bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic efficacy of visual subtypes and low attenuation area based on HRCT in the diagnosis of COPD
Authors: Zhu Dan , Qiao Chen , Dai Huiling , Hu Yunqian , Xi Qian 
Published: March 2022

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease. Current gold standard criteria, pulmonary function tests (PFTs) may result in underdiagnosis of potential COPD patients. Therefore, we hypothesize that the combination of high-resolution computed tomography (HRCT) and clinical basic characteristics will enable the identification of more COPD patients.

Methods
A total of 284 patients with respiratory symptoms who were current or former smokers were included in the study, and were further divided into 5 groups of GOLD grade I–IV and non-COPD according to PFTs. All patients underwent inspiratory HRCT scanning and low attenuation area (LAA) was measured. Then they were divided into seven visual subtypes according to the Fleischner Society classification system. Non-parametric tests were used for exploring differences in basic characteristics and PFTs between different groups of enrolled patients and visual subtypes. Binary logistic regression was to find the influencing factors that affected the patients’ outcome (non-COPD vs GOLD I-IV). The area under the receiver operating characteristic curve (AUC-ROC) was to explore the diagnostic efficacy of LAA, visual subtypes, and combined basic characteristics related to COPD for COPD diagnosis. Finally, based on the cut-off values of ROC analysis, exploring HRCT features in patients who do not meet the diagnostic criteria but clinically suspected COPD.

Results
With the worsening severity of COPD, the visual subtypes gradually progressed (p < 0.01). There was a significant difference in LAA between GOLD II–IV and non-COPD (p < 0.0001). The diagnostic efficacy of LAA, visual subtypes, and LAA combined with visual subtypes for COPD were 0.742, 0.682 and 0.730 respectively. The diagnostic efficacy increased to 0.923–0.943 when basic characteristics were added (all p < 0.001). Based on the cut-off value of ROC analysis, LAA greater than 5.6, worsening of visual subtypes, combined with positive basic characteristics can help identify some potential COPD patients.

Conclusion
The heterogeneous phenotype of COPD requires a combination of multiple evaluation methods. The diagnostic efficacy of combining LAA, visual subtypes, and basic characteristics achieves good consistency with current diagnostic criteria.
Navigating a newly diagnosed cancer through clinician-facilitated discussions of health-related patient values: a qualitative analysis
Authors: Lynch Kathleen A. , Bernal Camila , Romano Danielle R. , Shin Paul , Nelson Judith E. , Okpako Molly , Anderson Kelley , Cruz Elizabeth , Desai Anjali V. , Klimek Virginia M. , Epstein Andrew S. 
Published: March 2022

Abstract
Background
Advance care planning, the process through which patient values and goals are explored and documented, is a core quality indicator in cancer care. However, patient values are predominantly elicited at the end of life; patient values earlier in serious illness are not clearly delineated. The objective of this analysis is to assess the content of patient-verified summaries of health-related values among newly diagnosed cancer outpatients in order to develop a theoretical framework to guide future values discussions and optimize person-centered oncologic care.

Methods
Values summaries among patients with gastrointestinal (GI) cancers or myelodysplastic syndrome (MDS) were extracted from the medical record. Modified grounded theory analysis included interdisciplinary team coding of values summaries to identify key domains; code categorization; and identification of thematic constructs during successive consensus meetings. A final round of coding stratified themes by disease type.

Results
Analysis of 128 patient values summary documents from 67 patients (gastrointestinal [GI] cancers, n = 49; myelodysplastic syndrome [MDS], n = 18) generated 115 codes across 12 categories. Resultant themes demonstrated patients’ focus on retaining agency, personhood and interpersonal connection amidst practical and existential disruption caused by cancer. Themes coalesced into a theoretical framework with 5 sequenced constructs beginning with the cancer diagnosis, leading to 3 nesting constructs of individual identity (character), interpersonal (communication) preferences and needs, and social identity (connection), signifying sources of meaning and fulfillment. Values differences between GI cancer and MDS patients—including greater focus on normalcy, prognosis, and maintaining professional life among GI patients—reflected the distinct therapeutic options and prognoses across these disease groups.

Conclusions
Patient values reflect goals of meaning-making and fulfillment through individual agency and interpersonal supports in the setting of a newly diagnosed cancer. Early, nurse-led values discussions provide important and patient-specific data that are informative and likely actionable by clinicians in the delivery of person-centered care. Values can also facilitate discussions between patients and families and clarify patient preferences.
A newly identified mutation (c.2029 C > T) in SLC26A4 gene is associated with enlarged vestibular aqueducts in a Chinese family
Authors: Wu Ting , Cui Limei , Mou Yakui , Guo Wentao , Liu Dawei , Qiu Jingjing , Xu Cong , Zhou Jiamin , Han Fengchan , Sun Yan 
Published: March 2022

Abstract
Background
The enlarged vestibular aqueduct (EVA), associated with mutations in the SLC26A4 gene, characterized by non-syndromic hearing loss, is an autosomal recessive disorder. Here, we intended to investigate genetic causes of hearing loss in a Han Chinese man.

Method
First, whole-exome sequencing was performed to identify the gene mutations responsible for hearing loss in the proband. Sanger sequencing was used to verify the candidate mutations detected in the family. Next, we collected blood samples and clinical data from the three-generation pedigree. Finally, SLC26A4 mRNA and protein expression levels were detected by qPCR and western blotting.

Result
The proband suffered from bilateral progressive sensorineural hearing loss with EVA. The sequence analysis of SLC26A4 revealed that the proband and his sister both harbored a compound heterozygous mutation of c.2168A > G/c.2029C > T, inherited from their father and mother respectively. c.2029C > T mutation has not been recorded in the relevant literature previously. Relative mRNA levels of the SLC26A4 gene in individuals carrying a compound heterozygous mutation were significantly lower compared to a heterozygous mutation. SLC26A4 protein levels of 293t cells which transfected with recombinant plasmids [GV219-SLC26A4-mut (c.2029C > T) and GV219-SLC26A4-mut (c.2168A > G/c.2029C > T)] were significantly lower than normal control recombinant plasmids (GV219-SLC26A4-wt).

Conclusion
This study found a novel heterozygous mutation c.2029 (exon17) C > T compound with c.2168 (exon19) A > G in the SLC26A4 gene in a patient with EVA. The c.2029 (exon17) C > T mutation is proved to be pathogenic. This finding broadens the spectrum of variants in SLC26A4 gene.
In silico drug repositioning based on integrated drug targets and canonical correlation analysis
Authors: Chen Hailin , Zhang Zuping , Zhang Jingpu 
Published: March 2022

Abstract
Background
Besides binding to proteins, the most recent advances in pharmacogenomics indicate drugs can regulate the expression of non-coding RNAs (ncRNAs). The polypharmacological feature in drugs enables us to find new uses for existing drugs (namely drug repositioning). However, current computational methods for drug repositioning mainly consider proteins as drug targets. Meanwhile, these methods identify only statistical relationships between drugs and diseases. They provide little information about how drug-disease associations are formed at the molecular target level.

Methods
Herein, we first comprehensively collect proteins and two categories of ncRNAs as drug targets from public databases to construct drug–target interactions. Experimentally confirmed drug-disease associations are downloaded from an established database. A canonical correlation analysis (CCA) based method is then applied to the two datasets to extract correlated sets of targets and diseases. The correlated sets are regarded as canonical components, and they are used to investigate drug’s mechanism of actions. We finally develop a strategy to predict novel drug-disease associations for drug repositioning by combining all the extracted correlated sets.

Results
We receive 400 canonical components which correlate targets with diseases in our study. We select 4 components for analysis and find some top-ranking diseases in an extracted set might be treated by drugs interfacing with the top-ranking targets in the same set. Experimental results from 10-fold cross-validations show integrating different categories of target information results in better prediction performance than only using proteins or ncRNAs as targets. When compared with 3 state-of-the-art approaches, our method receives the highest AUC value 0.8576. We use our method to predict new indications for 789 drugs and confirm 24 predictions in the top 1 predictions.

Conclusions
To the best of our knowledge, this is the first computational effort which combines both proteins and ncRNAs as drug targets for drug repositioning. Our study provides a biologically relevant interpretation regarding the forming of drug-disease associations, which is useful for guiding future biomedical tests.
Clinical characteristics of plastic bronchitis in children: a retrospective analysis of 43 cases
Authors: Huang Jing-jing , Yang Xiao-qing , Zhuo Zhi-qiang , Yuan Lin 
Published: March 2022

Abstract
Background
With an increase in the diagnosis of plastic bronchitis (PB) cases, to enhance paediatricians’ knowledge and add to the few existing studies, we explored the clinical characteristics, diagnosis, and treatment of PB in children.

Methods
The clinicopathological data of 43 children admitted to the Xiamen Children’s Hospital and the Women and Children’s Hospital, affiliated to the Xiamen University from December 2016 to December 2019, were retrospectively analysed.

Results
All the children had cough, with 41 of them having associated fever. A peak temperature > 40 ℃ was observed in 25 children. Twenty-six children had shortness of breath, 27 had reduced respiratory sounds on the affected side, and 35 had audible moist rales on the affected side. Lactate dehydrogenase in all children increased to different degrees, and 29 had elevated D-dimer and fibrinogen degradation products. Lung imaging showed pulmonary consolidation and atelectasis, mainly in the bilateral lower lung lobes, in all the children. However, 31 had pleural effusion, mainly a small parapneumonic effusion. The infections were mainly caused by adenovirus and Mycoplasma pneumoniae. The casts in all 43 children were sucked or clamped out under bronchoscopy, and 10 were found to have type I PB on pathological examination. All children were treated with anti-infective therapy in addition to bronchoscopic cast removal. Thirty-one children were treated with methylprednisolone, and 16 with gamma globulin. Except for one child who was non-adherent to treatment, all other children showed improvement, or were cured and discharged from the hospital. Follow-up lung imaging at 3 months revealed that the lungs were fully re-expanded in 40 children. At the 6-month follow-up, six children had small airway lesions, four had obliterative bronchiolitis, and one had bronchiectasis.

Conclusions
Paediatric PB often occurs secondary to respiratory tract infections and progresses rapidly, with hyperpyrexia, cough, and shortness of breath as the main clinical manifestations. Pulmonary consolidation, atelectasis, and pleural effusion are seen on lung imaging, and early bronchoscopy and removal of casts in the trachea and bronchi are effective treatment options.
Diagnostic accuracy of the visceral adiposity index in patients with metabolic-associated fatty liver disease: a meta-analysis
Authors: Yi Xianhao , Zhu Shaihong , Zhu Liyong 
Published: March 2022

Abstract
Background
Conflicting results on the prognostic value of the visceral adiposity index (VAI) in patients with metabolic-associated fatty liver disease (MAFLD) have been reported. This study aimed to assess the diagnostic value of the VAI in MAFLD patients.

Methods
The Cochrane Library, PubMed, Embase, and other databases were searched to collect all documents that met the inclusion criteria from the establishment of the database to September 2021. The methodological quality of the included studies was assessed using the Newcastle–Ottawa Scale. The heterogeneity among the studies was analysed by the Cochran Q test and I2 test, and the appropriate model was selected according to the heterogeneity results. The diagnostic efficacy of the VAI was evaluated by sensitivity, specificity, and area under the curve, and a Fagan diagram was generated to evaluate the diagnostic ability of the VAI.

Results
A total of 9 studies were included. The overall quality of the included studies was good. Meta-analysis showed that the combined sensitivity of the VAI for the diagnosis of MAFLD was 0.70 [95% CI (0.69–0.71)], the combined specificity was 0.67 [95% CI (0.67–0.68)], the combined positive likelihood ratio was 2.08 [95% CI (1.87–2.31)], the combined negative likelihood ratio was 0.39 [95% CI (0.34–0.44)], and the combined diagnostic odds ratio was 5.81 [95% CI (4.73–7.14)]. The corresponding area under the curve was 0.79 [95% CI (0.75–0.82)]. Meta-regression analysis showed that the diagnostic method was a potential source of heterogeneity (P < 0.05). The Fagan diagram showed that the precision of MAFLD diagnosis was 70% when the pretest probability was set to 50% and then supplemented by the VAI.

Conclusions
The VAI is an independent predictor in the diagnosis of MAFLD and may be helpful in the detection of MAFLD. A VAI > 2.33 suggests that patients have a high probability of having MAFLD.
Construction of a new immune-related lncRNA model and prediction of treatment and survival prognosis of human colon cancer
Authors: Liu Sicheng , Peng Xingyu , Wu Xun , Bu Fanqin , Yu Zhonglin , Zhu Jinfeng , Luo Chen , Zhang Wenjun , Liu Jiang , Huang Jun 
Published: March 2022

Abstract
Background
An increasing number of studies have shown that immune-related long noncoding RNAs (lncRNAs) do not require a unique expression level. This finding may help predict the survival and drug sensitivity of patients with colon cancer.

Methods
We retrieved original transcriptome and clinical data from The Cancer Genome Atlas (TCGA), sorted the data, differentiated mRNAs and lncRNAs, and then downloaded immune-related genes. Coexpression analysis predicted immune-related lncRNAs (irlncRNAs) and univariate analysis identified differentially expressed irlncRNAs (DEirlncRNAs). We have also amended the lasso pending region. Next, we compared the areas under the curve (AUCs), counted the Akaike information standard (AIC) value of the 3-year receiver operating characteristic (ROC) curve, and determined the cutoff point to establish the best model to differentiate the high or low disease risk group of colon cancer patients.

Results
We reevaluated the patients regarding the survival rate, clinicopathological features, tumor-infiltrating immune cells, immunosuppressive biomarkers, and chemosensitivity. A total of 155 irlncRNA pairs were confirmed, 31 of which were involved in the Cox regression model. After the colon cancer patients were regrouped according to the cutoff point, we could better distinguish the patients based on adverse survival outcomes, invasive clinicopathological features, the specific tumor immune cell infiltration status, high expression of immunosuppressive biomarkers, and low chemosensitivity.

Conclusions
In this study, we established a characteristic model by pairing irlncRNAs to better predict the survival rate, chemotherapy efficacy, and prognostic value of patients with colon cancer.
Transhiatal esophagectomy as a treatment for locally advanced adenocarcinoma of the gastroesophageal junction: postoperative and oncologic results of a single-center cohort
Authors: Meillat Hélène , Niziers Vincent , Zemmour Christophe , Ewald Jacques , Ratone Jean-Philippe , Dermeche Slimane , Guiramand Jérôme 
Published: March 2022

Abstract
Background and purpose
To report the postoperative and oncological outcomes of transhiatal esophagectomy for locally advanced cancer of the gastroesophageal junction.

Methods
Medical records of 120 consecutive patients who underwent transhiatal esophagectomy for locally advanced cancer of the gastroesophageal junction with curative intent after neoadjuvant treatment between February 2006 and December 2018 at our center were reviewed.

Results
All patients received either chemotherapy (46.7%) or chemoradiation (53.3%). The 90-day mortality and overall morbidity rates were 0.8% and 56.7%, respectively. Respiratory complications were the most common (30.8%). Anastomotic leakage occurred in 19 patients (15.8%), who were treated by local wound care (n = 13) or surgical drainage (n = 6). Recurrent laryngeal nerve injury occurred in 12 patients (9.9%). The median length of hospital stay was 15.5 days. The rate of R0 resection was 95.8%, and the median number of nodes removed was 17.5. Over a median follow-up of 77 months, the rate of recurrence was 40.8%, and the overall survival rates at 1, 3, and 5 years were 91%, 75%, and 65%, respectively. The median survival time was not reached. In multivariate analysis, disease stage was the only independent significant prognostic factor.

Conclusions
Transhiatal esophagectomy is a safe and effective procedure with good long-term oncological outcomes for locally advanced tumors after neo-adjuvant treatment. It can be recommended for all patients with cancer of the gastroesophageal junction, regardless of the Siewert classification, tumor stage, and comorbidities.
The development and acceptability testing of an app-based smart survey system to record smoking behaviour, use of nicotine replacement therapy (NRT) and e-cigarettes
Authors: Huang Yue , Emery Joanne , Naughton Felix , Cooper Sue , McDaid Lisa , Dickinson Anne , Clark Miranda , Kinahan-Goodwin Darren , Thomson Ross , Phillips Lucy , Lewis Sarah , Orton Sophie , Coleman Tim 
Published: March 2022

Abstract
Objective
Nicotine replacement therapy (NRT) helps people stop smoking. Monitoring treatment adherence is important as poor adherence to NRT limits its effectiveness. As e-cigarettes contain nicotine, their use (‘vaping’) is likely to affect both NRT use and smoking. We wished to measure adherence to NRT, and to investigate relationships between NRT, vaping and smoking so we developed ‘NicUse’, a smartphone App linked to a cloud database for collecting data relevant to NRT adherence. We report user-acceptability and investigate data validity among pregnant people by comparing heaviness of smoking reported to NicUse surveys with contemporaneous exhaled carbon monoxide readings.

Results
Thirty five pregnant women participating in a pilot study were asked to install and use NicUse on their smartphones. 32/35 (91%) logged into NicUse, 31 (89%) completed one or more surveys, and 22 (63%) completed these on ≥ 20 of 28 study days. Twenty-four gave end-of-study user acceptability ratings; 23 (96%) agreed or strongly agreed NicUse was ‘Easy to use’ and ‘Instructions were clear’. There was a strong correlation between the number of daily cigarettes reported on NicUse and exhaled CO readings taken on study Day 7 (Pearson’s r = 0.95, p < 0.001). NicUse appears highly acceptable, and smoking data reported to it shows validity.
Gut microbiota reveals the environmental adaption in gastro-intestinal tract of wild boar in karst region of Southwest China
Authors: Cao Heqin , Yang Xiongwei , Peng Caichun , Wang Yeying , Guo Qunyi , Su Haijun 
Published: March 2022

Abstract
Background
Gut microbes has become one of the research hotspots in animal ecology, playing an important role in monitoring dietary adaptation and health status of host. However, there are few studies on the gut microbiota in the stomach, smallintestine (ileum), and large intestine (cecum, colon, and rectum) of wild boar.

Results
Alpha diversity and Beta diversity showed there were significant differences in the abundance and distribution of microbes in gastrointestinal tract of wild boar. Firmicutes and Bacteroidetes were the most dominant phyla in stomach, cecum, colon and rectum of wild boar, while Proteobacteria and Firmicutes were the most dominant in ileum. At genus level, there were different leading genera in stomach (Prevotella and Lactobacillus), small intestine (Escherichia-Shigella and Lactobacillus), and large intestine (Ruminococcaceae_UCG-005, Christensenellaceae_R-7_group, and Escherichia-Shigella). PICRUSt function predictive analysis suggested that there were significant differences in microbial metabolic pathways among five locations of wild boar.

Conclusions
This study comprehensively revealed the differences in composition of microbial community in gastrointestinal trac of wild boar. Future work links microbes with the metabolites to accurately reveal the health of wild boar.
Differential abscopal effect in extracranial and intracranial lesions after radiotherapy alone for vertebral bone metastasis of unknown primary: a case report
Authors: Ishikawa Yojiro , Umezawa Rei , Yamamoto Takaya , Takahashi Noriyoshi , Takeda Kazuya , Suzuki Yu , Jingu Keiichi 
Published: March 2022

Abstract
Background
The abscopal effect is a phenomenon in which a tumor located far from irradiated lesions regresses. We have experienced a case in which both intracranial and extracranial lesions showed an abscopal effect after radiotherapy for spinal metastases of unknown primary. We report the differential abscopal effect in extracranial and intracranial lesions.

Case presentation
A 57-year-old Japanese man was diagnosed with multiple lung nodules, bone metastases, and brain metastases. The results of pathological examination at the previous hospital he visited suggested adenocarcinoma of the lung. However, there was a possibility that the biopsy specimen was inadequate. Radiation therapy was performed on the ninth thoracic vertebra for a total dose of 39 Gy in 13 fractions because the lesion in the ninth thoracic vertebra was destructively extending. After thorough examination, the primary lesion could not be identified, and we made diagnosis of cancer of unknown primary. The patient did not want to receive systemic chemotherapy; however, all of the lesions except for the brain metastases had spontaneously shrunk 2 months after radiation therapy. Although the brain metastases had partially shrunk, whole-brain radiotherapy for a total dose of 36 Gy in 12 fractions was performed. Fifteen months after initial radiation therapy, the brain metastasis recurred, and Gamma Knife radiosurgery was additionally performed. The brain metastases disappeared after the radiosurgery. During a period of 30 months after radiation therapy for the ninth vertebra, the lesions of the trunk all maintained their shrinkage without systemic chemotherapy. Right cervical lymph node metastasis and brain metastases occurred 30 months after the initial radiation therapy. A biopsy of the right cervical lymph node led to the diagnosis of clear cell carcinoma. Although we considered additional radiation therapy or chemotherapy, the patient died 3 months after the progression of recurrence lesions.

Discussion and conclusions
We report a rare case in which radiotherapy alone for an extracranial metastatic lesion of a vertebra resulted in an abscopal effect on both extracranial and intracranial lesions. Notably, the abscopal effect in the intracranial lesions was weaker than that in the extracranial lesions.