bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modified EASIX predicts severe cytokine release syndrome and neurotoxicity after chimeric antigen receptor T cells
Authors: Pennisi Martina , Sanchez-Escamilla Miriam , Flynn Jessica R. , Shouval Roni , Alarcon Tomas Ana , Silverberg Mari Lynn , Batlevi Connie , Brentjens Renier J. , Dahi Parastoo B. , Devlin Sean M. , Diamonte Claudia , Giralt Sergio , Halton Elizabeth F. , Jain Tania , Maloy Molly , Mead Elena , Palomba Maria Lia , Ruiz Josel , Santomasso Bianca , Sauter Craig S. , Scordo Michael , Shah Gunjan L. , Park Jae H. , Yanez San Segundo Lucrecia , Perales Miguel-Angel 
Published: August 2021

Abstract
Patients who develop chimeric antigen receptor (CAR) T-cell–related severe cytokine release syndrome (CRS) and immune effector cell–associated neurotoxicity syndrome (ICANS) exhibit hemodynamic instability and endothelial activation. The EASIX (Endothelial Activation and Stress Index) score (lactate dehydrogenase [LDH; U/L] × creatinine [mg/dL]/platelets [PLTs; 109 cells/L]) is a marker of endothelial damage that correlates with outcomes in allogeneic hematopoietic cell transplantation. Elevated LDH and low PLTs have been associated with severe CRS and ICANS, as has C-reactive protein (CRP), while increased creatinine is seen only in a minority of advanced severe CRS cases. We hypothesized that EASIX and 2 new modified EASIX formulas (simplified EASIX, which excludes creatinine, and modified EASIX [m-EASIX], which replaces creatinine with CRP [mg/dL]), calculated peri-CAR T-cell infusion, would be associated with development of severe (grade ≥ 3) CRS and ICANS. We included 118 adults, 53 with B-acute lymphoblastic leukemia treated with 1928z CAR T cells (NCT01044069) and 65 with diffuse large B-cell lymphoma treated with axicabtagene ciloleucel or tisagenlecleucel. The 3 formulas showed similar predictive power for severe CRS and ICANS. However, low PLTs and high CRP values were the only variables individually correlated with these toxicities. Moreover, only m-EASIX was a significant predictor of disease response. m-EASIX could discriminate patients who subsequently developed severe CRS preceding the onset of severe symptoms (area under the curve [AUC] at lymphodepletion, 80.4%; at day −1, 73.0%; and at day +1, 75.4%). At day +3, it also had high discriminatory ability for severe ICANS (AUC, 73%). We propose m-EASIX as a clinical tool to potentially guide individualized management of patients at higher risk for severe CAR T-cell–related toxicities.
Pregnancy in women with an inferior vena cava filter: a tertiary center experience and overview of the literature
Authors: Bistervels Ingrid M. , Geerlings Abby E. , Bonta Peter I. , Ganzevoort Wessel , Zijlstra IJsbrand A.J. , Middeldorp Saskia 
Published: August 2021

Abstract
Patients with an inferior vena cava (IVC) filter that remains in situ encounter a lifelong increased risk of deep vein thrombosis and IVC filter complications including fracture, perforation, and IVC filter thrombotic occlusion. Data on the safety of becoming pregnant with an in situ IVC filter are scarce. The objective was to evaluate the risk of complications of in situ IVC filters during pregnancy. We performed a retrospective cohort study of pregnant patients with an in situ IVC filter from a tertiary center between 2000 and 2020. We collected data on complications of IVC filters and pregnancy outcomes. Additionally, we performed a systematic literature search in MEDLINE, Embase, and gray literature. We identified 7 pregnancies in 4 patients with in situ IVC filters with a mean time since IVC filter insertion of 3 years (range, 1-8). No complications of IVC filter occurred during pregnancy. Review of literature yielded five studies including 13 pregnancies in 9 patients. In 1 pregnancy a pre-existent, until then asymptomatic, chronic perforation of the vena cava wall by the IVC filter caused major bleeding and uterine trauma with fetal loss. Overall, the complication rate was 5%. It seems safe to become pregnant with an indwelling IVC filter that is intact and does not show signs of perforation, but because of the low number of cases, no firm conclusions about safety of in situ IVC filters during pregnancy can be drawn. We suggest imaging before pregnancy to reveal asymptomatic IVC filter complications.
Factors associated with do-not-resuscitate document completion among patients hospitalized in geriatric ward
Authors: Wu Chien-Yi , Jen Chun-Hao , Chuang Yun-Shiuan , Fang Tzu-Jung , Wu Yu-Hsuan , Wu Ming-Tsang 
Published: August 2021

Abstract
Background
With a rapidly aging population, there is an increasing need for do-not-resuscitate (DNR) and advance care planning (ACP) discussions. This study investigated the factors associated with signing DNR documents of older patients in the geriatric ward.

Methods
We conducted a retrospective cohort study at a geriatric ward in a tertiary hospital in Southern Taiwan. Three hundred and thirty-seven hospitalized older patients aged ≥65 years in the geriatric ward from 2018 to 2019. The Hospital Information System and electronic medical records were accessed to obtain details regarding patients’ demographics, daily living activities, serum albumin level, nutrition screening score, intensive care unit transferal, resuscitation procedure, days of hospital stay, and survival status on discharge, and DNR status was recorded retrospectively. Patients were classified into DNR and non-DNR groups, with t-tests and Chi-square tests applied to compare the differences between groups. Logistic regression was performed to predict factors related to the DNR documents.

Results
A total of 337 patients were included, 66 of whom had signed a DNR during hospitalization. After multivariate logistic regression, age 85 or more compared to age 65–74 (adjusted odds ratio, aOR 5.94), poor nutrition with screening score two or more (aOR 2.71), albumin level less than 3 (aOR 3.24), Charlson Comorbidity Index higher than 2 (aOR 2.46) and once transferred to ICU (aOR 5.11) were independently associated with DNR documentation during hospitalization.

Conclusions
Several factors related to DNR documents for geriatric patients were identified which could provide clinical information for physicians, patients, and their families to discuss DNR and ACP.
Colorectal cancer survival among Ministry of National Guard-Health Affairs (MNG-HA) population 2009–2017: retrospective study
Authors: Alyabsi Mesnad , Sabatin Fouad , Ramadan Majed , Jazieh Abdul Rahman 
Published: August 2021

Abstract
Background
Colorectal cancer (CRC) is the most diagnosed cancer among males and third among females in Saudi Arabia, with up to two-third diagnosed at advanced stage. The objective of our study was to estimate CRC survival and determine prognostic factors.

Methods
Ministry of National Guard- Health Affairs (MNG-HA) registry data was utilized to identify patients diagnosed with CRC between 2009 and 2017. Cases were followed until December 30th, 2017 to assess their one-, three-, and five-year CRC-specific survivals. Kaplan-Meier method and Cox proportional hazard models were used to assess survival from CRC.

Results
A total of 1012 CRC patients were diagnosed during 2009–2017. Nearly, one-fourth of the patients presented with rectal tumor, 42.89% with left colon and 33.41% of the cases were diagnosed at distant metastasis stage. The overall one-, three-, and five-year survival were 83, 65 and 52.0%, respectively. The five-year survival was 79.85% for localized stage, 63.25% for regional stage and 20.31% for distant metastasis. Multivariate analyses showed that age, diagnosis period, stage, nationality, basis of diagnosis, morphology and location of tumor were associated with survival.

Conclusions
Findings reveal poor survival compared to Surveillance, Epidemiology, and End Results (SEER) population. Diagnoses at late stage and no surgical and/or perioperative chemotherapy were associated with increased risk of death. Population-based screening in this population should be considered.
Robust biomarker discovery for hepatocellular carcinoma from high-throughput data by multiple feature selection methods
Authors: Zhang Zishuang , Liu Zhi-Ping 
Published: August 2021

Abstract
Background
Hepatocellular carcinoma (HCC) is one of the most common cancers. The discovery of specific genes severing as biomarkers is of paramount significance for cancer diagnosis and prognosis. The high-throughput omics data generated by the cancer genome atlas (TCGA) consortium provides a valuable resource for the discovery of HCC biomarker genes. Numerous methods have been proposed to select cancer biomarkers. However, these methods have not investigated the robustness of identification with different feature selection techniques.

Methods
We use six different recursive feature elimination methods to select the gene signiatures of HCC from TCGA liver cancer data. The genes shared in the six selected subsets are proposed as robust biomarkers. Akaike information criterion (AIC) is employed to explain the optimization process of feature selection, which provides a statistical interpretation for the feature selection in machine learning methods. And we use several methods to validate the screened biomarkers.

Results
In this paper, we propose a robust method for discovering biomarker genes for HCC from gene expression data. Specifically, we implement recursive feature elimination cross-validation (RFE-CV) methods based on six different classication algorithms. The overlaps in the discovered gene sets via different methods are referred as the identified biomarkers. We give an interpretation of the feature selection process based on machine learning using AIC in statistics. Furthermore, the features selected by the backward logistic stepwise regression via AIC minimum theory are completely contained in the identified biomarkers. Through the classification results, the superiority of interpretable robust biomarker discovery method is verified.

Conclusions
It is found that overlaps among gene subsets contain different quantitative features selected by the RFE-CV of 6 classifiers. The AIC values in the model selection provide a theoretical foundation for the feature selection process of biomarker discovery via machine learning. What’s more, genes containing in more optimally selected subsets make better biological sense and implication. The quality of feature selection is improved by the intersections of biomarkers selected from different classifiers. This is a general method suitable for screening biomarkers of complex diseases from high-throughput data.
Integrative enrichment analysis of gene expression based on an artificial neuron
Authors: Jiang Xue , Pan Weihao , Chen Miao , Wang Weidi , Song Weichen , Lin Guan Ning 
Published: August 2021

AbstractBackgroundHuntington’s disease is a kind of chronic progressive neurodegenerative disease with complex pathogenic mechanisms. To data, the pathogenesis of Huntington’s disease is still not fully understood, and there has been no effective treatment. The rapid development of high-throughput sequencing technologies makes it possible to explore the molecular mechanisms at the transcriptome level. Our previous studies on Huntington’s disease have shown that it is difficult to distinguish disease-associated genes from non-disease genes. Meanwhile, recent progress in bio-medicine shows that the molecular origin of chronic complex diseases may not exist in the diseased tissue, and differentially expressed genes between different tissues may be helpful to reveal the molecular origin of chronic diseases. Therefore, developing integrative analysis computational methods for the multi-tissues gene expression data, exploring the relationship between differentially expressed genes in different tissues and the disease, can greatly accelerate the molecular discovery process.MethodsFor analysis of the intra- and inter- tissues’ differentially expressed genes, we designed an integrative enrichment analysis method based on an artificial neuron (IEAAN). Firstly, we calculated the differential expression scores of genes which are seen as features of the corresponding gene, using fold-change approach with intra- and inter- tissues’ gene expression data. Then, we weighted sum all the differential expression scores through a sigmoid function to get differential expression enrichment score. Finally, we ranked the genes according to the enrichment score. Top ranking genes are supposed to be the potential disease-associated genes.ResultsIn this study, we conducted large amounts of experiments to analyze the differentially expressed genes of intra- and inter- tissues. Experimental results showed that genes differentially expressed between different tissues are more likely to be Huntington’s disease-associated genes. Five disease-associated genes were selected out in this study, two of which have been reported to be implicated in Huntington’s disease.ConclusionsWe proposed a novel integrative enrichment analysis method based on artificial neuron (IEAAN), which displays better prediction precision of disease-associated genes in comparison with the state-of-the-art statistical-based methods. Our comprehensive evaluation suggests that genes differentially expressed between striatum and liver tissues of health individuals are more likely to be Huntington’s disease-associated genes.
External fixation versus elastic stable intramedullary nailing in the treatment of open tibial shaft fractures in children
Authors: Hong Pan , Rai Saroj , Tang Xin , Liu Ruikang , Li Jin 
Published: August 2021

Abstract
Introduction
External fixator (EF) is a popular choice for open tibial fractures, but pin tract infection (PTI) and refracture are common complications. Elastic stable intramedullary nail (ESIN) has been reported in the treatment for open tibial fractures. This study aims to compare the clinical outcomes of EF vs. ESIN in the treatment for open tibial shaft fracture in children retrospectively.

Methods
Patients aged 5–11 years with Gustilo-Anderson II and IIIA tibial shaft fracture treated at our institute from January 2008 to January 2018 were reviewed retrospectively and categorized into EF and ESIN groups. Patients with pathological fracture, neuromuscular disorder, metabolic disease, previous tibial fracture or instrumentation, and polytrauma were excluded. Patients with follow-up < 24 months or incomplete medical records were also excluded.

Results
In all, 55 patients (33 males, 22 females) were included in the EF group, whereas 37 patients (21 males, 16 females) were included in the ESIN group. There was no statistically significant difference between the two groups concerning sex, age, body weight, duration from injury to surgery, Gustilo-Anderson (GA) classification, and concomitant injuries. There was no case of nonunion and malunion in either group. The angulation at the latest follow-up was higher in the EF group than the ESIN group (P < 0.01). The radiological union was faster in the ESIN group (7.0 ± 0.9 weeks) than those in the EF group (9.0 ± 2.2 weeks) (P < 0.01). Limb length discrepancy (LLD) was more in the EF group (12.1 ± 4.4, mm) than in the ESIN group (7.3 ± 4.3, mm) (P < 0.01).

Conclusion
ESIN is a viable option in selected patients of GA grade II and IIIA open tibial fractures with comparable clinical outcomes as external fixator. Pin tract infection is the most troublesome complication in the EF group while implant prominence is a nuisance in the ESIN group.
Poliovirus receptor (PVR)-like protein cosignaling network: new opportunities for cancer immunotherapy
Authors: Wu Baokang , Zhong Chongli , Lang Qi , Liang Zhiyun , Zhang Yizhou , Zhao Xin , Yu Yang , Zhang Heming , Xu Feng , Tian Yu 
Published: August 2021

AbstractImmune checkpoint molecules, also known as cosignaling molecules, are pivotal cell-surface molecules that control immune cell responses by either promoting (costimulatory molecules) or inhibiting (coinhibitory molecules) a signal. These molecules have been studied for many years. The application of immune checkpoint drugs in the clinic provides hope for cancer patients. Recently, the poliovirus receptor (PVR)-like protein cosignaling network, which involves several immune checkpoint receptors, i.e., DNAM-1 (DNAX accessory molecule-1, CD226), TIGIT (T-cell immunoglobulin (Ig) and immunoreceptor tyrosine-based inhibitory motif (ITIM)), CD96 (T cell activation, increased late expression (TACLILE)), and CD112R (PVRIG), which interact with their ligands CD155 (PVR/Necl-5), CD112 (PVRL2/nectin-2), CD111 (PVRL1/nectin-1), CD113 (PVRL3/nectin-3), and Nectin4, was discovered. As important components of the immune system, natural killer (NK) and T cells play a vital role in eliminating and killing foreign pathogens and abnormal cells in the body. Recently, increasing evidence has suggested that this novel cosignaling network axis costimulates and coinhibits NK and T cell activation to eliminate cancer cells after engaging with ligands, and this activity may be effectively targeted for cancer immunotherapy. In this article, we review recent advances in research on this novel cosignaling network. We also briefly outline the structure of this cosignaling network, the signaling cascades and mechanisms involved after receptors engage with ligands, and how this novel cosignaling network costimulates and coinhibits NK cell and T cell activation for cancer immunotherapy. Additionally, this review comprehensively summarizes the application of this new network in preclinical trials and clinical trials. This review provides a new immunotherapeutic strategy for cancer treatment.
Data from expressed sequence tags from the organs and embryos of parthenogenetic Haemaphysalis longicornis
Authors: Umemiya-Shirafuji Rika , Zhou Jinlin , Liao Min , Battsetseg Badgar , Boldbaatar Damdinsuren , Hatta Takeshi , Kuboki Thasaneeya , Sakaguchi Takeshi , Chee Huey Shy , Miyoshi Takeharu , Huang Xiaohong , Tsuji Naotoshi , Xuan Xuenan , Fujisaki Kozo 
Published: August 2021

Abstract
Objectives
Haemaphysalis longicornis is the most important tick species in Japan and has a wide range of vector capacity. Due to its veterinary and medical importance, this tick species has been used as a model for tick/vector biological studies. To identify the key molecules associated with physiological processes during blood feeding and embryogenesis, full-length cDNA libraries were constructed using the fat body, hemocytes-containing hemolymph, midgut, ovary and salivary glands of fed females and embryos of the laboratory colony of parthenogenetic H. longicornis. The sequences of cDNA from the salivary glands had been already released. However, the related information is still poor, and the other expressed sequence tags have not yet been deposited.

Data description
A total of 39,113 expressed sequence tags were obtained and deposited at the DNA DataBank of Japan. There were 7745 sequences from embryos, 7385 from the fat body, 8303 from the hemolymph including hemocytes, 7385 from the midgut, and 8295 from the ovary. The data, including expressed sequence tags from the salivary glands was summarized into Microsoft Excel files. Sharing this data resource with the tick research community will be valuable for the identification of novel genes and advance the progress of tick research.
Role of diagnostic imaging in psoriatic arthritis: how, when, and why
Authors: Crespo-Rodríguez Ana María , Sanz Sanz Jesús , Freites Dalifer , Rosales Zulema , Abasolo Lydia , Arrazola Juan 
Published: August 2021

AbstractPsoriasis is a common skin disease. Up to 30% of patients with psoriasis develop psoriatic arthritis (PsA) resulting, by far, the most prevalent coexisting condition. Heterogeneity of clinical and radiological presentation is a major challenge to diagnosis of PsA. Initial reports about PsA emphasized a benign course in most patients, but it is now recognized that psoriatic arthritis often leads to impaired function and a reduced quality of life. PsA is a progressive disease characterized by diverse clinical features, often resulting in diagnostic delay and treatment that are associated with poor clinical and structural outcomes. New effective treatments may halt PsA progression, and consequently, treatment goals have evolved from simple reduction of pain to achieving full remission or minimal disease activity. This emerging treat-to-target strategy paradigm emphasize a need for early diagnosis; sensitive imaging techniques may be of value in this process. While radiography and CT depict structural damage, US and MRI have emerged as helpful tools to evaluate magnitude and severity of active inflammatory lesions. This review aims to describe the role of imaging modalities in diagnosis, follow-up and prognosis of PsA.
The horizontal-to-vertical spectral ratio and its applications
Authors: Xu Rong , Wang Lanmin 
Published: August 2021

AbstractThe horizontal-to-vertical spectral ratio (HVSR) has been extensively used in site characterization utilizing recordings from microtremor and earthquake in recent years. This method is proposed based on ground pulsation, and then it has been applied to both S-wave and ambient noise, accordingly, in practical application also different. The main applications of HVSR are site classification, site effect study, mineral exploration, and acquisition of underground average shear-wave velocity structure. In site response estimates, the use of microtremors has been introduced long ago in Japan, while it has long been very controversial in this research area, as there are several studies reporting difficulties in recognizing the source effects from the pure site effects in noise recordings, as well as discrepancies between noise and earthquake recordings. In practice, the most reliable way is the borehole data, and the theoretical site response results were compared with the HVSR using shear wave to describe site response. This paper summarizes the applications of the HVSR method and draws conclusions that HVSR has been well applied in many fields at present, and it is expected to have a wider application in more fields according to its advantages.
“Let us define ourselves”: forced migrants’ use of multiple identities as a tactic for social navigation
Authors: Hack-Polay Dieu , Mahmoud Ali B. , Kordowicz Maria , Madziva Roda , Kivunja Charles 
Published: August 2021

AbstractBackgroundThe article examines how and why multiple identities are altered, used and discarded by forced migrants.MethodsThe research is located in the constructivist paradigm. We used thematic analysis to analyse data gathered through interviews with nineteen forced migrants.ResultsWe found that, though individual migrants can make deliberate choices about which identities to be associated with, they are constrained in the process by external socio-economic factors that lead them to adopt identities that are perceived to be advantageous to navigate the new social system. Moreover, the construction of forced migrants’ identity includes significant contextuality, transactionality and situatedness.ConclusionsOur research contributes to the literature on migrant identity practice concerning the stigma associated with forced migrant status and the extent to which migrants appraise their reception in exile as undignified. Additionally, examining migrant identities allows the researchers to apprehend the diverse facets of identity as far as migrants are concerned. Future research may draw a larger sample to examine other impactful dimensions of identity fluctuation, e.g. gender, education, social media, the extent of prior trauma, etc.