bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of high-fluoride toothpaste and mouth rinse on the prevention of demineralized lesions during orthodontic treatment: a randomized controlled trial
Authors: Enerbäck Hanna , Lövgren Mai Lin , Strömberg Nicklas , Westerlund Anna 
Published: July 2023

Abstract

Objective
To evaluate the effect of high-fluoride mouth rinse and high-fluoride toothpaste on the development of demineralized lesions (DLs) during orthodontic treatment.

Trial design
Three-armed parallel-group randomized controlled trial.

Methods
The trial was performed with 270 adolescent orthodontic patients. Randomization was performed in blocks of 30, enrolling the patients into one of the following groups: the fluoride mouth rinse (FMR) group receiving 0.2% sodium fluoride (NaF) mouth rinse plus 1450 ppm fluoride (F) toothpaste; high-fluoride toothpaste (HFT) group receiving 5000 ppm F toothpaste; and the Control (CTR) group receiving 1450 ppm F toothpaste. Inclusion criteria were patients scheduled for treatment in both arches with fixed appliances and age between 12 and 20 years. The primary outcome variable was the proportion of participants with at least one new demineralized lesion as assessed on digital photos taken before and after treatment, analysed by a blinded clinician. The analysis included all teeth or teeth in the aesthetic zone, i.e. all central incisors, lateral incisors, and canines. A random sample of 30 participants was assessed to check intra- and inter-reliability. For pairwise comparison between groups, Fisher’s non-parametric permutation test was used for continuous variables. Blinding was employed during the caries registration and data analysis.

Recruitment
October 2010 to December 2012

Results
In total, 270 patients were randomized, of which 22 were excluded during treatment. Therefore, 248 participants were included in the study. The number of patients with an increase of ≥1 DL, including only central- and lateral incisors and canines, during orthodontic treatment, was significantly lower in the HFT group, 51/85 60%, compared to the CTR group, 64/82 78%, RR 0.77 (CI 0.62; 0.95), P = .01 and in the FMR group, 47/81 58%, compared to the CTR group, RR 0.74 (CI 0.60; 0.92), P &lt; .01.

Conclusions
To prevent demineralized lesions in the aesthetic zone, high-fluoride mouth rinse and high-fluoride toothpaste may be recommended.

Limitations
The protocol was not registered, and the present study did not use a double-blinded design.
BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale
Authors: Piñeiro César , Pichel Juan C 
Published: July 2023

Abstract

Background
High-throughput sequencing technologies have led to an unprecedented explosion in the amounts of sequencing data available, which are typically stored using FASTA and FASTQ files. We can find in the literature several tools to process and manipulate those type of files with the aim of transforming sequence data into biological knowledge. However, none of them are well fitted for processing efficiently very large files, likely in the order of terabytes in the following years, since they are based on sequential processing. Only some routines of the well-known seqkit tool are partly parallelized. In any case, its scalability is limited to use few threads on a single computing node.

Results
Our approach, BigSeqKit, takes advantage of a high-performance computing–Big Data framework to parallelize and optimize the commands included in seqkit with the aim of speeding up the manipulation of FASTA/FASTQ files. In this way, in most cases, it is from tens to hundreds of times faster than several state-of-the-art tools. At the same time, our toolkit is easy to use and install on any kind of hardware platform (local server or cluster), and its routines can be used as a bioinformatics library or from the command line.

Conclusions
BigSeqKit is a very complete and ultra-fast toolkit to process and manipulate large FASTA and FASTQ files. It is publicly available at https://github.com/citiususc/BigSeqKit.
Real-World Effectiveness of Vedolizumab vs Anti-TNF in Biologic-naïve Crohn’s Disease Patients: A 2-year Propensity-score-adjusted Analysis from the VEDOIBD-Study
Authors: Bokemeyer Bernd , Plachta-Danielzik Sandra , di Giuseppe Romina , Efken Philipp , Mohl Wolfgang , Hoffstadt Martin , Krause Thomas , Schweitzer Axel , Schnoy Elisabeth , Atreya Raja , Teich Niels , Trentmann Leo , Ehehalt Robert , Hartmann Petra , Schreiber Stefan 
Published: July 2023

Abstract

Background
The aim of this observational, real-world evidence, modified intention-to-treat (mITT) study based on prospectively collected data from the VEDOIBD registry was to compare the effectiveness of vedolizumab (VEDO) vs antitumor necrosis factor (anti-TNF) in biologic-naïve Crohn’s disease (CD) patients.

Methods
Between 2017 and 2020, 557 CD patients starting therapy with VEDO or anti-TNF were consecutively enrolled in 45 IBD centers across Germany. Per study protocol, the analysis excluded biologic-experienced patients and those with a missing Harvey-Bradshaw Index score, resulting in a final sample of 327 biologic-naïve CD patients. Clinical remission was measured using the Harvey-Bradshaw Index at the end of induction therapy and after 1 and 2 years. Switching to a different therapy was considered an outcome failure. Propensity score adjustment with inverse probability of treatment weighting was used to correct for confounding.

Results
The effectiveness of both VEDO (n = 86) and anti-TNF (n = 241) was remarkably high for induction treatment, but VEDO performed significantly less well than anti-TNF (clinical remission: 56.3% vs 73.9%, P &lt; .05). In contrast, clinical remission after 2 years was significantly better for VEDO compared with anti-TNF (74.2% vs 44.7%; P &lt; .05; odds ratio, 0.45; 95% CI, 0.22-0.94). Remarkably, only 17% of patients switched from VEDO to another biologic vs 44% who received anti-TNF.

Conclusions
The results of this prospective, 2-year, real-world evidence study suggest that the choice of VEDO led to higher remission rates after 2 years compared with anti-TNF. This could support the role of VEDO as a first-line biologic therapy in CD.
Appendectomy and Risk of Advanced Colorectal Neoplasia in Inflammatory Bowel Disease: A Nationwide Population-based Cohort Study
Authors: Mark-Christensen Anders , Kristiansen Eskild Bendix , Myrelid Pär , Laurberg Søren , Erichsen Rune 
Published: July 2023

Abstract

Background
The aim of this study was to examine the association between appendectomy and advanced colorectal neoplasia (aCRN) in patients with inflammatory bowel disease (IBD).

Methods
Inflammatory bowel disease patients diagnosed in Denmark in the period 1977 to 2017 were identified from the Danish National Patient Registry. Inflammatory bowel disease patients who underwent appendectomy were matched with up to 10 IBD patients without appendectomy and followed until aCRN, death, or emigration. Absolute risks of aCRN were calculated, treating death and bowel resections as competing risks. Stratified Cox regression was used to calculate adjusted hazard ratios (aHRs) of aCRN, comparing IBD patients with appendectomy to IBD patients without appendectomy.

Results
We identified 3789 IBD patients with appendectomy and 37 676 IBD patients without appendectomy. A total of 573 patients (1.4%) developed aCRN, with an absolute risk of aCRN at 20 years of 4.9% (95% confidence interval [CI], 2.9%-7.7%) for ulcerative colitis (UC) patients with appendectomy after UC diagnosis compared with 2.8% (95% CI, 2.3%-3.3%) for UC patients without appendectomy. Appendectomy after UC was associated with an increased rate of aCRN 5 to 10 years (aHR, 2.5; 95% CI, 1.1-5.5) and 10 to 20 years after appendectomy (aHR, 2.3; 95% CI, 1.0-5.5). Appendectomy prior to UC diagnosis was not associated with an increased rate of aCRN, and Crohn’s disease was not associated with the rate of aCRN, regardless of timing or histological diagnosis of the appendix specimen.

Conclusions
Although appendectomy may have a positive effect on the clinical course of UC, our study suggests that this may come at the expense of a higher risk of aCRN.
The Limits of Liberalization: WTO Entry and Chinese State-Owned Firms
Authors: Tan Yeling , Davis Christina L 
Published: July 2023

Abstract
Does state ownership limit the liberalizing effects of the WTO? We examine the case of China, which is not only the largest exporting state but also lends active support to state-owned enterprises (SOEs) that could distort global trade. Using data on import purchases disaggregated by ownership from 1993 to 2012, we analyze how WTO entry affects the commercial orientation of state-owned and private imports. We demonstrate that after WTO entry, tariff cuts have a larger effect on private compared to SOE trade. We then show that state ownership alone does not block the WTO’s liberalizing effects. For most industries, SOEs and private firms are alike in their commercial orientation. However, where strategic goods targeted by industrial policy hold a large share of bilateral trade, lowering tariffs has no impact on SOE trade. These findings highlight the tensions between state-led economic models and global trade law premised upon market principles.
Contested Sacredness: The Struggle for Bears Ears
Authors: Keegan Brennan 
Published: July 2023

AbstractSouthern Utah and the Four Corners region is home to five Tribal nations, united by shared experiences of settler colonialism and a tie to the landscapes of Bears Ears National Monument. After years of Tribal advocacy to protect the site, President Obama designated the monument under the Antiquities Act in December 2016. A year later, President Trump reduced the 1.35-million-acre national monument by 85 percent to make way for uranium mining, officially sanctifying state control and natural resource extraction. Protests and lawsuits ensued. The legal status of Bears Ears continues to be contested. Religious freedom, capitalism, nationalism, environmental protection, and tourism have coalesced at the site in an example of the production, shift, and conflict of spatial relations. By mapping the constellation of spaces produced by the stakeholders, this article argues that a spatial lens points to moments of overlap and resolution as the case moves forward.
The impact of vaping ethanol-containing electronic cigarette liquids on roadside impairment investigations
Authors: Holt Alaina K , Anbil Akansha , Combs Madison M , Sales Erica R , Boone Edward L , Poklis Justin L , Greer Edgar L , Karaoghlanian Nareg , Breland Alison B , Peace Michelle R 
Published: July 2023

Abstract
Legal professionals and others have suggested that vaping electronic cigarettes (e-cigs) prior to or during ethanol breath testing may produce false positives. Preliminary breath tests (PBTs) and evidentiary breath tests (EBTs) measure ethanol in exhaled breath and standardized field sobriety tests (SFSTs) are used to assess impairment. Ethanol has been identified in e-cig liquids (e-liquids). Presented are a series of experiments designed to determine the mechanics of vaping ethanol using an e-cig and the effects of vaping ethanol on the SFSTs and breath tests used by law enforcement officers (LEO). Twelve participants (five females, age: 21–32 and seven males, age: 21–55), vaped either one or ten puffs of an e-liquid (0% or 20% ethanol). LEOs assessed impairment using SFSTs (12 and 42 min), PBTs (&lt;1, 27, 32, 37 and 57 min) and EBTs (2, 29, 34, 39 and 59 min) post-vaping. A self-assessment test was administered post-vaping (22 and 52 min). Baseline responses for all measures were collected prior to vaping. Results demonstrated that ethanol in the e-liquids was aerosolized by e-cigs and produced particles that could reach the deep lung tissue based on mean-mass diameter. Ethanol was detected by PBT &lt;3 min after participants vaped one (0.007–0.030 g/210 L) or ten puffs (013–0.074 g/210 L) of a 20% ethanol e-liquid. Ethanol was not detected by PBT at any subsequent time point. Ethanol was not detected by the EBT under any condition. Impairment was not indicated by the SFST. Some subjective effects were reported, but few statistically significant differences between conditions were indicated. A wait period prior to ethanol breath testing is not always mandated, depending on jurisdiction, or observed in all applications, such as workplace testing. The results demonstrate that a wait period must be employed to prevent vaping-related false-positive breath ethanol results.
A Pilot Replication Study of Implementing an Equine-Assisted Services Program Within a VA Residential Substance Use Disorder Treatment Program
Authors: Marchand William R , Smith Judy , Nazarenko Elena , Joubert Katryna , Black Heather , Osborne Makenna , Andersen Sarah , Bell Kylie , Baldwin Shannon , Klinger William , Connelly Heather , Sheppard Stephen , Hoopes Karl 
Published: July 2023

ABSTRACT

Introduction
Veterans have high rates of substance use disorders and other mental health conditions including post-traumatic stress disorder. Effective treatments for these conditions exist; however, high attrition rates and residual symptoms after completing treatment are common. Complementary treatment approaches could enhance treatment engagement and/or response among this population. We previously reported a study of one such intervention, an equine-assisted learning, and psychotherapy incorporating horses intervention provided to veterans admitted to a Veterans Health Care Administration residential substance abuse treatment program. The first aim of this study was to replicate the previous study assessing the safety, feasibility, and preliminary outcomes of this intervention. The second aim was to examine the effect of participants attending multiple intervention sessions.

Materials and Methods
Participants were 94 veterans who participated in one to six sessions of a 3–4-hour program consisting of both equine-assisted learning and psychotherapy incorporating horses. Pre- and post-session administration of the Positive and Negative Affect Scale, State-Trait Anxiety Inventory, and Craving Experience Questionnaire was utilized to assess changes in affect, anxiety, and craving. Wilcoxon signed-rank or paired two-tailed t-tests were utilized for pre- to post-session comparisons of the outcome measures for sessions 1–4. Generalized linear mixed-effects (GLME) models were constructed to determine the impact of dosage. GLME models were constructed to determine the impact of dosage.

Results
As with our previous study, the intervention was safe and feasible to utilize for this population. There were statistically significant pre- to post-session improvements, with medium-to-large effect sizes, for sessions 1–3 for negative affect and sessions 1 and 2 for positive affect, anxiety, and craving. The GLME models revealed no statistical significance for any of the predictors.

Conclusions
Taken together, this study and our previous investigation of this equine-assisted services intervention suggest that it is safe and feasible to utilize for veterans admitted to a residential substance abuse treatment program and we have now found short-term benefits in two separate studies. Thus, a randomized controlled trial of this intervention is warranted to demonstrate cause and effect and determine whether longer-term benefits are associated with the intervention. The finding that there was no additional benefit from attendance at more than two intervention sessions suggests that dose–response relationship studies of equine-assisted services interventions for veterans are needed.
Bins, Spans, and Tolerance: Three Theories of Microtiming Behavior
Authors: Danielsen Anne , Johansson Mats , Stover Chris 
Published: July 2023

AbstractThis study compares three recent theories of expressive microtiming in music. While each theory was originally designed to engage a particular musical genre—Anne Danielsen’s beat bins for funk, Neo-Soul, and other contemporary Black musical expressions, Chris Stover’s beat span for “timeline musics” from Africa and the African diaspora, and Mats Johansson’s rhythmic tolerance for Scandinavian fiddle music—we consider how they can productively coexist in a shared music-analytic space, each revealing aspects of musical structure and process in mutually reinforcing ways. In order to explore these possibilities, we bring all three theories to bear on a recording of Thelonious Monk’s “Monk’s Dream,” focusing on Monk’s piano gestures as well as the relationship between saxophonist Charlie Rouse’s improvised solo and Monk’s and bassist John Ore’s accompaniments.
A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination
Authors: Singh Jaideep , Liu Kevin G , Allen Aleique , Jiang Wei , Qin Peter Z 
Published: July 2023

Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The finding sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
On the rules of engagement for microRNAs targeting protein coding regions
Authors: Sapkota Sunil , Pillman Katherine A , Dredge B Kate , Liu Dawei , Bracken Julie M , Kachooei Saba Ataei , Chereda Bradley , Gregory Philip A , Bracken Cameron P , Goodall Gregory J 
Published: July 2023

Abstract
MiRNAs post-transcriptionally repress gene expression by binding to mRNA 3′UTRs, but the extent to which they act through protein coding regions (CDS regions) is less well established. MiRNA interaction studies show a substantial proportion of binding occurs in CDS regions, however sequencing studies show much weaker effects on mRNA levels than from 3′UTR interactions, presumably due to competition from the translating ribosome. Consequently, most target prediction algorithms consider only 3′UTR interactions. However, the consequences of CDS interactions may have been underestimated, with the reporting of a novel mode of miRNA-CDS interaction requiring base pairing of the miRNA 3′ end, but not the canonical seed site, leading to repression of translation with little effect on mRNA turnover. Using extensive reporter, western blotting and bioinformatic analyses, we confirm that miRNAs can indeed suppress genes through CDS-interaction in special circumstances. However, in contrast to that previously reported, we find repression requires extensive base-pairing, including of the canonical seed, but does not strictly require base pairing of the 3′ miRNA terminus and is mediated through reducing mRNA levels. We conclude that suppression of endogenous genes can occur through miRNAs binding to CDS, but the requirement for extensive base-pairing likely limits the regulatory impacts to modest effects on a small subset of targets.
Producing Agreements and Innovations in Collaborative Governance
Authors: Page Stephen B , Thomas Craig , Kern Michael , Murphy Amanda , Page Chris 
Published: July 2023

Abstract
Collaborative governance initiatives often seek innovative solutions to longstanding policy dilemmas, as well as agreements on those solutions among longtime political adversaries. Producing both innovations and agreements in combination is difficult: the diversity among collaborators that enable innovations can complicate their attempts to reach agreements, while unifying factors that support agreements may diminish the prospects for innovation. This article introduces three phases of collaborative agreement and pinpoints drivers of agreements on collaborative innovations. We analyze how each driver connects to the cross-pressure between unity and diversity in collaborative governance and generate propositions that relate each driver to the production of different phases of agreements. Our propositions indicate that collaborators seeking agreements on innovations must strike a balance between factors that support innovations (but may hinder agreements) and factors that support agreements (but may hinder innovations). We recommend ways practitioners can foster and sustain that balance by varying rules governing collaborative participation, information discovery, deliberation, and decisions. We conclude by proposing new research using our conceptual refinements to study whether specific conditions surrounding collaboration are associated with the achievement of different phases of agreement on collaborative innovations.