bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmablastic Lymphoma: A Clinicopathological Study from a Tertiary Care Cancer Center in South India
Authors: Mundada Manasi C. , Ahmed Faiq , Khera Rachna , Murthy Sudha , Rajappa Senthil , Santa A. , Mallavarapu Krishnamohan 
Published: December 2020

Abstract
Background Plasmablastic lymphoma (PBL) is a rare aggressive B cell lymphoma that is commonly encountered in patients with human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). In this case series, we describe the clinicopathological features of cases of PBL seen at a tertiary care center in South India.
Materials and Methods Medical records of patients diagnosed with PBL between January 2009 and November 2017 were reviewed. PBL was defined as per the World Health Organization 2016 classification for hematopoietic and lymphoid neoplasms. The slides were reviewed with hematoxylin and eosin along with immunohistochemistry (IHC) including CD45, CD20, PAX5, CD79a, CD3, CD5, CD138, MUMI, EMA, ALK, and Ki67. Epstein-Barr virus (EBV) association was documented by rapid in situ hybridization (RISH) studies wherever possible. The demographic data, clinical presentation, treatment details, and outcomes are elaborated using descriptive statistics.
Results During the study period, nine patients with PBL were identified. The median age at presentation was 47 years (range: 36–54 years). All patients had associated HIV/AIDS, eight (89%) had extranodal disease, and six (66%) had advanced clinical stage (stage III). All biopsies were positive for CD45, CD138, and MUM1, and negative for CD79a and T cell markers with a high Ki67 proliferation index (85–90%); CD20 was faint positive in one patient, and CD56 was positive in one (11%) patient. EBV-RISH was tested in two patients and was positive in one. Bone marrow was uninvolved in all the cases. At the time of last follow-up, three patients were alive. Treatment details were available in six patients. With frontline therapy, four patients achieved a complete remission (CR) and one patient developed progressive disease. Three of four patients in CR are alive till the last follow-up.
Conclusion PBL is a rare form of lymphoma with predominant association with HIV, extranodal location, and characteristic IHC pattern.
A Tertiary Cancer Center Experience of 52 Cases of Primary Ovarian Mucinous Adenocarcinomas
Authors: Das Gaurav , Sridevi V. , Natarajan Mohanaraj 
Published: December 2020

Abstract
Background Primary mucinous epithelial ovarian adenocarcinoma (mEOC) constitutes a small percentage (2–5%) of ovarian cancer. Our aim is to understand the clinicopathological characteristics and survival results of patients with mEOC after a long-term follow-up.
Materials and Methods This is a retrospective study of primary mEOC cases treated at a tertiary cancer center in India, from January 1, 2005, to December 31, 2012.
Results Out of 958 malignant ovarian tumors, 52 (5.43%) were mucinous adenocarcinoma. Nearly 71.2% of cases were of early-stage disease, and the remaining were of advanced-stage disease. After a follow-up period of 63 months (range: 1–138 months), the 5-year actuarial overall survival for stages I, II, III, and IV was 92.5, 70, 38.5, and 0%, respectively. Among advanced-stage tumors, half of them progressed without undergoing cytoreductive surgery and died.
Conclusion Most of the mEOC cases present in early stages and have good clinical outcome. Patients with advanced-stage disease do not respond well to standard chemotherapy regimens in use and have poor survival figures. The use of primary cytoreduction should be considered in the place of interval cytoreduction for advanced mEOC.
A Prospective Observational Study Comparing Long-Course Conventional Neoadjuvant Chemoradiotherapy with Short-Course Radiotherapy Followed by Consolidation Chemotherapy with Delayed Surgery in Locally Advanced Rectal Cancer
Authors: Thakur Niketa , Seam Rajeev K. , Gupta Manoj K. , Gupta Manish , Fotedar Vikas , Vats Siddharth , Rana Sakshi , Vias Poorva , Ahuja Rachit 
Published: December 2020

Abstract
Background Polish and Australian randomized studies compared short-course radiotherapy (RT) with immediate surgery and long-course chemoradiotherapy (CRT) with delayed surgery. In these studies, similar long-term survival and local control have been reported for both these approaches, but pathological complete response (pCR) is not better with short-course RT. Moreover, studies have shown better tumor downstaging with delayed surgery. In this context, the use of short-course RT with delayed surgery may have some advantages and needs to be tested in clinical trials.
Patients and Methods This was a two-arm, prospective, observational study, in which preoperative short-course RT followed by two cycles of chemotherapy was compared with the conventional neoadjuvant CRT in locally advanced rectal cancer. The primary end points were the rate of complete response and toxicity profile. The secondary end points were the rate of R0 resection, overall survival, and progression-free survival. The data obtained from the two arms were analyzed using Pearson’s chi-square test to determine the statistical significance between the two treatment arms.
Results The pCR rate was 6.7% in the study arm and 0 in the control arm (p = 0.343). The RO resection rates were 92.8 and 92.3% in the study and control arms, respectively. The rates of grade 3and 4 acute toxicity in the study and control arms were 14.2 and 61.5%, respectively (p = 0.011). The rates of grade 3 and 4 late toxicity in the study and control arms were 21.4 and 15.3%, respectively (p = 0.686).
Conclusions The pCR rates and the late toxicities in both arms are comparable. The major advantages of the 5 × 5 Gy regimen with chemotherapy in a neoadjuvant setting are a significant reduction in acute toxicities and better patient compliance along with similar efficacy as that of the standard regimen.
Perfusion fixation methods for preclinical biodistribution studies: A comparative assessment using automated image processing
Authors: Belhadjhamida Rania , Lea-Banks Harriet , Hynynen Kullervo 
Published: December 2020

Abstract
Studying the biodistribution of novel therapeutics and biomaterials in vivo requires effective and consistent perfusion and fixation of major organs. Standard methods for removing red blood cells (RBCs) and fixing tissue often involve transcardial perfusion, such as brain-targeted perfusion (via the left ventricle) or lung-targeted perfusion (via the right ventricle). Using autofluorescence measurements and a bespoke ImageJ macro to quantify RBC content from histology, we compared the efficacy and consistency of three whole-body perfusion techniques. We show that lung-targeted perfusion evacuates more blood from the lung vasculature than brain-targeted perfusion (20 ± 54% fewer RBCs), and that our novel approach of ‘dual-targeted’ perfusion (via the right and left ventricles sequentially) had even higher efficacy (30 ± 6% fewer RBCs). Furthermore, by combining aspects of brain- and lung-targeted methods, dual-targeted perfusion achieved the highest consistency in autofluorescence emissions from major organs (64% and 65% lower variance than brain- and lung-targeted perfusion respectively). Since RBC content and autofluorescence can be confounding factors in biodistribution studies using fluorescent probes, our findings and proposed novel approach offer insight into perfusion fixation techniques for pre-clinical studies.
Synthesis, characterization and photocatalytic activity using SiO2-TiO2 nanocomposites under UV light
Authors: Thongpool V , Phunpueok A , Jaiyen S , Rojviroon T 
Published: December 2020

Abstract
SiO2-TiO2 nanocomposites were synthesized by the sol-gel method with different SiO2 contents (0.125, 0.25, 0.50 and 0.75%wt). The characteristics of prepared samples were obtained from x-ray diffractometer (XRD), field emission scanning electron microscope (FESEM), UV–visible spectrophotometer, and Brunauer Emmett and Teller (BET) surface area analyzer. SiO2-TiO2 nanocomposites have higher UV absorption capability and a higher specific surface area compared to pure TiO2, resulting in improved dye degradation by photocatalytic activity. The results show that the dye degradation efficiency of 0.5SiO2-TiO2 is higher than pure TiO2. It can degrade the dye up to 96.91% within 2 h, while TiO2 was able to degrade dye at 88.62%.
A state-averaged orbital-optimized hybrid quantum–classical algorithm for a democratic description of ground and excited states
Authors: Yalouz Saad , Senjean Bruno , Günther Jakob , Buda Francesco , O’Brien Thomas E , Visscher Lucas 
Published: December 2020

Abstract
In the noisy intermediate-scale quantum (NISQ) era, solving the electronic structure problem from chemistry is considered as the ‘killer application’ for near-term quantum devices. In spite of the success of variational hybrid quantum/classical algorithms in providing accurate energy profiles for small molecules, careful considerations are still required for the description of complicated features of potential energy surfaces. Because the current quantum resources are very limited, it is common to focus on a restricted part of the Hilbert space (determined by the set of active orbitals). While physically motivated, this approximation can severely impact the description of these complicated features. A perfect example is that of conical intersections (i.e. a singular point of degeneracy between electronic states), which are of primary importance to understand many prominent reactions. Designing active spaces so that the improved accuracy from a quantum computer is not rendered useless is key to finding useful applications of these promising devices within the field of chemistry. To answer this issue, we introduce a NISQ-friendly method called ‘state-averaged orbital-optimized variational quantum eigensolver’ which combines two algorithms: (1) a state-averaged orbital-optimizer, and (2) a state-averaged VQE. To demonstrate the success of the method, we classically simulate it on a minimal Schiff base model (namely the formaldimine molecule CH2NH) relevant also for the photoisomerization in rhodopsin—a crucial step in the process of vision mediated by the presence of a conical intersection. We show that merging both algorithms fulfil the necessary condition to describe the molecule’s conical intersection, i.e. the ability to treat degenerate (or quasi-degenerate) states on the same footing.
Tuning optical and optoelectronic properties of gold nanoparticle and ZnO thin film hetero-structures
Authors: Sekhar Muddam Raja , Laha Ranjit , Kar Manoranjan 
Published: December 2020

Abstract
Thin film hetero-structures (TFHSs) involving metal oxide thin films and noble metal nanoparticles are very important for many optoelectronics based device applications. This work reports the growth, characterization, and tuning of photoluminescence and I–V properties of TFHSs involving zinc oxide (ZnO) and gold nanoparticles (GNPs). ZnO thin films and GNPs were respectively deposited by the Pulsed Laser Deposition (PLD) and DC sputtering with subsequent annealing. Three different TFHSs were prepared by varying the relative positions of ZnO and GNPs, namely Si-GNPs-ZnO, Si-ZnO-GNPs, and Si-ZnO-GNPs-ZnO. X-ray diffraction results confirmed the high crystallinity of the films, with single phase nature of the ZnO and GNPs. Scanning electron microscopy micrograph analysis confirmed that the morphology of structures containing both GNPs and ZnO is influenced by the bottom layer. Diffuse reflectance spectroscopy results also indicated that the position of GNPs relative to ZnO affects the plasmon resonance of GNPs as well as the overall optical properties of the TFHSs. Photoluminescence studies revealed that the presence of GNPs affects the defect concentration in the TFHSs. The I–V characteristics showed that the TFHSs where ZnO contains GNPs in embedded form are better suited for photodiode application. This study adds a new dimension to the research on optoelectronics devices.
Noncoding RNAs: modulators and modulatable players during infection-induced stress response
Authors: Chattopadhyay Partha , Srinivasa Vasudevan Janani , Pandey Rajesh 
Published: December 2020

AbstractThe human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncoding RNAs (ncRNAs) are significant contributors to the transcriptome pool with sizeable fraction from repetitive elements of the human genome, inclusive of Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs). ncRNAs are increasingly being implicated in diverse functional roles especially during conditions of stress. These stress responses are driven through diverse mediators, inclusive of long and short ncRNAs. ncRNAs such as MALAT1, GAS5, miR-204 and miR-199a-5p have been functionally involved during oxidative stress, endoplasmic reticulum (ER) stress and unfolded protein response (UPR). Also, within SINEs, Alu RNAs derived from primate-specific Alu repeats with ~11% human genome contribution, playing a significant role. Pathogenic diseases, including the recent COVID-19, leads to differential regulation of ncRNAs. Although, limited evidence suggests the need for an inquest into the role of ncRNAs in determining the host response towards pathogen challenge.
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms
Authors: Marín-Llaó Josep , Mubeen Sarah , Perera-Lluna Alexandre , Hofmann-Apitius Martin , Picart-Armada Sergio , Domingo-Fernández Daniel 
Published: December 2020

Abstract

Summary
High-throughput screening yields vast amounts of biological data which can be highly challenging to interpret. In response, knowledge-driven approaches emerged as possible solutions to analyze large datasets by leveraging prior knowledge of biomolecular interactions represented in the form of biological networks. Nonetheless, given their size and complexity, their manual investigation quickly becomes impractical. Thus, computational approaches, such as diffusion algorithms, are often employed to interpret and contextualize the results of high-throughput experiments. Here, we present MultiPaths, a framework consisting of two independent Python packages for network analysis. While the first package, DiffuPy, comprises numerous commonly used diffusion algorithms applicable to any generic network, the second, DiffuPath, enables the application of these algorithms on multi-layer biological networks. To facilitate its usability, the framework includes a command line interface, reproducible examples and documentation. To demonstrate the framework, we conducted several diffusion experiments on three independent multi-omics datasets over disparate networks generated from pathway databases, thus, highlighting the ability of multi-layer networks to integrate multiple modalities. Finally, the results of these experiments demonstrate how the generation of harmonized networks from disparate databases can improve predictive performance with respect to individual resources.

Availability and implementation
DiffuPy and DiffuPath are publicly available under the Apache License 2.0 at https://github.com/multipaths.

Supplementary information
Supplementary data are available at Bioinformatics online.
Development of a fixation-free fluorescence in situ hybridization for the detection of Salmonella species
Authors: Adebowale Oluwawemimo , Good Liam 
Published: December 2020

Abstract
Salmonella is one of the most important infectious bacteria causing severe gastroenteritis and deaths in humans and animals, and the prompt diagnosis is crucial for effective control and treatment. The detection of Salmonella still depends principally on culture-based methods, which is time-consuming and laborious. Recently, polyhexamethylene biguanide (PHMB) was discovered to have cellular delivery properties and its combination with the fluorescence in situ hybridization (FISH) method was exploited for oligomer delivery and the rapid detection of Salmonella spps in this study. Cell-associated fluorescence was quantified using Volocity® 3-D image analysis software (Volocity 6.3, PerkinElmer, Inc.). PHMB complexed with fluorophore—labelled species-specific oligomers permeabilized freshly grown viable strains of Salmonella cells and mediated strong cell-associated fluorescence signals. This strategy further enabled a fixation-free protocol and hybridization in a single reaction. Using the modified FISH method, monoculture Salmonella strains were validated as well as detected in artificially contaminated water and milk within a turnaround period of 5 h. The method was observed to be comparable with the standard FISH technique (sFISH; P &gt; 0.05). The findings suggest that fixation-free delivery and hybridization of oligomers using PHMB can provide a simplified and prompt strategy for Salmonella detection at the species level, and promote early management responses to the disease and appropriate antimicrobial therapy.
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle
Authors: Asplund Olof , Rung Johan , Groop Leif , Prasad B Rashmi , Hansson Ola 
Published: December 2020

Abstract

MuscleAtlasExplorer is a freely available web application that allows for the exploration of gene expression data from human skeletal muscle. It draws from an extensive publicly available dataset of 1654 skeletal muscle expression microarray samples. Detailed, manually curated, patient phenotype data, with information such as age, sex, BMI and disease status, are combined with skeletal muscle gene expression to provide insights into gene function in skeletal muscle. It aims to facilitate easy exploration of the data using powerful data visualization functions, while allowing for sample selection, in-depth inspection and further analysis using external tools.

Availability
MuscleAtlasExplorer is available at https://mae.crc.med.lu.se/mae2.
Recovery from respiratory failure after 49-day extracorporeal membrane oxygenation support in a critically ill patient with COVID-19: case report
Authors: Guo Fengwei , Deng Chao , Shi Tao , Yan Yang 
Published: December 2020

Abstract

Background
Respiratory failure is a life-threatening complication of coronavirus disease 2019 (COVID-19)-related acute respiratory distress syndrome. Extracorporeal membrane oxygenation (ECMO) in COVID-19 might offer promise based on our clinical experience. However, few critically ill cases with COVID-19 have been weaned off ECMO.

Case summary
A 66-year-old Chinese woman presented with fever (38.9°C), cough, dyspnoea, and headache. She had lymphopenia (0.72 × 109/L) and computed tomography findings of ground-glass opacities. Subsequently, she was confirmed to have respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. She was intubated after transfer to the intensive care unit due to respiratory failure and heart failure. However, her condition continued to deteriorate rapidly. Veno-veno ECMO was undertaken for respiratory and cardiac support due to refractory hypoxemic respiratory failure and bradyarrhythmia (45 b.p.m.). During hospitalization, she was also administered anti-viral treatment, convalescent plasma therapy, and continuous renal replacement therapy. She was maintained on ECMO before she had fully recovered from the condition that necessitated ECMO use and had a negative test for the nucleic acids of SARS-CoV-2 twice. Forty-nine days later, this patient was weaned from ECMO. At the most recent follow-up visit (3 months after weaning from ECMO), she received respiratory and cardiac rehabilitation and did not complain of any discomfort.

Discussion
As far as we know, the longest duration of ECMO treatment in this critical case with COVID-19 is supportive of ECMO as the most aggressive form of life support and the last line of defence during the COVID-19 epidemic.
Long-term durability of bicuspid aortic valve repair: a comparison of 2 annuloplasty techniques
Authors: de Meester Christophe , Vanovershelde Jean-Louis , Jahanyar Jama , Tamer Saadallah , Mastrobuoni Stefano , Van Dyck Michel , Navarra Emiliano , Poncelet Alain , Astarci Parla , el Khoury Gebrine , de Kerchove Laurent 
Published: December 2020

Abstract

OBJECTIVES
To compare long-term outcomes after bicuspid aortic valve (BAV) repair utilizing the Cabrol annuloplasty versus valve sparing Reimplantation technique.

METHODS
From 1996 to 2018, 340 consecutive patients underwent BAV repair. Eighty underwent Cabrol annuloplasty and 189 underwent Reimplantation. Exclusion criteria were re-repairs (n = 6), active endocarditis (n = 4), no annuloplasty (n = 41) and ring or suture annuloplasty (n = 20). We compared both groups for survival, reoperations, valve related events and recurrent severe aortic regurgitation (AR &gt; 2+). Inverse probability weighting (IPW) was used to balance the 2 groups. Cox regression analysis was used to identify outcome predictors.

RESULTS
After weighting, pre- and intraoperative characteristics were similar between groups, except for aorta replacement techniques and operative time, which was longer in the Reimplantation group (P &lt; 0.001). At 12 years, overall survival was similar between groups (IPW: Cabrol 97 ± 2% vs Reimplantation 94 ± 3%, P = 0.52). Freedom from reoperation and freedom from AR &gt; 2+ were significantly lower in the Cabrol group (reoperation IPW: 69 ± 9% vs 91 ± 4%, P = 0.004 and AR &gt; 2+ IPW: 71 ± 8% vs 97 ± 2%, P &lt; 0.001). The Reimplantation technique was the only independent predictor of reoperation (hazard ratio 0.31; confidence interval 0.19–0.7; P = 0.005).

CONCLUSIONS
In this study, comparing 2 annuloplasty strategies for BAV repair, we found statistically significant differences in long-term durability favouring the Reimplantation technique, and no differences in overall survival. The results support our current strategy of Reimplantation technique and repair of AR in patients with BAV. Cabrol annuloplasty is obsolete and should be generally abandoned in patients undergoing BAV repair for AR.