bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral health status after hematopoietic stem cell transplantations: Outcomes from an adult Italian population
Authors: Arduino Paolo G. , Gambino Alessio , Giaccone Luisa , Suria Marco , Carbone Mario , Carrozzo Marco , Broccoletti Roberto , Conrotto Davide 
Published: March 2022

AbstractAimTo describe oral cavity changes in patients who underwent a hematopoietic stem cell transplantation (HSCT).Methods and resultsA group of 32 patients was studied after a mean period of 48.8 months (±11.22) from HSCT; oral, dental, and periodontal status were collected and compared with those of healthy matched controls. Unstimulated whole salivary flow (UWS) and salivary pH were also measured. A validated questionnaire (EORTC QLQH&N‐35) was used for reported quality of life. Fifty‐nine percent of patients were affected by chronic graft‐versus‐host disease (cGVHD). Dental health and periodontal status were statistically worse than in controls (P = .003 and P = .008, respectively). Regarding the HSCT group, UWS was statistically lower, and EORTC QLQH&N‐35 significantly higher than those reported in controls (P = .000 for both). There was no statistical correlation between hypo‐salivation and conditioning, presence of cGVHD, type of medication used before and after transplantation, and time of follow‐up. A reduction in salivary pH has been noted only for patients with erosive oral lesions.ConclusionThe oral cavity of HSCT patients appeared to undergo substantial modifications and the quality of life was deeply compromised.
Alcohol use history increases the likelihood of suicide behavior among male chronic patients with schizophrenia in a Chinese population
Authors: Dai Qilong , Zhou Yongjie , Liu Ran , Wei Shuochi , Zhou Huixia , Tian Yang , Xia Luyao , Cervenka Gregory M , Wu Hanjing E , Wang Li , Zhang Xiangyang 
Published: March 2022

AbstractAimsThis study was designed to detect the association between the history of alcohol drinking and suicidality in schizophrenia (SCZ) inpatients in a Chinese population.MethodsWe recruited 616 male SCZ inpatients and collected demographic and clinical data. Five‐factor model of the Positive and Negative Syndrome Scale (PANSS) was used to assess their psychopathological symptoms.ResultsOur results showed that 31.33% of SCZ patients had a history of alcohol drinking. They had higher rates of lifetime suicide attempt and suicidal ideation than those without a history of alcohol drinking. Moreover, patients with a history of drinking were more likely to attempt suicide (14.51% vs. 7.09%; χ2 = 7.70, df = 1, p = 0.006), with an odds ratio (OR) of 2.22 and have suicidal ideation (29.02% vs. 17.49%; χ2 = 9.89, df = 1, p = 0.002), with an OR of 1.93. In addition, patients who used to drink alcohol were more likely to be smokers and had more severe positive and depressive symptoms (all p < 0.05).ConclusionsOur study indicates that history of alcohol drinking may increase the prevalence of lifetime suicide attempt and suicidal ideation in male patients with chronic SCZ. Moreover, the history of alcohol drinking may be associated with some demographic data and clinical symptoms.
The changing impact of cytomegalovirus among hematopoietic cell transplant recipients during the past decade: A single institutional cohort study
Authors: Johnsrud Joyce J. , Nguyen Isabelle T. , Domingo Walter , Raval Amit D. , Tang Yuexin , Narasimhan Balasubramanian , Efron Bradley , Brown Janice (Wes) 
Published: March 2022

AbstractBackgroundWith advancements in allogeneic hematopoietic cell transplantation (alloHCT), the need for cytomegalovirus (CMV) surveillance persists.MethodsWe present a retrospective analysis on the impact of CMV with preemptive therapy in 1065 alloHCT patients with donor and/or recipient CMV seropositivity from 2009 to 2019.ResultsFifty‐one percent developed clinically significant CMV infection (CMV‐CSI); 6.5% had CMV disease. In multivariate analysis stratified by serostatus and preparative regimen, the use of anti‐thymocyte globulin (hazard ratios 2.97, 95% confidence interval 2.00–4.42, p < .001) was associated with development of CMV‐CSI. Median length of stay for index hospitalization was longer in patients with CMV‐CSI (27 vs. 25 days, respectively; p = .002), as were rates (32.9% vs. 17.7%; p < .001) and duration (9 d vs. 6 d; p < .001) of rehospitalization, and median total inpatient days (28 d vs. 26 d; p < .001). Patients with CMV‐CSI had higher rates of neutropenia (47% vs. 20%; p < .001) and transfusion support (packed red blood cell, median 5 vs. 3; p < .001; platelets, median 3 vs. 3; p < .001).ConclusionPreemptive therapy does not negate the impact of CMV‐CSI on peri‐engraftment toxicity and healthcare utilization. This cohort represents a large single center study on the impact of CMV in the preletermovir era and serves as a real‐world comparator for assessing the impact of future prophylaxis.
Quantitative norovirus viral load is not affected by home storage of stool
Authors: Ison Michael G. , Tan Ming , Daud Amna , Huang Pengwei , Jiang Jason Xi 
Published: March 2022

AbstractIn preparation of a clinical trial of norovirus treatment, there were concerns raised by FDA about risk of self‐storage of stool from patients infected with norovirus affecting quantitative assessments of norovirus RNA. Specifically, most home freezers are frost‐free and may expose the samples to multiple rounds of freeze‐thaw. Stool samples collected by the study team were stored at different lengths in a frost‐free freezer and at −80°C. Quantitative PCRs of norovirus were performed on all samples using the same assay. By all measures, there was no significant change in measured viral load with home storage.
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Three-Dimensional Printing Ink Preparation and Process Analysis of Magnetorheological Elastomer With Complex Structure
Authors: Te Li , Jianhui Deng , Lili Liu , Haibo Liu , Boyao Cui , Qi Luo , Yongqing Wang 
Published: March 2022

Abstract
Magnetorheological elastomer (MRE) has great application prospects in the fields of shock absorption, isolation, sensing, and soft robots. However, the MRE precursor mixture cannot be printed directly due to its low viscosity and long curing time, which makes it difficult to manufacture MRE with complex structure, or multifunctional composite. Aiming at the MRE 3D printing dilemmas of material and process issues, a rheology modifier ink preparation method of MRE precursor mixture and a MRE 3D printing process that use MRE precursor mixtures to print directly with direct ink writing (DIW) are proposed. To obtain high-precision manufacturing process, the influence of process parameters such as nozzle diameter, extrusion pressure, feed speed, and nozzle height on the ink filaments is analyzed on the basis of theoretical models and experiments. The experiment results show that MREs with different characteristics and complex structures can be printed with high precision(≤0.2 mm), and the proposed MRE ink and 3D printing process are valid. To further verify the feasibility of 3D printing MRE, the magnetorheological effects of 3D-printed MRE samples are tested, and their stiffness can be improved under magnetic field conditions.
Interactions Between Shock Waves and Liquid Droplet Clusters: Interfacial Physics
Authors: Tripathi Mitansh , Ganti Himakar , Khare Prashant 
Published: March 2022

Abstract
This study quantitatively investigates the behaviors of single and multiple liquid cylinders placed in the path of a traveling normal shock wave using high-fidelity numerical simulations. The research is motivated by next-generation liquid-fueled scramjet and rotating detonation engines (RDE) where the liquid fuel interacts with shock waves and undergoes deformation, fragmentation, atomization, and vaporization before it mixes with the air and subsequently burns—the focus of this study is on the deformation and interfacial physics. The mathematical formulation to investigate this multiphase problem is based on a modified five-equation Kapila model that incorporates pressure-relaxation, viscous, and surface tension effects. A diffuse interface method is used to capture the liquid–gas interface. Two configurations are studied in this effort: (1) a single column of diameter 22 mm exposed to a shock wave traveling at Mach 2.4 and (2) a two identical cylinder system with diameters of 4.8 mm and 30 mm apart, and exposed to a shock wave moving a Mach number of 1.47. The computational results show excellent agreement with high-speed images and droplet deformation measured in the experiments. For both cases, it is found that the shock and the flow field in its wake leads to the flattening of the cylinder, followed by the formation of instability waves that are amplified by the baroclinic torque and the continuous reflections of the waves transmitted inside the liquid interior, eventually leading to ligament stripping. Based on the spatiotemporal evolution of the liquid and gaseous flowfields, time evolution of shock strength and parent droplet's mass and translation distance are also discussed.
Recurrent strokes and memory loss in a patient with triple-positive antiphospholipid antibody syndrome
Authors: Osuorji Chinenye , Bilal Jawad , Osuorji Ikenna 
Published: March 2022

Antiphospholipid syndrome may cause recurrent thromboembolic events of the microvasculature, arteries and veins. It is also characterised by a range of neurological and psychiatric dysfunctions, as well as complications during pregnancy. Patients with triple-positive antiphospholipid syndrome have persistently elevated levels of lupus anticoagulant (LA), anti-beta-2-glycoprotein I (B2GPI) and anticardiolipin antibodies (aCL). These patients also have a higher risk of initial or recurrent thrombosis.We report the case of a 36-year-old man who was presented with progressive memory loss and recurrent stroke. He had persistently elevated antiphospholipid antibody titres (LA, aCL-immunoglobulin G and B2GPI antibodies). These features persisted while the patient was receiving low-dose aspirin (LDA), 81mg daily. Vitamin K antagonist (VKA); warfarin, with the international normalised ratio (INR) maintained at 2–3 was then added to his treatment regimen. The VKA dose was maintained at - a higher therapeutic INR while LDA administration was continued to achieve resolution of the patient’s symptoms.
CD4 T cell dynamics shape the immune response to combination oncolytic herpes virus and BRAF inhibitor therapy for melanoma
Authors: Bozhanova Galabina , Hassan Jehanne , Appleton Lizzie , Jennings Victoria , Foo Shane , McLaughlin Martin , Chan Wah Hak Charleen ML , Patin Emmanuel C , Crespo-Rodriguez Eva , Baker Gabby , Armstrong Edward , Chiu Matthew , Pandha Hardev , Samson Adel , Roulstone Victoria , Kyula Joan , Vile Richard , Errington-Mais Fiona , Pedersen Malin , Harrington Kevin , Ono Masahiro , Melcher Alan 
Published: March 2022

BackgroundCombination herpes simplex virus (HSV) oncolytic virotherapy and BRAF inhibitors (BRAFi) represent promising immunogenic treatments for BRAF mutant melanoma, but an improved understanding of the immunobiology of combinations is needed to improve on the benefit of immune checkpoint inhibitors (ICI).MethodsUsing a BRAFV600E-driven murine melanoma model, we tested the immunogenicity of HSV/BRAFi in immunocompetent C57BL mice. In addition to standard FACS analysis, we used the ‘Timer of Cell Kinetics and Activity’ system, which can analyze the temporal dynamics of different T cell subsets. This immune data was used to inform the selection of ICI for triple combination therapy, the effects of which were then further characterized using transcriptomics.ResultsAdding BRAFi treatment to HSV improved anti-tumor effects in vivo but not in vitro. Immune characterization showed HSV or dual therapy led to fewer intratumoral Treg, although with a more activated phenotype, together with more effector CD8 +T cells. Tocky analysis further showed that HSV/BRAFi dual treatment reduced the Tocky signal (reflecting engagement with cognate antigen), in both Treg and conventional subsets of CD4+, but not in CD8 +cells. However, a higher percentage of Treg than of conventional CD4 +maintained frequent engagement with antigens on treatment, reflecting a predominance of suppressive over effector function within the CD4 +compartment. The only T cell subset which correlated with a reduction in tumor growth was within Tocky signal positive conventional CD4+, supporting their therapeutic role. Targeting CD25 high, antigen-engaged Treg with a depleting anti-CD25 ICI, achieved complete cures in 100% of mice with triple therapy. Transcriptomic analysis confirmed reduction in Foxp3 on addition of anti-CD25 to HSV/BRAFi, as well as increases in expression of genes reflecting interferon signaling and cytotoxic activity.ConclusionsCombination HSV/BRAFi is an immunogenic therapy for BRAF mutant melanoma, but cannot fully control tumors. Dual therapy results in changes in T cell dynamics within tumors, with relatively maintained antigen signaling in Treg compared with conv CD4+. Antigen-engaged CD4 +effectors correlate with tumor growth control, and depletion of Treg by addition of an anti-CD25 ICI, releasing suppression of conventional CD4 +effectors by Treg, enhances survival and activates immune signaling within tumors.
An Axiomatic Perspective on the Performance Effects of End-Host Path Selection
Authors: Scherrer Simon , Legner Markus , Perrig Adrian , Schmid Stefan 
Published: March 2022

In various contexts of networking research, end-host path selection has recently regained momentum as a design principle. While such path selection has the potential to increase performance and security of networks, there is a prominent concern that it could also lead to network instability (i.e., flow-volume oscillation) if paths are selected in a greedy, load-adaptive fashion. However, the extent and the impact vectors of instability caused by path selection are rarely concretized or quantified, which is essential to discuss the merits and drawbacks of end-host path selection.
In this work, we investigate the effect of end-host path selection on various metrics of networks both qualitatively and quantitatively. To achieve general and fundamental insights, we leverage the recently introduced axiomatic perspective on congestion control and adapt it to accommodate joint algorithms for path selection and congestion control, i.e., multi-path congestion-control protocols. Using this approach, we identify equilibria of the multi-path congestioncontrol dynamics and analytically characterize these equilibria with respect to important metrics of interest in networks (the "axioms") such as efficiency, fairness, and loss avoidance. We analyze how these axiomatic ratings for a general network change compared to a scenario without path selection, thereby obtaining an interpretable and quantititative formalization of the performance impact of end-host path-selection. Finally, we show that there is a fundamental trade-off in multi-path congestion-control protocol design between efficiency, stability, and loss avoidance on one side and fairness and responsiveness on the other side.
Anatomical investigation of wood from two old bridges as part of the historical record of the flora of the Atlantic Forest
Authors: Nascimento Silva Sabrina , Santos Kelly Cristina Moreira , Costa Warlen Silva , Castilhori Marcelo Fraga , Callado Cátia Henriques 
Published: March 2022

Summary
The anatomical study of wood used in Brazilian heritage, in association with other areas of knowledge, has provided important information about the cultural and social aspects of past generations and the composition and use of the flora of different regions. Our goal was to identify the wood used in the construction of two old bridges for the transport of people and cargo between Vila Dois Rios and Praia da Parnaioca, Ilha Grande, Angra dos Reis, state of Rio de Janeiro, Brazil. Anatomical features of the sampled woods were used for taxonomic identification by multiple-entry key for wood identification, followed by comparisons with anatomical descriptions of wood samples from xylarium, the literature, and databases. The search for information considered the common and/or scientific names of taxa attributed to the woods from the bridges, and whose natural occurrence is registered for Ilha Grande and/or the state of Rio de Janeiro. The results showed that the bridges were built with the wood of Zollernia ilicifolia (Brongn.) Vogel and Handroanthus sp. Mattos. Knowing that the site had labor, infrastructure, and raw materials during the period when the bridges were built, the results reveal aspects of the composition of the current and past flora of Ilha Grande.
The 2020 International Verification Methods Workshop Online: Major Outcomes and Way Forward
Authors: Casati Barbara , Dorninger Manfred , Coelho Caio A. S. , Ebert Elizabeth E. , Marsigli Chiara , Mittermaier Marion P. , Gilleland Eric 
Published: March 2022

Abstract
The International Verification Methods Workshop was held online in November 2020 and included sessions on physical error characterization using process diagnostics and error tracking techniques; exploitation of data assimilation techniques in verification practices, e.g., to address representativeness issues and observation uncertainty; spatial verification methods and the Model Evaluation Tools, as unified reference verification software; and meta-verification and best practices for scores computation. The workshop reached out to diverse research communities working in the areas of high-impact weather, subseasonal to seasonal prediction, polar prediction, and sea ice and ocean prediction. This article summarizes the major outcomes of the workshop and outlines future strategic directions for verification research.
Parallel sequence tagging for concept recognition
Authors: Furrer Lenz , Cornelius Joseph , Rinaldi Fabio 
Published: March 2022

Abstract
Background
Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial way, which is inherently prone to error propagation from NER to NEN. We propose a parallel architecture, where both NER and NEN are modeled as a sequence-labeling task, operating directly on the source text. We examine different harmonisation strategies for merging the predictions of the two classifiers into a single output sequence.

Results
We test our approach on the recent Version 4 of the CRAFT corpus. In all 20 annotation sets of the concept-annotation task, our system outperforms the pipeline system reported as a baseline in the CRAFT shared task, a competition of the BioNLP Open Shared Tasks 2019. We further refine the systems from the shared task by optimising the harmonisation strategy separately for each annotation set.

Conclusions
Our analysis shows that the strengths of the two classifiers can be combined in a fruitful way. However, prediction harmonisation requires individual calibration on a development set for each annotation set. This allows achieving a good trade-off between established knowledge (training set) and novel information (unseen concepts).
A comparison of transcriptome analysis methods with reference genome
Authors: Liu Xu , Zhao Jialu , Xue Liting , Zhao Tian , Ding Wei , Han Yuying , Ye Haihong 
Published: March 2022

Abstract
Background
The application of RNA-seq technology has become more extensive and the number of analysis procedures available has increased over the past years. Selecting an appropriate workflow has become an important issue for researchers in the field.

Methods
In our study, six popular analytical procedures/pipeline were compared using four RNA-seq datasets from mouse, human, rat, and macaque, respectively. The gene expression value, fold change of gene expression, and statistical significance were evaluated to compare the similarities and differences among the six procedures. qRT-PCR was performed to validate the differentially expressed genes (DEGs) from all six procedures.

Results
Cufflinks-Cuffdiff demands the highest computing resources and Kallisto-Sleuth demands the least. Gene expression values, fold change, p and q values of differential expression (DE) analysis are highly correlated among procedures using HTseq for quantification. For genes with medium expression abundance, the expression values determined using the different procedures were similar. Major differences in expression values come from genes with particularly high or low expression levels. HISAT2-StringTie-Ballgown is more sensitive to genes with low expression levels, while Kallisto-Sleuth may only be useful to evaluate genes with medium to high abundance. When the same thresholds for fold change and p value are chosen in DE analysis, StringTie-Ballgown produce the least number of DEGs, while HTseq-DESeq2, -edgeR or -limma generally produces more DEGs. The performance of Cufflinks-Cuffdiff and Kallisto-Sleuth varies in different datasets. For DEGs with medium expression levels, the biological verification rates were similar among all procedures.

Conclusion
Results are highly correlated among RNA-seq analysis procedures using HTseq for quantification. Difference in gene expression values mainly come from genes with particularly high or low expression levels. Moreover, biological validation rates of DEGs from all six procedures were similar for genes with medium expression levels. Investigators can choose analytical procedures according to their available computer resources, or whether genes of high or low expression levels are of interest. If computer resources are abundant, one can utilize multiple procedures to obtain the intersection of results to get the most reliable DEGs, or to obtain a combination of results to get a more comprehensive DE profile for transcriptomes.
Baseline neutrophil–lymphocyte ratio can be associated with hematoma expansion in patients with intracerebral hemorrhage: a retrospective observational study
Authors: Alimohammadi Ehsan , Bagheri Seyed Reza , Mardanpour Parand , Moradi Farid , Arjmandnia Fatemeh , Esmaeili Narges 
Published: March 2022

Abstract
Background
Hematoma expansion can be related to increased mortality and poor clinical outcomes in patients with intracerebral hemorrhage (ICH). So, early identification and prevention of hematoma expansion can be considered as an important therapeutic aim. This study aimed to evaluate the hypothesis that the neutrophil to lymphocyte ratio (NLR) is associated with hematoma expansion in ICH patients.

Methods
We retrospectively evaluated the clinical data of a total of 221 patients with ICH who were treated in our department between April 2018 and April 2021. The demographic, clinical, radiological, and laboratory test data including the NLR upon admission were investigated. A binary logistic regression analysis was used to assess the independent associations between different variables and hematoma expansion.

Results
A total of 221 patients with ICH were included. There were 122 (55.2%) males and 99 (44.8%) females. The mean age (years) at admission was 66.43 ± 8.28.
The hematoma expansion occurred in 57 (25.8%) cases. The results of the multivariate analysis showed that hematoma volume at baseline (OR, 3.12; 95% CI 1.78–5.02; P < 0.001), admission systolic blood pressure (OR, 2.87; 95% CI 1.79–4.34; P = 0.013), Glasgow Coma Scale (GCS) (OR, 1.94; 95% CI 1.45–2.93; P = 0.020), and NLR (OR, 1.74; 95% CI 1.16–2.60; P = 0.032) were correlated with hematoma expansion in these patients.

Conclusions
Our findings suggest that NLR can be a predictor of hematoma expansion in patients with ICH. This cost-effective and easily available biomarker could be used to early prediction of hematoma expansion in these patients.