bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological Characteristics and Prognosis of Squamous Cell Carcinoma of the Breast: A Population-Based Analysis
Authors: Han Yiqun , Wang Jiayu , Wang Zijing , Xu Binghe 
Published: October 2021

Background To better understand the clinicopathological features and prognostic profiles of squamous cell carcinoma (SCC) of the breast. Methods Information on breast cancer was obtained from the Surveillance, Epidemiology, and End Results database (2004–2016). Comparative analyses were carried out to investigate the heterogeneity in the clinicopathological characteristics and survival outcomes between SCC and invasive ductal carcinoma (IDC), while propensity score matching was conducted to analyze the variations among baseline characteristics. Prognostic factors for SCC of the breast were successively identified using Cox regression analysis. Results A total of 382 SCC patients and 561477 IDC patients were identified in this study. Comparatively, the SCC cohort exhibited a higher proportion of male individuals, poor differentiation, an advanced TNM stage, an increasing percentage of triple-negative (TN) subtype, an increasing rate of organ involvement, and less access to therapeutics. The aggressive profile was consistent in the TN subgroup, with a significantly higher proportion in SCC than in IDC (25.7% vs 6.8%). Prognosis of SCC was profoundly poorer than that of IDC (mOS, 78.6 months and 121.6 months, P < .0001; mBCSS 91.9 months vs 135.6 months, P < .0001), of which the inferior tendency remained stable among disease stage and therapeutic options, while no difference was detected in the 2 subgroups with the TN subtype. The 2-year survival rate was 66.9% and the 5-year survival rate was 51.4%, with the risk factors being older age, bilateral disease, advanced TNM stage, bone and visceral involvement, surgical intervention, radiation treatment, and chemotherapy. Conclusions This study systematically analyzed the heterogeneous characteristics of SCC of the breast in comparison with IDC. Squamous cell breast cancer presented with increasing aggressive behavior and inferior prognosis. Prospective studies should focus on this subgroup and introduce individualized therapeutic protocols in clinical practice.
Assessment of the Clinical Utility of Circulating Tumor Cells at Different Time Points in Predicting Prognosis of Patients With Small Cell Lung Cancer: A Meta-Analysis
Authors: Jiang Ai-Min , Zheng Hao-Ran , Liu Na , Zhao Rui , Ma Yu-Yan , Bai Shu-Heng , Tian Tao , Liang Xuan , Ruan Zhi-Ping , Fu Xiao , Yao Yu 
Published: October 2021

Objectives Numerous studies have elucidated that circulating tumor cells (CTCs) have significant prognostic value in various solid tumors. However, the prognostic value of CTCs in small cell lung cancer (SCLC) remains controversial. The current study was performed to investigate the prognostic significance of different time points of CTCs in SCLC. Methods PubMed, EMBASE, Web of Science, and Cochrane Library databases were retrieved for eligible studies. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated to investigate the association between CTCs level and overall survival (OS) and progression-free survival (PFS) in SCLC. Furthermore, subgroup analyses, sensitivity analysis, Begg’s and Egger’s tests were also conducted. Results Sixteen cohort studies with 1103 participants were eligible for this meta-analysis. Our results revealed that higher pretreatment CTCs level was significantly correlated with worse OS in SCLC no matter CellSearch (HR, 2.95; 95%CI, 1.56-5.58; P = .001) or other methods (HR, 2.37; 95%CI, 1.13-4.99; P = .023) was used to detect CTCs. Higher pretreatment CTCs status detected by CellSearch was associated with shorter PFS (HR, 3.75; 95%CI, 2.52-5.57; P < .001), while there was no significant association when other methods were adopted to CTC detection (HR, 2.04; 95%CI, .73-5.68; P = .172). Likewise, we observed that higher post-therapy CTCs level detected by both CellSearch (HR, 2.99; 95%CI, 1.51-5.93; P = .002) and other methods (HR, 4.79; 95%CI, 2.03-11.32; P < .001) was significantly correlated with decreased OS in SCLC. However, higher post-therapy CTCs count detected by CellSearch was not correlated with worse PFS (HR, 1.80; 95%CI, .83-3.90; P = .135). Sensitivity analysis demonstrated that the pooled data were still stable after eliminating studies one by one. However, significant publication bias was observed between pretreatment CTCs level detected by CellSearch and OS of SCLC. Conclusion Dynamic monitoring of CTCs level could be a non-invasive and effective tool to predict the disease progression and prognosis in patients with SCLC.
A case of nodular episcleritis mimicking a solitary giant episcleral mass
Authors: Zhou Lan , Wang Juanjuan , Xu Guihua , Wang Dingding , Wang Xiaoyi , Chen Zilin 
Published: October 2021

Purpose To describe an atypical nodular episcleritis mimicking a solitary giant episcleral mass, which is not attributed to any systemic diseases and identified only after immunohistochemical examination. Case report A sixty-year-old Chinese woman with systemic hypertension presented with 6-month history of giant, solitary and redness epibulbar mass arising from the superior aspect of her left eye. The lesion gradually enlarged, even with 6-month history of irregular topical steroid eye drops treatment. Imaging studies and laboratory test revealed a 10 mm × 8 mm episcleral mass absence of any infection indicator and autoimmune antibody changes. The mass was completely removed before its extension through the deep scleral, histopathologic examination revealed a nodular episcleritis composed of various chronic inflammatory cells infiltration. Topical steroid eye drops treatment combined with oral steroidal anti-inflammatory drugs was then administrated regularly for 1 month, and no recurrence occurred after 1-year follow-up. Conclusion Nodular anterior episcleritis is characterized by underlying chronic inflammation of the anterior episclera and can be presented as asymptomatic episcleral mass. Besides a thorough investigation systemically, tissue biopsy is required for definite diagnosis.
Lengthening and deformity correction in vascularized fibular autograft for a patient with Ewing sarcoma
Authors: Kwon Ki Bum , Chung Chin Youb , Park Moon Seok , Lee Kyoung Min , Sung Ki Hyuk 
Published: October 2021

We report the case of a pediatric patient with Ewing’s sarcoma of the tibia treated with vascularized fibular autograft where the resulting limb deformity and leg length discrepancy (LLD) were corrected using Ilizarov external fixator. A 14-year-old girl presented to our outpatient clinic with a deformity of the right proximal and distal tibia and an 11.7 cm of LLD after tumor reconstruction surgery. Deformity correction and limb lengthening were simultaneously performed using double corticotomy on the right proximal and distal tibia. One year postoperatively, the union of the right proximal tibia had progressed, but nonunion was observed at the right distal corticotomy site. To address this, osteosynthesis with tricortical iliac bone allograft was performed after the removal of the Ilizarov external fixator. After 6 months, the union of the distal tibia was confirmed, and the varus deformity of proximal and distal tibia improved. The LLD was also decreased, but the left lower limb was still longer by 3 cm. This report shows that vascularized fibular autografts can potentially be used for the gradual correction of LLD and deformities. However, for the treatment of multiple deformities in bones previously reconstructed with vascularized fibular graft, the possibility of impaired bone forming potential of the fibular graft should be considered.
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes
Authors: Pourreza Shahri Morteza , Kahanda Indika 
Published: October 2021

AbstractBackgroundIdentifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since experimental validation of protein-phenotype associations is prohibitive, automated tools capable of accurately extracting these associations from the biomedical text are in high demand. However, while the manual annotation of protein-phenotype co-mentions required for training such models is highly resource-consuming, extracting millions of unlabeled co-mentions is straightforward.ResultsIn this study, we propose a novel deep semi-supervised ensemble framework that combines deep neural networks, semi-supervised, and ensemble learning for classifying human protein-phenotype co-mentions with the help of unlabeled data. This framework allows the ability to incorporate an extensive collection of unlabeled sentence-level co-mentions of human proteins and phenotypes with a small labeled dataset to enhance overall performance. We develop PPPredSS, a prototype of our proposed semi-supervised framework that combines sophisticated language models, convolutional networks, and recurrent networks. Our experimental results demonstrate that the proposed approach provides a new state-of-the-art performance in classifying human protein-phenotype co-mentions by outperforming other supervised and semi-supervised counterparts. Furthermore, we highlight the utility of PPPredSS in powering a curation assistant system through case studies involving a group of biologists.ConclusionsThis article presents a novel approach for human protein-phenotype co-mention classification based on deep, semi-supervised, and ensemble learning. The insights and findings from this work have implications for biomedical researchers, biocurators, and the text mining community working on biomedical relationship extraction.
ClineHelpR: an R package for genomic cline outlier detection and visualization
Authors: Martin Bradley T. , Chafin Tyler K. , Douglas Marlis R. , Douglas Michael E. 
Published: October 2021

Abstract
Background
Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited, and users must often write custom, relatively complex code to do so.

Results
Here, we introduce the ClineHelpR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress. ClineHelpR bundles both input generation (i.e., filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMeval and RIdeogram.

Conclusions
Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms. Furthermore, the ClineHelpR extended functionality can evaluate genomic clines in the context of spatial and environmental features, allowing users to explore underlying processes potentially contributing to the observed patterns and helping facilitate effective conservation management strategies.
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix
Authors: Woźniak Tomasz , Sajek Małgorzata , Jaruzelska Jadwiga , Sajek Marcin Piotr 
Published: October 2021

Abstract
Background
The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs.

Results
Here, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE.

Conclusions
RNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.
Role of biliary stent and neoadjuvant chemotherapy in the pancreatic tumor microbiome
Authors: Nalluri Harika , Jensen Eric , Staley Christopher 
Published: October 2021

Abstract
Background
Intra-tumor microbiota have been implicated in pancreatic ductal adenocarcinoma (PDAC) development, treatment response and post-treatment survivorship. Moreover, therapeutic interventions targeting microbiota may improve the response to chemotherapy and immunotherapy, further emphasizing the critical need to understand the origins of and growth of bacteria within the pancreatic tumor microenvironment. Here, we studied the role of several clinical factors on the bacterial colonization of PDAC.

Results
We obtained matched tumor and normal pancreatic tissue specimens from 27 patients who had undergone surgical resection for PDAC between 2011 and 2015 from the University of Minnesota Biological Materials Procurement Network (BioNet). We found that 26 (48%) out of 54 pancreatic tissue samples harbored detectable bacterial communities using real-time PCR targeting the 16S rRNA gene. Bacterial colonization was detected significantly more frequently in samples from patients who had pancreatic head tumors, underwent Whipple procedure, or had preoperative biliary stent placement. There was also a significantly greater relative abundance of microbiota from the family Enterobacteriaceae among samples from patients who underwent biliary stent placement or neoadjuvant treatment with a combination of Gemcitabine and Paclitaxel.

Conclusions
These findings suggest that biliary stent placement and neoadjuvant chemotherapy are associated with specific alterations that promote the infiltration and growth of intra-tumor bacteria in the setting of PDAC. Further studies exploring whether specific bacterial communities could contribute to increased chemoresistance will be essential for optimizing medical therapies in the future.
Selection strategy of dextran sulfate sodium-induced acute or chronic colitis mouse models based on gut microbial profile
Authors: Xu Hao-Ming , Huang Hong-Li , Liu Yan-Di , Zhu Jia-Qi , Zhou You-Lian , Chen Hui-Ting , Xu Jing , Zhao Hai-Lan , Guo Xue , Shi Wei , Nie Yu-Qiang , Zhou Yong-Jian 
Published: October 2021

Abstract
Background
Dextran sulfate sodium (DSS) replicates ulcerative colitis (UC)-like colitis in murine models. However, the microbial characteristics of DSS-triggered colitis require further clarification. To analyze the changes in gut microbiota associated with DSS-induced acute and chronic colitis.

Methods
Acute colitis was induced in mice by administering 3% DSS for 1 week in the drinking water, and chronic colitis was induced by supplementing drinking water with 2.5% DSS every other week for 5 weeks. Control groups received the same drinking water without DSS supplementation. The histopathological score and length of the colons, and disease activity index (DAI) were evaluated to confirm the presence of experimental colitis. Intestinal microbiota was profiled by 16S rDNA sequencing of cecal content.

Results
Mice with both acute and chronic DSS-triggered colitis had significantly higher DAI and colon histopathological scores in contrast to the control groups (P < 0.0001, P < 0.0001), and the colon was remarkably shortened (P < 0.0001, P < 0.0001). The gut microbiota α-diversity was partly downregulated in both acute and chronic colitis groups in contrast to their respective control groups (Pielou index P = 0.0022, P = 0.0649; Shannon index P = 0.0022, P = 0.0931). The reduction in the Pielou and Shannon indices were more obvious in mice with acute colitis (P = 0.0022, P = 0.0043). The relative abundance of Bacteroides and Turicibacter was increased (all P < 0.05), while that of Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Rikenella, Alistipes, Alloprevotella, and Butyricicoccus was significantly decreased after acute DSS induction (all P < 0.05). The relative abundance of Bacteroides, Akkermansia, Helicobacter, Parabacteroides, Erysipelatoclostridium, Turicibacter and Romboutsia was also markedly increased (all P < 0.05), and that of Lachnospiraceae_NK4A136_group, Alistipes, Enterorhabdus, Prevotellaceae_UCG-001, Butyricicoccus, Ruminiclostridium_6, Muribaculum, Ruminococcaceae_NK4A214_group, Family_XIII_UCG-001 and Flavonifractor was significantly decreased after chronic DSS induction (all P < 0.05).

Conclusion
DSS-induced acute and chronic colitis demonstrated similar symptoms and histopathological changes. The changes in the gut microbiota of the acute colitis model were closer to that observed in UC. The acute colitis model had greater abundance of SCFAs-producing bacteria and lower α-diversity compared to the chronic colitis model.
Bacteriological and molecular characterization of Mycobacterium bovis isolates from tuberculous lesions collected among slaughtered cattle, Northwest Ethiopia
Authors: Ejo Mebrat , Haile Belete , Tariku Tsegaye , Nigatu Seleshe , Kebede Elias , Bitew Abebe Belete , Demessie Yitayew , Getaneh Gashaw , Alebie Atnaf , Girma Musse , Ota Fusao , Nuru Anwar 
Published: October 2021

Abstract
Background
In Ethiopia, the distribution of bovine tuberculosis (BTB) has long been known and documented as a major problem of animal health. However, the burden of circulating M. bovis strains is poorly understood in the country. Therefore; this study aimed to identify and characterize the mycobacterial isolates responsible for BTB in Northwest Ethiopia.

Methods
A cross-sectional study was conducted on tuberculous lesions that had been collected from slaughtered cattle between September 2018 to June 2019. Collected lesions were cultured and tested for tuberculous bacilli. The MPT64 assay and Genotype line probe assay (LPA) were used for identification of mycobacterial isolates, and region of deletion 4 (RD4) typing and spoligotyping were used to characterize the M. bovis strains.

Results
Of the total 1458 examined slaughtered cattle, only 62 (4.3, 95%CI; 0.0328–0.0542) had tuberculous lesions. The highest number of gross tuberculous lesions were observed from the lymph nodes of the thoracic cavity; at the mediastinal (40.3%, 25/62) and bronchial (22.6%, 14/62) lymph nodes. Of the 62 collected tuberculous lesions; 18 (29.0%) were culture positive for mycobacterium isolates, and only five isolates were confirmed for M. tuberculosis complex (MTBc) by the MPT64 assay and LPA. All the five MTBc isolates were positive for RD4 typing of M. bovis with a PCR product size of 446 bp, and no isolate was noticed to have M. tuberculosis. The detected M. bovis strains displayed five spoligotypes; with the common SB1176 and SB0133 M. bovis strains, although the two spoligotypes had not been previously reported.

Conclusion
The present study shows that BTB in North Gondar, Ethiopia, is caused by M. bovis strains SB1176 and SB0033, with low frequency. Thus, the finding highlights the importance of continuous surveillance for mycobacterial strains in cattle populations.
Clinical outcomes of an ultrathin-strut sirolimus-eluting stent in all-comers population: Thailand Orsiro registry
Authors: Suwannasom Pannipa , Athiksakul Siriporn , Thonghong Tasalak , Lertsuwunseri Vorarit , Chaipromprasit Jarkarpun , Srimahachota Suphot , Udayachalerm Wasan , Kuanprasert Srun , Buddhari Wacin 
Published: October 2021

Abstract
Background
Despite numerous studies supporting the outperformance of ultrathin-strut bioresorbable polymer sirolimus-eluting stent (Orsiro SES, Biotronik AG), the generalizability of the study results remains unclear in the Asian population. We sought to evaluate the clinical outcomes of the Orsiro SES in unselected Thai population.

Methods
The Thailand Orsiro registry was a prospective, open-label clinical study evaluating all patients with obstructive coronary artery disease implanted with Orsiro SES. The primary endpoint was target lesion failure (TLF) at 12 months. TLF is defined as a composite of cardiac death, target vessel myocardial infarction (TVMI), emergent coronary artery bypass graft (CABG), and clinically driven target lesion revascularization (CD-TLR). Patients with diabetes, small vessels (≤ 2.75 mm), chronic total occlusions (CTOs), and acute myocardial infarction (AMI) were pre-specified subgroups for statistical analysis.

Result
A total of 150 patients with 235 lesions were included in the analysis. Half of the patients (53.3%) presented with AMI, and 24% had diabetes. Among 235 lesions, 93(39.4%) were small vessels, and 24(10.2%) were chronic total occlusions. The primary endpoint, TLF at 12 months, occurred in eight patients (5.3%), predominately caused by cardiac death. By contrast, the incidences of TVMI and CD-TLR were null. The outcomes in pre-specified subgroup were not different from the overall population (all p > 0.05). One definite late stent thrombosis(0.7%) was incidentally observed during primary percutaneous coronary intervention to the non-target vessel.

Conclusion
The safety and efficacy of the ultrathin strut sirolimus-eluting stent in unselected cases are confirmed in the Thailand Orsiro registry. Despite the high proportion of pre-specified high-risk subgroups, the excellent stent performance was consistent with the overall population.
Trial Registration TCTR20190325001.