidic gene content and possessed conjugative elements carrying AMR genes, virulence factors and insertion sequences.
Conclusion:
This study presents the first comparative genomic analysis of XDR clinical Acinetobacter spp. from Bangladesh. It highlights the prevalence of different classes of beta-lactamases, mobilome-derived heterogeneity in genetic architecture and virulence gene variability in prominent Acinetobacter clonal complexes in the country. The findings of this study would be valuable in understanding the genomic epidemiology of A. baumannii clones and their association with closely related pathogenic species like A. nosocomialis in Bangladesh.
Changes in nutritional and bio-functional compounds and antioxidant capacity after mixed whole grain fermentation By
Authors: Wang Chih-Feng , Huang Cui-Rou , Lu Ying Chen 
Published: June 2022

Abstract
Whole grains are rich in nutrients. Microbial fermentation of grains increases their nutritional content and their antioxidant capacity. This study uses a mixed grain fermentation broth as a starter to ferment a mixture of eight grains: millet, wheat, sorghum, black rice, buckwheat, pear rice, black glutinous rice, and red quinoa. The fermentation was done for 13 weeks, to discern the quantitative changes in the concentration of amino acids, antioxidant capacity, GABA, glucuronic acid, ACE inhibition, total flavonoids and total phenols. After fermentation, the results indicated that the total phenols concentration increased by 2605%, total flavonoids increased by 1707%, ABTS radical scavenging capacity increased by 239%, DPPH radical scavenging capacity increased by 325%, GABA increased by 4810%, glucuronic acid increased by 4278%, and ACE inhibition activity increased by 69.28%.
Predictors of Morbidity in Revisional Bariatric Surgery and Bariatric Emergencies at an MBSAQIP-Accredited Community Hospital
Authors: Oviedo Rodolfo J. , Tomey Daniel , Martinino Alessandro , Nguyen-Lee Joseph , Lopez Alfred , Shenwai Priya , Nayak Tapan , Chai Jichong , Long Zhuoxin , Wiseman James 
Published: June 2022

Abstract
INTRODUCTION Bariatric surgery revisions and emergencies are associated with higher morbidity and mortality compared to primary bariatric surgery. No formal outcome benchmarks exist that distinguish MBSAQIP-accredited centers in the community from unaccredited institutions. METHODS A retrospective chart review was conducted on 53 bariatric surgery revisions and 61 bariatric surgical emergencies by a single surgeon at a high-volume community hospital accredited program from 2018 to 2020. Primary outcomes were complications or deaths occurring within 30-days of the index procedure. Secondary outcomes included operative time, leaks, surgical site occurrences (SSOs), and deep surgical site infections. RESULTS There were no significant differences in the demographic characteristics of the study groups. Mean operative time was significantly longer for revisions as compared to emergency operations (149.5 vs 89.4 minutes). Emergencies had higher surgical site infection (SSI) (5.7% vs 21.3%, p<0.05) and surgical site occurrence (SSO) (1.9% vs 29.5%, p<0.05) rates compared to revisions. Logistic regression analysis identified several factors to be predictive of increased risk of morbidity: pre-operative albumin <3.5 g/dL (p<0.05), recent bariatric procedure within the last 30 days (p<0.05), prior revisional bariatric surgery (p<0.05), prior duodenal switch (p<0.05), and pre-operative COPD (p<0.05). CONCLUSION Bariatric surgery revisions and emergencies have similar morbidity and mortality, far exceeding that of the primary operation. Outcomes comparable to those reported by urban academic centers can be achieved in community hospital MBSAQIP-accredited centers. Keywords: Revisional bariatric surgery, bariatric emergencies, community hospital, MBSAQIP
Spatial variation in fish assemblages is explained by hydrological connectivity
Authors: O’Mara Kaitlyn , Venarsky Michael , Stewart-Koster Ben , McGregor Glenn B. , Schulz Cameron , Marshall Jonathan , Bunn Stuart E. 
Published: June 2022

Abstract

Hydrological connectivity in river systems facilitates the movement of animals, nutrients, and energy across riverine landscapes but is threatened by climate change and water resource developments. These anthropogenic disturbances are expected to alter connectivity patterns in wet-dry tropical river systems that are driven by a highly variable seasonal flow regime. We studied the composition and functional diversity of fish assemblages across a large wet-dry tropical river system in northern Australia that is under consideration for new agricultural and water resource developments. We explored changes in the environment, species turnover, and relationships between environmental characteristics and fish species composition, quantifying how they were influenced by hydrological connectivity, to identify species and habitats at risk of impacts of reduced connectivity. Characteristics of the aquatic environment were significantly different between low connectivity, high connectivity, and off-channel sites, and these environmental characteristics were associated with changes in fish community composition. Fish species turnover occurred across the catchment, with unique assemblages in headwater sites. High turnover between adjacent sites of low connectivity suggested that reduced movement opportunity creates localized populations, and these differences in species presence/absence are likely to be exacerbated by reduced connectivity from water resource developments. Species turnover was also related to functional diversity, which itself varied across connectivity levels. Habitat specialists and species with functional traits that depend on hydrological connectivity, such as diadromous species, are most at risk from anthropogenic change. Protection of the flow regime and environmental characteristics that support these species is important for maintaining biodiversity.
Hippocampal neurons code individual episodic memories in humans
Authors: Kolibius Luca , Roux Frédéric , Parish George , Wal Marije Ter , Plas Mircea Van Der , Chelvarajah Ramesh , Sawlani Vijay , Rollings David , Lang Johannes , Gollwitzer Stephanie , Walther Katrin , Hopfengärtner Rüdiger , Kreiselmeyer Gernot , Hamer Hajo , Staresina Bernhard , Wimber Maria , Bowman Howard , Hanslmayr Simon 
Published: June 2022

Abstract
The hippocampus is an essential hub for episodic memory processing. However, how human hippocampal single neurons code multi-element associations remains unknown. Some argue that each hippocampal neuron codes for an invariant element within an episode. Instead, others have proposed that hippocampal neurons bind together all elements present in a discrete episodic memory. Here, we provide evidence for the latter. We show that individual neurons, which we term Episode Specific Neurons (ESNs), code discrete memory episodes. These ESNs do not reflect the coding of a particular element in the episode (i.e., concept or time). Instead, they code for the conjunction of the different elements that make up the episode.
Development and characterization of microsatellite markers in the African timber tree species Cylicodiscus gabunensis (Fabaceae)
Authors: Bhasin Oriana Bili , Sargeant Saskia , Hardy Olivier J. 
Published: June 2022

Abstract
I. Background: Cylicodiscus gabunensis (Fabaceae) or ‘Okan’ is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density and a natural regeneration deficit in dense forest. II. Methods and Results: We aimed to characterize polymorphic microsatellite markers that can be used to study patterns of genetic structure and gene flow (mating system, pollen and seed dispersal and inbreeding depression) and ultimately, help to develop sustainable forest management practices. We developed 24 polymorphic markers that can be amplified in three PCR multiplexes that were tested in 647 individuals of C. gabunensis from three populations. The number of alleles ranged from 4 to 27 and the average observed and expected heterozygosity across loci and populations were Ho = 0.585 (0.081-0.936) and He = 0.510 (0.076-0.914), respectively. III. Conclusions: This set of markers is a useful tool for exploring intra-specific diversity, genetic structure and gene flow of C. gabunensis.
Spindle cell melanoma masquerading as a lipoma: an interesting presentation of a rare cancer
Authors: Lamm Ryan , Lyons Walker , Gargano Stacey M , Willis Alliric I 
Published: June 2022

Abstract
Background: Overall survival is directly correlated to melanoma thickness and definitive surgical excision. Spindle cell melanoma is a rare subtype of malignant melanoma and particularly difficult to diagnose. Identification of histopathological features and referral to specialists are essential. Case presentation: We describe the case of an 86-year-old male who presented to his family medicine physician with complaints of a large 40 mm mass on his right posterior trunk which was clinically diagnosed as a lipoma. This mass was subsequently removed in his family physician’s office as an office procedure. Less than eight months post-excision, the tumor had erupted through the incision site. At time of surgical oncologist evaluation, the tumor was pedunculated and measured 92 mm at its greatest diameter. This tumor was subsequently biopsied to reveal spindle cell melanoma with thickness of at least 22 mm. Wide local excision was performed with complete removal of the tumor with negative margins.Conclusion: Our report supports the importance of early and correct diagnosis of cutaneous melanoma which can often be mistaken for other cutaneous lesions, both benign and malignant. In these situations, it is important to obtain a tissue biopsy and consult with specialists in pathology and surgical oncology/dermatology to ensure timely, appropriate treatment.
Anemia and It's Risk Factors among Patients with Type II Diabetes Mellitus, Alkhair Medical Center, Wad Medani, Gezira State, Sudan (2020)
Authors: Mohamedahmed Khalid Abdelsamea , Mohammed Rumisa Mobashar , Talha Albadawi Abdebagi 
Published: June 2022

Abstract
BackgroundAnemia is one of the common complications of diabetes mellitus, and their risk in diabetic patients is estimated to be 2–3 times higher than that of patients without diabetes. Therefore, having a major impact on the overall health and survival of diabetes patients. Globally, the prevalence of concurrent anemia and diabetes mellitus ranges from 14–45% in various ethnic populations worldwide.ObjectivesThe aim of this study was to determine the prevalence of anemia among type II diabetic patients.MethodologyThis is a cross-sectional laboratory-based study conducted in Alkhair Medical Center, Wad Medani, Gezira State, Sudan during March to December 2020 among 100 type II diabetic patients ((32 males and 68 females) their ages ranged between 30 and 90 years with mean (52.26 ± 13.58 years). Three ml of venous blood samples were collected from all participants in K3EDTA containers. A thin blood film was prepared and stained immediately. The RBCs parameters were performed using Sysmex XP-300 Automated Hematology Analyzer. SPSS computer program (v 25.0) was used for data analysis.ResultsThe study results showed that the prevalence of anemia among patients with type 2 Diabetes Mellitus were 7 (7%). 6 (85.7%) patients had mild anemia, and one (14.3%) had moderate anemia according to clinical degree of anemia based on hemoglobin level. 4 (57.14%) patients had microcytic hypochromic anemia, and 2 (28.57%) patients had normocytic normochromic anemia and one (14.29%) patients had macrocytic anemia based on RBCs indices and morphology. The prevalence of anemia is more in female (7.35%) than male (6.25%).ConclusionThe study concluded that anemia among patients with type II Diabetes Mellitus was 7%, mostly mild and microcytic hypochromic anemia; so improve their nutrition status among diabetic patients may help in reducing the anima during diabetes.
Bacterial composition analysis of colorectal tissue is affected by the degree of mucus adhesion
Authors: Tajima Yosuke , Okuda Shujiro , Hanai Tsunekazu , Hiro Junichiro , Masumori Koji , Koide Yoshikazu , Kamiya Tadahiro , Cheong Yeongcheol , Inaguma Gaku , Shimada Yoshifumi , Wakai Toshifumi , Akimoto Shingo , Matsuoka Hiroshi , Uyama Ichiro , Suda Koichi 
Published: June 2022

Abstract
The outer mucus layer of the colorectal epithelium is easily removable and colonized by commensal microbiota, while the inner mucus layer is firmly attached to the epithelium and devoid of bacteria. Although the specific bacteria penetrating the inner mucus layer can contact epithelial cells and trigger cancer development, most studies ignore the degree of mucus adhesion at sampling. Therefore, we evaluated whether bacteria adhering to tissues could be identified by removing the outer mucus layer. Our 16S rRNA gene sequencing analysis of 18 surgical specimens of human colorectal cancer revealed that Sutterella (P = 0.045) and Enterobacteriaceae (P = 0.045) were significantly enriched in the mucus covering the mucosa relative to the mucosa. Rikenellaceae (P = 0.026) was significantly enriched in the mucus covering cancer tissues compared with those same cancer tissues. Ruminococcaceae (P = 0.015), Enterobacteriaceae (P = 0.030), and Erysipelotrichaceae (P = 0.028) were significantly enriched in the mucus covering the mucosa compared with the mucus covering cancers. Fusobacterium (P = 0.038) was significantly enriched in the mucus covering cancers compared with the mucus covering the mucosa. Comparing the microbiomes of mucus and tissues with mucus removed may facilitate identifying bacteria that genuinely invade tissues and affect tumorigenesis.
Investigation of genes involved in lung cancer and their targeting by microRNAs
Authors: Arabameri Hossein , Salimi Alireza , Shademan Behrouz , Karami Behzad , Masjedi Sepideh , Nourazarian Alireza 
Published: June 2022

Abstract

Lung cancer is known as one of the most common cancers worldwide. Non-small cell lung cancer (NSCLC) is found in 85% of cases of lung cancer. In this study, we tried to identify genes that can be used to prevent cancer from progressing with inhibiting their expression by microRNAs. In fact, these gels can be targeted as a treatment. In this study, using the data obtained from the article, 37 genes were finally reached with the Venny 2.1 database. We then analyzed the genes involved in lung cancer, using databases such as DAVID, PANTHR, ENRICHER. Our work provides insight into PDGFRA, LAMC1, and MAP3K8 have critical roles in important pathways and biological process which can developed cancer such as; angiogenesis, integrin signalling pathway, and development process. for the first time, that mir-554 and mir-313 plays a critical role by inhibiting the proto- oncogene genes map3k8, PDGFR and lamc1.
Clinicopathological Characteristics of Pancreatic Neuroendocrine Tumours: Experience From an Indian Tertiary Care Centre
Authors: Prasad Pallavi , Verma Ritu , Gupta Neelima 
Published: June 2022

Abstract
Purpose: Pancreatic neuroendocrine tumours (pNETs) are among the most frequent neuroendocrine tumours. Although considered rare tumours, they have shown an increase in incidence and frequency over the last several years. We aimed to evaluate the clinicopathological features, and determine whether the location of the tumour has some impact on the difference in survival. Methods: The present study retrospectively analyzed the clinicopathological characteristics and outcomes of pNETs operated on between January 2007 to December 2019.Results: 12 patients (46.2%) presented with non-functional symptoms, and 14 (53.8%) had functional symptoms. The most frequent location of the tumour was the head (10) followed by the tail (9). No correlation was found between the primary location of the tumour with age or tumour grade. Metastatic disease was present in six patients, and liver was the commonest site. No correlation was observed between the primary location of the tumour and metastasis at presentation. 16 (61.5%) belonged to grade 1, 8 (30.8%) to grade 2 and 2 (7.7%) to grade 3. Metastasis at presentation was most common with grade-I tumours. Localised metastasis was more common in the body/tail group (9/13). There was no statistical significance between tumour grade or stage and the location of the tumour. The mainstay of treatment was surgical resection with or without adjuvant chemoradiotherapy. Conclusion: pNETs are a diverse group of tumors that exhibit heterogeneity in their pathologic, functional and clinical features. These tumours require a multimodality diagnostic approach and surgical resection is the mainstay of treatment. Histological grade was found to be the only independent prognostic factor affecting long-term survival.
The MCP2 and the wrist plus two tendons are the most affected and responsive joints/tendons out of the US7 score in patients with rheumatoid arthritis – an observational study
Authors: Podewski Annika Franziska , Glimm Anne-Marie , Fischer Imma , Bruyn George Arthur Willem , Hanova Petra , Hammer Hilde Berner , Aga Anna-Birgitte , Haavardsholm Espen A. , Ramiro Sofia , Burmester Gerd-Rüdiger , Backhaus Marina , Ohrndorf Sarah 
Published: June 2022

Abstract
Background: There is no international consensus on an optimal ultrasound score for monitoring of rheumatoid arthritis (RA) on patient-level yet. Our aim was to reassess the US7 score for the identification of the most frequently pathologic and responsive joint/tendon regions to optimize it and contribute to an international consensus. Furthermore, we aimed to evaluate the impact of disease duration on the performance of the score.Methods: RA patients were assessed at baseline and after 3 and 6 months of starting/changing DMARD therapy by the US7 score in greyscale (GS) and power Doppler (PD). The frequency of pathologic joint/tendon regions and their responsiveness to therapy were analyzed by Friedman test including the comparison of palmar vs. dorsal regions (Chi-square test). The responsiveness of different reduced scores and the amount of information retained from the original US7 score were assessed by standardized response mean/linear regression. Analyses were also performed separately for early and established RA.Results: A total of 435 patients (N=138 early RA) were included (56.5 (SD 13.1) years old, 8.2 (9.1) years disease duration, 80% female). The dorsal wrist, palmar MCP2, extensor digitorum communis (EDC) and carpi ulnaris (ECU) tendons were most frequently affected by GS/PD synovitis/tenosynovitis (wrist: 45%/43%; MCP2: 35%/28%; EDC: 30%/11% and ECU: 25%/11%) and significantly changed within 6 months of therapy (all p≤0.003 by GS/PD). The dorsal vs. palmar side of the wrist by GS/PD (p<0.001) and the palmar of the finger joints by PD (p<0.001) were more frequently pathologic. The reduced US7 score (GS/PD: dorsal MCP2, dorsal wrist, EDC and ECU, only GS: palmar MCP2) showed therapy response (SRM 0.433) after 6 months and retained 76% of the full US7 score’s information. No major differences between the groups of early and established RA could be detected.Conclusions: The wrist, MCP2, EDC and ECU tendons were most frequently pathologic and responsive to therapy in both early and established RA and should therefore be included in a comprehensive score for monitoring RA patients on patient-level.
Genome- scale metabolic model based engineering of Escherichia coli enhances recombinant single chain antibody fragment production
Authors: Behravan Aidin , hashemi atieh , Marashi Sayed-Amir , Fouladiha Hamideh 
Published: June 2022

Abstract
Escherichia coli is an attractive and cost-effective cell factory for producing recombinant proteins such as single-chain variable fragments (scFvs). AntiEpEX-scFv is a small antibody fragment that has received considerable attention for its ability to target the epithelial cell adhesion molecule (EpCAM), a cancer-associated biomarker of solid tumors. Due to its metabolic burden, scFv recombinant expression causes a remarkable decrease in the maximum specific growth rate of the scFv-producing strain. In the present study, a genome-scale metabolic model (GEM)-guided engineering strategy is proposed to identify gene targets for improved antiEpEX-scFv production in E. coli. For improving scFv production, flux balance analysis (FBA) and FVSEOF methods identified a number of potential genetic engineering targets localized in the glucose uptake system and pentose phosphate pathway. From the predicted targets, glk gene encoding glucokinase was chosen to be overexpressed in the parent strain Escherichia coli BW25113 (DE3). By overexpressing glk, the growth capacity of the recombinant E. coli strain was recovered. Moreover, the engineered strain with glk overexpression successfully lead to increased scFv production. This approach can be considered for the improvement of other recombinant proteins production.