bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Pre-TACE Radiomics Model to Predict HCC Progression and Recurrence in Liver Transplantation: A Pilot Study on a Novel Biomarker
Authors: Ivanics Tommy , Salinas-Miranda Emmanuel , Abreu Phillipe , Khalvati Farzad , Namdar Khashayar , Dong Xin , Deniffel Dominik , Gorgen Andre , Erdman Lauren , Jhaveri Kartik , Haider Masoom , Veit-Haibach Patrick , Sapisochin Gonzalo 
Published: January 2021

Background.Despite transarterial chemoembolization (TACE) for hepatocellular carcinoma (HCC), a significant number of patients will develop progression on the liver transplant (LT) waiting list or disease recurrence post-LT. We sought to evaluate the feasibility of a pre-TACE radiomics model, an imaging-based tool to predict these adverse outcomes.Methods.We analyzed the pre-TACE computed tomography images of patients waiting for a LT. The primary endpoint was a combined event that included waitlist dropout for tumor progression or tumor recurrence post-LT. The radiomic features were extracted from the largest HCC volume from the arterial and portal venous phase. A third set of features was created, combining the features from these 2 contrast phases. We applied a least absolute shrinkage and selection operator feature selection method and a support vector machine classifier. Three prognostic models were built using each feature set. The models’ performance was compared using 5-fold cross-validated area under the receiver operating characteristic curves.Results. Eighty-eight patients were included, of whom 33 experienced the combined event (37.5%). The median time to dropout was 5.6 mo (interquartile range: 3.6–9.3), and the median time for post-LT recurrence was 19.2 mo (interquartile range: 6.1–34.0). Twenty-four patients (27.3%) dropped out and 64 (72.7%) patients were transplanted. Of these, 14 (21.9%) had recurrence post-LT. Model performance yielded a mean area under the receiver operating characteristic curves of 0.70 (±0.07), 0.87 (±0.06), and 0.81 (±0.06) for the arterial, venous, and the combined models, respectively.Conclusions.A pre-TACE radiomics model for HCC patients undergoing LT may be a useful tool for outcome prediction. Further external model validation with a larger sample size is required.
Publication Rate of Abstracts Presented at the North American Neuro-Ophthalmology Society Annual Meeting From 2008 to 2017
Authors: Yuan Po Hsiang (Shawn) , MacLean Luke J. , Li Erica A. , Yin Shelly , Micieli Jonathan A. 
Published: January 2021

Background:
Conference abstracts serve an important role in the timely dissemination of scientific and clinical advancements, but most fail to be published. The goal of this study was to investigate the publication rate and factors associated with publication of abstracts presented at the North American Neuro-Ophthalmology Society (NANOS) Annual Meeting over a 10-year period.

Methods:
NANOS Annual Meeting abstracts from 2008 to 2017 were extracted and categorized into Walsh presentations, scientific platforms, or poster presentations. An original automated web scraping program was validated to search PubMed, Embase, Medline, and Google Scholar for publications. Publication date, journal, authors, study type, multicenter involvement, and financial disclosures were retrieved.

Results:
A total of 195 Walsh presentations, 231 scientific platform presentations, and 1735 scientific posters were included in the study with an overall publication rate of 31.5% (681/2,161). This was stable over the study period. Publication was the highest for scientific platforms (67.1%), followed by Walsh abstracts (36.4%) and poster presentations (27.2%). Multivariable analysis identified 3–4 authors, 5 or more authors, basic science, and sample size of 100 or more significantly correlated with subsequent publication. The top 3 countries for NANOS submissions were the United States, Canada, and South Korea, and the most frequent journal of publication was the Journal of Neuro-Ophthalmology.

Conclusions:
Publication rate of NANOS abstracts is comparable to other conferences in ophthalmology and the neurological sciences. Conference attendees should be aware that more than two-thirds of abstracts fail to be published and publication rates vary widely by type of submission.
Hospital-Acquired Pressure Injuries and Acute Skin Failure in Critical Care
Authors: Pittman Joyce , Beeson Terrie , Dillon Jill , Yang Ziyi , Mravec Michelle , Malloy Caeli , Cuddigan Janet 
Published: January 2021

PURPOSE
The purpose of this study was to examine clinical characteristics and risk factors for critically ill patients who develop pressure injuries and identify the proportion of validated unavoidable pressure injuries associated with the proposed risk factors for acute skin failure (ASF).

DESIGN:
Retrospective case-control comparative study.

SUBJECTS AND SETTING:
The sample comprised adult critically ill participants hospitalized in critical care units such as surgical, trauma, cardiovascular surgical, cardiac, neuro, and medical intensive care and corresponding progressive care units in 5 acute care hospitals within a large Midwestern academic/teaching healthcare system. Participants who developed hospital-acquired pressure injuries (HAPIs) and patients without HAPIs (controls) were included.

METHODS:
A secondary analysis of data from a previous study with HAPIs and matching data for the control sample without HAPIs were obtained from the electronic health record. Descriptive and multivariate logistic regression analyses were conducted.

RESULTS:
The sample comprised 475 participants; 165 experienced a HAPI and acted as cases, whereas the remaining 310 acted as controls. Acute Physiology and Chronic Health Evaluation (APACHE II) mean score (23.8, 8.7%; P < .001), mortality (n = 45, 27.3%; P = .002), history of liver disease (n = 28, 17%; P < .001), and unintentional loss of 10 lb or more in 1 month (n = 20, 12%; P = .002) were higher in the HAPI group. Multivariate logistic regression analysis identified participants with respiratory failure (odds ratio [OR] = 3.00; 95% confidence interval [CI], 1.27-7.08; P = .012), renal failure (OR = 7.48; 95% CI, 3.49-16.01; P < .001), cardiac failure (OR = 4.50; 95% CI, 1.76-11.51; P = .002), severe anemia (OR = 10.89; 95% CI, 3.59-33.00; P < .001), any type of sepsis (OR = 3.15; 95% CI, 1.44-6.90; P = .004), and moisture documentation (OR = 11.89; 95% CI, 5.27-26.81; P <.001) were more likely to develop a HAPI. No differences between unavoidable HAPI, avoidable HAPI, or the control group were identified based on the proposed ASF risk factors.

CONCLUSION:
This study provides important information regarding avoidable and unavoidable HAPIs and ASF. Key clinical characteristics and risk factors, such as patient acuity, organ failure, tissue perfusion, sepsis, and history of prior pressure injury, are associated with avoidable and unavoidable HAPI development. In addition, we were unable to support a relationship between unavoidable HAPIs and the proposed risk factors for ASF. Unavoidability of HAPIs rests with the documentation of appropriate interventions and not necessarily with the identification of clinical risk factors.
Suicide prevention efforts in the United States and their effectiveness
Authors: Barnhorst Amy , Gonzales Hilary , Asif-Sattar Rameesha 
Published: January 2021

Purpose of review
Suicide is a serious public health problem in the United States, and suicide rates have been increasing for more than a decade. Rural areas are more impacted than urban areas, reinforcing that social, cultural, and economic factors contribute to risk. This article reviews recent work about these contributors to suicide and how they may inform prevention efforts.

Recent findings
Current research has shown that suicide is more than a mental health problem with a psychiatric or medical solution. Universal screening and referral by gatekeepers target a large group with a low baseline risk, and there are few treatments proven to reduce death by suicide, as well as a severe shortage of mental health providers in the United States to provide them. Instead, suicide prevention polices can target various other factors that contribute to elevated suicide risk at the population level, including reducing socioeconomic deprivation and access to firearms, both of which are often higher in rural areas. Internet-based interventions also hold promise as they are highly scalable, accessible almost anywhere, and often anonymous.

Summary
Understanding factors that increase suicide risk guide development of evidence-based policies targeted at high-risk groups. Population-level interventions should be developed in collaboration with the target audience for cultural appropriateness.
Citrobacter koseri stimulates dendritic cells to induce IL-33 expression via abundant ATP production
Authors: Kataoka Hideo , Mori Taiki , Into Takeshi 
Published: January 2021

Introduction.Food allergies (FAs) occur due to intestinal immune dysfunction elicited by dysbiotic conditions. It was previously determined by us thatCitrobacterspecies propagate in the faeces of mice with FAs and worsen allergic symptoms by inducing the allergenic cytokine IL-33. Dendritic cells can play important roles in regulation of FA responses.Hypothesis.Citrobacterspecies propagating in intestines of mice worsen allergic symptoms by stimulating dendritic cells to induce IL-33 expression.Aim.The aim of the present study was to analyse whetherC. koseristimulates dendritic cells to induce IL-33 expression.Methodology.IL-33 expression was evaluated in a DC2.4 mouse dendritic cell line stimulated by live or heat-inactivatedC. koseriJCM1658, ATP, LPS extracted fromC. koseriJCM1658 or other enterobacteria by real-time PCR. The ATP concentration and number of live bacteria in the culture supernatant were measured simultaneously.Results.LiveC. koseriJCM1658 induced higher levels of IL-33 expression than other enterobacteria tested, but such a response was not elicited by heat-inactivatedC. koseriJCM1658. LPS extracted fromC. koseriJCM1658 did not induce IL-33 expression and suppressed liveC. koseriJCM1658-induced IL-33 expression via the activation of Toll-like receptor 4 signalling. Furthermore, ATP produced byC. koseriJCM1658 stimulated dendritic cells to induce IL-33 expression by stimulating the P2X7receptor, and LPS attenuated extracellular ATP-induced IL-33 expression.C. koseriJCM1658 was observed to proliferate more vigorously and produce more ATP than other enterobacteria.Conclusion.C. koseriacts as an allergenic bacterium through ATP production, stimulating dendritic cells to induce IL-33 expression, while LPS released from inactivatedC. koseriJCM1658 attenuates this allergenicity.
Late Pleistocene palaeoecology and phylogeography of woolly rhinoceroses
Authors: Rey-Iglesia Alba , Lister Adrian M. , Stuart Anthony J. , Bocherens Hervé , Szpak Paul , Willerslev Eske , Lorenzen Eline D. 
Published: January 2021

AbstractThe woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open vegetation in that region. Here, we analyzed carbon (δ13C) and nitrogen (δ15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,60014C years to ~14,000 years before present. Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data reveal ecological flexibility and geographical variation in woolly rhinoceros stable isotope compositions through time. In north-east Siberia, we detectedδ15N stability through time. This could reflect long-term environmental stability, and might have enabled the later survival of the species in the region. To further investigate the palaeoecology of woolly rhinoceroses, we compared their isotopic compositions with that of other contemporary herbivores. This analysis suggests possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius), and isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica) at different points in time. To provide phylogeographical context to the isotopic data, we analyzed 61 published mitochondrial control region sequences. The data show a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which show a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia had an impact on the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.
Intermittent radiotherapy as alternative treatment for recurrent high grade glioma: A modelling study based on longitudinal tumor measurements
Authors: Brüningk Sarah C. , Peacock Jeffrey , Whelan Christopher J. , Yu Hsiang-Hsuan M. , Sahebjam Solmaz , Enderling Heiko 
Published: January 2021

ABSTRACTRecurrent high grade glioma patients face a poor prognosis for which no curative treatment option currently exists. In contrast to prescribing high dose hypofractionated stereotactic radiotherapy (HFSRT, ≥ 6 Gyx5 in daily fractions) with debulking intent, we suggest a personalized treatment strategy to improve tumor control by delivering intermittent high dose treatment (iRT, ≥ 6 Gyx1 every six weeks). We performed a simulation analysis to compare HFSRT, iRT and iRT plus boost (≥ 6 Gyx3 in daily fractions at time of progression) based on a mathematical model of tumour growth, radiation response and patient-specific evolution of resistance to additional treatments (pembrolizumab and bevacizumab). Model parameters were fitted from tumour growth curves of 16 patients enrolled in the phase 1 NCT02313272 trial that combined HFSRT with bevacizumab and pembrolizumab. Then, iRT +/-boost treatments were simulated and compared to HFSRT based on time to tumor regrowth. The modelling results demonstrated that iRT+boost(-boost) treatment was equal or superior to HFSRT in 15(11) out of 16 cases and that patients that remained responsive to pembrolizumab and bevacizumab would benefit most from iRT. Time to progression could be prolonged through the application of additional, intermittently delivered fractions. iRT hence provides a promising treatment option for recurrent high grade glioma patients.
A Fractional Order Dengue Fever Model in the Context of Protected Travellers
Authors: Bonyah E. , Juga M. L. , Chukwu C. W. , Fatmawati  
Published: January 2021

AbstractClimate changes are affecting the control of many vector-borne diseases, particularly in Africa. In this work, a dengue fever model with protected travellers is formulated. Caputo-Fabrizio operator is utilized to obtain some qualitative information about the disease. The basic properties and the reproduction number is studied. The two steady states are determined and the local stability of the states are found to be asymptotically stable. The fixed pointed theory is made use to obtain the existence and uniqueness of solutions of the model. The numerical simulation suggests that the fractional-order affects the dynamics of dengue fever.
Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition
Authors: Ho Chi-Min , Jih Jonathan , Lai Mason , Li Xiaorun , Goldberg Daniel E. , Beck Josh R. , Zhou Z. Hong 
Published: January 2021

AbstractThe RhopH complex is implicated in malaria parasites’ ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here we enrich the endogenous RhopH complex in a native soluble form, comprising RhopH2, CLAG3.1 and RhopH3, directly from parasite cell lysates and determine its atomic structure using cryo electron microscopy, mass spectrometry, and the cryoID program. This first direct observation of an exportedP. falciparumtransmembrane protein—in a soluble, trafficking state and with atomic details of buried putative membrane-insertion helices—offers insights into assembly and trafficking of RhopH and other parasite-derived complexes to the erythrocyte membrane. Our study demonstrates the potential endogenous structural proteomics approach holds for elucidating the molecular mechanisms of hard-to-isolate complexes in their native, functional forms.
Climate warming changes synchrony of plants and pollinators
Authors: Freimuth Jonas , Bossdorf Oliver , Scheepens J. F. , Willems Franziska M. 
Published: January 2021

AbstractClimate warming changes the phenology of many species. When interacting organisms respond differently, climate change may disrupt their interactions and affect the stability of ecosystems. Here, we used GBIF occurrence records to examine phenology trends in plants and their associated insect pollinators in Germany since the 1980s. We found strong phenological advances in plants, but differences in the extent of shifts among pollinator groups. The temporal trends in plant and insect phenologies were generally associated with interannual temperature variation, and thus likely driven by climate change. When examining the synchrony of species-level plant-pollinator interactions, their temporal trends differed among pollinator groups. Overall, plant-pollinator interactions become more synchronized, mainly since the phenology of plants responded more strongly to climate change than that of the pollinators. However, if the observed trends continue, many interactions may become more asynchronous again in the future. Our study suggests that climate change affects the phenologies of both plants and insects, and that it also influences the synchrony of plant-pollinator interactions.
Distinct T cell chromatin landscapes in scleroderma subtypes
Authors: Dou Diana R. , Zhao Yang , Abe Brian , Li Rui , Zaba Lisa C. , Aren Kathleen , Carns Mary , Chung Lorinda S. , Hinchcliff Monique , Chang Howard Y. 
Published: January 2021

ABSTRACTSystemic sclerosis (SSc; scleroderma) is an autoimmune rheumatic disease that primarily affects biological females whose pathogenesis is poorly understood. The clinical hallmark is hardening of the skin, but internal organ dysfunction is the leading cause of death. Diagnosis and treatment are complicated by heterogeneity within the disease including variable lethality, fibrosis severity, serum autoantibody production, and internal organ involvement. Important gaps remain in our knowledge of the exact molecular and cellular pathways underlying distinct SSc subtypes. Herein, we identify genome-wide chromatin accessibility profiles of peripheral CD4+T cells to distinguish and better understand the observed heterogeneity in SSc patients. We identify a link between the presence of serum anticentromere autoantibodies (ACA) and elevated levels of T helper 2 (Th2) cells and increased chromatin access at gene loci encoding fibrosis-driving Th2 cytokines IL4, IL13, and IL4 receptor. Biological sex followed by autoantibody type are the predominant variables associated with differences in CD4+T cell epigenomic profiles, while mycophenolate mofetil treatment appeared to have no effect. These results suggest new mechanistic basis and therapeutic strategies to address SSc, especially the anti-ACA+ subset of patients who more frequently develop pulmonary arterial hypertension.
The pathway of starch synthesis inArabidopsis thalianaleaves
Authors: Fünfgeld Maximilian M.F.F. , Wang Wei , Ishihara Hirofumi , Arrivault Stéphanie , Feil Regina , Smith Alison M. , Stitt Mark , Lunn John E. , Niittylä Totte 
Published: January 2021

AbstractMany plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling,Arabidopsis thalianamutants that lack SUS activity in mesophyll cells (quadruplesus1234) or have no SUS activity (sextuplesus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in thepgmandadg1mutants that are blocked in the classical pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.Significance statementMutant analysis shows that sucrose synthase makes no significant contribution to transitory starch synthesis in Arabidopsis leaves, resolving a 20-year old controversy about one of the most important pathways of photosynthetic metabolism.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy
Authors: Baldwin Louise A. , Bartonicek Nenad , Yang Jessica , Wu Sunny Z. , Deng Niantao , Roden Daniel L. , Chan Chia-Ling , Al-Eryani Ghamdan , Zanker Damien J. , Parker Belinda S. , Swarbrick Alexander , Junankar Simon 
Published: January 2021

AbstractCancers evade the immune system in order to grow or metastasise through the process of cancer immunoediting. While immune checkpoint inhibitors have been effective for reactivating tumour immunity in some types of cancer, many other solid cancers, including breast cancer, remain largely non-responsive. Understanding the way non-responsive cancers evolve to evade immunity, what resistance pathways are activated and whether this occurs at the clonal level will improve immunotherapeutic design. We tracked cancer cell clones during the immunoediting process and determined clonal transcriptional profiles that allow immune evasion in murine mammary tumour growth in response to immunotherapy with anti-PD1 and anti-CTLA4. Clonal diversity was significantly restricted by immunotherapy treatment in both primary tumours and metastases. These findings demonstrate that immunoediting selects for pre-existing breast cancer cell populations and that immunoediting is not static, it is ongoing during metastasis and immunotherapy treatment. Isolation of immunotherapy resistant clones revealed unique and overlapping transcriptional signatures. The overlapping gene signature was associated with poor survival of basal-like breast cancer patients in two cohorts. At least one of these overlapping genes has an existing small molecule that can potentially be used to improve immunotherapy response.