bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of pressure controlled, volume controlled, and volume guaranteed pressure controlled modes in prone position in patients operated for lumbar disc herniation: A randomized trial
Authors: Gunenc Ferim Sakize , Seyidova İlkana , Ozbilgin Sule , Ur Koray , Hanci Volkan 
Published: February 2024

Background:
To compare pressure-controlled ventilation (PCV), volume-controlled ventilation (VCV), and pressure-controlled ventilation-volume guaranteed (PCV-VG) modes in patients undergoing spinal surgery in the prone position under general anesthesia.

Methods:
The study included 78 patients aged 20 to 80 years, American Society of Anesthesiologists 1–2, scheduled for lumbar spinal surgery. Patients included in the study were randomly divided into 3 groups Group-VCV; Group-PCV; Group-PCV-VG. Standard anesthesia protocol was applied. In addition to routine monitoring, train of four and BIS monitoring were performed. All ventilation modes were set with a target tidal volume of 6 to 8 mL/kg, FiO2: 0.40–0.45 and a respiratory rate of normocarbia. Positive end-expiratory pressure: 5 cm H2O, inspiration/expiration ratio = 1:2, and the maximum airway pressure:40 cm H2O. Hemodynamic, respiratory variables and arterial blood gases was measured, 15 minutes after induction of anesthesia in the supine position (T1), after prone position 15 minutes (T2), 30 minutes (T3), 45 minutes (T4), 60 minutes (T5), 75 minutes (T6), 90 minutes (T7).

Results:
There was no significant difference between the groups in patient characteristics. SAP, DAP, mean arterial pressure, and heart rate decreased after being placed in the prone position in all groups. Hemodynamic variables did not differ significantly between the groups. partial arterial oxygen pressure and arterial oxygen saturation levels in blood gas were found to be significantly higher in Group-PCV-VG compared to Group-PCV and Group-VCV in both the supine and prone positions. Ppeak and plateau airway pressure (Pplato) values increased and dynamic lung compliance (Cdyn) values decreased after placing the patients in the prone position in all groups. Lower Ppeak and Pplato values and higher Cdyn values were observed in both the supine and prone positions in the Group-PCV-VG group compared to the Group-PCV and Group-VCV groups.

Conclusion:
PCV-VG provides lower Ppeak and Pplato values, as well as better Cdyn, oxygenation values compared to PCV and VCV. So that PCV-VG may be an effective alternative mode of mechanical ventilation for patients in the prone position during lumbar spine surgery.
Improving Anticoagulation Care for Pediatric Oncology Patients: A Quality Improvement Initiative
Authors: Rodriguez Vilmarie , Mitchell Brockton S. , Stanek Joseph , Vasko Katherine , Giver Jean , Monda Kay , Canini Joan , Dunn Amy A. , Kumar Riten 
Published: February 2024

Background:
Cancer is associated with increased venous thromboembolism in children. Risk factors for venous thromboembolism in this cohort include using central venous catheters, mass effect from underlying malignancy, chemotherapy, and surgery. Anticoagulation management in this cohort is challenging, given recurrent episodes of thrombocytopenia, the need for invasive procedures, and coagulopathy. A quality improvement (QI) initiative was developed to improve hematology consultation services and provide documentation of an individualized anticoagulation care plan for this high-risk cohort.

Methods:
Through the use of QI methods, interviews of stakeholders, expert consensus, and review of baseline data, a multidisciplinary team was organized, and key drivers relevant to improving access to hematology consultations and documentation of individualized anticoagulation care plans were identified. We used a Plan-Do-Study-Act model to improve hematology consultations and documentation of anticoagulation care plan (process measure). Outcome measures were bleeding and thrombosis recurrence/progression.

Results:
Seventeen patients with oncologic and venous thromboembolism diagnoses were included as baseline data. Slightly over half of these patients [53% (n = 9)] had a hematology consultation, and 7 (43.8%) had documentation of an anticoagulation care plan. After implementing QI methods, all 34 patients (100%) received hematology consultations and documentation of an anticoagulation care plan, and this measure was sustained for 1 year. Bleeding and thrombosis rates were similar in the baseline and post-QI cohorts.

Conclusions:
QI interventions proved effective in sustaining access to hematology consultations and providing anticoagulation care plans for patients with concomitant improved anticoagulation plan documentation for patients.
<xhtml:span xmlns:xhtml="http://www.w3.org/1999/xhtml" xml:lang="en">First Italian case of&#160;<em>Serratia ficaria</em>&#160;infection in a woman with obstructive pancreatitis and review of the literature.
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Authors: Lucchi Giulia , Gibiino Giulia , binda Cecilia , Sbrancia Monica , Coluccio Chiara , Gatti Giulia , Taddei Francesca , Sambri Vittorio , Fabbri Carlo , Cricca Monica 
Published: February 2024

Introduction: Serratia ficaria, is a Gram-negative rod first identified in 1979 in the fig tree ecosystem. Since then, Serratia ficaria has been occasionally isolated from human specimens. According to literature, Serratia ficaria is an opportunistic pathogen that rarely affects human, when infection occurs it can lead to different clinical conditions, including gallbladder empyema, lithiasis, ophthalmitis, leg ulceration, respiratory infections.

Case presentation: We report the case of a 66-year-old woman in whom Serratia ficaria was the causative agent of acute obstructive jaundice. The woman was treated empirically with ceftriaxone and metronidazole before sphincterotomy.Serratia ficaria was isolated from bile samples collected by Endoscopic Retrograde Cholangiopancreatography (ERCP).

Conclusion: Serratia ficaria causes mild infections in most cases, however, severe infections such as soft tissue infections or septicemia are reported in the literature. In this case, ERCP was crucial in the diagnosis and treatment of the patient, which favorably resolved the infection.
Exploring muscle recruitment by Bayesian methods during motion
Authors: Amankwah M , Bersani A , Calvetti D , Davico G , Somersalo E , Viceconti M 
Published: February 2024

AbstractThe human musculoskeletal system is characterized by redundancy in the sense that the number of muscles exceeds the number of degrees of freedom of the musculoskeletal system. In practice, this means that a given motor task can be performed by activating the muscles in infinitely many different ways. This redundancy is important for the functionality of the system under changing external or internal conditions, including different diseased states. A central problem in biomechanics is how, and based on which principles, the complex of central nervous system and musculoskeletal system selects the normal activation patterns, and how the patterns change under various abnormal conditions including neurodegenerative diseases and aging. This work lays the mathematical foundation for a formalism to address the question, based on Bayesian probabilistic modeling of the musculoskeletal system. Lagrangian dynamics is used to translate observations of the movement of a subject performing a task into a time series of equilibria which constitute the likelihood model. Different prior models corresponding to biologically motivated assumptions about the muscle dynamics and control are introduced. The posterior distributions of muscle activations are derived and explored by using Markov chain Monte Carlo (MCMC) sampling techniques. The different priors can be analyzed by comparing the model predictions with actual observations.
Circadian period is compensated for repressor protein turnover rates in single cells
Authors: Gabriel Christian H. , del Olmo Marta , Widini Arunya Rizki , Roshanbin Rashin , Woyde Jonas , Hamza Ebrahim , Gutu Nica-Nicoleta , Zehtabian Amin , Ewers Helge , Granada Adrian , Herzel Hanspeter , Kramer Achim 
Published: February 2024

SummaryMost mammalian cells possess molecular circadian clocks generating widespread rhythms, e.g. in transcript and protein abundance. While circadian clocks are robust to fluctuations in the cellular environment, little is known about how circadian period is compensated for fluctuating metabolic states. Here, we exploit the heterogeneity of single cells both in circadian period and metabolic state, governing protein stability, to study their interdependence without the need for genetic manipulation. We generated cells expressing key circadian proteins (CRY1/2 and PER1/2) as endogenous fusions with fluorescent proteins and simultaneously monitored circadian rhythms and degradation in thousands of single cells. We found that the circadian period is compensated for fluctuations in the turnover rates of circadian repressor proteins and uncovered possible mechanisms using a mathematical model. In addition, the stabilities of the repressor proteins are circadian phase-dependent and correlate with the circadian period in a phase-dependent manner, in contrast to the prevailing model.
A learnable transition from low temperature to high temperature proteins with neural machine translation
Authors: Komp Evan , Phillips Christian , Alanzi Humood N. , Zorman Marlo , Beck David A. C. 
Published: February 2024

AbstractThis work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 million protein homologous pairs from organisms adapted to different temperatures, demonstrates promising capability in targeting thermal stability. A designed variant of theDrosophila melanogasterEngrailed Homeodomain shows increased stability at high temperatures, as validated by estimators and molecular dynamics simulations. Furthermore, NOMELT achieves zero-shot predictive capabilities in ranking experimental melting and half-activation temperatures across two protein families. It achieves this without requiring extensive homology data or massive training datasets as do existing zero-shot predictors by specifically learning thermophilicity, as opposed to all natural variation. These findings underscore the potential of leveraging organismal growth temperatures in context-dependent design of proteins for enhanced thermal stability.
Evaluation of melanocyte stem cell population in vitiliginous skin pre- and post-narrow-band UVB phototherapy
Authors: Dutta Abhik , Saha Dyuti , Poojary Manish , Nagesh T S , Jamora Colin 
Published: February 2024

AbstractVitiligo vulgaris is an autoimmune disorder characterized by the destruction of epidermal melanocytes leading to white lesions devoid of pigmentation. The destruction of epidermal melanocytes. Is driven by tissue-resident and circulatory immune cells that maintain an inflammatory milieu. Two percent of the global population suffer from vitiligo vulgaris, of which, prevalence is higher in the Indian population. Narrow-band UV-B (NBUVB) phototherapy is commonly used as an economical, non-invasive, and well-tolerated treatment modality. NBUVB promotes the migration of melanocyte stem cells (MelSC) to the epidermis, thus regaining pigmentation in affected individuals.Despite the widespread use of NBUVB in secondary and tertiary clinics in India, the status of melanocyte stem cells and immune cells, pre-and post-NBUVB is not well understood. We observe that following NBUVB phototherapy, melanocyte stem cells (pax3+) re-populate the epidermis and express melanogenesis markers (Tyrosinase, Trp2, kit) concomitant with a decrease in CD3+ T-cells within the skin. Our study reaffirms the therapeutic efficacy of NBUVB in promoting re-pigmentation in an Indian cohort of vitiligo patients. Further, NBUVB is effective in reducing overall immune load, widely considered a major contributor to the pathogenesis of the disease.
A lack of open data standards for large infrastructure project hampers social-ecological research in the Brazilian Amazon
Authors: Hyde J.L. , Swanson A.C. , Bohlman S.A. , Athayde S. , Bruna E.M. , Valle D.R. 
Published: February 2024

AbstractNew infrastructure projects are planned or under construction in several countries, including in the bioculturally diverse Amazon, Mekong, and Congo regions. While infrastructure development can improve human health and living standards, it may also lead to environmental degradation and social change. Accessible, high quality data about infrastructure projects is essential for both monitoring them and studying their social and environmental impacts. We investigated the availability and quality of data on infrastructure projects in the Brazilian Amazon by reviewing the academic literature and surveying researchers from the conservation and development community, then used the results of these surveys to identify critical data attributes for the gathering, organizing, and sharing of infrastructure data by social-ecological researchers and practitioners.Although data on infrastructure in the Brazilian Amazon were generally available, they were often of poor quality and lacked information critical for monitoring and research. Data were often difficult to find and reformat, resulting in loss of time and resources for researchers and other stakeholders. Discrepancies between researchers’ survey responses on data needs and the types of data used in peer-reviewed articles on infrastructure projects indicate the following information was often missing: geographic extent of the project, construction and operation dates, and project type (e.g., paved vs unpaved road). Including these data in a standardized format, along with making them more readily accessible by hosting them in public repositories and ensuring they are current and comprehensive, would facilitate research and improve planning, decision-making, and monitoring of existing and future infrastructure projects in Brazil and other developing countries.HighlightsInfrastructure projects across the globe spur economic development but also lead to social- ecological degradation.Researchers and practitioners need current and comprehensive data to better mitigate social- ecological changes from infrastructure.Infrastructure data are often unavailable, inaccessible, or incomplete.Finding and organizing datasets cost researchers hundreds of hours and may lead to abandoned projects.To promote better research outcomes, governments and NGOs should ensure datasets on infrastructure are accessible, current, comprehensive, and include such vital information as the project’s geographic extent, dates of construction and operation, project type, and essential technical data.
1.4 min Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry
Authors: Jiang Yuming , Meyer Jesse G. 
Published: February 2024

ABSTRACTNon-invasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method, which integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein coronas enrichment for high throughput and efficient plasma proteomic profiling. We realized over 280 protein identifications in 1.4 minutes collection time, which enables a potential throughput of approximately 1,000 samples daily. The identified proteins are involved in valuable pathways and 44 of the proteins are FDA approved biomarkers. The robustness and quantitative accuracy of this method were evaluated across multiple NPs and concentrations with a mean coefficient of variation at 17%. Moreover, different protein corona profiles were observed among various nanoparticles based on their distinct surface modifications, and all NP protein profiles exhibited deeper coverage and better quantification than neat plasma. Our streamlined workflow merges coverage and throughput with precise quantification, leveraging both DISPA and NP protein corona enrichments. This underscores the significant potential of DISPA when paired with NP sample preparation techniques for plasma proteome studies.
Time-varying mediation analysis for incomplete data with application to DNA methylation study for PTSD
Authors: Wei Kecheng , Xue Fei , Xu Qi , Yuan Yubai , Zhang Yuexia , Qin Guoyou , Wani Agaz H. , Aiello Allison E. , Wildman Derek E. , Uddin Monica , Qu Annie 
Published: February 2024

AbstractDNA methylation (DNAm) has been shown to mediate causal effects from traumatic experiences to post-traumatic stress disorder (PTSD). However, the scientific question about whether the mediation effect changes over time remains unclear. In this paper, we develop time-varying structural equation models to identify cytosine-phosphate-guanine (CpG) sites where DNAm mediates the effect of trauma exposure on PTSD, and to capture dynamic changes in mediation effects. The proposed methodology is motivated by the Detroit Neighborhood Health Study (DNHS) with high-dimensional and longitudinal DNAm measurements. To handle the non-monotone missing DNAm in the dataset, we propose a novel Longitudinal Multiple Imputation (LMI) method utilizing dependency among repeated measurements, and employ the generalized method of moments to integrate the multiple imputations. Simulations confirm that the proposed method outperforms existing approaches in various longitudinal settings. In DNHS data analysis, our method identifies several CpG sites where DNAm exhibits dynamic mediation effects. Some of the corresponding genes have been shown to be associated with PTSD in the existing literature, and our findings on their time-varying effects could deepen the understanding of the mediation role of DNAm on the causal path from trauma exposure to PTSD risk.
Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing
Authors: Abe Kaitlyn M. , Lim Ci Ji 
Published: February 2024

AbstractSample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis Abundant (LEA) proteins, which naturally bind to AWI, can protect samples from AWI damage during plunge freezing. This protection is demonstrated with two LEA proteins from nematodes and tardigrades, which rescued the cryo-EM structural determination outcome of two fragile multisubunit protein complexes.
RNA Splicing Junction Landscape Reveals Abundant Tumor-Specific Transcripts in Human Cancer
Authors: Li Qin , Li Ziteng , Chen Bing , Zhao Jingjing , Yu Hongwu , Hu Jia , Lai Hongyan , Zhang Hena , Li Yan , Meng Zhiqiang , Hu Zhixiang , Huang Shenglin 
Published: February 2024

AbstractRNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples across multiple sample types. We identified 29,051 tumor-specific transcripts (TSTs) in pan-cancer, with a majority of these TSTs being unannotated. Our findings show that TSTs are positively correlated with tumor stemness and linked to unfavorable outcomes in cancer patients. Additionally, TSTs display mutual exclusivity with somatic mutations and are overrepresented in transposable element-derived transcripts possessing oncogenic functions. Importantly, TSTs can generate neoepitopes that bind to MHC class I molecules for immunotherapy. Moreover, TSTs can be detected in blood extracellular vesicles from cancer patients. Our results shed light on the intricacies of RNA splicing and offer promising avenues for cancer diagnosis and therapy.In briefThis study thoroughly analyzed RNA splicing junctions in 34,775 samples and identified 29,051 tumor-specific transcripts (TSTs), which may serve as novel cancer driver genes, neoantigens, and circulating biomarkers.Graphical abstract
Granulosa cell-layer stiffening prevents the granulosa cells from escaping the post-ovulatory follicle
Authors: Wang Xiaodong , Liao Jianning , Shi Hongru , Zhao Yongheng , Ke Wenkai , Wu Hao , Liu Guoshi , Li Xiang , He Changjiu 
Published: February 2024

ABSTRACTOvulation is necessary for successful reproduction. After ovulation, cumulus cells and oocytes are released, while granulosa cells (GCs) remain trapped within the post-ovulatory follicle to form the corpus luteum. However, the mechanism underlying GC confinement has long been unclear. Here, we providein vitroandin vivoevidence demonstrating that the stiffening of GC-layer as an evolutionarily conserved mechanism that hinders GCs from escaping the post-ovulatory follicles. Spatial transcriptome analysis reveals that the assembly of focal adhesions is primarily responsible for this stiffening. Disrupting focal adhesion assembly through RNA interference results in the release of GCs from the post-ovulatory follicle, leading to the formation of an aberrant corpus luteum with reduced cell density and cavities. We also uncover that theLH (hCG) -cAMP-PKA-CREBsignaling axis stimulates focal adhesion assembly and induce GC-layer stiffening. Our findings introduce a novel concept of “GC-layer stiffening”, which offers valuable insights into the factors that prevent GCs escape from the post-ovulatory follicle.
The interplay between proton diffusion across biological membranes and their biophysical properties highlights the role of defects in mixed lipid membranes
Authors: Variyam Ambili Ramanthrikkovil , Rzycki Mateusz , Yucknovsky Anna , Stuchebrukhov Alexei A. , Drabik Dominik , Amdursky Nadav 
Published: February 2024

AbstractProton circuits within biological membranes are at the heart of natural bioenergetic systems, whereas different biological membranes are characterized by different lipid compositions. In this study, we investigate how the composition of mixed lipid membranes influences the proton transfer (PT) properties of the membrane by following the excited-state PT (ESPT) process from a tethered probe to the membrane with time-scales and length-scales of PT that are relevant to bioenergetic systems. Two processes can happen during ESPT: the initial PT from the probe to the membrane at short timescales, followed by diffusion of dissociated protons around the probe on the membrane, and the possible geminate recombination with the probe at longer timescales. Here, we use membranes that are composed of mixtures of phosphatidylcholine (PC) and phosphatidic acid (PA). We show that the changes in the ESPT properties are not monotonous with the concentration of the lipid mixture; at low concentration of PA in PC, we find that the membrane is a poor proton acceptor. Molecular dynamics simulations indicate that at this certain lipid mixture, the membrane has the least defects (more structured and unflawed). Accordingly, we suggest that defects can be an important factor in facilitating PT. We further show that the composition of the membrane affects the geminate proton diffusion around the probe, whereas, on a time-scale of tens of nanoseconds, the dissociated proton is mostly lateral restricted to the membrane plane in PA membranes, while in PC, the diffusion is less restricted by the membrane.