bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Factors of Sinonasal Squamous Cell Carcinomas Arising De Novo and From Inverted Papilloma
Authors: Li Yunxia , Wang Chengshuo , Wang Ru , Zhang Jiamin , Liu Honggang , Shi Qian , Chen Xiaohong , Hou Lizhen , Ma Hongzhi , Zhong Qi , Li Pingdong , Feng Ling , He Shizhi , Zhang Luo , Fang Jugao 
Published: July 2020

Background The prognostic factors and survival difference between inverted papilloma (IP)-associated sinonasal squamous cell carcinoma (SCC) and de novo SCC are unclear. Objective This study aimed to compare the clinical features and oncologic outcomes in patients with IP-associated SCC and de novo SCC; and additionally, to analyze the prognostic factors of the two types of SCCs. Methods Data from 173 SCC patients treated for IP-associated SCC (n = 89) and de novo SCC (n = 84), were reviewed retrospectively for demographic features, tumor characteristics, treatment modality, and clinical outcomes. 5-year overall survival (OS) and disease free survival (DFS) was analyzed using the Kaplan-Meier method, and Cox proportional hazards model was used to analyze factors influencing prognosis. Results A higher proportion of IP-associated SCC occurred in frontal and sphenoid sinus compared to de novo SCC. The two groups demonstrated similar 5-year OS and DFS (5-year OS: 63.3% and 55.4%, DFS: 45.4% and 50.1%, respectively). The metachronous tumor had a relatively better prognosis outcome than synchronous tumor and de novo SCC (5-year OS: 73.1%, 54.5% and 55.4%, respectively). Both groups showed similar loco-regional recurrence rates ( p > 0.05); however, de novo SCC tumors demonstrated an increased incidence of distant metastasis. Multivariate analysis indicated that age >70 years, advanced tumor stage and surgical margin were independent predictive factors for the risk of mortality (HR 2.047, 1.581 and 1.931, respectively). Conclusion IP-associated SCCs have an aggressive loco-regional tendency, whereas de novo SCCs have a higher aggressive distant metastatic propensity. Age, tumor stage and surgical positive margin are key factors for poor prognosis and should be routinely taken into consideration during treatment planning and subsequent surveillance.
A laboratory approach for the calibration of seismic data in the western part of the Swiss Molasse Basin: the case history of well Humilly-2 (France) in the Geneva area
Authors: Hefny Mahmoud , Zappone Alba , Makhloufi Yasin , de Haller Antoine , Moscariello Andrea 
Published: July 2020

AbstractA collection of 81 plugs were obtained from the Humilly-2 borehole (France), that reached the Permo-Carboniferous sediments at a depth of 3051 m. Experimental measurements of physical parameters and mineralogical analysis were performed to explore the links between sedimentary facies and seismic characteristics and provide a key tool in the interpretation of seismic field data in terms of geological formations. The plugs, cylinders of 22.5 mm in diameter and $$\sim$$
∼
30 mm in length were collected parallel and perpendicular to the bedding in order to explore their anisotropy. Ultrasound wave propagation was measured at increasing confining pressure conditions up to 260 MPa, a pressure where all micro-fractures are considered closed. The derivatives of velocities with pressure were established, allowing the simulation of lithological transitions at in-situ conditions. At room conditions, measured grain densities (kg/m3) range from 2630 to 2948 and velocities vary from 4339 to 6771 and 2460 to 3975 $${\text {m/s}}$$
m/s
for P- and S-waves propagation modes, respectively. The largest seismic-reflections coefficients were calculated for the interface between the evaporitic facies of the Keuper (Lettenkohle) and the underlying Muschelkalk carbonates (R$$_{\text {c}}=$$

c

=

0.3). The effective porosity has the range of 0.23% to 16.65%, while the maximum fluid permeability $$\left( \text {m}^{\text {2}}\right)$$

m
2

is 9.1 $$\times \text {10}^{-{\text {16}}}$$

×

10

-
16

. A positive correlation between porosity and ultrasound velocity has been observed for P- and S-waves. The link between velocities and modal content of quartz, dolomite, calcite, and micas has been explored. This paper presents a unique set of seismic parameters potentially useful for the calibration of seismic data in the Geneva Molasse Basin.
COVID-19 and andrology: Recommendations of the French-speaking society of andrology (Société d’Andrologie de langue Française SALF)
Authors: Hamdi S. , Bendayan M. , Huyghe E. , Soufir J.-C. , Amar E. , El Osta R. , Plotton I. , Delalande C. , Perrin J. , Leroy C. , Bouker A. , Pons H. , Lejeune H. , Robin G. , Boitrelle F. 
Published: July 2020

AbstractSARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) metamorphosed our medical practice. In early June 2020, more than 6,400,000 COVID-19 (coronavirus-19 disease) cases were diagnosed across the world and more than 380,000 deaths were linked to COVID-19. Many medical symptoms of COVID-19 were reported. We will focus, here, on potential impacts of COVID-19 on men’s andrological health. Our society (French-speaking society of andrology, SALF) also emitted some recommendations in the andrological management of men infected by SARS-CoV-2. First, considering the fever and the potential presence of SARS-CoV2 in semen, SALF recommends waiting for 3 months (duration of one spermatogenesis cycle and epididymal transit) before re-starting ART in the case of men diagnosed COVID-19 positive. Whatever the nature of testosterone and COVID-19 relationships, we recommend an andrological examination, sperm parameters, and hormonal evaluation at the time of the COVID-19 is diagnosed, and several months later. Furthermore, we are concerned by the potential morbid-mortality of the COVID-19, which mainly affects men. This “andrological bias”, if proven, must be reduced by specific andrological diagnosis, therapeutic and prophylactic measures. Research in this direction must be substantiated and financially supported over the next few months (years).
MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data
Authors: Shahryary Yadollah , Hazarika Rashmi R. , Johannes Frank 
Published: July 2020

AbstractBackgroundWhole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells. These surveys can easily generate hundreds or even thousands of WGBS datasets in a single study. The efficient pre-processing of these large amounts of data poses major computational challenges and creates unnecessary bottlenecks for downstream analysis and biological interpretation.ResultsTo offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data. MethylStar integrates well-established tools for read trimming, alignment and methylation state calling in a highly parallelized environment, manages computational resources and performs automatic error detection. MethylStar offers easy installation through a dockerized container with all preloaded dependencies and also features a user-friendly interface designed for experts/non-experts. Application of MethylStar to WGBS from Human, Maize andA. thalianashows favorable performance in terms of speed and memory requirements compared with existing pipelines.ConclusionsMethylStar is a fast, stable and flexible pipeline for high-throughput pre-processing of bulk or single-cell WGBS data. Its easy installation and user-friendly interface should make it a useful resource for the wider epigenomics community. MethylStar is distributed under GPL-3.0 license and source code is publicly available for download from githubhttps://github.com/jlab-code/MethylStar. Installation through a docker image is available fromhttp://jlabdata.org/methylstar.tar.gz
PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome
Authors: Zhang Hua , Xu Hanzhi , Liu Huiru , Pan Xiaolan , Xu Meng , Zhang Gege , He Maoxian 
Published: July 2020

Abstract
Background
The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain poorly understood. The transcriptome sequencing has been considered to understanding of the complexity of mechanisms of the growth of P. f. martensii. The recently released genome sequences of P. f. martensii, as well as emerging Pacific Bioscience (PacBio) single-molecular sequencing technologies, provide an opportunity to thoroughly investigate these molecular mechanisms.

Results
Herein, the full-length transcriptome was analysed by combining PacBio single-molecule long-read sequencing (PacBio sequencing) and Illumina sequencing. A total of 20.65 Gb of clean data were generated, including 574,561 circular consensus reads, among which 443,944 full-length non-chimeric (FLNC) sequences were identified. Through transcript clustering analysis of FLNC reads, 32,755 consensus isoforms were identified, including 32,095 high-quality consensus sequences. After removing redundant reads, 16,388 transcripts were obtained, and 641 fusion transcripts were derived by performing fusion transcript prediction of consensus sequences. Alternative splicing analysis of the 16,388 transcripts was performed after accounting for redundancy, and 9097 gene loci were detected, including 1607 new gene loci and 14,946 newly discovered transcripts. The original boundary of 11,235 genes on the chromosomes was corrected, 12,025 complete open reading frame sequences and 635 long non-coding RNAs (LncRNAs) were predicted, and functional annotation of 13,482 new transcripts was achieved. Two thousand three hundred eighteen alternative splicing events were detected. A total of 228 differentially expressed transcripts (DETs) were identified between the largest (L) and smallest (S) pearl oysters. Compared with the S, the L showed 99 and 129 significantly up-and down-regulated DETs, respectively. Six of these DETs were further confirmed by quantitative real-time RT-PCR (RT-qPCR) in independent experiment.

Conclusions
Our results significantly improve existing gene models and genome annotations, optimise the genome structure, and in-depth understanding of the complexity and diversity of the differential growth patterns of P. f. martensii.
Epidemiology, species distribution, and predictive factors for mortality of candidemia in adult surgical patients
Authors: Zhang Wei , Song Xingpeng , Wu Hao , Zheng Rui 
Published: July 2020

Abstract
Background
We evaluated the epidemiology, clinical characteristics, microbiology, outcomes, and risk factors for mortality of candidemia in adult surgical patients in Shenyang from 2012 to 2018.

Methods
We designed a retrospective observational study of adult patients with candidemia in a teaching hospital including three hospital campuses. Data regarding clinical and demographic characteristics were collected from the patient’s medical records.

Results
Of the 236 cases of candidemia, 172 (72.9%) were identified in surgical patients, including 146 (84.9%) general surgeries, 11 (6.4%) urologic surgeries, 6 (3.5%) thoracic surgeries, and others. Higher proportions of solid tumors, total parenteral nutrition, the presence of a urinary catheter, and the presence of a gastric tube were observed in surgical patients with candidemia versus non-surgical ones, whereas the percentages of hematological malignancy, diabetes mellitus, and renal replacement therapy were relatively lower in surgical patients. Renal failure, leukopenia, and thrombocytopenia were less common laboratory findings in surgical patients with candidemia than compared to non-surgical ones. Among surgical patients with candidemia, Candida parapsilosis was the predominant species (43%), followed by C. albicans (33.7%), C. glabrata (11%), C. tropicalis (8.1%), and others (4.1%). Overall susceptibility, susceptible dose dependent or intermediate susceptibility, and resistance to fluconazole were detected in 73.3, 19.8, and 3.5% Candida isolates from surgical patients, respectively, but no resistance to amphotericin B was observed. Overall, the 30-day mortality in surgical patients was 19.2%. At multivariable analysis, independent risk factors for death in surgical patients with candidemia were ICU stay, thrombocytopenia, and C. albicans infection.

Conclusions
Surgical patients account for the majority of candidemia cases. Among patients with recent surgery, risk factors for species distribution, antifungal sensitivity patterns of Candida isolates causing candidemia, and independent risk factors for mortality should be evaluated and considered for a better outcome in the antifungal treatment.
Fibroadenoma versus phyllodes tumor: a vexing problem revisited!
Authors: Tummidi Santosh , Kothari Kanchan , Agnihotri Mona , Naik Leena , Sood Prashant 
Published: July 2020

Abstract
Background
Fibroepithelial lesions of the breast include fibroadenoma (FA) and phyllodes tumor (PT). Fibroadenomas are benign while phyllodes tumor range from benign, indolent neoplasms to malignant tumors capable of distant metastasis. Our study was to determine the select cytologic features that can accurately distinguish FA from PT.

Methods
A retrospective review was performed of patients who had histopathology follow up of FA or PT and on whom a pre-operative fine needle aspiration was performed. Cytologic criteria i.e. epithelial component, stromal component and background cellularity were assessed.

Results
46 FA and 24 PT were specimens were reviewed. Median age and tumor size for FA and PT were 23.0 and 39.0 years, and 2.0 and 5.0 cm, respectively. Univariate analysis and regression models based on generalized estimating equations revealed that large opened out, folded epithelial sheets, frayed and irregular stromal fragment contours, spindle stromal cell nuclei, spindle cell nuclei in the background and background cell atypia are significant cytological predictors of PT. The GEE regression model achieved 78.9% diagnostic accuracy (p <  0.001) in identifying PT based on cytological features. Median epithelial: stromal ratio was 3.4 and 2.6 for FA and PT, respectively.

Conclusion
Presence of large, opened out, folded epithelial sheets, frayed and irregular stromal contours with spindle nuclei, background spindle cells and atypia can help distinguish PT from FA.
A single-arm confirmatory trial of pazopanib in patients with paclitaxel-pretreated primary cutaneous angiosarcoma: Japan Clinical Oncology Group study (JCOG1605, JCOG-PCAS protocol)
Authors: Oashi Kohei , Shibata Taro , Namikawa Kenjiro , Takahashi Akira , Yokota Kenji , Nakano Eiji , Teramoto Yukiko , Tsutsumida Arata , Maeda Taku , Yamazaki Naoya ,   the Dermatologic Oncology Group of the Japan Clinical Oncology Group
Published: July 2020

Abstract
Background
Paclitaxel is a standard of care for patients with primary cutaneous angiosarcoma of the scalp and face. However, no standard second-line treatment for paclitaxel-resistant patients has ever been established. Since primary cutaneous angiosarcoma expresses a high level of vascular endothelial growth factor receptor, the multitargeted tyrosine kinase inhibitor pazopanib seemed to be the most promising agent, and several retrospective studies have demonstrated its activity against this disease. However, the efficacy and safety of pazopanib in paclitaxel-resistant patients with primary cutaneous angiosarcoma have never been evaluated in a clinical trial.

Methods
In February 2018 the Dermatologic Oncology Group of Japan Clinical Oncology Group started a single-arm confirmatory trial to evaluate the efficacy and safety of pazopanib as a second-line treatment for patients with primary cutaneous angiosarcoma whose disease was resistant to paclitaxel or who were unable to tolerate paclitaxel (JCOG1605, JCOG-PCAS). Patients with primary cutaneous angiosarcoma not associated with lymphedema or radiation, progressing despite first-line paclitaxel monotherapy are included in the study. No prior systemic chemotherapy other than paclitaxel is permitted. Pazopanib is administered orally at an initial dosage of 800 mg once daily. Dose modifications for adverse events are made according to the dose reduction criteria described in the protocol. Treatment is continued until recurrence, disease progression, unacceptable toxic effects, patient refusal, or death. The primary endpoint is progression-free survival, secondary endpoints include overall survival, response rate, disease control rate, adverse events, and serious adverse events. We plan to recruit 30 participants in 5.5 years from 23 Japanese institutions. The follow-up period is set as 1 year after completion of accrual. The study protocol was approved by the Japan Clinical Oncology Group Protocol Review Committee in December 2017. Ethical approval for this study was granted by Ethics Committee of each institute.

Discussion
If the primary endpoint is met, pazopanib will be regarded as a standard of care for paclitaxel-resistant patients for whom no standard second-line treatment is established.

Trials registration
Registry number: UMIN000031438 [http://www.umin.ac.jp/ctr/index.htm]. Date of Registration: 23/Feb/2018. Date of First Participant Enrollment: 8/Mar/2018.
The relationship between retroperitoneal lymphadenectomy and survival in advanced ovarian cancer patients
Authors: Fang Chenyan , Zhang Yingli , Zhao Lingqin , Chen Xi , Xia Liang , Zhang Ping 
Published: July 2020

Abstract
Background
Systematic retroperitoneal lymphadenectomy has been widely used in the surgical treatment of advanced ovarian cancer patients. Nevertheless, the corresponding therapeutic may not provide a survival benefit. The aim of this study was to assess the effect of systematic retroperitoneal lymphadenectomy in such patients.

Methods
Patients with advanced ovarian cancer (stage III-IV, according to the classification presented by the International Federation of Gynecology and Obstetrics) who were admitted and treated in Zhejiang Cancer Hospital from January 2004 to December 2013 were enrolled and reviewed retrospectively. All patients were optimally or suboptimally debulked (absent or residual tumor < 1 cm) and divided into two groups. Group A (no-lymphadenectomy group, n = 170): patients did not undergo lymph node resection; lymph nodes resection or biopsy were selective. Group B (n = 240): patients underwent systematic retroperitoneal lymphadenectomy.

Results
A total of 410 eligible patients were enrolled in the study. The patients’ median age was 51 years old (range, 28–72 years old). The 5-year overall survival (OS) and 2-year progression-free survival (PFS) rates were 78 and 24% in the no-lymphadenectomy group and 76 and 26% in the lymphadenectomy group (P = 0.385 and 0.214, respectively). Subsequently, there was no significant difference in 5-year OS and 2-year PFS between the two groups stratified to histological types (serous type or non-serous type), the clinical evaluation of negative lymph nodes or with macroscopic peritoneal metastasis beyond pelvic (IIIB-IV). Multivariate Cox regression analysis indicated that systematic retroperitoneal lymphadenectomy was not a significant factor influencing the patients’ survival. Patients in the lymphadenectomy group had a higher incidence of postoperative complications (incidence of infection treated with antibiotics was 21.7% vs. 12.9% [P = 0.027]; incidence of lymph cysts was 20.8% vs. 2.4% [P < 0.001]).

Conclusions
Our study showed that systematic retroperitoneal lymphadenectomy did not significantly improve survival of advanced ovarian cancer patients with residual tumor < 1 cm or absent after cytoreductive surgery, and were associated with a higher incidence of postoperative complications.
Choroidal origin of endogenous Candida endophthalmitis
Authors: Breazzano Mark P. 
Published: July 2020

AbstractEndogenous Candida endophthalmitis (ECE) has been established with microscopic histopathology, both by autopsy and experimentation, to primarily originate from and involve the choroid. Zhuang et al. examined a series of patients with ECE using spectral-domain optical coherence tomography (SD-OCT) imaging and present a new classification scheme. The authors conclude the majority of lesions are primarily retinal in location without report of choroidal involvement. This discrepancy may be explained by posterior shadowing artifact and lack of discernment from associated retinal findings like infarction. These considerations are necessary in reviewing SD-OCT, characterizing ECE, and proposing new classification systems.
Clinical characteristics and prognosis of Total Rhegmatogenous retinal detachment: a matched case-control study
Authors: Sung Jae-Yun , Lee Min-Woo , Won Yeo-Kyoung , Lim Hyung-Bin , Kim Jung-Yeul 
Published: July 2020

Abstract
Background
Although many studies have reported clinical features, surgical outcomes of rhegmatogenous retinal detachment (RRD), studies focusing on total RRD are rare. In this study, we investigate the clinical characteristics, risk factors, and prognosis of total RRD.

Methods
A retrospective chart review was performed on cases of 44 total RRD and an age- and sex-matched 88 partial RRD. Two groups were compared for clinical characteristics, risk factors, and prognosis.

Results
The prevalence of total RRD in all cases of retinal detachment was 4.4%. Pseudophakic eye, ocular trauma, and proliferative vitreoretinopathy (PVR) were significantly associated with a risk of total RRD (P = .002, P = .003, and P < .001, respectively). In the total RRD group, retinal breaks were located in both superior and inferior parts of the retina, and macular holes and giant retinal tears were frequently found. The best-corrected visual acuity (log MAR) before surgery and final best-corrected visual acuity after surgery were 2.23 ± 0.45 and 1.88 ± 0.96, which was significantly poorer than in the partial RRD group (P < .001). The success rate after primary surgery was 75.0% in the total RRD group, which was significantly lower than partial RRD group (P < .001). Old age, pseudophakic eye, and macular hole as the type of retinal break were highly associated with low success rate. (P = .010, P = .0500, and P = .002).

Conclusions
Patients with total RRD had higher recurrence rate and poorer visual outcome after surgery than patients with focal RRD. Old age, pseudophakic eye, and presence of macular hole were important risk factors for recurrence after total RRD repair. Additional surgical procedures should be considered to combine with vitrectomy to achieve better surgical outcomes in these patients.