bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure
Authors: Newell Andrew J , Jima Dereje , Reading Benjamin , Patisaul Heather B 
Published: July 2023

AbstractToxicogenomics is a critical area of inquiry for hazard identification and to identify both mechanisms of action and potential markers of exposure to toxic compounds. However, data generated by these experiments are highly dimensional and present challenges to standard statistical approaches, requiring strict correction for multiple comparisons. This stringency often fails to detect meaningful changes to low expression genes and/or eliminate genes with small but consistent changes particularly in tissues where slight changes in expression can have important functional differences, such as brain. Machine learning offers an alternative analytical approach for “omics” data that effectively sidesteps the challenges of analyzing highly dimensional data. Using 3 rat RNA transcriptome sets, we utilized an ensemble machine learning approach to predict developmental exposure to a mixture of organophosphate esters (OPEs) in brain (newborn cortex and day 10 hippocampus) and late gestation placenta of male and female rats, and identified genes that informed predictor performance. OPE exposure had sex specific effects on hippocampal transcriptome, and significantly impacted genes associated with mitochondrial transcriptional regulation and cation transport in females, including voltage-gated potassium and calcium channels and subunits. To establish if this holds for other tissues, RNAseq data from cortex and placenta, both previously published and analyzed via a more traditional pipeline, were reanalyzed with the ensemble machine learning methodology. Significant enrichment for pathways of oxidative phosphorylation and electron transport chain was found, suggesting a transcriptomic signature of OPE exposure impacting mitochondrial metabolism across tissue types and developmental epoch. Here we show how machine learning can complement more traditional analytical approaches to identify vulnerable “signature” pathways disrupted by chemical exposures and biomarkers of exposure.
The shape of water: adaptations of cochlea morphology in seals and otters
Authors: Taszus Roxana , del Rio Joaquin , Stoessel Alexander , Nowotny Manuela 
Published: July 2023

Abstract
Seals (Pinnipedia) and otters (Lutrinae) are two major taxa of the mammalian order Carnivora that independently adapted to a semi-aquatic lifestyle. Their sensory capabilities, including hearing, are still not fully understood. Notably, the functional morphology of amphibious hearing presents an interesting example for studying convergent evolution. We therefore investigated the shape and dimensions of morphological traits of the inner ear and the surrounding structures involved in sound perception using Micro-Computer Tomography (µCT) data of 52 skulls belonging to 38 species of the carnivoran subgroup Caniformia. Principal component analysis (PCA) of cochlea shape variables revealed that 82% of shape variation is explained by PC1 and PC2. A number of traits (e.g. cochlea shape, reduction in cochlea turns, flattening of the cochlea, relative size of tympanum and round window) are significantly different from terrestrial Caniformia. We also found an external cochlea foramen in all Pinnipedia, which is likely related to coping with pressure compensation during diving. Finally, we demonstrate that hearing parameters, such as characteristic hearing frequency, correlate with changes in the morphological traits that separate seals and otters from other Caniformia. Our data suggest that large parts of the morphology of ear region of these semi-aquatic carnivorans have independently adapted to allow hearing in air and water.
The Comparative Dermal Stimulation Potential of Constant-Volume and Constant-Amount Diluted Calcium Hydroxylapatite Injections Versus the Concentrated Form
Authors: Botsali Aysenur , Erbil Hakan , Eşme Pelin , Gamsızkan Mehmet , Aksoy Ali Okan , Caliskan Ercan 
Published: July 2023

INTRODUCTION
Biostimulation properties of diluted and hyperdiluted calcium hydroxylapatite (CaHA) injections have become increasingly popular. However, the existing data are insufficient to certify a particular dose–response pattern.

OBJECTIVE
To assess and compare the dermal stimulation potentials of different concentrations of CaHA injections.

MATERIALS AND METHODS
Two independent experiments (Experiment-1: constant injection volume vs Experiment-2: constant CaHA amount) included 4 study groups each, and these experimental groups were placed consecutively on the abdominal skin of a juvenile Yorkshire pig. Histopathological and immunohistochemical stainings were performed on punch biopsy materials collected 4 months after the injection day.

RESULTS
The fibroblast count significantly decreased upon dilution from 1:3 to 1:19 in experiment 1 (p = .000) but still higher than the control group. In experiment 1, the collagen density of the concentrated form was more elevated than the 1:19 dilution and the negative control groups (p = .034 and .000, respectively) but similar to the 1:3 dilution (p = .123). No significant difference was observed between the groups regarding collagen density with a standard amount of CaHA (0.2 mL, 30%) (p > .05).

CONCLUSION
Despite the efficacy being more pronounced till 1:3 dilution, hyperdiluted CaHA at any dilution ratio up to 1:19 can provide a higher fibroblast count than the negative control group.
Arterial partial pressure of oxygen as a marker of airway closure does not correlate with the efficacy of pre-oxygenation
Authors: Larsson Alexander , Östberg Erland , Edmark Lennart 
Published: July 2023

BACKGROUND
The prerequisites for the early formation of anaesthesia-related atelectasis are pre-oxygenation with its resulting high alveolar oxygen content, and airway closure. Airway closure increases with age, so it seems counterintuitive that atelectasis formation during anaesthesia does not. One proposed explanation is that pre-oxygenation is impaired in the elderly by airway closure present in the waking state. The extent of airway closure cannot be assessed at the bedside, but arterial partial pressure of oxygen (P
aO2) as a surrogate variable of the resulting ventilation to perfusion mismatch can.

OBJECTIVE
The primary aim was to test the hypothesis that a decreased efficacy of pre-oxygenation, measured as the fraction of end-tidal oxygen (FE’O2) after 3 min of pre-oxygenation, correlates with decreased P
aO2 on room air. We also re-investigated the influence on FE’O2 by age.

DESIGN
Prospective observational study.

SETTING
Two regional hospitals, Västerås and Köping County Hospitals, Västmanland, Sweden, between 30 October 2018 and 17 September 2021.

PARTICIPANTS
We included 120 adults aged 40 to 79 years presenting for elective noncardiac surgery.

INTERVENTION
An arterial blood gas was sampled before commencing pre-oxygenation.

RESULTS
No linear correlation was found between FE’O2 at 3 min and P
aO2 or age (Pearson's r = −0.038, P = 0.684; and Pearson's r = −0.113, P = 0.223, respectively). The mean ± SD FE’O2 at 3 min for the population studied was 0.87 ± 0.05.

CONCLUSION
The lack of correlation between FE’O2 at 3 min and P
aO2 or age during pre-oxygenation has implications for further studies concerning the interaction between airway closure and atelectasis. After 3 min of pre-oxygenation, FE’O2, even in the elderly, indicated a high enough alveolar oxygen concentration to promote atelectasis after induction, therefore, it is still unclear why atelectasis formation diminishes after middle age.

TRIAL REGISTRATION
ClinicalTrials.gov NCT03395782
Current State of Entry-level Physical Therapy Oncology Curricula in the United States: A Faculty Survey
Authors: Harrington Shana E. , VanHoose Lisa , Westlake Frances 
Published: July 2023

Introduction.
The purpose of this study was to determine the extent of oncology rehabilitation education in current physical therapist educational programs in the United States, including oncology rehabilitation content characteristics, delivery, and instructional resources.

Review of Literature.
By 2030, more than 21 million survivors of cancer in the United States (US) will be living with multisystem side effects depending on the treatment delivered. In addition, the sociopsychological factors associated with cancer treatment require that physical therapists are equipped with a unique body of knowledge, skills, and abilities. Insufficient cancer rehabilitation education is problematic across the health care spectrum.

Subjects.
Program directors at 235 US physical therapist educational programs.

Methods.
An online survey was developed in REDCap using the American Board of Physical Therapy Specialist's Description of Specialty Practice: Oncology Physical Therapy as a guide. An electronic link to the survey was sent to the email of the chair/program director at 235 Commission for the Accreditation of Physical Therapy Education–accredited programs.

Results.
The overall response rate was 40.4% (95/235) and represented 36 of the 50 states. Private universities represented 54.3% of the responses, and 65% of the surveys were completed by core faculty. Four programs reported having an independent oncology course, ranging from 1 to 3 credit hours. Integrated content hours averaged 14.8 contact hours (range: 1–60) in the 69 reporting programs. Fifty-four percent of respondents were aware of published rehabilitation cancer guidelines. The majority of respondents (62%) felt their students received adequate instruction related to oncology rehabilitation. Certified lymphedema therapists (68%) were primarily responsible for teaching the oncology content. Goodmans' Pathophysiology text was most reported (87%), whereas 38% used evidence-based research in Rehabilitation Oncology Journal. About half of the respondents (52%) reported offering students full-time clinical experiences in oncology rehabilitation.

Discussion and Conclusions.
This survey demonstrated how oncology rehabilitation education is incorporated into physical therapist educational programs and highlights areas for improvement. The results from this study lay the groundwork for developing core competencies for prelicensure education in oncology rehabilitation.
Challenges and Opportunities for Physical Therapist Education Research: Results From an American Council of Academic Physical Therapy Needs Assessment Survey
Authors: Dickson Tara , Eckert Jody , Pabian Patrick , Greco Jamie 
Published: July 2023

Introduction.
The physical therapy (PT) profession has cited a need for education research, yet the needs of researchers are not fully understood. Furthermore, there continues to be a limited understanding of where resources are most needed to support and advance education research. The purpose of this study was to identify barriers and opportunities for education research to support PT faculty.

Review of Literature.
Scholarly productivity may be related to the attainment of an academic doctoral degree, research culture within an institution, and faculty time devoted to research. There is a lack of knowledge about what factors relate to the production of education research and the types of support needed for education researchers.

Subjects.
Two hundred sixteen PT education researchers.

Methods.
An open survey invitation was sent through email through the American Council of Academic Physical Therapy newsletter. A multiple regression analysis was used to determine factors that were associated with scholarly productivity of education researchers in PT. Open responses to a question regarding needed resources for engagement in education research were qualitatively analyzed.

Results.
The multiple regression analysis yielded a large effect (R2 = 0.31), demonstrating that faculty years of experience, faculty rank, and having an academic doctoral degree were correlated with scholarly productivity. “Faculty time/workload” was considered “very important” or higher to the production of education research by 87% of respondents. This item was rated of highest importance on the survey. Mentorship was considered the most important external resource, with 69% of respondents rating it as “very important” or higher, whereas “other personal commitments (ie, family care, household management, other community-related volunteer commitments)” was the most important personal factor (rated by 70% of the respondents as “very important” or higher). Open-ended responses further suggest that institution logistics, appropriate dissemination venues, and funding are areas of need to foster success in engaging in education research.

Discussion and Conclusion.
Results highlight challenges and opportunities for resource investment in education research. Among these are time and funding. Existing professional networking and educational opportunities need to be continually evaluated for their effectiveness. Further development should focus on mitigating these barriers while considering the logistics of the researcher's institution.
Management of patients with idiopathic pulmonary fibrosis and lung cancer: challenges in clinical practice
Authors: Karampitsakos Theodoros , Sampsonas Fotios , Herazo-Maya Jose D. , Tzouvelekis Argyris 
Published: July 2023

Purpose of reviewIdiopathic pulmonary fibrosis (IPF) is the nonmalignant, chronic lung disease with the worst prognosis. Prevalent comorbidities including lung cancer exert a negative impact on patients’ survival. However, there is considerable lack of knowledge on the diagnostic and therapeutic management of patients diagnosed with both clinical entities. This review article presents the main challenges in the management of patients with IPF and lung cancer and highlights future perspectives.Recent findingsRecent registries for patients with IPF demonstrated that approximately 10% of patients developed lung cancer. Importantly, incidence of lung cancer was increasing remarkably over time in patients with IPF. Patients with IPF and otherwise technically operable lung cancer who underwent surgical resection had improved survival compared with those who did not undergo surgery. However, specific precautions perioperatively are crucial. Finally, the first randomized-controlled, phase 3 trial (J-SONIC trial) showed no significant difference in exacerbation-free survival for chemotherapy-naive patients with IPF and advanced nonsmall cell lung cancer that were allocated to receive carboplatin and nab-paclitaxel every 3 weeks with or without nintedanib.SummaryLung cancer is prevalent in IPF. Management of patients with IPF and lung cancer is challenging. A consensus statement aiming to attenuate confusion is greatly anticipated.
Pulmonary alveolar proteinosis – current and future therapeutical strategies
Authors: Jehn Lutz-Bernhard , Bonella Francesco 
Published: July 2023

Purpose of review
We discuss the most recent advances in the treatment of pulmonary alveolar proteinosis (PAP), an ultra-rare syndrome.

Recent findings
Whole lung lavage (WLL) remains the gold standard of treatment for PAP syndrome. For the autoimmune form, recent trials with inhaled granulocyte-macrophage colony-stimulating factor (GM-CSF) confirmed the efficacy in up to 70% of cases, especially under continuous administration. In patients with hereditary PAP with underlying GM-CSF receptor mutations, ex vivo autologous hematopoietic stem-cell gene therapy and reimplantation of autologous ex vivo gene-corrected macrophages are promising approaches.

Summary
There are no drugs approved for PAP at present, but cause-based treatments such as GM-CSF augmentation and pulmonary macrophage transplantation are paving the way for targeted therapy for this complex syndrome.
Lessons learned in developing a chronic thromboembolic pulmonary hypertension program
Authors: Bair Nancy D. , Heresi Gustavo A. 
Published: July 2023

Purpose of review
Chronic thromboembolic pulmonary hypertension (CTEPH) is a deadly underdiagnosed form of pulmonary hypertension, traditionally treated with surgical extraction of thrombo-fibrotic lesions via pulmonary thrombendarterectomy (PTE) surgery. More recently, treatment options have expanded to pulmonary vasodilator medical therapy and balloon pulmonary angioplasty (BPA). This has led to increased awareness and detection of CTEPH, as well as growing interest in performing PTE and BPA. This review will describe the steps required to build a successful CTEPH team in the context of the rapidly evolving treatment of CTEPH.

Recent findings
CTEPH care requires a multidisciplinary team, including a Pulmonologist or Cardiologist expert in Pulmonary Hypertension, a PTE surgeon, a BPA interventionalist, a dedicated radiologist, cardiothoracic anesthesia and Vascular Medicine or Hematology. Careful assessment of precise imaging and hemodynamic data is needed for operability assessment in the context of the experience of the CTEPH team and surgeon. Medical therapy and BPA are indicated for inoperable CTEPH and residual CTEPH after PTE. Increasingly, multimodality approaches, including surgery, BPA and medical therapy are utilized for best outcomes.

Summary
An expert CTEPH center requires a multidisciplinary team with dedicated specialists, and time to develop the experience and expertise to achieve high volumes and good outcomes.
Pulmonary hypertension in interstitial lung disease and in chronic obstructive pulmonary disease: different entities?
Authors: Piccari Lucilla , Aguilar-Colindres Ricardo , Rodríguez-Chiaradía Diego A. 
Published: July 2023

Purpose of reviewPulmonary hypertension (PH) is a common complication of both chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD), classified as Group 3 PH. To which extent PH presents and behaves similarly in COPD and ILD is unclear. This review examines the similarities and differences in pathogenesis, clinical presentation, natural history and treatment response of PH in COPD and ILD.Recent findingsThe latest studies on PH in chronic lung disease have re-evaluated the role of traditionally held etiopathogenetic factors such as tobacco exposure and hypoxia, although new ones such as airborne pollutant and genetic mutations are increasingly recognized. We examine common and diverging factors involved in PH development in COPD and ILD, as well as common and diverging clinical features of presentation, natural history and response to treatment and highlight areas for future research.SummaryThe development of PH in lung disease significantly worsens the morbidity and mortality of patients with COPD and ILD. However, recent findings show importance of recognizing distinct patterns and behaviors of pulmonary vascular disease, taking into account the specific underlying lung disease and severity of the hemodynamic involvement. Further studies are needed to build evidence on these aspects, especially in early disease.
Twenty versus 40 back-and-forth needle movements for endoscopic ultrasound-guided fine-needle biopsy of solid pancreatic masses: a prospective, crossover, randomized study
Authors: Hu Xinyi , Yu Fang , Cao Tingting , Chen Xiaojia , Nie Haihang , Zhang Zhang , Wang Fan , Wang Hongling , Fang Jun , Zhao Qiu 
Published: July 2023

Background and aims
In endoscopic ultrasound (EUS)-fine-needle biopsy (FNB) of solid pancreatic mass lesions, the number of times the needle moves back and forth within the lesion might affect the collection of the sample and the subsequent diagnostic accuracy. Thus, this study was designed to compare the diagnostic adequacy between different numbers of back-and-forth movements in EUS-FNB.

Methods
Fifty-five patients with solid pancreatic masses underwent EUS-FNB sampling with the needle (22-gauge) moved 20 times (MTT) and 40 times (MFT) randomly and sequentially for a total of four alternating passes. We compared the acquisition rate of appropriate and adequate specimens for histologic assessment and diagnostic accuracy.

Results
Finally, 55 patients (35 men and 20 women) were included in the study. We found that 56.4% (31/55) and 60% (33/55) of the specimens obtained using MTT and MFT, respectively, could be adequately diagnosed histologically (P = 0.815, McNemar test). The diagnostic accuracy of MTT and MFT was 72.7% (40/55) and 80% (44/55), respectively (P = 0.289, McNemar test). The overall diagnostic accuracy was 89.1%.

Conclusion
There was no significant statistical difference between the histopathological diagnostic samples obtained in MTT and those obtained in MFT. Therefore, a large number of back-and-forth movements of the needle should be avoided during EUS-FNB, which can help reduce the operation time and may reduce the risk of intraoperative and postoperative complications (Clinical trial registration number: ChiCTR2000031106).
Vimentin-targeted radiopeptide 99mTc-HYNIC-(tricine/EDDA)-VNTANST: a promising drug for pulmonary fibrosis imaging
Authors: Rezaeianpour Maliheh , Mazidi Seyed Mohammad , Nami Reza , Geramifar Parham , Mosayebnia Mona 
Published: July 2023

Objective
Idiopathic pulmonary fibrosis (IPF) is a fatal disease characterized by the accumulation of extracellular matrix. Because there is no effective treatment for advanced IPF to date, its early diagnosis can be critical. Vimentin is a cytoplasmic intermediate filament that is significantly up-regulated at the surface of fibrotic foci with a crucial role in fibrotic morphological changes.

Methods
In the present study, VNTANST sequence as a known vimentin-targeting peptide was conjugated to hydrazinonicotinic acid (HYNIC) and labeled with 99mTc. The stability test in saline and human plasma and log P determination were performed. Next, the biodistribution study and single photon emission computed tomography (SPECT) integrated with computed tomography (CT) scanning were performed in healthy and bleomycin-induced fibrosis mice models.

Results
The 99mTc-HYNIC-(tricine/EDDA)-VNTANST showed a hydrophilic nature (log P = −2.20 ± 0.38) and high radiochemical purity > 97% and specific activity (336 Ci/mmol). The radiopeptide was approximately 93% and 86% intact in saline and human plasma within 6 h, respectively. The radiopeptide was substantially accumulated in the pulmonary fibrotic lesions (test vs. control = 4.08 ± 0.08% injected dose per gram (ID/g) vs. 0.36 ± 0.01% ID/g at 90 min postinjection). SPECT-CT images in fibrosis-bearing mice also indicated the fibrotic foci and kidneys.

Conclusion
Because there is no available drug for the treatment of advanced pulmonary fibrosis, early diagnosis is the only chance. The 99mTc-HYNIC-(tricine/EDDA)-VNTANST could be a potential tracer for SPECT imaging of pulmonary fibrosis.