bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrence of ovarian squamous cell carcinoma with MET gene copy number variation: a case report and review of literature
Authors: Dong Xuhui , Yuan Lei , Yao Liangqing 
Published: May 2020

Abstract
Background: Malignant transformation such as ovarian squamous cell carcinoma (SCC) in ovarian mature cystic teratoma (OMCT) is a rare tumor. The gene mutation of ovarian SCC remains unclear. We herein report a recurrent case of ovarian squamous cell carcinoma with MET gene copy number variation. Case presentation: A 60-year-old woman presented with recurrence of ovarian SCC 8 months after primary surgery. Adhesiolysis, right abdominal wall mass excision, prosthetics, enterectomy, enterostomy and partial cystectomy were performed by laparoscope. Pathologic examination demonstrated metastatic squamous cell carcinoma in ileocecus, rectum and abdominal wall muscle. MET gene copy number was elevated with copy number of six in this case. Postoperatively, the patient was treated with four cycles of combination chemotherapy with docetaxel and carboplatin. The patient was free of disease at 20 months’ follow-up. Conclusions: Optimal cytoreductive surgery combined with platinum-based chemotherapy is recommended currently for not only primary tumor but also recurrence. For patients with malignant transformation in OMCT, prompt diagnosis and individualized treatment are crucial for better prognosis. Increased copy number of MET may be correlated with her poor PFS and can be a potential therapeutic target for this case.
Yolk Sac tumor differentiation in urothelial carcinoma of the urinary bladder: A case report and differential diagnosis
Authors: Espejo-Herrera Nadia , Mundó Enric Condom 
Published: May 2020

Abstract
Background: Yolk sac tumor (YST) is a germ cell neoplasm that arises predominantly in the gonads, but can also derive from somatic neoplasms in extragonadal locations. These latter cases have been documented in several organs, although reports from the urinary tract are limited. To our knowledge, this is the first report of a bladder urothelial carcinoma with a predominant component of YST differentiation.Case presentation: We present a unique case of a 76-year-old man with a recurrent urinary bladder tumor, initially interpreted as a high grade urothelial carcinoma with glandular differentiation. In the recurrent tumor, diverse histological patterns were identified, including glandular, hepatoid and sarcomatoid. This tumor showed positivity for AFP, GLP3 and SALL4, and negativity for CK7 and EMA. Fluorescent in situ hybridization study showed a polysomic pattern of chromosome 12. All these findings led to the final diagnosis of a YST derived from urothelial carcinoma. Conclusions: YST differentiation should be considered in the differential diagnosis of a high grade urothelial carcinoma, particularly when glandular and other unusual patterns are observed.
Analysis of primary oral and oropharyngeal squamous cell carcinoma in inhabitants of Beijing, China—A 10-year continuous single-center study
Authors: Bai Xuexiao , Zhang Jie , Wei Li 
Published: May 2020

Abstract
Background This study aimed to describe some of the characteristics of the inhabitants of Beijing with oral and oropharyngeal squamous cell carcinoma(OSCC) who had received treatment at Stomatology Hospital of Peking University and to analyze the survival rate and the prognostic factors of patients following surgical treatment.. Methods Data of 603 consecutive cases with primary OSCC between 2004 and 2013 were obtained from the Stomatology Hospital of Peking University. Clinical data including age, sex, living district, primary site，TNM stage, history of drinking and smoking, pathological differentiation, treatment, survival were retrospectively analyzed. Results The male: female ratio was 1.1:1. The frequency of site involvement in descending order were tongue(34.3%), gingiva(25.0%), buccal mucosa(13.8%), oral floor(9.0%), oropharynx(8.5%), lip(6.3%) and palate(3.2%). Female OSCC patients tended to be significantly older than men with OSCC (P < 0.05). The percentage of patients with stages III-IV OSCC was 52.4%. The results revealed that 65.3% of male patients and only 6.3% of female patients smoked or drank. The overall 5-year survival rate was 64%. Female patients had a worse prognosis than male patients. Among the patients who received surgery, tumor size and lymph node involvement were independent prognostic factors. Smoking and drinking were not prognostic factors.Conclusion Among the Beijing inhabitants who were diagnosed with OSCC and treated in our hospital in the past 10 years, more than half of them were in the advanced stage, and the cancer stage was the main prognostic factor of oral cancer. Therefore, the recognition of oral cancer should be strengthened, and early detection and treatment of OSCC should be achieved to improve the survival rate.
Multiple HPV 16 infection with two strains: a possible marker of neoplastic progression
Authors: Bruno Maria Teresa , Scalia Guido , Cassaro Nazario , Boemi Sara 
Published: May 2020

Abstract
Background. We studied the cases of single and multiple HPV infection and analyzed the correlation with negative cases, and preneoplastic and neoplastic lesions of the uterine cervix with the aim of making a contribution to the prognostic factor under discussionMethods: 909 women undergoing second level screening because they had been positive at cervical cytology were enrolled. All the patients underwent colposcopy and cervical biopsy with viral genotyping. We divided mHPV infection based on the number of genotypes present: infections with 2 strains, 3 strains, 4 strains and 5 or more strains.Statistical analysis The analysis of the data was made using the χ2 test. Contingency tables were created to evaluate the correlation between single, multiple and CIN2+ infections. Values with p <0.05 were considered statistically significant.Results: The presence of genotype HPV16 in our study was associated with a 12 times greater risk of developing a high-grade lesion, OR = 12.70. The patients with single infections had the highest incidence of CIN2+ (34.1 %) with respect to those with multiple infections (10.6%).When we studied in the mHPV infection the prevalence of the combinations between the genotypes, we found that in mHPV16 infections, the combinations HPV16, 18 and HPV16, 31 were the most frequent (55.5%) in CIN3 lesion.ConclusionsOur results suggest that single HPV infections have a greater risk of developing SCC with respect to multiple infections. Multiple HPV infections are relevant only in the first phase of the lesion (CIN1-CIN2), while they are absent in carcinomas, where infections are of a single genotype. In particular, among multiple infections, HPV16 infection with 2 HR genotypes is associated significantly with CIN2 / CIN3 (21/30) and has 4 times greater risk of developing a high-grade lesion. Thus, it is probable that only specific combinations of HPV (HPV16,18 - HPV 16,31) can be associated with a clinically significant impact, while other combinations can simply be correlated because of a common infection or diagnostic method used. Therefore, multiple HPV16 infections with two high-risk genotypes is a major risk of CIN2/CIN3.
Alkaline organosolv pretreatment of different sorghum stem parts for enhancing the total reducing sugar yields and p-coumaric acid release
Authors: Li Dandan , Long Liangkun , Ding shaojun 
Published: May 2020

Abstract
Background: The sorghum stem can be divided into the pith and rind parts with obvious differences in cell type and chemical composition, thus arising the different recalcitrance to enzyme hydrolysis and demand for different pretreatment conditions. The introduction of organic solvents in the pretreatment can reduce over-degradation of cellulose and hemicellulose, but significance of solvent addition in pretreatment of different parts of sorghum stem is still unclear. Valorization of each component is critical for economy of sorghum biorefinery. Therefore, in this study, NaOH-ethanol pretreatment condition for different parts of the sorghum stem was optimized in order to maximize p-coumaric acid release and total reducing sugar recovery. Result: Ethanol addition improved p-coumaric acid release and delignification efficiency, but significantly reduced hemicellulose deconstruction in NaOH-ethanol pretreatment. Optimization using the response surface methodology revealed that the pith, rind and whole stem require different NaOH-ethanol pretreatment conditions for maximal p-coumaric acid release and xylan preservation. By respective optimal NaOH-ethanol pretreatment, the p-coumaric acid release yields reached 94.07%, 97.24% and 95.05% from pith, rind and whole stem, which increased by 8.16%, 8.38% and 8.39% compared to those of NaOH pretreated samples. The xylan recoveries of pith, rind and whole stem reached 76.80%, 88.46% and 85.01%, respectively, which increased by 47.75%, 15.11% and 35.97% compared to NaOH pretreatment. Adding xylanase significantly enhanced the enzymatic saccharification of pretreated residues. The total reducing sugar yields after respective optimal NaOH-ethanol pretreatment and enzymatic hydrolysis reached 84.06%, 82.29% and 84.09% for pith, rind and whole stem, respectively, which increased by 29.56%, 23.67% and 25.56% compared to those of NaOH pretreated samples. Considering the economic cost on the separation of the different parts, whole stem of sorghum stem can be directly used as feedstock in industrial biorefinery. Conclusion: These results indicated that NaOH-ethanol is effective for the efficient fractionation and pretreatment of sorghum biomass. This work will help to understand the differences of different parts of sorghum stem under NaOH-ethanol pretreatment, thereby improving the full-component utilization of sorghum stem.
Enzymatic Activity and Brine Shrimp Lethality of Venom From the Large Brown Spitting Cobra (Naja Ashei) and Its Neutralization by Antivenom
Authors: Okumu Mitchel Otieno , Mbaria James Mucunu , Gikunju Joseph Kangangi , Mbuthia Paul Gichohi , Madadi Vincent Odongo , Ochola Francis Okumu 
Published: May 2020

Abstract
Objective: Naja ashei is a snake of medical importance in Kenya, Ethiopia, Somalia, Uganda, and Tanzania. However, little is known about the enzymatic and toxic activities of Naja ashei venom and crucially, the capacity of commercially available antivenom to neutralize these effects. This study aimed to fill this gap by evaluating the enzymatic and toxic activities of N. ashei venom as well as the capacity of commercially available antivenoms to neutralize these effects. Results: The enzymatic/snake venom phospholipase A2/svPLA2 activity of Naja ashei venom is dose-dependent while the toxic effects of the venom in the brine shrimp animal model are dose and time-dependent. Commercially available antivenoms have poor neutralization capacity against the svPLA2 activity of Naja ashei venom. One ml of commercial antivenom manufactured in Mexico neutralized 0.21 mg of Naja ashei venom. However, the antivenom manufactured in India was ineffective against Naja ashei venom-induced brine shrimp lethality.
Summed rest score in gated myocardial perfusion imaging is a good predicator for treatment-related cardiotoxicity after anthracycline chemotherapy in diffuse large B-cell lymphoma patients
Authors: Lin Yan , Wang Jianfeng , Xu Min , Qiu Chun , Xu Peng , Shang Limei , He Bai , Wang Fei , Yue Yanhua , Guo Yanting , Li Feng , Dong Weimin , Xie Xiaobao , Wang Yuetao , Gu Weiying 
Published: May 2020

Abstract
Background: Anthracycline chemotherapy is commonly used in the treatment of diffuse large B-cell lymphoma (DLBCL) patients. Treatment-related cardiotoxicity (TRC) may be observed during treatment and may induce severe cardiac failure or cardiac arrhythmia as the main cause of death, even several years after chemotherapy implementation. Herein, we performed a study to investigate the prognostic value of gated myocardial perfusion imaging (G-MPI) summed rest score (SRS) for the early detection of TRC caused by anthracycline chemotherapy in DLBCL patients.Methods: A total of 36 DLBCL patients were enrolled, and a series of parameters from the same individual patient were compared between baseline and after the end of the 6th R-CHOP chemotherapeutic regimen. According to whether TRC occurred during the observation period, the patients were divided into two groups, and parameters related to cardiac function were compared.Results: SRS in G-MPI and QTc interval in electrocardiogram were significantly different before and after chemotherapy (P = 0.012 and P = 0.015, respectively).By comparing parameters related to cardiac function between the TRC group (n = 22) and the no-TRC group (n = 14), only SRS was significantly different (P = 0.012). Multivariate logistic regression analysis showed that the SRS level was the only independent predicator for TRC (P = 0.018, HR = 6.053, 95% CI: 1.364-26.869). Receiver operating characteristic curve analysis identified an optimal SRS cutoff of >1for predicting TRC after anthracycline chemotherapy (P＜ 0.001).Conclusion: The G-MPI SRS level was an early indicator for TRC surveillance in DLBCL patients after anthracycline chemotherapy, thus contributing to early treatment and a subsequent decrease in mortality caused by such cardiovascular complications.
Immune Transcripts of the Pacific Oyster, Crassostrea gigas Larvae that Change in Expression as a Result of Bacteria Challenge
Authors: Fang Jing , Cai Xiaohui , Mao Fengyi , Li Hongyu , Chen Honglin , Qian Minhua , Hambrook Jacob M , Hanington Patrick C , Wu Xinzhong 
Published: May 2020

Abstract
Background: Marine molluscs living in intertidal and estuarine areas, such as oysters, face numerous pathogen challenges during their development. Infection from bacteria such as Vibrio alginolyticus, represents a major factor affecting larval development and frequently leads to high mortality of the pacific oyster, Crassostrea gigas. The oyster immune response is known to play an important role in protecting the animal during development by mitigating the consequences of infection. Results: In this study, we undertook a comprehensive analysis of the immune response of C. gigas to V. alginolyticus challenge. We sequenced the transcriptome of C. gigas at 0, 6, 12, 24, 48 and 72 hours post infection. After RNA-seq, the raw reads are available through the NCBI Sequence Read Archive under accession number PRJNA623063. After filtering, a total of 58.24 Gb clean reads were produced and assembled using the reference genome of C. gigas. The distribution of quality Q30 was higher than 90.88% for each sample and the GC content ranged from 41.27% to 42.91%. When compared with sequences in the COG, GO, KEGG, Swiss-Prot, and NR databases, there were 1267, 1112, 2187, 682, 1133 differentially expressed genes annotated at 6, 12, 24, 48, 72 hours post infection respectively. Numerous immune-related genes displayed differential expression that varied over time: toll-like receptors, tripartite motif proteins, Lectin-like factors, scavenger receptors, signaling pathway components such as Myeloid differentiation factor 88, and stress proteins such as Heat shock 70 kDa protein were all found to be higher in abundance following V. alginolyticus challenge compared to control. For analysis, these genes were divided into several categories such as pattern recognition receptors, fibrinogen-like proteins, damage associated molecular patterns, complement factors, etc. These general categories allowed us to generate an immune response profile for C. gigas over the first 72 hours of infection. These results indicate that bacterial infection induce a complex pattern of immune gene expression in C. gigas larvae. Conclusion: Our study will facilitate targeted investigation into the function of specific immune factors that may explain the diversity and evolution of invertebrate immune molecules and lead to the development of effective measures to improve the performance of oyster culture.
Characteristics of Acute Ischemic Stroke in Hospitalized Patients in Tibet: A Retrospective Comparative Study
Authors: Lu Yuxuan , Zhuoga Cidan , Jin Haiqiang , Zhu Feiqi , Zhao Yuhua , Ding Zhijie , He Shihua , Du Ailian , Xu Jun , Luo Jingjing , Sun Yongan 
Published: May 2020

Abstract
BackgroundLots of studies of acute ischemic stroke (AIS) had been conducted at low altitude regions, and related findings were used to instruct clinic management while corresponding studies at high altitude were few. This study aimed to analyse AIS clinic characteristics at high altitude regions by conducting a hospital-based comparative study between Tibet and Beijing.MethodsThis study included diagnoses of AIS patients from People’s Hospital of Tibet Autonomous Region (PHOTAR) and Peking University First Hospital (PUFH) between 1st January 2014, and 31st December 2017, where data including patient demographics, treatment time, onset season, risk factors, infarction location, laboratory data, image examination results, treatments, and AIS subtype were collected and compared. Continuous and categorical variables were analysed with a two-sample t-test or Wilcoxon rank sum test and chi-square test, respectively. Significant risk factors were examined with binary logistic regression analysis.ResultsIn total, 236 and 1021 inpatients from PHOTAR and PUFH were included, respectively. The PHOTAR patients were younger than the PUFH patients (P < 0.001). Young adult stroke, erythrocytosis, and hyperhomocysteinemia were more frequent in PHOTAR patients (all P < 0.001). Other vascular risk factors, including hypertension, diabetes mellitus, hyperlipidaemia, and smoking and alcohol consumption history, were less prevalent in PHOTAR patients than in PUFH patients. The rate of intravenous thrombolysis and intravenous thrombolysis window time were also lower in PHOTAR patients (both P < 0.001). PHOTAR groups also tended to have anterior circulation infarction. Erythrocytosis and hyperhomocysteinemia were independent risk factors in PHOTAR, and here young adults accounted for a larger proportion of stroke cases.ConclusionIn Tibet, the average age of AIS patients were less, and anterior circulation infarctions were also more common. Erythrocytosis and hyperhomocysteinemia may contribute to these differences. Here young adult stroke also accounted for a higher proportion, and this may be associated with erythrocytosis. Our findings present the first hospital-based comparative study in Tibet and may contribute to policies for stroke prevention in this region.
Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales
Authors: De Maayer Pieter , Pillay Talia , Coutinho Teresa A 
Published: May 2020

Abstract
Background
Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of these structures is highly energy intensive and as such flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility.
Results
Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales.
Conclusions
Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report for the first time on the occurrence of two peritrichous flagellar loci in some enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.
GWAS unveils features between early- and late-flowering pearl millets
Authors: Diack Oumar , Kanfany Ghislain , Gueye Mame Codou , Sy Ousmane , Fofana Amadou , Tall Hamidou , Serba Desalegn D. , Zekraoui Leila , Berthouly-Salazar Cécile , Vigouroux Yves , Diouf Diaga , KANE NDJIDO ARDO 
Published: May 2020

Abstract
Background
Pearl millet, a dietary food for around 100 million people in Africa and in India, has a large diversity due to an extensive genetic diversity combined with a high degree of admixture with wild relatives. In Senegal, two major morphotypes are distinguished: early-flowering and late-flowering millets. The phenotypic variabilities according to the flowering time plays an important role in pearl millet adaptation to climate variability. A better understanding of the genetic makeup of these variabilities would allow breeding of pearl millet fitting different climatic areas. In this study, we aimed to characterize the genetic basis of these phenotypic differences.
Results
We defined a core collection capturing most of the diversity of cultivated pearl millet of Senegal, which includes 60 early-flowering Souna and 31 late-flowering Sanio. This panel was evaluated during the 2016 and 2017 rainy seasons at Nioro for 16 agro-morphological traits. Phenological and phenotypes traits linked with yield, flowering time, and biomass helped differentiated early- and late-flowering millets. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) with minor allele frequencies of more than 5% were identified. Sparse Non-Negative Matrix Factorization (sNMF) analysis confirms the genetic structure in 2 gene pools associated with flowering time differences. Moreover, 2 chromosomal regions on linkage groups 3 (~ 89.7 Mb) and 6 (~ 68.1 Mb) differentiated the early-flowering into 2 clusters. Genome-wide analysis study (GWAS) was used to associate phenotypic variation to the SNPs and 18 genes were linked to flowering time, plant height, nodal tiller number, and biomass (P-value ˂ 2.3E-06).
Conclusions
The diversity of early- and late-flowering pearl millet landraces of Senegal was captured using a heuristic approach. Key phenology and phenotypic traits, SNPs, ad candidate genes underlying flowering time, tillering, biomass and plant height of pearl millet were identified. Chromosome rearrangements in LG 3 and 6 were implicated as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes would have paramount importance in breeding strategies under climate change scenarios.