bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predator metamorphosis and its consequence for prey risk assessment
Authors: Thapa Himal , Crane Adam L , Achtymichuk Gabrielle H , Sadat Sultan M M , Chivers Douglas P , Ferrari Maud C O 
Published: March 2024

Abstract
Living with a diverse array of predators provides a significant challenge for prey to learn and retain information about each predator they encounter. Consequently, some prey respond to novel predators because they have previous experience with a perceptually similar predator species, a phenomenon known as generalization of predator recognition. However, it remains unknown whether prey can generalize learned responses across ontogenetic stages of predators. Using wood frog tadpole (Lithobates sylvaticus) prey, we conducted two experiments to explore the extent of predator generalization of different life stages of two different predators: (1) predacious diving beetles (Dytiscus sp.) and (2) tiger salamanders (Ambystoma mavortium). In both experiments, we used chemical alarm cues (i.e., injured conspecific cues) to condition tadpoles to recognize the odor of either the larval or adult stage of the predator as risky. One day later, we tested tadpoles with either the larval or adult predator odor to determine whether they generalized their learned responses to the other life stages of the predator. Tadpoles generalized between larval and adult beetle odors but failed to generalize between larval and adult salamander odors. These results suggest that the odor of some predator species changes during metamorphosis to an extent that reduces their recognisability by prey. This “predator identity reset” increases the number of threats to which prey need to attend.
Partial order relation–based gene ontology embedding improves protein function prediction
Authors: Li Wenjing , Wang Bin , Dai Jin , Kou Yan , Chen Xiaojun , Pan Yi , Hu Shuangwei , Xu Zhenjiang Zech 
Published: March 2024

Abstract
Protein annotation has long been a challenging task in computational biology. Gene Ontology (GO) has become one of the most popular frameworks to describe protein functions and their relationships. Prediction of a protein annotation with proper GO terms demands high-quality GO term representation learning, which aims to learn a low-dimensional dense vector representation with accompanying semantic meaning for each functional label, also known as embedding. However, existing GO term embedding methods, which mainly take into account ancestral co-occurrence information, have yet to capture the full topological information in the GO-directed acyclic graph (DAG). In this study, we propose a novel GO term representation learning method, PO2Vec, to utilize the partial order relationships to improve the GO term representations. Extensive evaluations show that PO2Vec achieves better outcomes than existing embedding methods in a variety of downstream biological tasks. Based on PO2Vec, we further developed a new protein function prediction method PO2GO, which demonstrates superior performance measured in multiple metrics and annotation specificity as well as few-shot prediction capability in the benchmarks. These results suggest that the high-quality representation of GO structure is critical for diverse biological tasks including computational protein annotation.
Tutorial on survival modeling with applications to omics data
Authors: Zhao Zhi , Zobolas John , Zucknick Manuela , Aittokallio Tero 
Published: March 2024

AbstractMotivationIdentification of genomic, molecular and clinical markers prognostic of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, and how these potential risk factors complement clinical characterization of patient outcomes for survival prognosis. However, the massive sizes of the omics datasets, along with their correlation structures, pose challenges for studying relationships between the molecular information and patients’ survival outcomes.ResultsWe present a general workflow for survival analysis that is applicable to high-dimensional omics data as inputs when identifying survival-associated features and validating survival models. In particular, we focus on the commonly used Cox-type penalized regressions and hierarchical Bayesian models for feature selection in survival analysis, which are especially useful for high-dimensional data, but the framework is applicable more generally.Availability and implementationA step-by-step R tutorial using The Cancer Genome Atlas survival and omics data for the execution and evaluation of survival models has been made available at https://ocbe-uio.github.io/survomics.
Two-phase designs with failure time processes subject to nonsusceptibility
Authors: Mao Fangya , Cheung Li C , Cook Richard J 
Published: March 2024

ABSTRACTEpidemiological studies based on 2-phase designs help ensure efficient use of limited resources in situations where certain covariates are prohibitively expensive to measure for a full cohort. Typically, these designs involve 2 steps: In phase I, data on an outcome and inexpensive covariates are acquired, and in phase II, a subsample is chosen in which the costly variable of interest is measured. For right-censored data, 2-phase designs have been primarily based on the Cox model. We develop efficient 2-phase design strategies for settings involving a fraction of long-term survivors due to nonsusceptibility. Using mixture models accommodating a nonsusceptible fraction, we consider 3 regression frameworks, including (a) a logistic “cure” model, (b) a proportional hazards model for those who are susceptible, and (c) regression models for susceptibility and failure time in those susceptible. Importantly, we introduce a novel class of bivariate residual-dependent designs to address the unique challenges presented in scenario (c), which involves 2 parameters of interest. Extensive simulation studies demonstrate the superiority of our approach over various phase II subsampling schemes. We illustrate the method through applications to the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.
Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network
Authors: Blackburn David C , Boyer Doug M , Gray Jaimi A , Winchester Julie , Bates John M , Baumgart Stephanie L , Braker Emily , Coldren Daryl , Conway Kevin W , Rabosky Alison Davis , de la Sancha Noé , Dillman Casey B , Dunnum Jonathan L , Early Catherine M , Frable Benjamin W , Gage Matt W , Hanken James , Maisano Jessica A , Marks Ben D , Maslenikov Katherine P , McCormack John E , Nagesan Ramon S , Pandelis Gregory G , Prestridge Heather L , Rabosky Daniel L , Randall Zachary S , Robbins Mark B , Scheinberg Lauren A , Spencer Carol L , Summers Adam P , Tapanila Leif , Thompson Cody W , Tornabene Luke , Watkins-Colwell Greg J , Welton Luke J ,   the oVert Project Team, Stanley Edward L 
Published: March 2024

Abstract
The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.
CYR61 confers chemoresistance by upregulating survivin expression in triple-negative breast cancer
Authors: Kim Hyungjoo , Son Seogho , Ko Yunhyo , Lim Hogeun , Lee Joohyung , Lee Kyung-Min , Shin Incheol 
Published: March 2024

Abstract
Cysteine-rich angiogenic inducer 61 (CYR61) is a protein from the CCN family of matricellular proteins that play diverse regulatory roles in the extracellular matrix. CYR61 is involved in cell adhesion, migration, proliferation, differentiation, apoptosis, and senescence. Here, we show that CYR61 induces chemoresistance in triple-negative breast cancer (TNBC). We observed that CYR61 is overexpressed in TNBC patients, and CYR61 expression correlates negatively with the survival of patients who receive chemotherapy. CYR61 knockdown reduced cell migration, sphere formation and the cancer stem cell (CSC) population and increased the chemosensitivity of TNBC cells. Mechanistically, CYR61 activated Wnt/β-catenin signaling and increased survivin expression, which are associated with chemoresistance, the epithelial–mesenchymal transition, and CSC-like phenotypes. Altogether, our study demonstrates a novel function of CYR61 in chemotherapy resistance in breast cancer.
Experimental validation of double-fed induction generator in oscillating water column using circulatory system-based optimization
Authors: Elnaghi Basem E , Ismaiel Ahmed M , Abdel-Kader Fathy El Sayed , Mohammed Reham H , Abelwhab M N 
Published: March 2024

Abstract
This paper validates the optimal operation for a grid-connected double-fed induction generator (DFIG) in an oscillating water column power plant (OWCPP). This study presents a novel optimization technique called the circulatory system-based optimization (CSBO) approach to develop six adaptive fuzzy logic controllers (AFLCs) with 30 parameters and compare them to chaotic-billiards optimization (C-BO) and genetic algorithm (GA). The proposed controller is also compared with a proportional–integral differential (PID) controller based on a self-adaptive global-best harmony search (SGHS). CSBO-based AFLCs are fully investigated under different scenarios and experimented with using a real-time interface DSP1104. The results of using CSBO–AFLCs revealed a fast time response, fast convergence, less overshoot and minimal error compared with those achieved with C-BO–AFLC, SGHS–PID and GA–AFLC during different case studies. The CSBO-based AFLCs ensure maximum power from the DFIG in an OWCPP and enhance dynamic response with very low errors. The results show that the CSBO shows better power tracking by 25% as compared with C-BO, by 45% when compared with the GA and by 56% when compared with PID. Moreover, the integral absolute errors of six controllers are investigated to demonstrate the feasibility of CSBO–AFLC. The root mean square of the errors of six controllers using CSBO is improved by 68.27% when compared with GA, by 22.57% when compared with C-BO and by 38.42% when compared with PID. These indicators demonstrate the feasibility of CSBO when compared with other algorithms with the same OWCPP.
Comparison of clinical and laboratory data of adult patients with cutaneous IgA vasculitis and non-IgA vasculitis
Authors: Gambichler Thilo , Bui Duyên , Domin Belanna , Ardabili Larisa , Devrim Yusa , Abu Rached Nessr , Susok Laura 
Published: March 2024

Abstract

Background
Immune complex vasculitides may be subdivided into adult IgA small vessel vasculitis (aIgA-SVV; i.e. adult Henoch–Schönlein purpura) and non-IgA-SVV (hypersensitivity vasculitis, etc.).

Objectives
To evaluate the clinical and laboratory parameters of inpatients fulfilling the diagnostic criteria for aIgA-SVV and non-IgA-SVV.

Methods
Twenty-nine adults aged ≥ 20 years with aIgA-SVV [according to the European League Against Rheumatism/Paediatric Rheumatology International Trials Organisation/Paediatric Rheumatology European Society (EULAR/PRINTO/PRES) criteria] and 53 adults with non-IgA-SVV (according to the 2012 revised International Chapel Hill Consensus Conference Nomenclature of Vasculitides) were compared with respect to a variety of clinical and laboratory parameters by uni- and multivariable analyses.

Results
Compared with patients with aIgA-SVV, the platelet-to-lymphocyte ratio was significantly higher in patients with non-IgA-SVV. Serum C3 levels and mean corpuscular haemoglobin concentration in patients with non-IgA-SVV were significantly lower compared with patients with aIgA-SVV. Proteinuria and haematuria were significantly more common in patients with aIgA SVV, and were significantly correlated with systemic immune-inflammation biomarkers only in patients with aIgA-SVV. In patients with aIgA-SVV, higher lactate dehydrogenase and C-reactive protein were strong independent predictors for the presence of proteinuria and proteinuria. In patients with non-IgA-SVV, female sex was a protective factor for proteinuria, while skin lesions on the upper extremities proved to be a significant independent predictor of haematuria.

Conclusions
We detected several clinical and laboratory differences between patients with aIgA-SVV and non-IgA-SVV. Distinct predictors for renal involvement were not observed in either group, indicating that aIgA-SVV and non-IgA-SVV are similar conditions but do not appear to represent the same entity.
Factors influencing olfactory function in an adult general population sample: the CHRIS study
Authors: Gögele Martin , Emmert David , Fuchsberger Christian , Frasnelli Johannes 
Published: March 2024

Abstract
The sense of smell allows for the assessment of the chemical composition of volatiles in our environment. Different factors are associated with reduced olfactory function, including age, sex, as well as health and lifestyle conditions. However, most studies that aimed at identifying the variables that drive olfactory function in the population suffered from methodological weaknesses in study designs and participant selection, such as the inclusion of convenience sample or only of certain age groups, or recruitment biases.
We aimed to overcome these issues by investigating the Cooperative Health Research in South Tyrol (CHRIS) cohort, a population-based cohort, by using a validated odor identification test. Specifically, we hypothesized that a series of medical, demographic and lifestyle variables is associated with odor identification abilities. In addition, our goal was to provide clinicians and researchers with normative values for the Sniffin’ Sticks identification set, after exclusion of individuals with impaired nasal patency.
We included 6,944 participants without acute nasal obstruction and assessed several biological, social, and medical parameters. A basic model determined that age, sex, years of education, and smoking status together explained roughly 13% of the total variance in the data. We further observed that variables related to medical (positive screening for cognitive impairment and for Parkinson’s disease, history of skull fracture, stage 2 hypertension) and lifestyle (alcohol abstinence) conditions had a negative effect on odor identification scores. Finally, we provide clinicians with normative values for both versions of the Sniffin’ Sticks odor identification test, i.e. with 16 items and with 12 items.
Relationship between the mixed venous-to-arterial carbon dioxide gradient and the cardiac index in acute pulmonary embolism
Authors: Yuriditsky Eugene , Zhang Robert S , Bakker Jan , Horowitz James M , Zhang Peter , Bernard Samuel , Greco Allison A , Postelnicu Radu , Mukherjee Vikramjit , Hena Kerry , Elbaum Lindsay , Alviar Carlos L , Keller Norma M , Bangalore Sripal 
Published: March 2024

Abstract

Aims
Among patients with acute pulmonary embolism (PE) undergoing mechanical thrombectomy, the cardiac index (CI) is frequently reduced even among those without a clinically apparent shock. The purpose of this study is to describe the mixed venous-to-arterial carbon dioxide gradient (CO2 gap), a surrogate of perfusion adequacy, among patients with acute PE undergoing mechanical thrombectomy.

Methods and results
This was a single-centre retrospective study of consecutive patients with PE undergoing mechanical thrombectomy and simultaneous pulmonary artery catheterization over a 3-year period. Of 107 patients, 97 had simultaneous mixed venous and arterial blood gas measurements available. The CO2 gap was elevated (&gt;6 mmHg) in 51% of the cohort and in 49% of patients with intermediate-risk PE. A reduced CI (≤2.2 L/min/m2) was associated with an increased odds [odds ratio = 7.9; 95% confidence interval (CI) 3.49–18.1, P &lt; 0.001] for an elevated CO2 gap. There was an inverse relationship between the CI and the CO2 gap. For every 1 L/min/m2 decrease in the CI, the CO2 gap increased by 1.3 mmHg (P = 0.001). Among patients with an elevated baseline CO2 gap &gt;6 mmHg, thrombectomy improved the CO2 gap, CI, and mixed venous oxygen saturation. When the CO2 gap was dichotomized above and below 6, there was no difference in the in-hospital mortality rate (9 vs. 0%; P = 0.10; hazard ratio: 1.24; 95% CI 0.97–1.60; P = 0.085).

Conclusion
Among patients with acute PE undergoing mechanical thrombectomy, the CO2 gap is abnormal in nearly 50% of patients and inversely related to the CI. Further studies should examine the relationship between markers of perfusion and outcomes in this population to refine risk stratification.
Heart transplantation in a patient with infective endocarditis bridged with Impella 5.5: a case report
Authors: Khan Nadeem A , Shukrullah Bassam , Eckman Peter M , Hryniewicz Katarzyna M 
Published: March 2024

Abstract

Background
Infective endocarditis (IE) is a feared complication after surgical valve replacement accounting for 10% to 30% of all cases of IE. Our case is unique as we present a decompensated heart failure patient with IE who urgently needed mechanical circulatory support (MCS) to stabilize while IE was treated. We used Impella to bridge him to sterile state before heart transplant was done. This case highlights the importance of different strategies for bridge to heart transplant in decompensated heart failure patients with endocarditis.

Case summary
We describe a case of 62-year-old male who initially presented with severe shortness of breath with minimal exertion, weight gain, and lower extremity oedema diagnosed with acute on chronic systolic heart failure (HF) exacerbation (ACC stage D, NYHA class IV). Initial blood cultures and extensive work-up for IE were negative. He continued to decompensate haemodynamically despite inotropic support and the decision was to proceed with durable left ventricular assist device (LVAD) as bridge to orthotopic heart transplantation (OHT). Immediately prior to LVAD implantation, patient’s blood cultures became positive for Cutibacterium acnes. Echocardiogram revealed IE on bioprosthetic aortic valve. Patient therefore underwent urgent aortic valve replacement (AVR) and was stabilized with Impella 5.5.

Discussion
We highlight a case where MCS with Impella was used as a bridge to transplant in a decompensated HF patient who was septic. Patient was listed for OHT but was found to be septic due to IE and had to undergo AVR to achieve infection source control prior to undergoing heart transplant. Impella was used effectively to stabilize ACC stage D/NYHA class IV patient while he recovered from AVR and endocarditis before his blood cultures cleared up and he was listed for OHT. He successfully underwent OHT after 3 weeks.
Multi-modal treatment in a pregnant woman with untreated cardiac sarcoidosis complicated by cardiac dysfunction and ventricular arrhythmias: a case report and literature review
Authors: Yoshii Tomohiro , Kanzaki Hideaki , Aoki-Kamiya Chizuko , Izumi Chisato 
Published: March 2024

Abstract

Background
The treatment of cardiac sarcoidosis during pregnancy is inherently challenging owing to its impact on the foetus.

Case summary
We report a case of a 30-year-old pregnant woman with untreated cardiac sarcoidosis. One year prior to admission, she underwent permanent pacemaker implantation for complete atrioventricular block. Left ventricular ejection fraction (EF) showed a declining trend, and ventricular tachycardia (VT) was documented. Following an extensive evaluation, the patient was diagnosed with active cardiac sarcoidosis, and the pregnancy was detected at the same time. Considering the high risk of mortality and cardiovascular complications in pregnant patients with decreased EF and VT, we meticulously discussed the optimal timing of multi-modal treatment, including bisoprolol, eplerenone, sotalol, and prednisolone and cardiac resynchronization therapy with a defibrillator, and its effect on the foetus. These interventions improved the EF to 49%, and the baby was successfully delivered without adverse events or neonatal complications developing. At 8 months’ post-partum, the mother and the baby were doing well, and the EF was 45%.

Discussion
Cardiac sarcoidosis can lead to adverse outcomes for both the mother and the foetus. However, with multi-modal treatment individually optimized and implemented by a multi-disciplinary team of specialists in each field, even pregnant women with untreated cardiac sarcoidosis who present with reduced EF and VT can achieve safe childbirth.
Three-dimensional printed moulds to obtain silicone hearts with congenital defects for paediatric heart-surgeon training
Authors: Frei Mélanie , Reymond Philippe , Wacker Julie , van Steenberghe Mathieu , Beghetti Maurice , Sologashvili Tornike , Vallée Jean-Paul 
Published: March 2024

Abstract

OBJECTIVES
Many types of congenital heart disease are amenable to surgical repair or palliation. The procedures are often challenging and require specific surgical training, with limited real-life exposure and often costly simulation options. Our objective was to create realistic and affordable 3D simulation models of the heart and vessels to improve training.

METHODS
We created moulded vessel models using several materials, to identify the material that best replicated human vascular tissue. This material was then used to make more vessels to train residents in cannulation procedures. Magnetic resonance imaging views of a 23-month-old patient with double-outlet right ventricle were segmented using free open-source software. Re-usable moulds produced by 3D printing served to create a silicone model of the heart, with the same material as the vessels, which was used by a heart surgeon to simulate a Rastelli procedure.

RESULTS
The best material was a soft elastic silicone (Shore A hardness 8). Training on the vessel models decreased the residents’ procedural time and improved their grades on a performance rating scale. The surgeon evaluated the moulded heart model as realistic and was able to perform the Rastelli procedure on it. Even if the valves were poorly represented, it was found to be useful for preintervention training.

CONCLUSIONS
By using free segmentation software, a relatively low-cost silicone and a technique based on re-usable moulds, the cost of obtaining heart models suitable for training in congenital heart defect surgery can be substantially decreased.