bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between ovarian follicular development and Hippo pathway in polycystic ovary syndrome
Authors: Huang Zichao , Xu Tianyue , Liu Chunling , Wu Honghui , Weng Linglin , Cai Jieyu , Liang Na , Ge Hongshan 
Published: January 2024

Abstract
Background
For women of childbearing age, the biggest problem caused by polycystic ovary syndrome (PCOS) is infertility, which is mainly caused by anovulation, abnormal follicular development, proliferation of small antral follicles, and cystic follicles. The mechanism underlying its occurrence is not clear. The abnormal proliferation and development of follicles in PCOS patients is a complex process, which is affected by many factors. The objective of this study was to investigate the relationship between the Hippo pathway and follicular development in PCOS, and to further explore this relationship by using the YAP inhibitor verteporfin (VP).

Method
30 3-week-old BALB/C female rats were randomly divided into control group (n = 10), DHEA group (n = 10) and DHEA + VP group (n = 10). The morphology of ovary and the degree of follicular development were observed by HE staining, and the expression and location of AMH in ovarian follicles were observed by immunofluorescence. The ovarian reserve function index AMH, cell proliferation index PCNA and the ratio of Hippo pathway related proteins MST, LATS, YAP, P-YAP and P-YAP/YAP were detected by Western blot.

Results
After dividing 30 3-week-old female mice into control, dehydroepiandrosterone (DHEA; model of PCOS), and DHEA + VP groups, we found that the number of small follicles increased in the DHEA group compared to the control group. Additionally, in the DHEA group compared to the control group, anti-müllerian hormone (AMH; ovarian reserve index) increased, proliferating cell nuclear antigen (PCNA; cell proliferation index) decreased, and upstream (MST and LATS) and downstream (YAP and p-YAP) proteins in the Hippo pathway increased, though the p-YAP/YAP ratio decreased. VP ameliorated the increases in AMH, MST, LATS, YAP and p-YAP, but did not ameliorate the decrease in the p-YAP/YAP ratio.

Conclusions
This study indicates that the increased small follicles in the ovaries and changes in ovarian reserve and cell proliferation may be closely related to Hippo pathway activation. This suggests that the Hippo pathway may be an important pathway affecting the proliferation and development of follicles and the occurrence of PCOS.
Driving pressure of respiratory system and lung stress in mechanically ventilated patients with active breathing
Authors: Stamatopoulou Vaia , Akoumianaki Evangelia , Vaporidi Katerina , Stamatopoulos Efstathios , Kondili Eumorfia , Georgopoulos Dimitrios 
Published: January 2024

Abstract
Background
During control mechanical ventilation (CMV), the driving pressure of the respiratory system (ΔPrs) serves as a surrogate of transpulmonary driving pressure (ΔPlung). Expiratory muscle activity that decreases end-expiratory lung volume may impair the validity of ΔPrs to reflect ΔPlung. This prospective observational study in patients with acute respiratory distress syndrome (ARDS) ventilated with proportional assist ventilation (PAV+), aimed to investigate: (1) the prevalence of elevated ΔPlung, (2) the ΔPrs-ΔPlung relationship, and (3) whether dynamic transpulmonary pressure (Plungsw) and effort indices (transdiaphragmatic and respiratory muscle pressure swings) remain within safe limits.

Methods
Thirty-one patients instrumented with esophageal and gastric catheters (n = 22) were switched from CMV to PAV+ and respiratory variables were recorded, over a maximum of 24 h. To decrease the contribution of random breaths with irregular characteristics, a 7-breath moving average technique was applied. In each patient, measurements were also analyzed per deciles of increasing lung elastance (Elung). Patients were divided into Group A, if end-inspiratory transpulmonary pressure (PLEI) increased as Elung increased, and Group B, which showed a decrease or no change in PLEI with Elung increase.

Results
In 44,836 occluded breaths, ΔPlung ≥ 12 cmH2O was infrequently observed [0.0% (0.0–16.9%) of measurements]. End-expiratory lung volume decrease, due to active expiration, was associated with underestimation of ΔPlung by ΔPrs, as suggested by a negative linear relationship between transpulmonary pressure at end-expiration (PLEE) and ΔPlung/ΔPrs. Group A included 17 and Group B 14 patients. As Elung increased, ΔPlung increased mainly due to PLEI increase in Group A, and PLEE decrease in Group B. Although ΔPrs had an area receiver operating characteristic curve (AUC) of 0.87 (95% confidence intervals 0.82–0.92, P < 0.001) for ΔPlung ≥ 12 cmH2O, this was due exclusively to Group A [0.91 (0.86–0.95), P < 0.001]. In Group B, ΔPrs showed no predictive capacity for detecting ΔPlung ≥ 12 cmH2O [0.65 (0.52–0.78), P > 0.05]. Most of the time Plungsw and effort indices remained within safe range.

Conclusion
In patients with ARDS ventilated with PAV+, injurious tidal lung stress and effort were infrequent. In the presence of expiratory muscle activity, ΔPrs underestimated ΔPlung. This phenomenon limits the usefulness of ΔPrs as a surrogate of tidal lung stress, regardless of the mode of support.
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Authors: Abbas Ahmed , Chandratre Khyati , Gao Yunpeng , Yuan Jiapei , Zhang Michael Q. , Mani Ram S. 
Published: January 2024

AbstractThe three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac, and H3K27me3 but works well with just RAD21 signal. Integrative analysis reveals novel insights into the role of CTCF motif, its orientation, and CTCF binding on cohesin-mediated chromatin interactions.
Efficacy of navigation system-assisted distraction osteogenesis for hemifacial microsomia based on artificial intelligence for 3 to 18 years old: study protocol for a randomized controlled single-blind trial
Authors: Liu Xiangqi , Zhang Ziwei , Han Wenqing , Zhao Zhijie , Kim Byeong Seop , Yan Yingjie , Chen Xiaojun , Wang Xuetong , Li Xin , Yang Xianxian , Wang Bingshun , Xu Haisong , Lin Li , Chai Gang 
Published: January 2024

Abstract
Background
Mandibular distraction osteogenesis (MDO) is a major part of the treatment for hemifacial microsomia patients. Due to the narrow surgical field of the intraoral approach, osteotomy accuracy is highly dependent on the surgeons’ experience. Electromagnetic (EM) tracking systems can achieve satisfying accuracy to provide helpful real-time surgical navigation. Our research team developed an EM navigation system based on artificial intelligence, which has been justified in improving the accuracy of osteotomy in the MDO in animal experiments. This study aims to clarify the effect of the EM navigation system in improving the MDO accuracy for hemifacial microsomia patients.

Methods
This study is designed as a single-centered and randomized controlled trial. Altogether, 22 hemifacial microsomia patients are randomly assigned to the experiment and control groups. All patients receive three-dimensional CT scans and preoperative surgical plans. The EM navigation system will be set up for those in the experiment group, and the control group will undergo traditional surgery. The primary outcome is the surgical precision by comparing the osteotomy position of pre- and postoperative CT scan images through the Geomagic Control software. The secondary outcomes include mandibular symmetry (occlusal plane deviation angle, mandibular ramus height, and body length), pain scale, and complications. Other indications, such as the adverse events of the system and the satisfactory score from patients and their families, will be recorded.

Discussion
This small sample randomized controlled trial intends to explore the application of an EM navigation system in MDO for patients, which has been adopted in other surgeries such as orthognathic procedures. Because of the delicate structures of children and the narrow surgical view, accurate osteotomy and protection of nearby tissue from injury are essential for successful treatment. The EM navigation system based on artificial intelligence adopted in this trial is hypothesized to provide precise real-time navigation for surgeons and optimally improve patient outcomes, including function and aesthetic results. The results of this trial will extend the application of new navigation technology in pediatric plastic surgery.

Trial registration
Chinese Clinical Trial Registry ChiCTR2200061565. Registered on 29 June 2022.
Effectiveness of a blended school-based mindfulness program for the prevention of co-rumination and internalizing problems in Dutch secondary school girls: a cluster randomized controlled trial
Authors: Vuijk Patricia , Bul Kim , Buil Marieke , Rauws Marloes , Curie Keshia , Amesz Charlotte , Weerheijm Ron , Riper Heleen 
Published: January 2024

Abstract
Background
A growing body of literature indicates that adolescent girls who talk with close friends about interpersonal problems or worries in an excessive, speculative way, and with an intense focus on distress (i.e., co-rumination) are at heightened risk for developing internalizing symptoms and disorders as well as reduced friendship quality. However, to date, there are no prevention programs available that target high levels of co-rumination between adolescent girls. As such, we developed the blended school-based mindfulness prevention program Happy Friends, Positive Minds (HFPM) that targets co-rumination at the dyadic level, i.e., between two close female friends. The aim of this trial is to evaluate the effectiveness of HFPM to reduce co-rumination and internalizing problems and to enhance wellbeing and social-emotional behavior in Dutch adolescent girls.

Methods
A cluster Randomized Controlled Trial (cRCT) will be conducted to evaluate HFPM effectiveness. We will recruit 160 female friendship dyads (n = 320 girls) aged 13 to 15 years who will be characterized by high levels of self-reported co-rumination. The cRCT has two arms: (1) an intervention condition in which 160 girls (80 friendship dyads) will receive the 14-week HFPM program in two consecutive cohorts (cohort 1 in academic year 2023/2024 and cohort 2 in academic year 2024/2025, and (2) a control condition in which 160 girls (80 dyads) will receive care-as-usual (CAU) in two consecutive cohorts (cohort 1 in academic year 2023/2024 and cohort 2 in academic year 2024/2025). Data will be collected at baseline (T0), during the program (T1;T2; T3), immediately after the program (T4), and at 1-year follow-up (T5). Participant-level self-reported risk for (early onset) depression and anxiety, self-reported and observed co-rumination, self- and friend-reported friendship quality, self-reported positive and negative affect, self-reported interpersonal responses to positive affect, and self-reported anhedonia symptoms will be the outcome variables.

Discussion
This study will provide insights into the short-term and long-term effects of the HFPM program on girls’ internalizing problems, wellbeing, and social-emotional behavior.

Trial registration
International Standard Randomized Controlled Trials, identifier: ISRCTN54246670. Registered on 27 February 2023.
Unsupervised spatially embedded deep representation of spatial transcriptomics
Authors: Xu Hang , Fu Huazhu , Long Yahui , Ang Kok Siong , Sethi Raman , Chong Kelvin , Li Mengwei , Uddamvathanak Rom , Lee Hong Kai , Ling Jingjing , Chen Ao , Shao Ling , Liu Longqi , Chen Jinmiao 
Published: January 2024

AbstractOptimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-supervised learning mechanism to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. SEDR achieved higher clustering performance on manually annotated 10 × Visium datasets and better scalability on high-resolution spatial transcriptomics datasets than existing methods. Additionally, we show SEDR’s ability to impute and denoise gene expression (URL: https://github.com/JinmiaoChenLab/SEDR/).
Phenotypic and genotypic assessment of iron acquisition in diverse bovine-associated non-aureus staphylococcal strains
Authors: Reydams Helena , Toledo-Silva Bruno , Mertens Kristien , Piepers Sofie , Vereecke Nick , Souza Fernando Nogueira , Haesebrouck Freddy , De Vliegher Sarne 
Published: January 2024

AbstractAlthough the role of iron in bacterial infections has been well described for Staphylococcus (S.) aureus, iron acquisition in (bovine-associated) non-aureus staphylococci and mammaliicocci (NASM) remains insufficiently mapped. This study aimed at elucidating differences between four diverse bovine NASM field strains from two species, namely S. chromogenes and S. equorum, in regards to iron uptake (with ferritin and lactoferrin as an iron source) and siderophore production (staphyloferrin A and staphyloferrin B) by investigating the relationship between the genetic basis of iron acquisition through whole genome sequencing (WGS) with their observed phenotypic behavior. The four field strains were isolated in a previous study from composite cow milk (CCM) and bulk tank milk (BTM) in a Flemish dairy herd. Additionally, two well-studied S. chromogenes isolates originating from a persistent intramammary infection and from a teat apex were included for comparative purpose in all assays. Significant differences between species and strains were identified. In our phenotypical iron acquisition assay, while lactoferrin had no effect on growth recovery for all strains in iron deficient media, we found that ferritin served as an effective source for growth recovery in iron-deficient media for S. chromogenes CCM and BTM strains. This finding was further corroborated by analyzing potential ferritin iron acquisition genes using whole-genome sequencing data, which showed that all S. chromogenes strains contained hits for all three proposed ferritin reductive pathway genes. Furthermore, a qualitative assay indicated siderophore production by all strains, except for S. equorum. This lack of siderophore production in S. equorum was supported by a quantitative assay, which revealed significantly lower or negligible siderophore amounts compared to S. aureus and S. chromogenes. The WGS analysis showed that all tested strains, except for S. equorum, possessed complete staphyloferrin A (SA)-synthesis and export operons, which likely explains the phenotypic absence of siderophore production in S. equorum strains. While analyzing the staphyloferrin A and staphyloferrin B operon landscapes for all strains, we noticed some differences in the proteins responsible for iron acquisition between different species. However, within strains of the same species, the siderophore-related proteins remained conserved. Our findings contribute valuable insights into the genetic elements associated with bovine NASM pathogenesis.
Factors determining fine-scale spatial genetic structure within coexisting populations of common beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.), and sessile oak (Q. petraea (Matt.) Liebl.)
Authors: Sandurska Elżbieta , Ulaszewski Bartosz , Meyza Katarzyna , Sztupecka Ewa , Burczyk Jarosław 
Published: January 2024

Abstract
Key message
Naturally regenerating populations of common beech, pedunculate, and sessile oaks develop strong spatial genetic structures at adult and seedling stages. Significant genetic relationship occurs between individuals growing up to 60 m apart. This indicates the minimum distance separating trees from which seeds used for reforestation should be harvested to avoid the adverse effects of excessive relatedness among offspring.

Context
Spatial genetic structure is an inherent characteristic of naturally regenerating plant populations and has practical implications in forests for the management of genetic resources.

Aims
We investigated the extent of spatial genetic structure in three broad-leaved forest tree species (common beech—Fagus sylvatica L.; pedunculate oak—Quercus robur L.; and sessile oak—Q. petraea (Matt.) Liebl.) coexisting in the same nature reserve, explored its variation among species and different life stages (adults/offspring), and tested its possible determinants.

Methods
We explored patterns of spatial distribution of individuals, and using microsatellites, we estimated parameters of spatial genetic structure based on kinship relationships, considering possible sources of variation.

Results
In adults, the strongest spatial genetic structure was found for Q. petraea (Sp = 0.0187), followed by F. sylvatica (Sp = 0.0133), and the weakest in Q. robur (Sp = 0.0080). It was uniform across different age classes in pedunculate oak but decreased with age in sessile oak. No apparent relationship between age and spatial genetic structure was found in beech. Offspring exhibited significant spatial genetic structure (ranging from 0.0122 in beech to 0.0188 in sessile oak). The cohorts of seedlings having both parents present within the study site had stronger spatial genetic structures than cohorts of seedlings with only one local parent.

Conclusion
Spatial genetic structure is strong in naturally regenerating populations of heavy-seeded forest trees. Pollen immigration from outside of a local forest stand can significantly decrease the extent of spatial genetic structure in offspring generations.
Psychometric properties of principals’ attitudes toward inclusive education (PATIE) scale: Arabic version
Authors: Aldosari Mubarak S. 
Published: January 2024

Abstract
Background
Inclusive education is critical for the successful integration of students with disabilities into general education schools, and principals’ attitudes play a crucial role in this process. Despite the recognized significance of attitudes, there remains a gap in understanding these attitudes among principals in Arabic-speaking regions concerning inclusive education practices. This study aims to bridge this gap by validating and assessing the reliability of the Arabic version of the Principals’ Attitudes Toward Inclusive Education (PATIE) scale.

Methods
To measure these attitudes in the Arab region, the current study validated and assessed the reliability of the Arabic version of the Principals’ Attitudes Toward Inclusive Education (PATIE) scale using a sample of 391 principals from schools that have in place inclusion programs for students with disabilities. Confirmatory factor analysis (CFA) was employed to validate the scale’s structural, discriminant, and convergent validity, while Cronbach’s alpha and composite reliability (CR) were utilized to evaluate the scale’s reliability.

Results
The results demonstrated the strong validity and reliability of the Arabic version of the PATIE, with all five factors displaying good reliability.

Conclusions
These findings suggest that the scale can effectively measure attitudes toward inclusive education in Arabic-speaking countries. This study’s implications for research and practice are significant, as they underscore the importance of positive attitudes among principals in promoting inclusive education and provide a validated tool for measuring these attitudes.
CNS tumor with CREBBP::BCORL1 Fusion and pathogenic mutations in BCOR and CREBBP: expanding the spectrum of BCOR-altered tumors
Authors: Barresi Valeria , Cardoni Antonello , Miele Evelina , Pedace Lucia , Masotto Barbara , Nardini Claudia , Barresi Sabina , Rossi Sabrina 
Published: January 2024

AbstractThe fifth edition of the World Health Organization (WHO) classification of central nervous system (CNS) tumors introduced the new tumor type CNS tumor with BCOR internal tandem duplication (ITD), characterized by a distinct DNA methylation profile and peculiar histopathological features, including a circumscribed growth pattern, ependymoma-like perivascular pseudorosettes, microcystic pattern, absent or focal GFAP immunostaining, OLIG2 positivity, and BCOR immunoreactivity. We describe a rare case of a CNS tumor in a 45-year-old man with histopathological and immunohistochemical features overlapping the CNS tumor with BCOR internal tandem duplication (ITD) but lacking BCOR immunostaining and BCOR ITD. Instead, the tumor showed CREBBP::BCORL1 fusion and pathogenic mutations in BCOR and CREBBP, along with a DNA methylation profile matching the “CNS tumor with EP300:BCOR(L1) fusion” methylation class. Two CNS tumors with fusions between CREBBP, or its paralog EP300, and BCORL1, and approximately twenty CNS tumors with CREBBP/EP300::BCOR fusions have been reported to date. They exhibited similar ependymoma-like features or a microcystic pattern, along with focal or absent GFAP immunostaining, and shared the same DNA methylation profile. Given their morphological and epigenetic similarities, circumscribed CNS tumors with EP300/CREBBP::BCOR(L1) fusions and CNS tumors with BCOR ITD may represent variants of the same tumor type. The ependymoma-like aspect coupled with the lack of diffuse GFAP immunostaining and the presence of OLIG2 positivity are useful clues for recognizing these tumors in histopathological practice. The diagnosis should be confirmed after testing for BCOR(L1) gene fusions and BCOR ITD.
pH-dependent virucidal effects of weak acids against pathogenic viruses
Authors: Hu Weiyin , Shimoda Hiroshi , Tsuchiya Yoshihiro , Kishi Mikiya , Hayasaka Daisuke 
Published: January 2024

Abstract
Background
Weak acids, such as acetic acid, show virucidal effects against viruses, and disinfectants are considered effective virucidal agents possibly because of their low pH, depending on the proton concentration. This study aimed to evaluate the efficacy of different weak acids (acetic, oxalic, and citric acids) and eligible vinegars under different pH conditions by comparing their inactivation efficacies against enveloped and non-enveloped viruses.

Methods
Acetic, oxalic, and citric acids were adjusted to pH values of 2, 4 and 6, respectively. They were also diluted from 1 M to 0.001 M with distilled water. Enveloped influenza A virus (FulV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and non-enveloped feline calicivirus (FCV) were treated with adjusted weak acids for up to 30 min. These viruses were also reacted with white distilled vinegar (WDV) and grain-flavored distilled vinegar (GV) for up to 30 min. Infectious viral titers after the reactions were expressed as plaque-forming units per mL.

Results
Acetic acid showed virucidal effects against FulV at pH 4, whereas citric and oxalic acids did not. Acetic and citric acids inactivated SARS-CoV-2 at pH 2, whereas oxalic acid did not. All acids showed virucidal effects against FVC at pH 2; however, not at pH 4. The virucidal effects of the serially diluted weak acids were also reflected in the pH-dependent results. WDV and GV significantly reduced FulV titers after 1 min. SARS-CoV-2 was also susceptible to the virucidal effects of WDV and GV; however, the incubation period was extended to 30 min. In contrast, WDV and GV did not significantly inactivate FCV.

Conclusions
The inactivation efficacy of weak acids is different even under the same pH conditions, suggesting that the virucidal effect of weak acids is not simply determined by pH, but that additional factors may also influence these effects. Moreover, eligible vinegars, the main component of which is acetic acid, may be potential sanitizers for some enveloped viruses, such as FulV, in the domestic environment.