bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-World Performance of a Comprehensive Genomic Profiling Test Optimized for Small Tumor Samples
Authors: Tomlins Scott A. , Hovelson Daniel H. , Suga Jennifer M. , Anderson Daniel M. , Koh Han A. , Dees Elizabeth C. , McNulty Brendan , Burkard Mark E. , Guarino Michael , Khatri Jamil , Safa Malek M. , Matrana Marc R. , Yang Eddy S. , Menter Alex R. , Parsons Benjamin M. , Slim Jennifer N. , Thompson Michael A. , Hwang Leon , Edenfield William J. , Nair Suresh , Onitilo Adedayo , Siegel Robert , Miller Alan , Wassenaar Timothy , Irvin William J. , Schulz William , Padmanabhan Arvinda , Harish Vallathucherry , Gonzalez Anneliese , Mansoor Abdul Hai , Kellum Andrew , Harms Paul , Drewery Stephanie , Falkner Jayson , Fischer Andrew , Hipp Jennifer , Kwiatkowski Kat , Lazo de la Vega Lorena , Mitchell Khalis , Reeder Travis , Siddiqui Javed , Vakil Hana , Johnson D. Bryan , Rhodes Daniel R. 
Published: August 2021

PURPOSETissue-based comprehensive genomic profiling (CGP) is increasingly used for treatment selection in patients with advanced cancer; however, tissue availability may limit widespread implementation. Here, we established real-world CGP tissue availability and assessed CGP performance on consecutively received samples.MATERIALS AND METHODSWe conducted a post hoc, nonprespecified analysis of 32,048 consecutive tumor tissue samples received for StrataNGS, a multiplex polymerase chain reaction (PCR)–based comprehensive genomic profiling (PCR-CGP) test, as part of an ongoing observational trial ( NCT03061305 ). Sample characteristics and PCR-CGP performance were assessed across all tested samples, including exception samples not meeting minimum input quality control (QC) requirements (< 20% tumor content [TC], < 2 mm2tumor surface area [TSA], DNA or RNA yield < 1 ng/µL, or specimen age > 5 years). Tests reporting ≥ 1 prioritized alteration or meeting TC and sequencing QC were considered successful. For prostate carcinoma and lung adenocarcinoma, tests reporting ≥ 1 actionable or informative alteration or meeting TC and sequencing QC were considered actionable.RESULTSAmong 31,165 (97.2%) samples where PCR-CGP was attempted, 10.7% had < 20% TC and 59.2% were small (< 25 mm2tumor surface area). Of 31,101 samples evaluable for input requirements, 8,089 (26.0%) were exceptions not meeting requirements. However, 94.2% of the 31,101 tested samples were successfully reported, including 80.5% of exception samples. Positive predictive value of PCR-CGP for ERBB2 amplification in exceptions and/or sequencing QC-failure breast cancer samples was 96.7%. Importantly, 84.0% of tested prostate carcinomas and 87.9% of lung adenocarcinomas yielded results informing treatment selection.CONCLUSIONMost real-world tissue samples from patients with advanced cancer desiring CGP are limited, requiring optimized CGP approaches to produce meaningful results. An optimized PCR-CGP test, coupled with an inclusive exception testing policy, delivered reportable results for > 94% of samples, potentially expanding the proportion of CGP-testable patients and impact of biomarker-guided therapies.
PLP2 drives collective cell migration via ZO-1-mediated cytoskeletal remodeling at the leading edge in human colorectal cancer cells
Authors: Ghosh Dipanjana , Dutta Ankita , Kashyap Anjali , Upmanyu Neeraj , Datta Sunando 
Published: August 2021

ABSTRACT
Collective cell migration (CCM), in which cell–cell integrity remains preserved during movement, plays an important role in the progression of cancer. However, studies describing CCM in cancer progression are majorly focused on the effects of extracellular tissue components on moving cell plasticity. The molecular and cellular mechanisms of CCM during cancer progression remain poorly explored. Here, we report that proteolipid protein 2 (PLP2), a colonic epithelium-enriched transmembrane protein, plays a vital role in the CCM of invasive human colorectal cancer (CRC) epithelium by modulating leading-edge cell dynamics in 2D. The extracellular pool of PLP2, secreted via exosomes, was also found to contribute to the event. During CCM, the protein was found to exist in association with ZO-1 (also known as TJP1) and to be involved in the positioning of the latter at the migrating edge. PLP2-mediated positioning of ZO-1 at the leading edge further alters actin cytoskeletal organization that involves Rac1 activation. Taken together, our findings demonstrate that PLP2, via its association with ZO-1, drives CCM in CRC epithelium by modulating the leading-edge actin cytoskeleton, thereby opening up new avenues of cancer research.
This article has an associated First Person interview with the first author of the paper.
The loss of the ‘pelvic step’ in human evolution
Authors: Thompson Nathan E. , Rubinstein Danielle , Parrella-O'Donnell William , Brett Matthew A. , Demes Brigitte , Larson Susan G. , O'Neill Matthew C. 
Published: August 2021

ABSTRACT
Human bipedalism entails relatively short strides compared with facultatively bipedal primates. Unique non-sagittal-plane motions associated with bipedalism may account for part of this discrepancy. Pelvic rotation anteriorly translates the hip, contributing to bipedal stride length (i.e. the ‘pelvic step’). Facultative bipedalism in non-human primates entails much larger pelvic rotation than in humans, suggesting that a larger pelvic step may contribute to their relatively longer strides. We collected data on the pelvic step in bipedal chimpanzees and over a wide speed range of human walking. At matched dimensionless speeds, humans have 26.7% shorter dimensionless strides, and a pelvic step 5.4 times smaller than bipedal chimpanzees. Differences in pelvic rotation explain 31.8% of the difference in dimensionless stride length between the two species. We suggest that relative stride lengths and the pelvic step have been significantly reduced throughout the course of hominin evolution.
The effects of lactic acid bacteria and yeasts as probiotics on the growth performance, relative organ weight, blood parameters, and immune responses of broiler: A meta-analysis
Authors: Sjofjan Osfar , Adli Danung Nur , Harahap Rakhmad Perkasa , Jayanegara Anuraga , Utama Dicky Tri , Seruni Ainun Pizar 
Published: August 2021

Introduction: The number of publications in Scopus on this topic increased from less than 50 in 1995 to more than 250 in 2015. In other hand, inconsistency in results about the correlation between yeast and lactic acid bacteria as probiotics has been evident since the early publications on use in broilers. Methods: A meta-analysis was conducted to determine relationship between lactic acid bacteria and yeast as probiotics to broiler diets on the growth performance, relative organ weight, blood parameters, and immune response of the broiler. A database was designed based on published data that reported the use of probiotics on the broiler. The method used for selecting articles was based on the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) method. Articles selected were taken from PubMed, Web of science, Scopus, Google Scholar, and Science direct databases as well as individual. Results: The final database consists of 49 in vivo articles, 93 studies, and 225 treatments. The analysis statement in the system was a PROC MIXED procedure of SAS software. The level of probiotic increased (p <0.001) body weight, body weight gain, and feed intake of broiler. There was a reduction (p <0.01) on feed conversion ratio and mortality on the level probiotic given to broiler. Supplementation of probiotics in broiler diet increased (p <0.001) the weight of liver, spleen, gizzard, bursa of fabricius and carcass yield, while reduced (p<0.001) abdominal fat weight. The probiotic given increased the total of red and white blood cells (both at p < 0.001) but did not affect lymphocyte. Discussion: It can be concluded the yeast act as supporting agent that serves lactic acid bacteria as probiotic increases the growth performance, relative organ weight, blood parameters, and immune response of the broiler.
A protocol for a systematic review of behaviour change techniques used in the context of stillbirth prevention
Authors: Escañuela Sánchez Tamara , Byrne Molly , Meaney Sarah , O'Donoghue Keelin , Matvienko-Sikar Karen 
Published: August 2021

Background: Stillbirth is a devastating pregnancy outcome that affects approximately 3.5 per 1000 births in high-income countries. Previous research has highlighted the importance of focusing prevention efforts on targeting risk factors and vulnerable groups. A wide range of risk factors has been associated with stillbirth before, including maternal behaviours such as back sleep position, smoking, alcohol intake, illicit drug use, and inadequate attendance at antenatal care. Given the modifiable nature of these risk factors, there has been an increase in the design of behaviour change interventions targeting such behaviours to reduce the risk of stillbirth. Objectives: The aim of this study is to identify all behavioural interventions with a behavioural component designed and trialled for the prevention of stillbirth in high-income countries, and to identify the behaviour change techniques (BCTs) used in such interventions using the Behaviour Change Techniques Taxonomy V1 (BCTTv1). Inclusion criteria: Interventions will be included in this review if they (1) have the objective of reducing stillbirth rates with a focus on behavioural risk factors; (2) are implemented in high-income countries; (3) target pregnant women or women of childbearing age; and (4) are published in research articles. Methods: A systematic search of the literature will be conducted. The results of the search will be screened against our inclusion criteria by two authors. The following data items will be extracted from the selected papers: general information, study characteristics, participant and intervention/approach details. The Cochrane Effective Practice and Organization of Care (EPOC) risk of bias criteria will be used to assess the methodological quality of included studies. Intervention content will be coded for BCTs as present (+) or absent (-) by two authors using the BCTTv1, discrepancies will be discussed with a third author. A narrative synthesis approach will be used to present the results of this systematic review.
Cost-effectiveness of Microsoft Academic Graph with machine learning for automated study identification in a living map of coronavirus disease 2019 (COVID-19) research
Authors: Shemilt Ian , Arno Anneliese , Thomas James , Lorenc Theo , Khouja Claire , Raine Gary , Sutcliffe Katy , Preethy D'Souza , Kwan Irene , Wright Kath , Sowden Amanda 
Published: August 2021

Background: Conventionally, searching for eligible articles to include in systematic reviews and maps of research has relied primarily on information specialists conducting Boolean searches of multiple databases and manually processing the results, including deduplication between these multiple sources. Searching one, comprehensive source, rather than multiple databases, could save time and resources. Microsoft Academic Graph (MAG) is potentially such a source, containing a network graph structure which provides metadata that can be exploited in machine learning processes. Research is needed to establish the relative advantage of using MAG as a single source, compared with conventional searches of multiple databases. This study sought to establish whether: (a) MAG is sufficiently comprehensive to maintain our living map of coronavirus disease 2019 (COVID-19) research; and (b) eligible records can be identified with an acceptably high level of specificity. Methods: We conducted a pragmatic, eight-arm cost-effectiveness analysis (simulation study) to assess the costs, recall and precision of our semi-automated MAG-enabled workflow versus conventional searches of MEDLINE and Embase (with and without machine learning classifiers, active learning and/or fixed screening targets) for maintaining a living map of COVID-19 research. Resource use data (time use) were collected from information specialists and other researchers involved in map production. Results: MAG-enabled workflows dominated MEDLINE-Embase workflows in both the base case and sensitivity analyses. At one month (base case analysis) our MAG-enabled workflow with machine learning, active learning and fixed screening targets identified n=469 more new, eligible articles for inclusion in our living map – and cost £3,179 GBP ($5,691 AUD) less – than conventional MEDLINE-Embase searches without any automation or fixed screening targets. Conclusions: MAG-enabled continuous surveillance workflows have potential to revolutionise study identification methods for living maps, specialised registers, databases of research studies and/or collections of systematic reviews, by increasing their recall and coverage, whilst reducing production costs.
Cantilever deflection optical fiber sensor based on a chirped fiber
grating Fabry–Perot cavity
Authors: Xie Zhanwu , Yan Haitao , Zhang Hongtao , Zhao Xiaoyan , Han Daofu 
Published: August 2021

A cantilever deflection fiber-optic sensor based on chirped fiber grating (CFG)
Fabry–Perot (FP) cavity had been proposed and experimental
demonstrated. Two CFBGs with the same chirped coefficient direction
and grating parameters are written in one single-mode fiber by UV mask
exposure to form the CFG-FP cavity. The central wavelength of two CFGs
is 1549.6072 nm, the 3 dB bandwidth is 2.9897 nm, and the physical
cavity length of two CFGs is 1 cm. The grating region of two CFGs are
straightness fixed on a cantilever beam, forming a sensor. Then the
optical properties of this sensor are tested with different stresses
at different positions of the cantilever beam. The experimental
results show that this sensor can obtain linear displacement of a
cantilever beam, overcoming the abilities of the FBG sensor, which
only performed point measurement defect. The wavelength drift
sensitivity of the sensor is 2.31 pm/g, and linearity is 0.99916. This
sensor has great application value in the precise measurement of
cantilever beam type and two-dimensional scale strain.
E-Government und Datensouveränität – Einblicke und Lösungsansätze
Authors: Heine Moreen , Wessel Daniel 
Published: August 2021

ZusammenfassungDie Digitalisierung hat alle Lebensbereiche erreicht – so auch den öffentlichen Sektor. Um bequeme E‑Government-Angebote bereitstellen zu können, müssen bürgerbezogene Daten zwischen Verwaltungen geteilt werden. Gleichzeitig verfolgen viele Kommunen Smart-City-Strategien und sind dabei auch auf den Zugang zu Daten der Bürger angewiesen. Damit stellt die Digitalisierung und Digitale Transformation im öffentlichen Sektor zunehmend mehr Anforderungen an die Datensouveränität der Bürger. Im privaten Bereich geschieht dieses Teilen und die Weitergabe von Daten häufig unreflektiert oder wenig informiert. Zwar stimmen viele Personen zu, dass ihnen Datenschutz wichtig sei, diese Einstellung zeigt sich allerdings oft nicht im Verhalten (Privacy Paradox). Ziel des Beitrags ist es, basierend auf aktueller Forschung, für die Datensouveränität relevante Eigenschaften von Websites im privaten und öffentlichen Kontext anhand von exemplarischen Fällen zu beschreiben. Unterschieden wird dabei zwischen öffentlichen Angeboten (z. B. Bürgerportale von Kommunen), besonders regulierten Angeboten (z. B. Portale von Banken und Versicherungen) und privaten Angeboten, deren Geschäftsmodell darauf beruht, möglichst umfangreiche Daten über ihre Nutzer zu sammeln (z. B. Soziale Netzwerke). Ziel ist es, Eigenschaften der Websites zu erfassen, die Auswirkungen auf die Datensouveränität auf Nutzerseite haben können und Gestaltungsempfehlungen zur Erhöhung der Datensouveränität, insbesondere für den öffentlichen Sektor, abzuleiten.
Quantifying the effect of Wakefield et al. (1998) on skepticism about MMR vaccine safety in the U.S.
Authors: Motta Matthew , Stecula Dominik 
Published: August 2021

Background
Efforts to trace the rise of childhood vaccine safety concerns in the US often suggest Andrew Wakefield and colleagues’ retracted 1998 Lancet study (AW98)–which alleged that the MMR vaccine can cause children to develop autism–as a primary cause of US vaccine skepticism. However, a lack of public opinion data on MMR safety collected before/after AW98’s publication obscures whether anecdotal accounts are indicative of a potentially-causal effect.

Methods
We address this problem using a regression discontinuity framework to study change in monthly MMR injury claims (N = 74,850; from 1990–2019) from the Vaccine Adverse Events Reporting System (VAERS) to proxy concern about vaccine safety. Additionally, we suggest a potential mechanism for the effect of AW98 on vaccine skepticism, via automated sentiment analyses of MMR-related news stories (N = 674; from 1996–2000) in major television and newspaper outlets.

Results
AW98 led to an immediate increase of about 70 MMR injury claims cases per month, averaging across six estimation strategies (meta-analytic effect = 70.44 [52.19, 88.75], p < 0.01). Preliminary evidence suggests that the volume of negative media attention to MMR increased in the weeks following AW98’s publication, across four estimation strategies (meta-analytic effect = 9.59% [3.66, 15.51], p < 0.01).

Conclusions
Vaccine skepticism increased following the publication of AW98, which was potentially made possible by increased negative media coverage of MMR.

Significance
Childhood vaccine skepticism presents an important challenge to widespread vaccine uptake, and undermines support for pro-vaccine health policies. In addition to advancing our understanding of the previously-obscured origins of US vaccine skepticism, our work cautions that high-profile media attention to inaccurate scientific studies can undermine public confidence in vaccines. We conclude by offering several recommendations that researchers and health communicators might consider to detect and address future threats to vaccine confidence.
Leveraging Fecal Microbial Markers to Improve the Diagnostic Accuracy of the Fecal Immunochemical Test for Advanced Colorectal Adenoma
Authors: Zhang Yuhan , Lu Ming , Lu Bin , Liu Chengcheng , Ma Yiming , Liu Li , Miao Xiaoping , Qin Junjie , Chen Hongda , Dai Min 
Published: August 2021

INTRODUCTION:
Fecal immunochemical tests (FITs) detect colorectal adenoma inefficiently. The gut microbiota participates in colorectal cancer development. We aimed to explore fecal microbial signatures for advanced adenomas and evaluate their diagnostic value and complementary capacity to FIT.

METHODS:
Using 16S rRNA sequencing, we studied gut microbiota in feces from 1,546 subjects in a screening setting, including 268 patients with advanced adenomas, 490 patients with nonadvanced adenomas, and 788 healthy subjects. Feature selections were performed using linear discriminant analysis effect size, multivariate association with linear models, and least absolute shrinkage and selection operator. The diagnostic performance of microbial signatures and their auxiliary role to FITs and the added value of the Asia-Pacific Colorectal Screening score were evaluated. We applied 0.632+ bootstrapping to adjust the potential overfitting.

RESULTS:
We identified 13 microbial signatures to show the joint diagnostic value for advanced adenoma, with genus Tyzzerella 4 demonstrating the highest adjusted area under the curve (AUC) of 0.545 (95% confidence interval [CI], 0.520–0.610). The 13-bacteria increased the adjusted AUC to 0.607 (95% CI, 0.548–0.660). Compared with individual FIT (adjusted AUC = 0.527; 95% CI, 0.519–0.571), 13-bacteria and FITs collectively reached an adjusted AUC of 0.641 (95% CI, 0.579–0.691). At cutoff values yielding specificities of 90% and 80%, the adjusted sensitivities were 28.4% (95% CI, 19.3–36.8) and 41.1% (95% CI, 29.9–49.4), respectively. The Asia-Pacific Colorectal Screening score further boosted the adjusted AUC to 0.706 (95% CI, 0.648–0.750).

DISCUSSION:
In this study using fecal samples from a screening setting, the identified microbial signatures could complement FITs for detecting advanced adenomas. Gut microbiota can act as a promising tool to optimize the current colorectal cancer screening modalities.
Regularization based discriminative feature pattern selection for the classification of Parkinson cases using machine learning
Authors: Kaliyan Kamalakannan , Ganesan Anandharaj 
Published: August 2021

Abstract

Objectives
This paper focuses on developing a regularization-based feature selection approach to select the most effective attributes from the Parkinson’s speech dataset. Parkinson’s disease is a medical condition that progresses as the dopamine-producing nerve cells are affected. Early diagnosis often reduces the effect on the individuals, minimizes the advancement over time. In recent times, intelligent computational models are used in many complex cases to diagnose a clinical condition with high precision. These models are intended to find meaningful representation from the data to diagnose the disease. Machine learning acts as a tool, gears up the model learning process through a mathematical baseline. But, not in all cases, machine learning will be demanded to perform optimally. It comes with a few constraints, mainly the representation of the data. The learning models expect a clean, noise-free input, which in-turns produces better discriminative patterns over different categories of classes.

Methods
The proposed model identified five candidate features as predictors. This feature subset is trained with different varieties of supervised classifiers to trace out the best-performing model.

Results
The results are validated through accuracy, precision, recall, and receiver’s operational characteristic curves. The proposed regularization- based feature selection model outperformed the benchmark algorithms by attaining 100% accuracy on most of the classifiers, other than linear discriminant analysis (99.90%) and naïve Bayes (99.51%).

Conclusions
This paper exhibits the need for intelligent models to analyze complex data patterns to assist medical practitioners in better disease diagnosis. The results exhibit that the regularization methods find the best features based on their importance score, which improved the model performance over other feature selection methods.
Multimodal magnetic resonance imaging analysis in the characteristics of Wilson’s disease: A case report and literature review
Authors: Wang Yun , Jia Zejin , Lyu Yuelei , Dong Qian , Li Shujuan , Hu Wenli 
Published: August 2021

Abstract
Wilson’s disease (WD) is an inherited disorder of copper metabolism. Multimodal magnetic resonance imaging (MRI) has been reported to provide evidence of the extent and severity of brain lesions. However, there are few studies related to the diagnosis of WD with multimodal MRI. Here, we reported a WD patient who was subjected to Sanger sequencing, conventional MRI, and multimodal MRI examinations, including susceptibility-weighted imaging (SWI) and arterial spin labeling (ASL). Sanger sequencing demonstrated two pathogenic mutations in exon 8 of the ATP7B gene. Slit-lamp examination revealed the presence of Kayser–Fleischer rings in both eyes, as well as low serum ceruloplasmin and high 24-h urinary copper excretion on admission. Although the substantia nigra, red nucleus, and lenticular nucleus on T1-weighted imaging and T2-weighted imaging were normal, SWI and ASL showed hypointensities in these regions. Besides, decreased cerebral blood flow was found in the lenticular nucleus and the head of caudate nucleus. The patient recovered well after 1 year and 9 months of follow-up, with only a Unified Wilson Disease Rating Scale score of 1 for neurological symptom. Brain multimodal MRI provided a thorough insight into the WD, which might make up for the deficiency of conventional MRI.