bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beta-PSMC: uncovering more detailed population history using beta distribution
Authors: Liu Junfeng , Ji Xianchao , Chen Hua 
Published: November 2022

Abstract
Background
Inferring the demographic history of a population is essential in population genetic studies. Though the inference methods based on the sequentially Markov coalescent can present the population history in detail, these methods assume that the population size remains unchanged in each time interval during discretizing the hidden state in the hidden Markov model. Therefore, these methods fail to uncover the detailed population history in each time interval.

Results
We present a new method called Beta-PSMC, which introduces the probability density function of a beta distribution with a broad variety of shapes into the Pairwise Sequentially Markovian Coalescent (PSMC) model to refine the population history in each discretized time interval in place of the assumption that the population size is unchanged. Using simulation, we demonstrate that Beta-PSMC can uncover more detailed population history, and improve the accuracy and resolution of the recent population history inference. We also apply Beta-PSMC to infer the population history of Adélie penguin and find that the fluctuation in population size is contrary to the temperature change 15–27 thousand years ago.

Conclusions
Beta-PSMC extends PSMC by allowing more detailed fluctuation of population size in each discretized time interval with the probability density function of beta distribution and will serve as a useful tool for population genetics.
DDX1 is a prognostic biomarker and correlates with immune infiltrations in hepatocellular carcinoma
Authors: Yuan Mengping , Xu Jinyong , Cao Shuguang , Sun Shuangshuang 
Published: November 2022

AbstractHepatocellular carcinoma (HCC) is one of the leading lethal malignant tumors worldwide. DEAD-box (DDX) family helicases are implicated in numerous human cancers. However, the role of DDX1 in HCC has not yet been fully elucidated. We downloaded gene expression data and clinical information data of HCC from The Cancer Genome Atlas and International Cancer Genome Consortium (ICGC) database and conducted subsequent analyses using the R package and online portal. The results revealed that HCC tissues had higher DDX1 expression compared with either paired or unpaired normal tissues. The increased DDX1 expression was closely related to the advanced pathological grade and histologic grade of HCC. Further analysis suggested that patients with high DDX1 expression contributed to poor prognosis The Cox regression analysis revealed that the expression level of DDX1 was an independent prognostic factor for HCC. In addition, an ICGC cohort was used for external validation. The cBio-Portal, MethSurv, and UALCAN database were used for evaluating the genomic mechanism. Moreover, the Tumor Immune Estimation Resource dataset and QUANTISEQ algorithm revealed that DDX1 expression positively correlates with immune infiltrating cells. We also identified the DDX1-related differentially expressed genes (DEGs) and explored their biological functions by GO, KEGG, and GSEA analyses, which indicated that DDX1 may regulate the progression of HCC. In general, increased DDX1 expression predicts a poor prognosis and drives the progression of HCC.
CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data
Authors: Tippani Madhavi , Pattie Elizabeth A. , Davis Brittany A. , Nguyen Claudia V. , Wang Yanhong , Sripathy Srinidhi Rao , Maher Brady J. , Martinowich Keri , Jaffe Andrew E. , Page Stephanie Cerceo 
Published: November 2022

Abstract
Background
Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are lacking. Existing methods lack scalability to accommodate high-throughput comparisons between multiple lines, across developmental timepoints, or across pharmacological manipulations.

Results
To address this need we developed CaPTure, a scalable, automated Ca2+ imaging analysis pipeline (https://github.com/LieberInstitute/CaPTure). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates cell- and network-specific metrics that facilitate phenotypic discovery. The method is compatible with parallel processing on computing clusters without requiring significant user input or parameter modification.

Conclusion
CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems.
Morphogenesis and cell wall composition of trichomes and their function in response to salt in halophyte Salsola ferganica
Authors: Liu Yanxia , Ma Yali , Aray Hanat , Lan Haiyan 
Published: November 2022

Abstract
Background
To survive harsh environmental conditions, desert plants show various adaptions, such as the evolution of trichomes, which are protective epidermal protrusions. Currently, the morphogenesis and function of trichomes in desert plants are not well understood. Salsola ferganica is an annual halophyte distributed in cold deserts; at the seedling stage, its rod-shaped true leaves are covered with long and thick trichomes and are affected by habitat conditions. Therefore, we evaluated the trichomes on morphogenesis and cell wall composition of S. ferganica compared to Arabidopsis thaliana and cotton, related gene expression, and preliminary function in salt accumulation of the leaves.

Results
The trichomes of S. ferganica were initiated from the epidermal primordium, followed by two to three rounds of cell division to form a multicellular trichome, while some genes associated with them were positively involved. Cell wall composition analysis showed that different polysaccharides including heavily methyl-esterified and fully de-esterified pectins (before maturation, probably in the primary wall), xyloglucans (in the mid-early and middle stages, probably in the secondary wall), and extensin (during the whole developmental period) were detected, which were different from those found in trichomes of Arabidopsis and cotton. Moreover, trichome development was affected by abiotic stress, and might accumulate salt from the mesophyll cells and secrete outside.

Conclusions
S. ferganica has multicellular, non-branched trichomes that undergo two to three rounds of cell division and are affected by abiotic stress. They have a unique cell wall composition which is different from that of Arabidopsis and cotton. Furthermore, several genes positively or negatively regulate trichome development. Our findings should contribute to our further understanding of the biogenesis and adaptation of plant accessory structures in desert plant species.
Implementing an audit and feedback cycle to improve adherence to the Choosing Wisely Canada recommendations: clustered randomized trail
Authors: Singer Alexander , Kosowan Leanne , Abrams Elissa M. , Katz Alan , Lix Lisa , Leong Katrina , Paige Allison 
Published: November 2022

Abstract
Background
Audit and Feedback (A&F), a strategy aimed at promoting modified practice through performance feedback, is a method to change provider behaviour and reduce unnecessary medical services. This study aims to assess the use of A&F to reduce antibiotic prescribing for viral infections and antipsychotic prescribing to patients with dementia.

Methods
Clustered randomized trial of 239 primary care providers in Manitoba, Canada, participating in the Manitoba Primary Care Research Network. Forty-six practices were randomly assigned to one of three groups: control group, intervention 1 (recommendations summary), intervention 2 (recommendations summary and personalized feedback). We assessed prescribing rates prior to the intervention (2014/15), during and immediately after the intervention (2016/17) and following the intervention (2018/19). Physician characteristics were assessed.

Results
Between 2014/15–2016/17, 91.6% of providers in intervention group 1 and 95.9% of providers in intervention group 2 reduced their antibiotic and antipsychotic prescribing rate by ≥ 1 compared to the control group (77.6%) (p-value 0.0073). This reduction was maintained into 2018/19 at 91.4%. On multivariate regression alternatively funded providers had 2.4 × higher odds of reducing their antibiotic prescribing rate compared to fee-for-service providers. In quantile regression of providers with a reduction in antibiotic prescribing, alternatively funded (e.g. salaried or locum) providers compared to fee-for-service providers were significant at the 80th quantile.

Conclusions
Both A&F and recommendation summaries sent to providers by a trusted source reduced unnecessary prescriptions. Our findings support further scale up of efforts to engage with primary care practices to improve care with A&F.

Trial registration
ClinicalTrials.gov NCT05385445, retrospectively registered, 23/05/2022.
How to create value with unobtrusive monitoring technology in home-based dementia care: a multimethod study among key stakeholders
Authors: Wrede Christian , Braakman-Jansen Annemarie , van Gemert-Pijnen Lisette 
Published: November 2022

Abstract
Background
There is a growing interest to support extended independent living of people with dementia (PwD) via unobtrusive monitoring (UM) technologies which allow caregivers to remotely monitor lifestyle, health, and safety of PwD. However, these solutions will only be viable if developers obtain a clear picture of how to create value for all relevant stakeholders involved and achieve successful implementation. The aim of this study was therefore to explore the value proposition of UM technology in home-based dementia care and preconditions for successful implementation from a multi-stakeholder perspective.

Methods
We conducted an expert-informed survey among potential stakeholders (n = 25) to identify key stakeholders for UM technology in home-based dementia care. Subsequently, focus groups and semi-structured interviews were conducted among 5 key stakeholder groups (n = 24) including informal caregivers (n = 5), home care professionals (n = 5), PwD (n = 4), directors and managers within home care (n = 4), and policy advisors within the aged care and health insurance sector (n = 6). The sessions addressed the value proposition- and business model canvas and were analyzed using thematic analysis.

Results
Stakeholders agreed that UM technology should provide gains such as objective surveillance, timely interventions, and prevention of unnecessary control visits, whereas pains mainly included information overload, unplannable care due to real-time monitoring, and less human interaction. The overall design-oriented need referred to clear situation classifications including urgent care (fall- and wandering detection), non-urgent care (deviations in eating, drinking, sleeping), and future care (risk predictions). Most important preconditions for successful implementation of UM technology included inter-organizational collaboration, a shared vision on re-shaping existing care processes, integrated care ICT infrastructures, clear eligibility criteria for end-users, and flexible care reimbursement systems.

Conclusions
Our findings can guide the value-driven development and implementation of UM technology for home-based dementia care. Stakeholder values were mostly aligned, although stakeholders all had their own perspective on what UM technology should accomplish. Besides, our study highlights the complexity of implementing novel UM technology in home-based dementia care. To achieve successful implementation, organizational and financial preconditions, as well as digital data exchange between home care organizations, will be important.
Understanding older patients’ willingness to have medications deprescribed in primary care: a protocol for a cross-sectional survey study in nine European countries
Authors: Lüthold Renata Vidonscky , Jungo Katharina Tabea , Weir Kristie Rebecca , Geier Anne-Kathrin , Scholtes Beatrice , Kurpas Donata , Wild Dorothea M. G. , Petrazzuoli Ferdinando , Thulesius Hans , Lingner Heidrun , Assenova Radost , Poortvliet Rosalinde K. E. , Lazic Vanja , Rozsnyai Zsofia , Streit Sven 
Published: November 2022

Abstract
Introduction
To reduce inappropriate polypharmacy, deprescribing should be part of patients’ regular care. Yet deprescribing is difficult to implement, as shown in several studies. Understanding patients’ attitudes towards deprescribing at the individual and country level may reveal effective ways to involve older adults in decisions about medications and help to implement deprescribing in primary care settings. In this study we aim to investigate older adults’ perceptions and views on deprescribing in different European countries. Specific objectives are to investigate the patients’ willingness to have medications deprescribed by medication type and to have herbal or dietary supplements reduced or stopped, the role of the Patient Typology (on medication perspectives), and the impact of the patient-GP relationship in these decisions.

Methods and analysis
This cross-sectional survey study has two parts: Part A and Part B. Data collection for Part A will take place in nine countries, in which per country 10 GPs will recruit 10 older patients (≥65 years old) each (n = 900). Part B will be conducted in Switzerland only, in which an additional 35 GPs will recruit five patients each and respond to a questionnaire themselves, with questions about the patients’ medications, their willingness to deprescribe those, and their patient-provider relationship. For both Part A and part B, a questionnaire will be used to assess the willingness of older patients with polypharmacy to have medications deprescribed and other relevant information. For Part B, this same questionnaire will have additional questions on the use of herbal and dietary supplements.

Discussion
The international study design will allow comparisons of patient perspectives on deprescribing from different countries. We will collect information about willingness to have medications deprescribed by medication type and regarding herbal and dietary supplements, which adds important information to the literature on patients’ preferences. In addition, GPs in Switzerland will also be surveyed, allowing us to compare GPs’ and patients’ views and preferences on stopping or reducing specific medications. Our findings will help to understand patients’ attitudes towards deprescribing, contributing to improvements in the design and implementation of deprescribing interventions that are better tailored to patients’ preferences.
Clinical study on the use of advanced magnetic resonance imaging in lupus nephritis
Authors: Chen Yan-Xia , Zhou Wa , Ye Yin-Quan , Zeng Lei , Wu Xian-Feng , Ke Ben , Peng Hao , Fang Xiang-Dong 
Published: November 2022

Abstract
Objectives
To investigate the correlation between the histopathology of the kidney and clinical indicators in patients with lupus nephritis (LN) using magnetic resonance imaging (MRI).

Methods
A total 50 female participants were enrolled in the study. Thirty patients with LN were divided into types 2, 3, 4, and 5, according to their pathological features. The control group consisted of 20 healthy female volunteers. Serum creatinine, C3, C1q, and anti-ds-DNA were measured. Conventional MRI, DTI, DWI, and BOLD scanning was performed to obtain the FA, ADC, and R2* values for the kidney.

Results
Compared with the control group, FA and the ADC were decreased in patients with LN, while the R2* value was increased (P < 0.05). The overall comparison of the SLEDAI (Activity index of systemic lupus erythematosus) score, total pathological score, AI, and serum creatinine C3 showed that these were significantly different between the two groups (P < 0.05). FA and the ADC were negatively correlated with urinary, blood ds-DNA, and serum creatinine and positively correlated with C1q (P < 0.05). The R2* value was positively correlated with urinary NGAL, blood ds-DNA, and serum creatinine (P < 0.05). FA and the ADC were negatively correlated with the SLEDAI score, total pathological score, AI, CI, nephridial tissue C3, and C1q. The R2* value was positively correlated with the SLEDAI score, total pathological score, AI, CI, nephridial tissue C3, and C1q (P < 0.05).

Conclusions
MRI examination in female patients with LN was correlated with pathologic test results, which may have clinical significance in determining the disease’s severity, treatment, and outcome.
Monitoring one heart to help two: heart rate variability and resting heart rate using wearable technology in active women across the perinatal period
Authors: Rowan Shon P. , Lilly Christa L. , Claydon Elizabeth A. , Wallace Jenna , Merryman Karen 
Published: November 2022

Abstract
Background
Characterizing normal heart rate variability (HRV) and resting heart rate (RHR) in healthy women over the course of a pregnancy allows for further investigation into disease states, as pregnancy is the ideal time period for these explorations due to known decreases in cardiovascular health. To our knowledge, this is the first study to continuously monitor HRV and RHR using wearable technology in healthy pregnant women.

Methods
A total of 18 healthy women participated in a prospective cohort study of HRV and RHR while wearing a WHOOP® strap prior to conception, throughout pregnancy, and into postpartum. The study lasted from March 2019 to July 2021; data were analyzed using linear mixed models with splines for non-linear trends.

Results
Eighteen women were followed for an average of 405.8 days (SD = 153). Minutes of logged daily activity decreased from 28 minutes pre-pregnancy to 14 minutes by third trimester. A steady decrease in daily HRV and increase in daily RHR were generally seen during pregnancy (HRV Est. = − 0.10, P < 0.0001; RHR Est. = 0.05, P < 0.0001). The effect was moderated by activity minutes for both HRV and RHR. However, at 49 days prior to birth there was a reversal of these indices with a steady increase in daily HRV (Est. = 0.38, P < 0.0001) and decrease in daily RHR (Est. = − 0.23, P < 0.0001), regardless of activity level, that continued into the postpartum period.

Conclusions
In healthy women, there were significant changes to HRV and RHR throughout pregnancy, including a rapid improvement in cardiovascular health prior to birth that was not otherwise known. Physical activity minutes of any type moderated the known negative consequences of pregnancy on cardiovascular health. By establishing normal changes using daily data, future research can now evaluate disease states as well as physical activity interventions during pregnancy and their impact on cardiovascular fitness.
Artificial rupture of membranes as a mode for induction of labor in women with a previous cesarean section- a retrospective cohort study
Authors: Dick Aharon , Gutman-Ido Einat , Chill Henry Hillel , Karavani Gilad , Ryvkin Ina , Porat Shay , Rosenbloom Joshua Isaac 
Published: November 2022

Abstract
Background
Induction of labor in women with a previous cesarean section (CS) is associated with increased rates of uterine rupture and failed attempt for vaginal delivery. Prostaglandins use is contraindicated in this population, limiting available options for cervical ripening.

Objective
To evaluate the efficacy and safety of artificial rupture of membranes (AROM) as a mode of Induction of labor (IOL) in women with a previous cesarean section.

Methods
A retrospective cohort study conducted in a single tertiary care center between January 2015 and October 2020. Women with one previous cesarean section and a current singleton term pregnancy requiring IOL, with an unfavorable cervix, were included. The primary outcome was a successful vaginal delivery (VBAC); secondary outcomes were rates of chorioamnionitis, uterine rupture and low Apgar score (< 7).

Results
Of the 665 women who met the inclusion criteria, 492 (74%) did not receive subsequent oxytocin and 173 (26%) did. There were significant differences in the baseline characteristics between these two groups, including maternal age, cervical dilation at presentation, parity, and a history of a previous VBAC. Among women who were induced solely by AROM the rate of a successful TOLAC was higher (81.3% vs 73.9%), total time of IOL was shorter (mean 8.7 h vs.16.1 h) and the risk of chorioamnionitis was lower (7.3% vs 18.4%). When subdividing the women who received oxytocin into early (< 12 h after AROM) vs late (> 12 h after AROM) administration, there were no significant changes in the rates of successful VBAC or of chorioamnionitis.

Conclusion
AROM as a single mode of IOL in women with a previous CS is a safe and efficient practice with high rates of successful VBAC. When spontaneous labor does not develop, there is no advantage to delay the administration of oxytocin.
The Effectiveness of an Intensive Inpatient Psychotherapy Program for Chronic Depression: A naturalistic comparison with wait list
Authors: Eielsen Mikkel , Ulvenes Pål Gunnar , Røssberg Jan Ivar , Høstmælingen Andreas , Soma Christina S. , Wampold Bruce E. 
Published: November 2022

Abstract
Background
Patients with chronic depression (CD) typically have an early symptom onset, more psychiatric comorbidities, more treatment attempts, and more frequent and longer inpatient hospitalizations than patients with major depressive disorders. The main purpose of this study was to investigate the effectiveness of an intensive inpatient psychotherapy program for patients with chronic depression (CD). The primary research question was whether two intensive psychodynamic inpatient treatments, affect phobia therapy (APT) and VITA, were superior to an outpatient wait list condition, receiving treatment as usual (TAU), at completion of treatment. To investigate if a potential difference between the intensive treatment and the wait list control group was dependent on a specific psychotherapeutic model, the study contrasted two therapies with similar intensity, but different theoretical rationales.

Methods
Two hundred eighty patients with CD were included in a naturalistic study. Patients were assessed at four time points; assessment, start of therapy, end of therapy and 1-year follow-up. Three comparisons were performed with patients matched across groups; Intensive inpatient treatment program (APT + VITA) vs wait list during treatment, APT vs VITA during treatment and APT vs VITA during follow-up. The outcome measure was the BDI-II.

Results
Intensive inpatient treatment program vs. wait list showed a significant difference in favor of the intensive treatment. No significant differences were found between APT and VITA during therapy or follow-up; but both groups had large effect sizes during treatment, which were maintained during follow-up.

Conclusions
The intensive inpatient psychotherapy program showed superior effect on chronic depression over an outpatient wait list condition receiving treatment as usual (TAU), but no significant differences were found between the two intensive inpatient psychodynamic treatments. The results provide support for the effectiveness of an intensive inpatient psychotherapy program in treatment of chronic and severe disorders, such as CD, which could be of benefit for policymakers and the health care sector as they are allocating recourses efficiently.

Trial registration
This study has been retrospectively registered on ClinicalTrials.gov (NCT05221567) on February 3rd, 2022.