bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal Transcribed Spacers Enable Species-Level Metataxonomic Analysis of Ciliated Protozoa
Authors: Somasundaram Sripoorna , Yu Zhongtang 
Published: February 2025

Abstract
Traditional morphology-based ciliate classification is often time-consuming and inaccurate, necessitating molecular approaches. Although 18S rRNA gene sequencing is widely used for taxonomic analyses of ciliates, its high degree of conservation makes it challenging to achieve species-level resolution. This study explores the potential of internal transcribed spacers (ITS1 and ITS2) and the 28S rRNA gene to improve taxonomic resolution beyond that offered by 18S rRNA gene in free-living and host-associated ciliates. A comparative analysis of ITS, the 18S, and 28S rRNA gene sequences retrieved from public databases indicated that ITS regions exhibit greater inter- and intra-specific sequence dissimilarity compared to 18S rRNA gene, supporting existing literature. We then designed universal primers targeting the ITS and 28S rRNA gene for freshwater and rumen ciliates. These primers were rigorously evaluated for their inclusiveness, specificity, and amplification efficiency using in-silico PCR, experimental PCR, followed by sequencing and metataxonomic analyses of the ciliate communities. In-silico analyses revealed inclusiveness exceeding 80%, while experimental analyses validated their specificity. Metataxonomic analyses of ciliates demonstrated that the ITS and 28S rRNA gene captured significantly greater taxonomic diversity than 18S rRNA gene. Also, ITS1 offered superior taxonomic resolution by detecting the most ciliate species that went unnoticed by the 18S rRNA gene. These findings underscore the superiority of ITS1, and to a lesser extent ITS2, as taxonomic markers for enhancing the resolution of freshwater and rumen ciliate communities. We recommend ITS1 as an alternative marker to overcome the limitations of 18S rRNA gene-based approaches in free-living and host-associated ciliate taxonomy.
Synthetic DNA Spike-in Standards for Cross-Domain Absolute Quantification of Microbiomes by rRNA Gene Amplicon Sequencing
Authors: Tourlousse Dieter M , Sekiguchi Yuji 
Published: February 2025

Abstract
Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of twelve unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.
HSF1 and CPSF1 affect milk fat and protein synthesis by regulating the AKT/mTOR signaling pathway
Authors: Chen Zhujun , Zhang Xinyi , Teng Jun , Jiang Li , Zhang Qin 
Published: February 2025

Abstract
In our previous genome-wide association study on milk production traits in Chinese Holstein cows, HSF1 (heat shock factor 1) and CPSF1 (cleavage and polyadenylation specific factor 1) were found to be strongly associated with milk fat and protein percentages. However, their roles in milk fat and protein synthesis and the underlying mechanism are still largely unknown. In this study, we verified the effects of their expressions on milk fat and milk protein synthesis in MAC-T cells. We showed that HSF1 can participate in the AKT/mTOR signaling pathway, one of the most important pathways for fat and protein synthesis, through its interaction with the AKT protein, and influence the downstream genes in this pathway to regulate milk fat and milk protein synthesis. We also found that HSF1, as a transcription factor, can bind to the promoter region of CPSF1 to regulate its transcription and expression, which in turn modulates the expression of SREBP1 and thereby influences the synthesis of milk fat.
Empty Education: A Dialogue of Nishitani and Rancière
Authors: Kuusela Anttoni E A , Hietamäki Sari 
Published: February 2025

Abstract
In this article, we study the educational views of two philosophers from two different intellectual traditions: those of the East and West. We aim to explore comparative philosophy, a method intrinsic to the Kyoto School, as a practice, using it to engage the ideas of Nishitani Keiji and Jacques Rancière in dialogue. This dialogue takes place between Nishitani’s concept of emptiness and Rancière’s concept of equality. Taking inspiration from what Anton Luis Sevilla has termed ‘negative education’, we propose an alternative philosophy of education: empty education. To develop our new concept, we examine the importance of emptiness and equality in education, focusing on the fruitful and emancipatory encounters they promote. We contend that a reciprocal relationship between the I and the Thou is essential for bypassing the unequal relations and stultifying processes found in education.
Estimating the number of primary versus incidental COVID-19 hospitalizations in Santa Clara County
Authors: Smith Rosamond , D’Agostino Alexis , Stoddard Pamela , Kamal Ahmad , Kelsey Kate , Li Linlin , Lin Wen , Enanoria Wayne T A , Rudman Sarah L , Hoover Christopher 
Published: February 2025

Abstract

Background
The goal of this study is to evaluate whether ICD-10 discharge data can be used to accurately differentiate primary COVID-19 hospitalizations, which are specifically due to COVID-19, from incidental COVID-19 hospitalizations for monitoring COVID-19 trends in one large county health department. We sought to explore the use of machine learning algorithms for enhancing surveillance capabilities in a local public health setting.

Methods
Discharge data for 5,122 Santa Clara County hospitalizations with a positive SARS-CoV-2 PCR or antigen test occurring between December 15, 2021 and August 15, 2022 were used to train a series of models for classifying primary COVID-19 hospitalizations, using chart review as a gold standard. Area under the receiver operator characteristic curve (AUROC) was used as the evaluation metric.

Results
Each model performed well when trained on the full set of available predictors. AUROC values ranged from 0.808 (random forest) to 0.818 (SuperLearner). After evaluating each model, we implemented a reporting process based on the LASSO (Least Absolute Shrinkage and Selection Operator) logistic regression, as the performance was comparable with the SuperLearner and it had the advantage of being transparent and familiar to health department staff.

Conclusions
In Santa Clara County, ICD-10 discharge data was successfully used to develop a low burden method for monitoring primary COVID-19 hospitalization, demonstrating one way that predictive algorithms can help local health jurisdictions meet surveillance needs while minimizing manual effort.
The Movement System and Diagnosis: Are we There Yet?
Authors: McClure Philip 
Published: February 2025

Abstract
In the 29th Maley lecture, Phil McClure PT, PhD, FAPTA, shares a Perspective regarding the movement system and diagnosis. Despite declarations from the House of Delegates over 10 years ago, the concept of a movement system has not been widely embraced in either education or practice. In this perspective, he offers critical analysis and 3 proposals that could potentially make the concept of a movement system more relevant and meaningful. The first is to operationally define the movement system, arguing that the current definition is too vague and not operational, and therefore not meaningful. The second is to intentionally separate the movement system from any specific diagnostic classification scheme which would allow the focus to remain on movement and movement analysis. He argues that diagnostic classification schemes require a biopsychosocial framework and that movement, while important, cannot be the only consideration. The third proposal is that diagnostic schemes must be developed by clinical scientists through appropriate research guided by sound theory, not by administrative or political process. He further argues that a greater focus on determining which patients are likely to be helped by physical therapists is necessary and offered the example of developing “appropriateness criteria” as a tool towards promoting value-based care. Achieving broad consensus around these proposals could unify our professional focus and assist toward the vision of optimizing movement to enhance the human experience.
Cancer Incidence and Mortality in Familial Adenomatous Polyposis Syndrome
Authors: Feldman Dan , Rodgers-Fouche Linda H. , Ukaegbu Chinedu , Yurgelun Matthew B. , Syngal Sapna , Chung Daniel C. 
Published: February 2025

BACKGROUND:
Risk-reducing colectomy in familial adenomatous polyposis syndrome is the standard of care. This has increased the importance of surveillance for extra-colonic malignancies in post-colectomy individuals.

OBJECTIVE:
We sought to define the present-day incidence of all cancers and mortality in familial adenomatous polyposis.

DESIGN:
Retrospective longitudinal cohort study.

SETTINGS:
Two large academic hospitals.

PATIENTS:
Eligible patients carried an APC pathogenic variant or met clinical criteria for familial adenomatous polyposis.

MAIN OUTCOMES MEASURES:
Cancer diagnosis, mortality, associated risk factors.

RESULTS:
A total of 358 patients were identified. The percentage who exhibited a classic familial adenomatous polyposis phenotype was 63.7%; 21.2% were de novo, and 82.7% had a colectomy. Colorectal cancer was the most common cancer (N = 59, 16.5%). Colorectal cancer diagnoses were associated with de novo familial adenomatous polyposis (odds ratio 7.8 [95% CI 3.51-17.35; p < 0.001]). Thyroid, duodenal/small bowel, gastric, and neuroendocrine tumors were reported in 7.5%, 3.1%, 2.8%, and 2.5% of patients, respectively. Rates of cancer were similar in classic and attenuated familial adenomatous polyposis. Thirty-nine patients (10.9%) died at a mean age of 49.6±17.1 years. Twenty-six deaths were malignancy-related, and colorectal cancer was the leading cause (N = 10). All colorectal cancer-related deaths occurred in individuals with classic familial adenomatous polyposis, and 9/10 were not previously diagnosed with the syndrome. Gastric and duodenal/small bowel cancer were the second leading causes (4 deaths each), and all occurred after colectomy. Fifty-nine percent of all deaths were attributable to a familial adenomatous polyposis-related malignancy or morbidity.

LIMITATIONS:
Retrospective clinical data.

CONCLUSIONS:
Colorectal cancer remains the most common malignancy and cause of death in familial adenomatous polyposis. However, nearly all colorectal cancer-related deaths occurred in individuals unaware of their familial adenomatous polyposis diagnosis, and none occurred in the attenuated syndrome. In patients who had a colectomy, gastric and duodenal/small bowel cancers are now the leading causes of death. See Video Abstract.
Effect of Low-Load Blood Flow Restriction Training and High-Load Resistance Training on Quadriceps Strength, Dynamic Stability, and Functional Performance
Authors: Adhitya I Putu Gde Surya , Aryana I Gusti Ngurah Wien , Kurniawati Ida , Thanaya Sayu Aryantari Putri , Utama Made Bang Redy 
Published: February 2025

Objective:
Blood flow restriction (BFR) is a method used to affix a pneumatic cuff to the uppermost part of a leg. Blood flow restriction is often combined with low load-blood flow restriction training (LL-BFRt) to enhance strength and promote muscle hypertrophy. Therefore, this research aimed to examine the effect of LL-BFRt, sham LL-BFRt, and high load-resistance training (HL-Rt) on quadriceps strength (QS), dynamic stability, and functional performance.

Design:
Single-blinded randomized trial method.

Setting:
A private physical therapy clinic in Bali, Indonesia.

Participants:
Data were collected from 63 basketball and rugby players assigned to 3 intervention groups, namely, LL-BFRt, sham LL-BFRt, and HL-Rt, through block randomization.

Independent Variables:
Each participant received intervention consisting of 45-minute sessions twice per week for 8 weeks.

Outcome Measures:
Quadriceps strength, star excursion balance test (SEBT), and single-leg hop test (SLHT) were evaluated in baseline, 4 weeks, and 8 weeks of the intervention period.

Results:
In LL-BFRt and HL-Rt groups, QS, SEBT, and SLHT scores were significantly improved during 8-week intervention period, except in sham LL-BFRt group. Furthermore, there was a significant improvement in LL-BFRt (

QS: 9.2-33.5 Newton;

SEBT: 1.2-11.1 cm;

SLHT: 1.3-9.8 cm, P-values < 0.05) and HL-Rt groups (

QS: 15.4-35.9 Newton;

SEBT: 2.2-9.0 cm;

SLHT: 4.5-15.8 cm, P < 0.05) compared with sham LL-BFRt.

Conclusions:
The improvements attained by participants using LL-BFRt and HL-Rt were comparable and capable of improving QS, SEBT, and SLHT more than sham LL-BFRt.

Trial Registration:
NCT05951036.
Self-advocacy Among Women With Uterine Malignancies
Authors: Chen Xiaojie , Xu Xiaohan , Du Yunhong , Liu Wei , Zhang Xiao , Wang Li 
Published: February 2025

Abstract

Background:
Self-advocacy plays a crucial role in the mental health and treatment outcomes of oncology patients, particularly those with uterine malignancies. Despite its significance, research on the self-advocacy levels and influencing factors among Chinese patients with uterine malignancies remains limited.

Objectives:
To assess the self-advocacy levels among Chinese patients with uterine malignancies and identify the demographic, psychological resilience, and decision self-efficacy factors that influence self-advocacy.

Methods:
This cross-sectional study was conducted from March 1 to September 1, 2023, involving 220 inpatients with uterine malignancies from three tertiary hospitals in Shandong Province, China. Participants were recruited using convenience sampling and completed the General Information Questionnaire, Female Cancer Survivorship Self-advocacy Scale, Connor–Davidson Resilience Scale, and Decision Self-efficacy Scale.

Results:
The average self-advocacy score among participants was 59.44 ± 10.14. Significant positive correlations were found between self-advocacy, psychological resilience, and decision self-efficacy. The random forest algorithm identified decision self-efficacy, psychological resilience, family average income, type of medical insurance, educational level, and residence as the six most important influencing factors, with the optimal model performance observed when lambda (λ) = 1.191. Multiple linear regression analysis further confirmed that decision self-efficacy, psychologic resilience, family average income, educational level, and residence were significant predictors of self-advocacy.

Discussion:
The self-advocacy levels of Chinese patients with uterine malignancies were relatively low, with decision self-efficacy, psychological resilience, and socioeconomic factors significantly influencing their self-advocacy abilities. Future targeted interventions should focus on enhancing patients’ decision self-efficacy and psychological resilience, thereby guiding them to actively respond and participate in decision-making, ultimately improving self-advocacy among patients with uterine malignancies.
Budget Impact of Eliminating Medicaid Prior Authorizations for Antiretrovirals in Washington State
Authors: Golden Matthew R. , Taketomo Ryan T. , Pistoresi Ryan , Sullivan Donna 
Published: February 2025

Background
In 2023, Washington state Medicaid eliminated prior authorizations (PAs) for antiretrovirals (ARVs). We estimated the budget impact of this policy change on Medicaid ARV expenditures, 2023-2027.

Methods
Models used 2022 net drug costs reflecting costs minus rebates. Our base case pre-exposure prophylaxis (PrEP) model assumed changes in the proportions of PrEP users on tenofovir disoproxil fumarate/emtricitabine (TDF/FTC), tenofovir alafenamide/emtricitabine (TAF/FTC), and cabotegravir (CAB) based on 2021-2022 data (prior to elimination of PAs). We compared base case costs to models assuming changes in PrEP prescribing observed 2022-2023 (first year after elimination of PAs), and models assuming an accelerated increase in TAF/FTC and CAB use. For HIV treatment, models assumed ARV changes based on 2021-2022 data (Base Model), changes based on data from 2022-2023 (No PA – Stable Increase), and a model based on 2022-2023 data but with a declining rate of change in the adoption of bictegravir/TAF/FTC and CAB/rilpivirine (No PA – Declining Increase). We estimated the number of persons with HIV (PWH) who might be housed using money required to meet new ARV costs using 2023 local Ryan White Program costs for emergency or temporary housing.

Results
Elimination of PAs will increase Medicaid expenditures for ARVs by an estimated $109.9-$157.7 million over 5 years. This cost would pay for 5 years of housing for approximately 820-1,177 people, or 61-88% of unstably housed PWH in Washington state.

Conclusions
Elimination of Medicaid PAs will result in substantial new costs. Changes in drug formulary policy should consider opportunity costs.
Systematic Review and Meta-Analysis of Prevalence and Population-Level Factors Contributing to Posttraumatic Stress Disorder in Pediatric Intensive Care Survivors
Authors: Hay Rebecca E. , O’Hearn Katie , Zorko David J. , Lee Laurie A. , Mooney Sarah , McQuaid Cara , Albrecht Lisa , Henshall David E. , Dannenberg Vanessa Campes , Flamenghi Veronica , Thibault Celine , Lee Wai Kit , Shi Min Ko Michelle , Cree Michele , St. Louis Julia , Heneghan Julia A. , Leung Karen Ka Yan , Wood Andrea , López-Barón Eliana , Temsah Mohamad-Hani , Almazyad Mohammed , Retallack Jennifer , Reddy Mounika , Aldairi Nedaa , Palomino Rubén Eduardo Lasso , Choong Karen , Du Pont-Thibodeau Geneviève , Ducharme-Crevier Laurence , Tsampalieros Anne , Hayawi Lamia , McNally James Dayre M. , Garcia Guerra Gonzalo 
Published: February 2025

Objectives:
In survivors of illnesses or surgeries requiring PICU admission, there is a risk of posttraumatic stress disorder (PTSD). We aimed to estimate PTSD prevalence and potential contributing factors in survivors of PICU admission.

Data Sources:
We performed a PROSPERO registered systematic review (CRD42022348997; Registered August 2022) using MEDLINE, Embase, CINAHL, and Cochrane Central Register of Controlled Trials (CENTRAL) databases, 2000 to 2022, with no language restrictions.

Study Selection:
Observational or interventional studies evaluating the incidence or prevalence of PTSD in patients’ after PICU admission and/or contributing factors to PTSD. We used studies describing patients younger than 18 years old. Since there were a large number of citations, we used an integrated crowdsourcing and machine-learning model for citation screening. Each citation was reviewed independently and in duplicate by two reviewers at each stage of screening and abstraction.

Data Extraction:
Data items included study and participant demographics, details of case definition (PTSD screening), and risk factors.

Data Synthesis:
We followed the Preferred Reporting items for Systematic Reviews and Meta-analysis guidelines. Random-effects models were used to analyze PTSD prevalence and subgroup differences. In 24 citations meeting final review criteria, 19 had data for meta-analysis. There were 1898 PICU survivors with a median (interquartile range) cohort size of 59 (49–76). PTSD prevalence in the studies ranged from 3% to 37%; PTSD occurred in 529 of 1898 survivors (I
2 = 72%). Factors influencing PTSD variability included timing of assessment (p < 0.01) with the highest prevalence (29%) at 6 months and the type of assessment instrument (n = 10; range, 4–27%; p = 0.04). There was lower prevalence of PTSD (8%) in postoperative cardiac patients (p < 0.01). Last, we failed to find an association between PICU length of stay and PTSD prevalence (p = 0.62; I
2 = 80%).

Conclusions:
PICU follow-up studies from 2000 to 2022 indicate that one-in-three of admissions surviving to 6 months have PTSD. However, there are population, study design factors and heterogeneity in PTSD assessment that indicate more standardization in this research is needed.
Temporary Femoral Central Venous Catheters in the PICU: Two-Center, Retrospective Cohort Study of Catheter Tip Position and Symptomatic Venous Thromboembolism, 2016–2021
Authors: Good Ryan J. , Ahern Emily , Weber Mark D. , Miller Kristen R. , DeVine Mackenzie , Mehta Sanjiv D. , Conlon Thomas W. , Himebauch Adam S. 
Published: February 2025

Objectives:
We aimed to determine the frequency and variables associated with low femoral central venous catheter (fCVC) tip position. We also examined the association between tip position and symptomatic venous thromboembolism (VTE).

Design:
Retrospective cohort from two PICUs.

Setting:
Quaternary academic children’s hospitals, 2016–2021.

Patients:
Children (age <18 yr) in the PICU who underwent temporary fCVC placement.

Interventions:
None.

Measurements and Main Results:
Low fCVC tip position occurs when the tip is inferior to the fifth lumbar vertebra (L5) on a postprocedural abdominal radiograph. Of 936 patients: 56.3% were 1–12 years old, and 80.0% had normal weight-for-age z score. fCVC tip position was low in 67.3% of patients. In the multivariable model, older age, earlier years of placement, and higher weight-for-age were associated with low fCVC tip position. Symptomatic fCVC-associated VTE occurred in 8.8% of patients, with a rate of 16.5 per 1000 CVC days (interquartile range, 13.1–20.5 per 1000 CVC days). The percentage of VTE in low vs. recommended fCVC tip position and VTE (8.6% vs. 9.2%) were equivalent (two one-sided z-tests; p < 0.001). Furthermore, in the multivariable model, we failed to identify an association between low fCVC tip position, relative to the recommended tip position, and greater odds of VTE (OR, 1.58 [95% CI, 0.92–2.69). However, we cannot exclude the possibility of low fCVC tip position being associated with up to 2.6-fold greater odds of symptomatic VTE.

Conclusions:
In our two PICUs, 2016–2021, low fCVC tip position occurred in two-thirds of placements and was associated with older age and higher weight-for-age patients. fCVC-associated VTE occurred in one-in-11-catheter placements, with the raw percentage of fCVCs and subsequent VTE in low and recommended tip position being equivalent. However, the multivariable modeling indicates that future research into the relationship between tip position and VTE requires ongoing surveillance and work.