bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation of bitter components of the asparagus juices during lactic acid bacteria fermentation
Authors: Guan Chengran , Yuan Yuan , Zhang Wenjuan , Ding Xiangli , Zhang Chenchen , Chen Dawei , Lu Maolin , Gu Ruixia , Chen Xia 
Published: September 2021

ABSTRACT
To investigate the bitterness status of asparagus juices during lactic acid fermentation, Limosilactobacillus fermentum Xd, Lacticaseibacillus paracasei Yd, Lactiplantibacillus plantarum 5-7-3, and their various combinations were used for single and mixed fermentation of asparagus juices. The fermentation characteristics and variation of the main bitter substances were studied. For the single and cofermented samples, the viable counts, pH value, and acidity were ranged from 8.33-8.65 lg CFU/mL, 3.58-3.86, and 6.29-6.52 g/kg, respectively. By sensory evaluation, the bitterness of every fermented sample was continuously reduced by at least 77% during fermentation, and the corresponding content of total saponins, flavonoids, and 9 bitter amino acids showed varying degrees of declination. These results suggested that it was feasible to develop novel low-bitter asparagus juices fermented by the lactic acid bacteria used in this study.
Bioinformatics mentorship in a resource limited setting
Authors: Jjingo Daudi , Mboowa Gerald , Sserwadda Ivan , Kakaire Robert , Kiberu Davis , Amujal Marion , Galiwango Ronald , Kateete David , Joloba Moses , Whalen Christopher C 
Published: September 2021

Abstract

Background
The two recent simultaneous developments of high-throughput sequencing and increased computational power have brought bioinformatics to the forefront as an important tool for effective and efficient biomedical research. Consequently, there have been multiple approaches to developing bioinformatics skills. In resource rich environments, it has been possible to develop and implement formal fully accredited graduate degree training programs in bioinformatics. In resource limited settings with a paucity of expert bioinformaticians, infrastructure and financial resources, the task has been approached by delivering short courses on bioinformatics—lasting only a few days to a couple of weeks. Alternatively, courses are offered online, usually over a period of a few months. These approaches are limited by both the lack of sustained in-person trainer–trainee interactions, which is a key part of quality mentorships and short durations which constrain the amount of learning that can be achieved.

Methods
Here, we pioneered and tested a bioinformatics training/mentorship model that effectively uses the available expertise and computational infrastructure to deliver an in-person hands-on skills training experience. This is done through a few physical lecture hours each week, guided personal coursework over the rest of the week, group discussions and continuous close mentorship and assessment of trainees over a period of 1 year.

Results
This model has now completed its third iteration at Makerere University and has successfully mentored trainees, who have progressed to a variety of viable career paths.

Conclusions
One-year (intermediate) skills based in-person bioinformatics training and mentorships are viable, effective and particularly appropriate for resource limited settings.
Social Work Senior Managers as Street-Level Policymakers
Authors: Sery Anat , Weiss-Gal Idit 
Published: September 2021

AbstractThis study enhances the knowledge regarding the role of senior managers of street-level organisations in reshaping social policy on the ground, a subject that has been side-lined in research. The study focused on the ways senior managers of local government social services in Israel, all of whom are social workers by law, implemented emergency material assistance (EMA). This form of assistance is formulated by the central government but administered by local government. A qualitative research design based on semi-structured interviews with sixteen senior managers from diverse localities was employed. Findings showed that senior managers played a major role in the reconstruction of EMA on the ground. They reshaped policy in some or all of its major aspects. Both contextual factors and ideological factors impacted their policy decisions. The contextual factors were budgetary constraints, accessibility of resources from localities or charities, and socio-economic status of the locality. The ideological factors were managers’ attitudes towards the policy, the place of material assistance in the social service, risk, and perceptions of poverty and people living in poverty. These factors led to divergences in material assistance across localities, while conservative and poverty-aware attitudes guided managers as they navigated between state–agent and citizen–agent roles.
‘Marriage is Going to Fix It’: Indigenous Women’s Experiences with Early Childbearing, Early Marriage and Intimate Partner Violence
Authors: McKinley Catherine E , Lilly Jennifer 
Published: September 2021

AbstractIntimate partner violence (IPV), early childbearing (ECB) and early marriage (EM) are interconnected to the historical oppression of patriarchal colonialism imposed upon Indigenous peoples throughout the world by colonising nations, such as the UK. The artefacts of colonial oppression persist in both colonising nations and those that have been colonised through social norms of patriarchal oppression perpetuated upon women with far-reaching consequences. Indigenous women of the US experience higher rates of IPV, ECB and EM than any other ethnic group—which pose risks to women’s physical, psychological, socioeconomic and educational status. The purpose of this study is to explore Indigenous women’s experiences with ECB and EM through a critical ethnography with two US tribes. Through reconstructive analysis the following themes emerged: (i) ECB as a Precursor to Marriage; (ii) Unequal and Overburdened Marriages; (iii) ECB, EM and IPV; and (iv) Continued Harmful Effects of Multiple Abusive Relationships. Indigenous women’s experiences of ECB and EM are connected to patriarchal historical oppression that systematically dehumanises and oppresses Indigenous women, who were once treated with respect and esteem. Decolonisation and re-visualisation to promote the status of women and girls are needed to offset women’s constrained wellness, socio-political status and safety.
An MRI radiomics approach to predict survival and tumour-infiltrating macrophages in gliomas
Authors: Li Guanzhang , Li Lin , Li Yiming , Qian Zenghui , Wu Fan , He Yufei , Jiang Haoyu , Li Renpeng , Wang Di , Zhai You , Wang Zhiliang , Jiang Tao , Zhang Jing , Zhang Wei 
Published: September 2021

Abstract
Preoperative MRI is one of the most important clinical results for the diagnosis and treatment of glioma patients. The objective of this study was to construct a stable and validatable preoperative T2-weighted MRI-based radiomics model for predicting the survival of gliomas.
A total of 652 glioma patients across three independent cohorts were covered in this study including their preoperative T2-weighted MRI images, RNA-seq and clinical data. Radiomic features (1731) were extracted from preoperative T2-weighted MRI images of 167 gliomas (discovery cohort) collected from Beijing Tiantan Hospital and then used to develop a radiomics prediction model through a machine learning-based method. The performance of the radiomics prediction model was validated in two independent cohorts including 261 gliomas from the The Cancer Genomae Atlas database (external validation cohort) and 224 gliomas collected in the prospective study from Beijing Tiantan Hospital (prospective validation cohort). RNA-seq data of gliomas from discovery and external validation cohorts were applied to establish the relationship between biological function and the key radiomics features, which were further validated by single-cell sequencing and immunohistochemical staining.
The 14 radiomic features-based prediction model was constructed from preoperative T2-weighted MRI images in the discovery cohort, and showed highly robust predictive power for overall survival of gliomas in external and prospective validation cohorts. The radiomic features in the prediction model were associated with immune response, especially tumour macrophage infiltration.
The preoperative T2-weighted MRI radiomics prediction model can stably predict the survival of glioma patients and assist in preoperatively assessing the extent of macrophage infiltration in glioma tumours.
Mentoring at the Boundary: Interdisciplinarity and the International Student of Color in Communication
Authors: Murty Madhavi 
Published: September 2021

Abstract
In this paper, I will discuss mentoring within the discipline of Communication by centering international scholars, who are translated as people of color in the U.S. and are engaged with questions drawn from the context of their nations of origin. How do you enable such a scholar to traverse boundaries national and disciplinary with the selfassurance that ostensibly comes from feeling at home? Briefly discussing the history of the institutionalization of Communication as an academic discipline, I ask what it means to mentor scholars of color engaged with transnational work within a space that centers the nation-state as a bounded territory, in general and the U.S. in particular. Drawing on transnational and women of color feminist theorization and praxis, I also draw out the productive collaborations and relationships forged when mentoring reveals the processes through which the discipline reiterates its boundaries.
Frontoparietal Anatomical Connectivity Predicts Second Language Learning Success
Authors: Sander Kaija , Barbeau Elise B , Chai Xiaoqian , Kousaie Shanna , Petrides Michael , Baum Shari , Klein Denise 
Published: September 2021

Abstract
There is considerable individual variability in second language (L2) learning abilities in adulthood. The inferior parietal lobule, important in L2 learning success, is anatomically connected to language areas in the frontal lobe via the superior longitudinal fasciculus (SLF). The second and third branches of the SLF (SLF II and III) have not been examined separately in the context of language, yet they are known to have dissociable frontoparietal connections. Studying these pathways and their functional contributions to L2 learning is thus of great interest. Using diffusion MRI tractography, we investigated individuals undergoing language training to explore brain structural predictors of L2 learning success. We dissected SLF II and III using gold-standard anatomical definitions and related prelearning white matter integrity to language improvements corresponding with hypothesized tract functions. SLF II properties predicted improvement in lexical retrieval, while SLF III properties predicted improvement in articulation rate. Finer grained separation of these pathways enables better understanding of their distinct roles in language, which is essential for studying how anatomical connectivity relates to L2 learning abilities.
Overcoming Data Bottlenecks in Genomic Pathogen Surveillance
Authors: Afolayan Ayorinde O , Bernal Johan Fabian , Gayeta June M , Masim Melissa L , Shamanna Varun , Abrudan Monica , Abudahab Khalil , Argimón Silvia , Carlos Celia C , Sia Sonia , Ravikumar Kadahalli L , Okeke Iruka N , Donado-Godoy Pilar , Aanensen David M , Underwood Anthony ,   NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance, Harste Harry , Kekre Mihir , Muddyman Dawn , Taylor Ben , Wheeler Nicole , David Sophia , Arevalo Alejandra , Fernanda Valencia Maria , Osma Castro Erik C D , Nagaraj Geetha , Govindan Vandana , Prabhu Akshata , Sravani D , Shincy M R , Rose Steffimole , Ravishankar Kundur N , Oaikhena Anderson O , Ajiboye Jolaade J , Ewomazino Odih Erkison , Lagrada Marietta L , Macaranas Polle Krystle V , Olorosa Agnettah M , Herrera Elmer M , Molloy Ali , Stelling John , Vegvari Carolin 
Published: September 2021

AbstractPerforming whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, national, and global scales. To derive WGS-based outputs, a series of processes are required, beginning with sample and metadata collection, followed by nucleic acid extraction, library preparation, sequencing, and analysis. Throughout this pathway there are many data-related operations required (informatics) combined with more biologically focused procedures (bioinformatics). For a laboratory aiming to implement pathogen genomics, the informatics and bioinformatics activities can be a barrier to starting on the journey; for a laboratory that has already started, these activities may become overwhelming. Here we describe these data bottlenecks and how they have been addressed in laboratories in India, Colombia, Nigeria, and the Philippines, as part of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance. The approaches taken include the use of reproducible data parsing pipelines and genome sequence analysis workflows, using technologies such as Data-flo, the Nextflow workflow manager, and containerization of software dependencies. By overcoming barriers to WGS implementation in countries where genome sampling for some species may be underrepresented, a body of evidence can be built to determine the concordance of antimicrobial sensitivity testing and genome-derived resistance, and novel high-risk clones and unknown mechanisms of resistance can be discovered.
Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment
Authors: Sawhney Sanjam S , Johnson Caitlin , Shupe Angela , Fine Jeremy , Dantas Gautam , Burnham Carey-Ann D , Yarbrough Melanie L 
Published: September 2021

Abstract

Background
The urinary tract is not sterile and is populated by microbial communities that influence urinary health. Men who have sex with men (MSM) are understudied yet have increased risk factors for genitourinary infections. Our objective was to interrogate the composition of MSM urinary microbiota.

Methods
Midstream urine specimens (n = 129) were collected from MSM (n = 63) and men seen for routine care (clinical cohort, n = 30). Demographics and sexual/medical history were documented. Specimens underwent culture using standard-of-care and enhanced methods designed to isolate fastidious and anaerobic microorganisms. Isolates were identified by MALDI-TOF mass spectrometry or 16S rRNA gene sequencing.

Results
The MSM cohort was younger (mean (SD), 35.4 (11.26) years) compared to the clinical cohort (62.7 (15.95) years). Organism recovery was significantly increased using enhanced vs standard culture for the MSM (mean of 9.1 vs 0.6 species/sample [P &lt; 0.001]) and clinical (7.8 vs 0.9 species/sample [P &lt; 0.001]) cohorts. The microbial composition of MSM urine specimens was dominated by Gram-positive and anaerobic microbes and clustered distinctly from that of clinical urine specimens. Composition of microbial species recovered within the same subject was dynamic between urine specimens but more similar relative to inter-individual comparisons. Principal coordinate analysis showed no correlation between urinary microbiota composition and age, recent antibiotic use, sexually transmitted infection/HIV status, or sexual practices.

Conclusions
Enhanced culture recovered a large diversity of microbial species from MSM urine specimens, especially taxa typically associated with mucosal surfaces. These findings may increase understanding of urologic disease in MSM and improve diagnostic methods for detection of genitourinary infections.
Youtube Trending Videos: Boosting Machine Learning Results Using Exploratory Data Analysis
Authors: Khanam Sana , Tanweer Safdar , Khalid Syed Sibtain 
Published: September 2021

Abstract
With the emergence of social media and the Internet, bulks of data are generated every day in different fields. However, filtering out useful information, which can be turned into knowledge, requires significant effort. This can be achieved using various Big Data Technologies, statistics, data mining and a variety of machine learning algorithms that corporates and businesses are using to improve their performance every day for a long time now. In this paper, we analyze YouTube trending video data that analyses the target that grabs the user’s attention over a relatively short time. We present our analysis by measuring, mining, analyzing and comparing key aspects of time-series YouTube data with respect to its view and audience response statistics from 40 000 trending YouTube videos collected over 205 days. We have performed an exploratory data analysis (EDA) on all of it's aspect to get data insights and used statistics to find similarities between them to understand viewing pattern of different video categories. We also compare and observe the variation of activity over time with the nature of the event that affects the quality of our analysis. We make the viewership pattern clear belonging to each category separately by direct analysis. The results and findings can help us predict the category of the video that could probably be trending next in the upcoming days and help individuals get boosted views and performance when they upload video as per the predictions and analysis.
The Relationship Between Endoscopic and Clinical Recurrence in Postoperative Crohn’s Disease: A Systematic Review and Meta-analysis
Authors: Ble Alessandro , Renzulli Cecilia , Cenci Fabio , Grimaldi Maria , Barone Michelangelo , Sedano Rocio , Chang Joshua , Nguyen Tran M , Hogan Malcolm , Zou Guangyong , MacDonald John K , Ma Christopher , Sandborn William J , Feagan Brian G , Merlo Pich Emilio , Jairath Vipul 
Published: September 2021

Abstract

Background and Aims
We aimed to quantify the magnitude of the association between endoscopic recurrence and clinical recurrence [symptom relapse] in patients with postoperative Crohn’s disease.

Methods
Databases were searched to October 2, 2020, for randomised controlled trials [RCTs] and cohort studies of adult patients with Crohn’s disease with ileocolonic resection and anastomosis. Summary effect estimates for the association between clinical recurrence and endoscopic recurrence were quantified by risk ratios [RR] and 95% confidence intervals [95% CI]. Mixed-effects meta-regression evaluated the role of confounders. Spearman correlation coefficients were calculated to assess the relationship between these outcomes as endpoints in RCTs. An exploratory mixed-effects meta-regression model with the logit of the rate of clinical recurrence as the outcome and the rate of endoscopic recurrence as a predictor was also evaluated.

Results
In all, 37 studies [N = 4053] were included. For eight RCTs with available data, the RR for clinical recurrence for patients who experienced endoscopic recurrence was 10.77 [95% CI 4.08 to 28.40; GRADE moderate certainty evidence]; the corresponding estimate from 11 cohort studies was 21.33 [95% CI 9.55 to 47.66; GRADE low certainty evidence]. A single cohort study showed a linear relationship between Rutgeerts score and clinical recurrence risk. There was a strong correlation between endoscopic recurrence and clinical recurrence treatment effect estimates as trial outcomes [weighted Spearman correlation coefficient 0.51].

Conclusions
The associations between endoscopic recurrence and subsequent clinical recurrence lend support to the choice of endoscopic recurrence to monitor postoperative disease activity and as a primary endpoint in clinical trials of postoperative Crohn’s disease.
Cardiovascular magnetic resonance imaging in suspected cardiac tumour: a multicentre outcomes study
Authors: Shenoy Chetan , Grizzard John D , Shah Dipan J , Kassi Mahwash , Reardon Michael J , Zagurovskaya Marianna , Kim Han W , Parker Michele A , Kim Raymond J 
Published: September 2021

AbstractAimsCardiovascular magnetic resonance (CMR) imaging is a key diagnostic tool for the evaluation of patients with suspected cardiac tumours. Patient management is guided by the CMR diagnosis, including no further testing if a mass is excluded or if only a pseudomass is found. However, there are no outcomes studies validating this approach.Methods and resultsIn this multicentre study of patients undergoing clinical CMR for suspected cardiac tumour, CMR diagnoses were assigned as no mass, pseudomass, thrombus, benign tumour, or malignant tumour. A final diagnosis was determined after follow-up using all available data. The primary endpoint was all-cause mortality. Among 903 patients, the CMR diagnosis was no mass in 25%, pseudomass in 16%, thrombus in 16%, benign tumour in 17%, and malignant tumour in 23%. Over a median of 4.9 years, 376 patients died. Compared with the final diagnosis, the CMR diagnosis was accurate in 98.4% of patients. Patients with CMR diagnoses of pseudomass and benign tumour had similar mortality to those with no mass, whereas those with malignant tumour [hazard ratio (HR) 3.31 (2.40–4.57)] and thrombus [HR 1.46 (1.00–2.11)] had greater mortality. The CMR diagnosis provided incremental prognostic value over clinical factors including left ventricular ejection fraction, coronary artery disease, and history of extracardiac malignancy (P &lt; 0.001).ConclusionIn patients with suspected cardiac tumour, CMR has high diagnostic accuracy. Patients with CMR diagnoses of no mass, pseudomass, and benign tumour have similar long-term mortality. The CMR diagnosis is a powerful independent predictor of mortality incremental to clinical risk factors.
New evidence: Cryoballoon ablation vs. antiarrhythmic drugs for first-line therapy of atrial fibrillation
Authors: Andrade Jason G , Chierchia Gian-Battista , Kuniss Malte , Wazni Oussama M 
Published: September 2021

Abstract
Atrial fibrillation (AF) is a commonly encountered chronic and progressive heart rhythm disorder, characterized by exacerbations and remissions. Contemporary clinical practice guidelines recommend a trial of antiarrhythmic drugs (AADs) as the initial therapy for sinus rhythm maintenance; however, these medications have modest efficacy and are associated with significant adverse effects. Recently, several trials have demonstrated that an initial treatment strategy of cryoballoon catheter ablation significantly improves arrhythmia outcomes (e.g. freedom atrial tachyarrhythmia and reduction in arrhythmia burden), produces clinically meaningful improvements in patient-reported outcomes (e.g. symptoms and quality of life), and significantly reduces subsequent healthcare resource utilization (e.g. hospitalization), without increasing the risk of serious or any adverse events. These findings are relevant to patients, providers, and healthcare systems, helping inform the decision regarding the initial choice of rhythm-control therapy in patients with treatment-naïve AF.