bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging Cherenkov emission for quality assurance of high-dose-rate brachytherapy
Authors: Yogo Katsunori , Matsushita Akihiro , Tatsuno Yuya , Shimo Takahiro , Hirota Seiko , Nozawa Marika , Ozawa Shuichi , Ishiyama Hiromichi , Yasuda Hiroshi , Nagata Yasushi , Hayakawa Kazushige 
Published: February 2020

AbstractWith advances in high-dose-rate (HDR) brachytherapy, the importance of quality assurance (QA) is increasing to ensure safe delivery of the treatment by measuring dose distribution and positioning the source with much closer intervals for highly active sources. However, conventional QA is time-consuming, involving the use of several different measurement tools. Here, we developed simple QA method for HDR brachytherapy based on the imaging of Cherenkov emission and evaluated its performance. Light emission from pure water irradiated by an 192Ir γ-ray source was captured using a charge-coupled device camera. Monte Carlo calculations showed that the observed light was primarily Cherenkov emissions produced by Compton-scattered electrons from the γ-rays. The uncorrected Cherenkov light distribution, which was 5% on average except near the source (within 7 mm from the centre), agreed with the dose distribution calculated using the treatment planning system. The accuracy was attributed to isotropic radiation and short-range Compton electrons. The source positional interval, as measured from the light images, was comparable to the expected intervals, yielding spatial resolution similar to that permitted by conventional film measurements. The method should be highly suitable for quick and easy QA investigations of HDR brachytherapy as it allows simultaneous measurements of dose distribution, source strength, and source position using a single image.
Plantaricin NC8 αβ exerts potent antimicrobial activity against Staphylococcus spp. and enhances the effects of antibiotics
Authors: Bengtsson Torbjörn , Selegård Robert , Musa Amani , Hultenby Kjell , Utterström Johanna , Sivlér Petter , Skog Mårten , Nayeri Fariba , Hellmark Bengt , Söderquist Bo , Aili Daniel , Khalaf Hazem 
Published: February 2020

AbstractThe use of conventional antibiotics has substantial clinical efficacy, however these vital antimicrobial agents are becoming less effective due to the dramatic increase in antibiotic-resistant bacteria. Novel approaches to combat bacterial infections are urgently needed and bacteriocins represent a promising alternative. In this study, the activities of the two-peptide bacteriocin PLNC8 αβ were investigated against different Staphylococcus spp. The peptide sequences of PLNC8 α and β were modified, either through truncation or replacement of all L-amino acids with D-amino acids. Both L- and D-PLNC8 αβ caused rapid disruption of lipid membrane integrity and were effective against both susceptible and antibiotic resistant strains. The D-enantiomer was stable against proteolytic degradation by trypsin compared to the L-enantiomer. Of the truncated peptides, α1–22, β7–34 and β1–20 retained an inhibitory activity. The peptides diffused rapidly (2 min) through the bacterial cell wall and permeabilized the cell membrane, causing swelling with a disorganized peptidoglycan layer. Interestingly, sub-MIC concentrations of PLNC8 αβ substantially enhanced the effects of different antibiotics in an additive or synergistic manner. This study shows that PLNC8 αβ is active against Staphylococcus spp. and may be developed as adjuvant in combination therapy to potentiate the effects of antibiotics and reduce their overall use.
Disrupted principal network organisation in multiple sclerosis relates to disability
Authors: Charalambous Thalis , Clayden Jonathan D. , Powell Elizabeth , Prados Ferran , Tur Carmen , Kanber Baris , Chard Declan , Ourselin Sebastien , Wheeler-Kingshott Claudia A. M. Gandini , Thompson Alan J. , Toosy Ahmed T. 
Published: February 2020

AbstractStructural network-based approaches can assess white matter connections revealing topological alterations in multiple sclerosis (MS). However, principal network (PN) organisation and its clinical relevance in MS has not been explored yet. Here, structural networks were reconstructed from diffusion data in 58 relapsing-remitting MS (RRMS), 28 primary progressive MS (PPMS), 36 secondary progressive (SPMS) and 51 healthy controls (HCs). Network hubs’ strengths were compared with HCs. Then, PN analysis was performed in each clinical subtype. Regression analysis was applied to investigate the associations between nodal strength derived from the first and second PNs (PN1 and PN2) in MS, with clinical disability. Compared with HCs, MS patients had preserved hub number, but some hubs exhibited reduced strength. PN1 comprised 10 hubs in HCs, RRMS and PPMS but did not include the right thalamus in SPMS. PN2 comprised 10 hub regions with intra-hemispheric connections in HCs. In MS, this subnetwork did not include the right putamen whilst in SPMS the right thalamus was also not included. Decreased nodal strength of the right thalamus and putamen from the PNs correlated strongly with higher clinical disability. These PN analyses suggest distinct patterns of disruptions in MS subtypes which are clinically relevant
Different dynamical behaviors induced by slow excitatory feedback for type II and III excitabilities
Authors: Zhao Zhiguo , Li Li , Gu Huaguang 
Published: February 2020

AbstractNeuronal excitability is classified as type I, II, or III, according to the responses of electronic activities, which play different roles. In the present paper, the effect of an excitatory autapse on type III excitability is investigated and compared to type II excitability in the Morris-Lecar model, based on Hopf bifurcation and characteristics of the nullcline. The autaptic current of a fast-decay autapse produces periodic stimulations, and that of a slow-decay autapse highly resembles sustained stimulations. Thus, both fast- and slow-decay autapses can induce a resting state for type II excitability that changes to repetitive firing. However, for type III excitability, a fast-decay autapse can induce a resting state to change to repetitive firing, while a slow-decay autapse can induce a resting state to change to a resting state following a transient spike instead of repetitive spiking, which shows the abnormal phenomenon that a stronger excitatory effect of a slow-decay autapse just induces weaker responses. Our results uncover a novel paradoxical phenomenon of the excitatory effect, and we present potential functions of fast- and slow-decay autapses that are helpful for the alteration and maintenance of type III excitability in the real nervous system related to neuropathic pain or sound localization.
Epithelial-mesenchymal transition gene signature is associated with prognosis and tumor microenvironment in head and neck squamous cell carcinoma
Authors: Jung Ah Ra , Jung Chan-Hun , Noh Joo Kyung , Lee Young Chan , Eun Young-Gyu 
Published: February 2020

AbstractIn this study we assessed the clinical significance of an epithelial-mesenchymal transition (EMT) gene signature and explored its association with the tumor microenvironment related to immunotherapy in patients with head and neck squamous cell carcinoma (HNSCC). Genes were selected when mRNA levels were positively or negatively correlated with at least one well-known EMT marker. We developed an EMT gene signature consisting of 82 genes. The patients were classified into epithelial or mesenchymal subgroups according to EMT signature. The clinical significance of the EMT signature was validated in three independent cohorts and its association with several immunotherapy-related signatures was investigated. The mesenchymal subgroup showed worse prognosis than the epithelial subgroup, and significantly elevated PD-1, PD-L1, and CTLA-4 levels, and increased interferon-gamma, cytolytic, T cell infiltration, overall immune infiltration, and immune signature scores. The relationship between PD-L1 expression and EMT status in HNSCC after treatment with TGF-β was validated in vitro. In conclusion, the EMT gene signature was associated with prognosis in HNSCC. Additionally, our results suggest that EMT is related to immune activity of the tumor microenvironment with elevated immune checkpoint molecules.
Health-Related Quality of Life – an Underestimated Factor to Evaluate the Treatment Success after Open Wedge HTO Surgery: Prospective 6-Years Follow-Up
Authors: Herbst Moritz , Kuwashima Umito , Ahrend Marc-Daniel , Gueorguiev Boyko Guergov , Schröter Steffen , Ihle Christoph 
Published: February 2020

Abstract
Background The subjective health related quality of life in patients with degenerative joint diseases is an important variable to evaluate the treatment outcome. In this study, mid-term results of open wedge HTO were analysed and compared to the subjective quality of life (SF 36) of the general population. Furthermore, the relationships of preoperative assessed subscales of the health-related quality of life (SF 36) and the conversion to knee arthroplasty were analysed.
Methods The cohort consisted of 120 patients who were prospectively followed-up after open wedge HTO. At five follow-up points of time, patients were examined and asked about their subjective, health-related quality of life using the SF 36 score.
Results 104 patients were included and evaluated until the last follow-up (mean: 81.2 ± 11.3 months after open wedge HTO; follow-up rate: 86.7%). Six years after open wedge HTO, similar values in several psychologic subscales of the SF 36 (BP, GH, V, MH) and the mental health component summary score (MCS) compared to the general population were found. The physical health component summary score (PCS) showed a significant improvement relative to the preoperative values. Nine out of 104 patients (8.7%) received a knee arthroplasty (50.1 ± 25.0 months). Low preoperative values of the subscales “physical functioning” (PF) and “bodily pain” (BP) were identified as risk factors in terms of conversion to a total knee arthroplasty.
Conclusions Patients with medial unicompartimental knee osteoarthrosis treated with open wedge HTO showed very good results. The health-related quality of life was nearly as high as in the general population. Patients with preoperative low physical function and high pain values have a higher risk to have a conversion to knee arthroplasty. Surgeons should be aware of these factors if an open wedge HTO is considered.
A Three Point Assessment Protocol for Tympanoplasty Outcomes: A Retrospective Analysis
Authors: Naina P. , Pokharel Apar , Syed Kamran Asif , John Mary , Varghese Ajoy Mathew , Kurien Mary 
Published: February 2020

Abstract
Introduction The surgical outcome of chronic otitis media (COM) of the mucosal type in the pediatric population with high rates of recurrent tympanic membrane perforation is indeed a concern for the attending surgeon.
Objective The present study was done to evaluate the outcome of tympanoplasty in children with chronic otitis media mucosal type.
Methods A retrospective analysis of the medical records of all children, aged < 16 years old, who underwent tympanoplasty for COM of the mucosal type was performed. These patients were addressed by a three-point assessment, for predicting outcome of tympanoplasty, which included the age of the patient, addressing the nasal/pharyngeal issues, and the status of the COM (discharging or dry). Surgical success was assessed in terms of graft uptake and improvement of hearing. Factors affecting the surgical outcome were also analyzed.
Results A total of 90 children underwent type 1 tympanoplasty; 7 were lost to follow-up and 10 had incomplete audiometric results. In the 73 tympanoplasties analyzed, graft uptake was seen in 91.7% of the patients. Children with longer duration of ear discharge (> 8 years) had greater hearing loss. Children aged > 8 years old showed statistically significant higher chance of graft uptake (p = 0.021). Five of the six children who had graft rejection had bilateral disease.
Conclusion A three-point assessment in the management of pediatric COM of the mucosal type offers good outcomes with post-tympanoplasty graft uptake rates > 90%.
Electronic and optical properties of zinc based hybrid organic-inorganic compounds
Authors: Sahoo Trilochan , Anene Uchenna A , Nayak Sanjeev K , Alpay S Pamir 
Published: February 2020

Abstract
There is significant interest in hybrid organic-inorganic (HOI) compounds since these materials offer multiple functionalities and properties that can be tailored at the mesoscopic and nanoscale levels. HOIs investigated for photovoltaic applications typically contain lead or mercury. There is considerably less work done on Zn-based HOIs. These could potentially be considered in biomedical applications due to presence of organic components and the biocompatibility of Zn cations. Using a systematic materials selection approach, we have carried out a detailed search of Zn-HOI compounds in two comprehensive experimental crystallographic repositories: Inorganic Crystal Structure Database and American Mineralogist Crystal Structure Database. Thirteen Zn-HOI compounds are discovered: CuZnO2(CO3), Zn(C2O4), ((CH3)2NH2)Zn3(PO4)(HPO4)2, (CH3NH3)Zn4(PO4)3, Zn(N(CH2PO3H)3)(H2O)3, (CH3NH3)Zn(HCO2)3, Zn4(CO3)2, Zn8(HPO4)16(C2H8N)8, Zn5(CO3)2, (Mg2Zn)8(CO3)2(OH), Zn7(CO3)2(OH)10, Ca3Zn2(PO4)CO3(OH).2H2O, and Zn(CO3). We have then performed first principles calculations via density functional theory with hybrid functional treatment to determine the electronic band gap and optical response of these materials. Our computations show that eleven of the thirteen compounds have insulating properties with band gaps ranging from 2.8 eV to 6.9 eV. Ten of these are found to have a high absorbance in the far ultra-violet (FUV) region of 200–112 nm wavelength. For example, the absorption coefficient of (CH3NH3)Zn(HCO2)3 is ∼0.75 × 105 cm−1 for F2 excimer laser energy (wavelength ∼157 nm) which is more than three orders higher than the average tissue absorbance (∼101.5 cm−1) and the refractive index of 1.85 is larger than typical biological matter which is in the range 1.36–1.49. These results suggest that Zn-HOIs could potentially find applications in photothermolysis and UV protection.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
Authors: Schwarz Michael , Welzel Marius , Kabdullayeva Tolganay , Becker Anke , Freisleben Bernd , Heider Dominik 
Published: February 2020

Abstract

Summary
The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes.

Availability and implementation
MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim.

Contact
dominik.heider@uni-marburg.de

Supplementary information
Supplementary data are available at Bioinformatics online.
Supervised learning is an accurate method for network-based gene classification
Authors: Liu Renming , Mancuso Christopher A , Yannakopoulos Anna , Johnson Kayla A , Krishnan Arjun 
Published: February 2020

Abstract

Background
Assigning every human gene to specific functions, diseases and traits is a grand challenge in modern genetics. Key to addressing this challenge are computational methods, such as supervised learning and label propagation, that can leverage molecular interaction networks to predict gene attributes. In spite of being a popular machine-learning technique across fields, supervised learning has been applied only in a few network-based studies for predicting pathway-, phenotype- or disease-associated genes. It is unknown how supervised learning broadly performs across different networks and diverse gene classification tasks, and how it compares to label propagation, the widely benchmarked canonical approach for this problem.

Results
In this study, we present a comprehensive benchmarking of supervised learning for network-based gene classification, evaluating this approach and a classic label propagation technique on hundreds of diverse prediction tasks and multiple networks using stringent evaluation schemes. We demonstrate that supervised learning on a gene’s full network connectivity outperforms label propagaton and achieves high prediction accuracy by efficiently capturing local network properties, rivaling label propagation’s appeal for naturally using network topology. We further show that supervised learning on the full network is also superior to learning on node embeddings (derived using node2vec), an increasingly popular approach for concisely representing network connectivity. These results show that supervised learning is an accurate approach for prioritizing genes associated with diverse functions, diseases and traits and should be considered a staple of network-based gene classification workflows.

Availability and implementation
The datasets and the code used to reproduce the results and add new gene classification methods have been made freely available.

Contact
arjun@msu.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
Fast and robust ancestry prediction using principal component analysis
Authors: Zhang Daiwei , Dey Rounak , Lee Seunggeun 
Published: February 2020

Abstract

Motivation
Population stratification (PS) is a major confounder in genome-wide association studies (GWAS) and can lead to false-positive associations. To adjust for PS, principal component analysis (PCA)-based ancestry prediction has been widely used. Simple projection (SP) based on principal component loadings and the recently developed data augmentation, decomposition and Procrustes (ADP) transformation, such as LASER and TRACE, are popular methods for predicting PC scores. However, the predicted PC scores from SP can be biased toward NULL. On the other hand, ADP has a high computation cost because it requires running PCA separately for each study sample on the augmented dataset.

Results
We develop and propose two alternative approaches: bias-adjusted projection (AP) and online ADP (OADP). Using random matrix theory, AP asymptotically estimates and adjusts for the bias of SP. OADP uses a computationally efficient online singular value decomposition algorithm, which can greatly reduce the computation cost of ADP. We carried out extensive simulation studies to show that these alternative approaches are unbiased and the computation speed can be 16–16 000 times faster than ADP. We applied our approaches to the UK Biobank data of 488 366 study samples with 2492 samples from the 1000 Genomes data as the reference. AP and OADP required 0.82 and 21 CPU hours, respectively, while the projected computation time of ADP was 1628 CPU hours. Furthermore, when inferring sub-European ancestry, SP clearly showed bias, unlike the proposed approaches.

Availability and implementation
The OADP and AP methods, as well as SP and ADP, have been implemented in the open-source Python software FRAPOSA, available at github.com/daviddaiweizhang/fraposa.

Contact
leeshawn@umich.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
In Their Own Words: Joel Cracraft
Authors: Verdier James M 
Published: February 2020

Abstract
In Their Own Words chronicles the stories of scientists who have made great contributions to their fields, particularly within the biological sciences. These short oral histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and in our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This oral history is with Joel Cracraft, curator in the Department of Ornithology at the American Museum of Natural History. He previously served as president of the American Institute of Biological Sciences. Note: Both the text and audio versions have been edited for clarity and length.
The fallacy of indexed effective orifice area charts to predict prosthesis–patient mismatch after prosthesis implantation
Authors: Vriesendorp Michiel D , De Lind Van Wijngaarden Rob A F , Head Stuart J , Kappetein Arie-Pieter , Hickey Graeme L , Rao Vivek , Weissman Neil J , Reardon Michael J , Moront Michael G , Sabik Joseph F , Klautz Robert J M 
Published: February 2020

Abstract

Aims
Indexed effective orifice area (EOAi) charts are used to determine the likelihood of prosthesis–patient mismatch (PPM) after aortic valve replacement (AVR). The aim of this study is to validate whether these EOAi charts, based on echocardiographic normal reference values, can accurately predict PPM.

Methods and results
In the PERIcardial SurGical AOrtic Valve ReplacemeNt (PERIGON) Pivotal Trial, 986 patients with aortic valve stenosis/regurgitation underwent AVR with an Avalus valve. Patients were randomly split (50:50) into training and test sets. The mean measured EOAs for each valve size from the training set were used to create an Avalus EOAi chart. This chart was subsequently used to predict PPM in the test set and measures of diagnostic accuracy (sensitivity, specificity, and negative and positive predictive value) were assessed. PPM was defined by an EOAi ≤0.85 cm2/m2, and severe PPM was defined as EOAi ≤0.65 cm2/m2. The reference values obtained from the training set ranged from 1.27 cm2 for size 19 mm up to 1.81 cm2 for size 27 mm. The test set had an incidence of 66% of PPM and 24% of severe PPM. The EOAi chart inaccurately predicted PPM in 30% of patients and severe PPM in 22% of patients. For the prediction of PPM, the sensitivity was 87% and the specificity 37%. For the prediction of severe PPM, the sensitivity was 13% and the specificity 98%.

Conclusion
The use of echocardiographic normal reference values for EOAi charts to predict PPM is unreliable due to the large proportion of misclassifications.
Hepatitis C Virus Treatment as Prevention: Challenges and Opportunities in Men Who Have Sex With Men
Authors: Rockstroh Jürgen Kurt , Boesecke Christoph 
Published: February 2020

Abstract
Since 2002, a global epidemic of acute hepatitis C virus (HCV) infection has been noted in men who have sex with men (MSM). Transmission of HCV, particularly in the context of traumatic sex practices that increase the risk of blood-blood contacts (eg, anal sex and fisting), was initially found in human immunodeficiency virus (HIV)–coinfected and more recently in HIV-uninfected MSM, especially those receiving pre-exposure prophylaxis (PrEP). Early HCV treatment with all-oral direct-acting antiviral combination therapy has been associated with very high HCV cure rates of up to 100%. Indeed, immediate treatment of recently acquired HCV directly after new HCV diagnosis, or after 4 weeks if no 2-log10 drop in HCV RNA level occurs, promises rapid HCV elimination. Reports from the Netherlands, Switzerland, and the United Kingdom all show that with increased treatment uptake in this particular patient group, dramatic reductions in new HCV infections can be achieved. A general consensus on how to best screen for and manage acute HCV infections, along with broad access to rapid HCV therapy initiation, is crucial to attaining HCV elimination, a goal that is challenged by high HCV reinfection rates among MSM.