bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods
Authors: Tully Benjamin J. , Finkel Steven E. , Corzett Christopher H. 
Published: December 2023

ABSTRACTBackgroundPCR-based diagnostics, predominantly utilized for pathogen detection, have faced challenges in broader microbial profiling due to disparities in genomic data availability. This study addresses this limitation by exploiting the surge in the number of microbial genomes, facilitated by advancements in next-generation sequencing (NGS) and metagenomic-assembled genomes. The primary aim was to develop and validate quantitative PCR (qPCR) assays for a wide range of gut commensals, traditionally overlooked due to inadequate genomic information. We sought to compare the efficacy of these qPCR assays against established NGS microbiome profiling methodologies - 16S amplicon and metagenomic sequencing.MethodsWe designed 110 species-specific qPCR assays for gut commensals using a novel proprietaryin silicopipeline and validated the assays against stool samples from three healthy donors. The quantitative microbiome profiles were compared to taxonomic profiles generated by standard bioinformatic approaches for 16S amplicon and metagenomic sequencing. 16S amplicons were analyzed as amplicon sequence variants produced by DADA2 and metagenomic sequences were analyzed by multiple iterations of MetaPhlAn (versions 2, 3, and 4) and Kraken2/Bracken paired with two different genomic databases. The qPCR assays were assessed for their ability to detect low abundance microbes and their correlation with NGS results, focusing on taxonomic resolution and limits of quantification.ResultsThe qPCR assays demonstrated high concordance with advanced metagenomic and the ineffectiveness of 16S amplicon methods to achieve species-level assignments. qPCR microbiome profiles were more highly correlated with the most current bioinformatic methods than the bioinformatics methods were to each other. The profile comparisons also highlight how the continued use of older bioinformatics protocols can limit results and lead to misinterpretation of data. Notably, qPCR identified taxa undetected or underestimated by metagenomic approaches, revealing limitations in current bioinformatics tools for differentiating closely related species and quantifying low abundance taxa.ConclusionsThis study establishes qPCR as a robust tool for large-scale microbiome profiling, offering enhanced accuracy, sensitivity, and quantitative capabilities compared to standard NGS methods. Our findings advocate for the integration of qPCR in standardizing microbiome detection, providing a pathway towards developing human microbiome profiling platforms capable of accurate species quantification. The adoption of qPCR assays could lead to more consistent, reliable, and cost-effective microbiome research and diagnostics.
Auditory High Entropy Response (A-HER): A Novel Paradigm for Studying Brain Processing of Uncertain Information
Authors: Liang Xiaoqi , Zhu Qianyun , Zhang Zhiguo , Hu Zhenxing , Liang Zhen , Li Linling , Zhang Li , Xiao Xuezhen , Huang Gan 
Published: December 2023

AbstractThis paper introduces a novel experimental paradigm - Auditory High Entropy Response (A-HER), which maximizes the information entropy of auditory stimulus sequences. This allows us to study how the brain processes complex information, rather than isolated individual events. Our analysis of the frequency response of the frontal theta rhythm induced by A-HER indicated a significant increase in signal-to-noise ratio and repeatability compared to zero-entropy Auditory Steady-State Response (A-SSR) and low-entropy mismatch negativity (MMN). We further investigated whether the A-HER response was induced by stimulus sequence differences or uncertainty, and studied its propagation rules. Different principles between evoked and entrained were found in A-HER and A-SSR. In conclusion, the A-HER paradigm, by maximizing stimulus sequence uncertainty, offers a new approach to analyzing how the brain processes uncertain information. It has potential for diagnosing and researching neurological and mental diseases, and for brain-computer interfaces, thus potentially impacting neuroscience, cognitive science, and psychology.
Comment on ‘Accumbens cholinergic interneurons dynamically promote dopamine release and enable motivation’
Authors: Taniguchi James , Melani Riccardo , Chantranupong Lynne , Wen Michelle J. , Mohebi Ali , Berke Joshua , Sabatini Bernardo , Tritsch Nicolas 
Published: December 2023

AbstractAcetylcholine is widely believed to modulate the release of dopamine in the striatum of mammals. Experiments in brain slices clearly show that synchronous activation of striatal cholinergic interneurons is sufficient to drive dopamine release via axo-axonal stimulation of nicotinic acetylcholine receptors. However, evidence for this mechanismin vivohas been less forthcoming. A recent paper ineLife(Mohebiet al., 2023) reported that, in awake behaving rats, optogenetic activation of striatal cholinergic interneurons with blue light readily evokes dopamine release measured with the red fluorescent sensor RdLight1. Here, we show that blue light alone alters the fluorescent properties of RdLight1 in a manner that may be misconstrued as phasic dopamine release, and that this artefactual photoactivation can account for the effects attributed to cholinergic interneurons. Our findings indicate that measurements of dopamine using the red-shifted fluorescent sensor RdLight1 should be interpreted with caution when combined with optogenetics. In light of this and other publications that did not observe large acetylcholine-evoked dopamine transientsin vivo, the conditions under which such release occurs in behaving animals remain unknown.
GABA Increases Sensory Transmission In Monkeys
Authors: Mahrous Amr A. , Liang Lucy , Balaguer Josep-Maria , Ho Jonathan C. , Hari Krishnapriya , Grigsby Erinn M. , Karapetyan Vahagn , Damiani Arianna , Fields Daryl P. , Gonzalez-Martinez Jorge A. , Gerszten Peter C. , Bennett David J. , Heckman C.J. , Pirondini Elvira , Capogrosso Marco 
Published: December 2023

ABSTRACTSensory input flow is central to voluntary movements. For almost a century, GABA was believed to modulate this flow by inhibiting sensory axons in the spinal cord to sculpt neural inputs into skilled motor output. Instead, here we show that GABA can also facilitate sensory transmission in monkeys and consequently increase spinal and cortical neural responses to sensory inputs challenging our understanding of generation and perception of movement.
Population genomic analysis reveals high inbreeding in a Hawksbill turtle population nesting in Singapore
Authors: Tiong Regine Hui Yi , Dacanay Justine , Uchida Akira , Desai Archita Sanjay , Kalsi Namrata , Tong Collin , Kim Hie Lim 
Published: December 2023

AbstractSeven species of marine turtles remain in a world currently threatened by anthropogenic activities and climate change, standing at the precipice of extinction. Urgent conservation endeavours are imperative to safeguard their survival and preserve the biodiversity of marine ecosystems. Yet, genetic studies on these turtles have leaned on restricted genetic markers, such as the mitochondrial control region. The markers could provide incomplete or biased estimations of genetic diversity and population structure, thereby limiting precise conservation strategies. Here, we have generated ade novogenome assembly and high-quality whole-genome population datasets from hawksbill turtles nesting and foraging in Singapore. This initiative aims to contribute to unbiased, fine-resolution genetic data on the species, conducting a comprehensive population genomic study. Our analysis results demonstrated a remarkable enhancement in genetic markers. While we identified five different haplotypes defined by five variants within 69 mitochondrial control region sequences, the analysis of 35 whole genome sequences uncovered approximately 12 million single nucleotide polymorphisms (SNPs). Within the Singapore hawksbill turtle population, our whole-genome analysis revealed a pronounced degree of inbreeding, with most samples sharing at least a first cousin relationship. Furthermore, within a multiple-paternity nest, we identified related parents. Additionally, our inference of demographic history underscored the impact of past climate change on the decreasing hawksbill turtle population. We believe this pioneering study will substantially enhance the field of conservation genetic study of marine turtles.
Development and validation of multivariable predictive models for recurrence and mortality following nonoperative management of sigmoid volvulus
Authors: Loria Anthony , Cai Xueya , Gao Shan , Zhao Tony , Juviler Peter , Li Yue , Cupertino Paula , Fleming Fergal J. 
Published: December 2023

AbstractAimSigmoid volvulus is a challenging condition, and deciding between elective surgery or expectant management can be complex. The aim of this study was to develop a tool for predicting the risk of recurrent sigmoid volvulus and all‐cause mortality within 1 year following initial nonoperative management.MethodThis is a retrospective cohort study using Medicare claims data from 2016 to 2018 of beneficiaries admitted urgently/emergently for volvulus, undergoing colonic decompression and discharged alive without surgery (excluding those discharged to hospice). The primary outcomes were recurrent sigmoid volvulus and all‐cause mortality within 1 year. Proportional hazards models and logistic regression were employed to identify risk factors and develop prediction equations, which were subsequently validated.ResultsAmong the 2078 patients managed nonoperatively, 36.1% experienced recurrent sigmoid volvulus and 28.6% died within 1 year. The prediction model for recurrence integrated age, sex, race, palliative care consultations and four comorbidities, achieving area under the curve values of 0.63 in both the training and testing samples. The model for mortality incorporated age, palliative care consultations and nine comorbidities, with area under the curve values of 0.76 in the training and 0.70 in the testing sample.ConclusionThis study provides a straightforward predictive tool that utilizes easily accessible data to estimate individualized risks of recurrent sigmoid volvulus and all‐cause mortality for older adults initially managed nonoperatively. The tool can assist clinicians and patients in making informed decisions about such risks. While the accuracy of the calculator was validated, further confirmation through external validation and prospective studies would enhance its clinical utility.
Down‐regulation of miR‐21‐5p by pirfenidone to inhibit fibroblast proliferation in the treatment of acquired tracheal stenosis
Authors: Li Wentao , Huang Pingping , Wei Jinmei , Tan Sen , Liu Guangnan , Yang Qiu , Wang Guangfa 
Published: December 2023

AbstractObjectiveTreatment options for acquired tracheal stenosis (ATS) are limited due to a series of pathophysiological changes including inflammation and cell proliferation. Micro ribonucleic acid‐21‐5p (miR‐21‐5p) may promote the excessive proliferation of fibroblasts. However, various types of fibrosis can be prevented with pirfenidone (PFD). Currently, the effect of PFD on miR‐21‐5p and its biological function has not been clarified. In this study, PFD was evaluated as a potential treatment for ATS by inducing fibroblast proliferation in lipopolysaccharide (LPS)‐induced fibroblasts by targeting miR‐21‐5p.MethodsFor 48 h, 1 g/ml LPS was used to generate fibroblasts in vitro, followed by the separation of cells into four groups: control, PFD, mimic, and mimic + PFD. The Cell Counting Kit‐8 (CCK‐8) technique was adopted to measure the proliferation of fibroblasts. Real‐time quantitative polymerase chain reaction (RT‐qPCR) and Western blot (WB) were used to measure the relative expressions of tumor necrosis factor‐α (TNF‐α), transforming growth factor‐β1 (TGF‐β1), drosophila mothers against decapentaplegic 7 (Smad7) and collagen type I alpha 1(COL1A1) messenger RNA (mRNA) and proteins, respectively.Results(1) At 0, 24, 48, and 72 h, fibroblast growth was assessed using the CCK‐8 method. Compared with the control group, the mimic group showed the highest fibroblast viability, and the PFD group showed the lowest fibroblast viability. However, fibroblast viability increased in the mimic + PFD group but decreased in the mimic one. (2) RT‐qPCR and WB showed that the mimic group exhibited a significant up‐regulation in the relative expressions of TNF‐α, TGF‐β1, and COL1A1 mRNA and proteins but a down‐regulation in the relative expression of Smad7 mRNA and protein compared with the control one. In the PFD group, the results were the opposite. Nevertheless, the relative expressions of TNF‐α, TGF‐β1, and COL1A1 mRNA and proteins were increased, whereas that of Smad7 mRNA was decreased in the mimic + PFD group. The change was less in the mimic group.ConclusionPFD may have a preventive and curative effect on ATS by inhibiting fibroblast proliferation and the fibrotic process and possibly through down‐regulating miR‐21‐5p and up‐regulating Smad7 and its mediated fibrotic and inflammatory responses.
A meta‐analysis examining the impact of intrawound treatment on reducing deep surgical site infections during instrumented spine surgery
Authors: Zhou Liqiang , Xing Shuxing 
Published: December 2023

AbstractThe purpose of the meta‐analysis was to evaluate and compare the effect of intrawound management on decreasing deep surgical site infections (SSIs) in instrumented spinal surgery (SS). The results of this meta‐analysis were analysed, and the odds ratio (OR) and mean difference (MD) with 95% confidence intervals (CIs) were calculated using dichotomous or contentious random or fixed effect models. For the current meta‐analysis, 29 examinations spanning from 2006 to 2022 were included, encompassing 11 181 people who had instrumented SS. Intrawound management had a significantly lower deep SSI when using vancomycin (OR, 0.34; 95% CI, 0.25–0.44, p < 0.001) and povidone‐iodine as intrawound management (OR, 0.24; 95% CI, 0.13–0.42, p < 0.001) compared to control in instrumented SS subjects. The data that was looked at showed that using vancomycin and povidone‐iodine as intrawound management had a much lower deep SSI than using a control group of instrumented SS subjects. However, given that some studies included a small number of subjects, attention should be given to their values.
Parathyroidectomy Improves Bone Density in Women With Primary Hyperparathyroidism and Preoperative Osteopenia
Authors: Frey Samuel , Gérard Maxime , Guillot Pascale , Wargny Matthieu , Bach-Ngohou Kalyane , Bigot-Corbel Edith , Renaud Moreau Nelly , Caillard Cécile , Mirallié Eric , Cariou Bertrand , Blanchard Claire 
Published: December 2023

Abstract

Context
Osteoporosis and/or bone fractures are indications of parathyroidectomy in primary hyperparathyroidism (PHPT), especially in women. However, the benefit of surgery in patients with osteopenia remains unclear.

Objective
To evaluate bone mineral density (BMD) and bone remodeling biomarkers changes 1 year after parathyroidectomy in women with PHPT.

Design
In the prospective, monocentric, observational prospective cohort with primary hyperparathyroidism patients (CoHPT) cohort, women operated for sporadic PHPT since 2016 with ≥1 year follow-up were included. BMD (dual-X ray absorptiometry) and bone remodeling biomarkers [cross-linked C-telopeptide (CTX), procollagen type 1 N-terminal propeptide (P1NP), and bone-specific alkaline phosphatases] were assessed before and 1 year after parathyroidectomy.

Setting
Referral center.

Patients
A total of 177 women with PHPT (62.5 ± 13.3 years, 83.1% menopausal, 43.9% osteopenic, and 45.1% osteoporotic) were included.

Intervention
Parathyroidectomy.

Main Outcome Measure
BMD change between before and 1 year after parathyroidectomy.

Results
Parathyroidectomy resulted in significant increase in BMD and decrease in serum bone remodeling biomarker concentrations. In the 72 patients with baseline osteopenia, mean BMD significantly increased at the lumbar spine [+0.05 g/cm2 (95% confidence interval [CI], 0.03–0.07)], the femoral neck [+0.02 g/cm2 (95% CI 0.00–0.04)], the total hip [+0.02 g/cm2 (95% CI 0.01–0.02)], and the forearm [+0.01 (95% CI 0.00–0.02)], comparable to osteoporotic patients. Among osteopenic patients, those with individual BMD gain (&gt;0.03 g/cm2) at ≥1 site had higher preoperative serum CTX, P1NP, and urine calcium concentrations than those without improvement.

Conclusion
Parathyroidectomy significantly improved BMD and remodeling biomarkers in women with osteopenia, thereby supporting the benefit of parathyroidectomy in these patients. Preoperative serum CTX and P1NP concentrations could be useful to predict expected BMD gain.
Stably Unusual
Authors: Waller Thomas 
Published: December 2023

Abstract
This article critically compares two recent approaches to the problem of aesthetic autonomy: Dave Beech’s Art and Value and Nicholas Brown’s Autonomy. By recentering the differences between these critics’ works around Marx’s categories of subsumption, it evaluates the fraught relationship between labor and aesthetics, economy and form, art and the market. Although Beech provides a persuasive account of art’s “economic exceptionalism,” his focus on the qualitative irreducibility of artistic labor risks losing sight of what is socially unique about aesthetic production. Likewise, and inversely, while Brown’s original account of art’s internal overcoming of the commodity-form provides a generative way to rethink aesthetics in modernism’s wake, it rests on a periodizing claim for the total domination of the capitalist market that equivocates on whether artistic labor can truly be “really subsumed” under capital. The article concludes by pondering the political dimension to these theories of autonomy, which mirror in important ways debates within communization circles over subsumption, programmatism, and the aesthetics of revolution.
Cholangitis and Interruptions of Neoadjuvant Chemotherapy Associate with Reduced Overall and Progression-Free Survival in Pancreatic Cancer
Authors: Vehviläinen Sini , Kuuliala Antti , Udd Marianne , Nurmi Anna , Peltola Katriina , Haglund Caj , Kylänpää Leena , Seppänen Hanna 
Published: December 2023

Abstract
Background
Interrupting chemotherapy may explain the reduced overall survival (OS) in patients with pancreatic cancer (PC) with cholangitis. Endoscopic biliary decompression (BD) with metallic stents results in fewer chemotherapy interruptions and a lower cholangitis rate compared with plastic stents. We aimed to determine the impact of cholangitis, neoadjuvant treatment (NAT) interruptions and biliary stent choice on PC patients’ survival.

Methods
We conducted a retrospective analysis of 162 patients with cancer of the head of the pancreas undergoing pancreatoduodenectomy after NAT and BD documenting progression-free survival (PFS) and OS. Data on BD, cholangitis, stent type, surgical radicality, and chemotherapy were collected. Survival was estimated based on the Kaplan–Meier method by using the log-rank test and multivariate Cox regression analysis.

Results
Median OS and PFS for patients with cholangitis (n = 33, 20%) were 26 and 8 months (95% confidence interval [CI] 20–32 and 5–10 months), respectively, compared with 36 and 17 months (95% CI 31–41 and 12–21 months; p < 0.001 for OS; p = 0.002 for PFS) for patients without cholangitis. Among patients without NAT interruptions median OS and PFS were 35 and 17 months (95% CI 31–40 and 12–21 months), falling to 26 and 7 months (95% CI 18–30 and 5–10 months) among those who experienced an NAT interruption caused by biliary stent failure (n = 26, 16%) (p = 0.039 for OS; p < 0.001 for PFS). We found no difference in OS or PFS between stent types.

Conclusions
Cholangitis and NAT interruptions reduce OS and PFS among PC patients.
Developing and testing the feasibility of a new internet-based intervention–A case study of people with stroke and occupational therapists
Authors: Barcheus Ida-Maria , Ranner Maria , Nyman Anneli , Månsson Lexell Eva , Larsson-Lund Maria 
Published: December 2023

Introduction
Internet-based interventions are called for within rehabilitation to meet the limited access to support for self-management after stroke. Therefore, a new intervention program, “Strategies for Empowering activities in Everyday life” (SEE) was developed. The aim of this study was to explore and describe how clients with stroke and their occupational therapists experienced the SEE intervention process and whether SEE has the potential to promote an active everyday life.

Methods
A qualitative descriptive case study was designed. Four people with stroke (two of each sex, mean age 66,5 years) and their two occupational therapists (one of each sex) were included. A mix of data collection methods as interviews, assessments, registration forms and fieldnotes was used to uncover the participants’ experiences and potential changes. Data were analysed with pattern matching.

Findings
The analysed data formed three categories: “Not being able to take on the internet-based intervention”, “Being facilitated in the change process of everyday life through the internet-based intervention”, and “Providing a new internet-based intervention is a transition from ordinary practice”. These categories included two to four subcategories that reflected aspects of SEE feasibility and acceptability with a focus on content and delivery.

Conclusion
The first test of the intervention indicates that the content and delivery of SEE can be feasible and acceptable both for clients and occupational therapists. The findings suggest that SEE has the potential to support clients’ self-reflections and their adoption of strategies that influence engagement in daily activities and satisfaction with life in various ways. Further research with large-scale studies is needed.
EXAMPLE CRIMINOLOGICAL DETERMINANTS OF THE SPREAD OF THE IDEOLOGY OF TERRORISM IN EDUCATIONAL ORGANIZATIONS OF HIGHER EDUCATION AND PROFESSIONAL EDUCATIONAL ORGANIZATIONS
Authors: Стародубцева М.А. 
Published: December 2023

The article examines the facts of the spread of the ideology of terrorism in educational organizationsas manifestations of «idealistic» terrorism, according to the classification proposed by Yu.M. Antonyan.From the point of view of criminology, terrorism is understood as a diverse phenomenon. In this regard,it is necessary to determine what type of terrorism educational organizations face. Next, it is necessary tohighlight the determinants of the spread of the ideology of terrorism in educational organizations.The analysis of criminal cases according to the elements of Art. 205.2 of the Criminal Code of theRussian Federation and a survey of teachers and teachers of a number of educational organizations in theAltai Territory makes it possible to determine the determinants of the spread of the ideology of terrorismin educational organizations. The traditional division of the determinants of crime into general social,socio-psychological and personal needs to be clarified in relation to terrorist crimes committed by youngpeople studying in educational organizations. Among the general social determinants of terrorist crime in educational organizations, the main role is played by the social qualities of young people. Among the sociopsychological determinants, the main role is played by shortcomings in family education and the formalismof preventive measures. The analysis of criminal cases allows us to conclude that among the families of thoseaccused and on trial for committing terrorist crimes in educational organizations, pedagogically incorrectlyoriented families prevail, where, for one reason or another, psychological contact with the child has notbeen established.