bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping intrinsic electromechanical responses at the nanoscale via sequential excitation scanning probe microscopy empowered by deep data
Authors: Huang Boyuan , Esfahani Ehsan Nasr , Li Jiangyu 
Published: September 2018

Abstract
Ever-increasing hardware capabilities and computation powers have enabled acquisition and analysis of big scientific data at the nanoscale routine, though much of the data acquired often turn out to be redundant, noisy and/or irrelevant to the problems of interest, and it remains nontrivial to draw clear mechanistic insights from pure data analytics. In this work, we use scanning probe microscopy (SPM) as an example to demonstrate deep data methodology for nanosciences, transitioning from brute-force analytics such as data mining, correlation analysis and unsupervised classification to informed and/or targeted causative data analytics built on sound physical understanding. Three key ingredients of such deep data analytics are presented. A sequential excitation scanning probe microscopy (SE-SPM) technique is first developed to acquire high-quality, efficient and physically relevant data, which can be easily implemented on any standard atomic force microscope (AFM). Brute-force physical analysis is then carried out using a simple harmonic oscillator (SHO) model, enabling us to derive intrinsic electromechanical coupling of interest. Finally, principal component analysis (PCA) is carried out, which not only speeds up the analysis by four orders of magnitude, but also allows a clear physical interpretation of its modes in combination with SHO analysis. A rough piezoelectric material has been probed using such a strategy, enabling us to map its intrinsic electromechanical properties at the nanoscale with high fidelity, where conventional methods fail. The SE in combination with deep data methodology can be easily adapted for other SPM techniques to probe a wide range of functional phenomena at the nanoscale.
Repulsion of fallback matter due to central energy source in supernova
Authors: Shigeyama Toshikazu , Kashiyama Kazumi 
Published: September 2018

Abstract
The flow of fallback matter being shocked and repelled back by an energy deposition from a central object is discussed using newly found self-similar solutions. We show that there exists a maximum mass-accretion rate if the adiabatic index of the flow is less than or equal to 4/3. Otherwise, we can find a solution with an arbitrarily large accretion rate by appropriately shrinking the energy deposition region. Applying the self-similar solution to supernova fallback, we discuss how the fate of newborn pulsars or magnetars depends on the fallback accretion and their spin-down power. Combining the maximum accretion rate with the condition for the fallback accretion to bury the surface magnetic field into the crust, we argue that supernova fallback with a rate of $\dot{M}_{\rm fb} \sim 10^{-(4\mbox{-}6)}\, M_{\odot }\:$s−1 could be the main origin of the diversity of Galactic young neutron stars, i.e., rotation-powered pulsars, magnetars, and central compact objects.
Recent updates on cancer immunotherapy
Authors: Liu Ming , Guo Fukun 
Published: September 2018

Abstract
Traditional cancer therapies include surgery, radiation, and chemotherapy, all of which are typically non-specific approaches. Cancer immunotherapy is a type of cancer treatment that helps the immune system fight cancer. Cancer immunotherapy represents a standing example of precision medicine: immune checkpoint inhibitors precisely target the checkpoints; tumor infiltrating lymphocytes, TCR T cells, and CAR T cells precisely kill cancer cells through tumor antigen recognition; and cancer vaccines are made from patient-derived dendritic cells, tumor cell DNA, or RNA, or oncolytic viruses, thus offering a type of personalized medicine. This review will highlight up-to-date advancement in most, if not all, of the immunotherapy strategies.
Intraperitoneal Local Anesthetic Instillation and Postoperative Infusion Improves Functional Recovery Following Colectomy: A Randomized Controlled Trial
Authors: Duffield Jaime A. , Thomas Michelle L. , Moore James W. , Hunter R. Andrew , Wood Carolyn , Gentili Sheridan , Lewis Mark 
Published: September 2018

BACKGROUND:
Intraperitoneal local anesthetic is an analgesic technique for inclusion in the polypharmacy approach to postoperative pain management in enhanced recovery after surgery programs. Previously, augmentation of epidural analgesia with intraperitoneal local anesthetic was shown to improve functional postoperative recovery following colectomy.

OBJECTIVE:
This study determines whether intraperitoneal local anesthetic improves postoperative recovery in patients undergoing colectomy, in the absence of epidural analgesia, with standardized enhanced recovery after surgery perioperative care.

DESIGN:
This is a multisite, double-blinded, randomized, placebo-controlled trial (ClinicalTrials.gov Identifier NCT02449720).

SETTINGS:
This study was conducted at 3 hospital sites in South Australia.

PATIENTS:
Eighty-six adults undergoing colectomy were stratified by approach (35 open; 51 laparoscopic), then randomly assigned to intraperitoneal local anesthetic (n = 44) and control (n = 42) groups.

INTERVENTIONS:
Patients in the intraperitoneal local anesthetic group received an intraoperative intraperitoneal ropivacaine 100-mg bolus both pre- and postdissection and 20 mg/h continuous postoperative infusion for 48 hours. Patients in the control group received a normal saline equivalent.

MAIN OUTCOME MEASURES:
Functional postoperative recovery was assessed by using the surgical recovery scale for 45 days; postoperative pain was assessed by using a visual analog scale; and opioid consumption, use of rescue ketamine, recovery of bowel function, time to readiness for discharge, and perioperative complications were recorded.

RESULTS:
The intraperitoneal local anesthetic group reported improved surgical recovery scale scores at day 1 and 7, lower pain scores, required less rescue ketamine, and passed flatus earlier than the control group (p < 0.05). The improvement in surgical recovery scale at day 7 and pain scores remained when laparoscopic colectomy was considered separately. Opioid consumption and time to readiness for discharge were equivalent.

LIMITATIONS:
This study was powered to detect a difference in surgical recovery scale, but not the other domains of recovery, when the intraperitoneal local anesthetic group was compared with control.

CONCLUSIONS:
We conclude that instillation and infusion of intraperitoneal ropivacaine for patients undergoing colectomy, including by the laparoscopic approach, decreases postoperative pain and improves functional postoperative recovery. We recommend routine inclusion of intraperitoneal local anesthetic into the multimodal analgesia component of enhanced recovery after surgery programs for laparoscopic colectomy. See Video Abstract at http://links.lww.com/DCR/A698.
Oculocardiac Reflex as a Late Presentation of Orbital Floor Fracture
Authors: Başağaoğlu Berkay , Steinberg Ashley , Tung Irene T. , Olorunnipa Shola , Maricevich Renata S. 
Published: September 2018

Abstract
Delayed repair of orbital trapdoor fractures can jeopardize the viability of entrapped contents and prolong recovery. Variation in presentations, both clinically and radiographically, complicate prompt diagnosis. The oculocardiac reflex may be the only indication of fracture with entrapped orbital contents, but, unfortunately, the reflex has variable onset patterns and can mimic common diagnoses. Therefore, the authors present the case of a 14-year-old male with a right orbital floor fracture, who presented with delayed symptoms secondary to an oculocardiac reflex. The vagal sequelae of the reflex, including gastric hyperactivity and headache, were experienced approximately 1 week after the injury and caused the patient to be misdiagnosed with gastroenteritis and status migrainosus, on 2 separate hospital visits. After admission to the hospital due to progressive symptoms, a CT scan showed concerns for a subacute orbital blowout fracture. The patient underwent orbital floor exploration with findings of scarred orbital fat herniating into a healing fracture site. Repositioning of the fat into the orbit resulted in immediate resolution of the patient's symptoms. Awareness of the presenting characteristics of the oculocardiac reflex can lead to prompt diagnosis and maximize clinical outcomes.
miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRBase
Authors: Xu Taosheng , Su Ning , Liu Lin , Zhang Junpeng , Wang Hongqiang , Zhang Weijia , Gui Jie , Yu Kui , Li Jiuyong , Le Thuc Duy 
Published: September 2018

AbstractBackgroundmiRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses.ResultsWe introducemiRBaseConverter,an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/miRBaseConverter/). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application athttp://nugget.unisa.edu.au:3838/miRBaseConverter.miRBaseConverterhas a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources.ConclusionsThe Bioconductor packagemiRBaseConverterand the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.
Deep Learning Based Retrieval System for Gigapixel Histopathology Cases and Open Access Literature
Authors: Otálora Sebastian , Schaer Roger , Jimenez-del-Toro Oscar , Atzori Manfredo , Müller Henning 
Published: September 2018

ABSTRACTClinical practice is getting increasingly stressful for pathologists due to increasing complexity and time constraints. Histopathology is slowly shifting to digital pathology, thus creating opportunities to allow pathologists to improve reading quality or save time using Artificial Intelligence (AI)-based applications. We aim to enhance the practice of pathologists through a retrieval system that allows them to simplify their workflow, limit the need for second opinions, while also learning in the process. In this work, an innovative retrieval system for digital pathology is integrated within a Whole Slide Image (WSI) viewer, allowing to define regions of interest in images as queries for finding visually similar areas using deep representations. The back-end similarity computation algorithms are based on a multimodal approach, allowing to exploit both text information and content-based image features. Shallow and deep representations of the images were evaluated, the later showed a better overall retrieval performance in a set of 112 whole slide images from biopsies. The system was also tested by pathologists, highlighting its capabilities and suggesting possible ways to improve it and make it more usable in clinical practice. The retrieval system developed can enhance the practice of pathologists by enabling them to use their experience and knowledge to properly control artificial intelligence tools for navigating repositories of images for decision support purposes.
Taxonomic revision of Leopold and Rudolf Blaschka Glass Models of Invertebrates 1888 Catalogue, with correction of authorities
Authors: Callaghan Eric , Egger Bernhard , Doyle Hazel , Reynaud Emmanuel G. 
Published: September 2018

AbstractThe glass models of invertebrates crafted by Leopold and Rudolf Blaschka were made between 1863 and 1889. Production ceased when the glassmakers turned their attention to what is now known as the Ware Collection of Blaschka Glass Models of Plants, created for the Harvard Museum of Natural History. Nearly 130 years have passed since their last published catalogue of species in 1888 and the nomenclature they applied is now a confusing mix that includes many junior synonyms and unavailable names. This is an issue for many museums and universities which owns Blaschka models as uncertain identifications may compromised interpretation of this rediscovered legacy. Nowadays, many museums and universities hold collections of those glass invertebrates but misspelled, mislabelled or simply apply the century old taxonomy of 1888. Here, we provide a valuable resource for curators and enthusiasts alike. We studied and updated the final catalogue 1888 from the Blaschkas’ Dresden-based workshop. We first focused on major taxonomical changes from taxa to species, as well as on an analysis of the acknowledged authorities. We found that only 35.3% of the models retain their original names, while 3.7% lack any known synonym and their identity remains open to interpretation. Finally, two of the authorities listed in the catalogue, Ernst Haeckel and Philip Henry Gosse, were incorrectly acknowledged for an extensive range of models. This study is the first of its kind on the Blaschka collection, and it will help in the identification and naming of Blaschka models worldwide.
Radiomics Analysis Using Stability Selection Supervised Principal Component Analysis for Right-censored Survival Data
Authors: Yan Kang K. , Wang Xiaofei , Lam Wendy , Vardhanabhuti Varut , Lee Anne W.M. , Pang Herbert 
Published: September 2018

AbstractRadiomics is a newly emerging field that involves the extraction of a large number of quantitative features from biomedical images through the use of data-characterization algorithms. Radiomics provides a noninvasive approach for personalized therapy decision by identifying distinctive imaging features for predicting prognosis and therapeutic response. So far, many of the published radiomics studies utilize existing out of the box algorithms to identify the prognostic markers from biomedical images that are not specific to radiomics data. T o better utilize biomedical image, we propose a novel machine learning approach, stability selection supervised principal component analysis (SSSuperPCA) that identify a set of stable features from radiomics big data coupled with dimension reduction for right censored survival outcomes. In this paper, we describe stability selection supervised principal component analysis for radiomics data with right-censored survival outcomes. The proposed approach allows us to identify a set of stable features that are highly associated with the survival outcomes, control the per-family error rate, and predict the survival in a simple yet meaningful manner. We evaluate the performance of SSSuperPCA using simulations and real data sets for non-small cell lung cancer and head and neck cancer, and compare it with other machine learning algorithms. The results demonstrate that our method has a competitive edge over other existing methods in identifying the prognostic markers from biomedical big imaging data for the prediction of right-censored survival outcomes. An R package SSSuperPCA is available at the website:http://web.hku.hk/∼herbpang/SSSuperPCA.html
Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?
Authors: Tiger Li Zheng-Rong , Zarnitsyna Veronika I. , Lowen Anice C. , Weissman Daniel , Koelle Katia , Kohlmeier Jacob E. , Antia Rustom 
Published: September 2018

AbstractThe high-degree conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow T cell-inducing vaccines effective across different strains and subtypes. This conservation is not fully explained by functional constraint, since additional mutation(s) can compensate the replicative fitness loss of IAV escape-variant. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may only have a modest effect on transmission. Second, polymorphism of human MHC-I gene restricts the advantage of an escape-variant to only a small fraction of human population, who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell-escapevariants may result in compensatory increase in the responses to other epitopes of IAV. A combination of population genetics and epidemiological models is used to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape-variants. We conclude that the invasion of an escape-variant will be very slow with a timescale of decades or longer, even if the escape-variant does not have a replicative fitness loss. Our results suggest T cell-inducing vaccines may not engender the rapid evolution of IAV and serve as a foundation for future modeling works on the long-term effectiveness and impacts of T cell-inducing influenza vaccines. (Word count: 221)ImportanceUniversal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear to which extent the T cell-inducing vaccines will select for viruses that escape the T cell responses. Our mathematical models suggest how the nature of CD8 T cell protection contributes to the conservation of the CD8 T cell epitopes of influenza A virus. Also, it points out the essential biological parameters and questions that need addressing by future experimental works. (Word count: 91)
FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression
Authors: Plewka Patrycja , Szczesniak Michal Wojciech , Stepien Agata , Zywicki Marek , Pacak Andrzej , Colombo Martino , Makalowska Izabela , Ruepp Marc-David , Raczynska Katarzyna Dorota 
Published: September 2018

ABSTRACTFUS is a multifunctional protein involved in many steps of RNA metabolism, including transcription, splicing, miRNA processing and replication-dependent histone gene expression. In this paper, we show for the first time that FUS binds and negatively regulates the levels of a subset of snoRNAs in cells. Scanning of available human small RNA databases revealed the existence of smaller RNA fragments that can be processed from FUS-dependent snoRNAs. Therefore, we suggest that FUS mediates the biogenesis of snoRNA-derived small RNAs, called sdRNAs. Furtherin silicoapproaches enabled us to predict putative targets of selected FUS-dependent sdRNAs. Our results indicate that sdRNAs may bind to different regions of target mRNAs as well as to noncoding transcripts and influence the posttranscriptional level or translation of these targets.SIGNIFICANCE STATEMENTRNA metabolism is orchestrated by a complex network of RNA-protein interactions and involves various classes of RNA molecules. Small nucleolar RNAs (snoRNAs) are commonly considered essential components of the ribosome biogenesis pathway. However, recent studies have revealed that snoRNAs can also be fragmented into small entities called snoRNA-derived RNAs (sdRNAs), which have been linked to multiple cancer types and thus may serve as next-generation prognostic or diagnostic biomarkers. In this paper, a multifunctional protein, FUS, was shown to be involved in the biogenesis of snoRNA-derived fragments. Furthermore, we combined bioinformatic analyses with complementary experimental approaches to elucidate the role of FUS-dependent sdRNAs in gene expression regulation. Our findings reveal the considerable regulatory potential of this new class of small noncoding RNAs.
Mutation of influenza A virus PA-X decreases pathogenicity in chicken embryos and can increase the yield of reassortant candidate vaccine viruses
Authors: Hussain Saira , Turnbull Matthew L. , Wise Helen M. , Jagger Brett W. , Beard Philippa M. , Kovacikova Kristina , Taubenberger Jeffery K. , Vervelde Lonneke , Engelhardt Othmar G , Digard Paul 
Published: September 2018

AbstractThe PA-X protein of influenza A virus has roles in host cell shut-off and viral pathogenesis. While most strains are predicted to encode PA-X, strain-dependent variations in activity have been noted. We found that PA-X protein from A/PR/8/34 (PR8) strain had significantly lower repressive activity against cellular gene expression compared with PA-Xs from the avian strains A/turkey/England/50-92/91 (H5N1) (T/E) and A/chicken/Rostock/34 (H7N1). Loss of normal PA-X expression, either by mutation of the frameshift site or by truncating the X-ORF, had little effect on the infectious virus titre of PR8 or PR8 7:1 reassortants with T/E segment 3 grown in embryonated hens’ eggs. However, in both virus backgrounds, mutation of PA-X led to decreased embryo mortality and lower overall pathology; effects that were more pronounced in the PR8 strain than the T/E reassortant, despite the low shut-off activity of the PR8 PA-X. Purified PA-X mutant virus particles displayed an increased ratio of HA to NP and M1 compared to their WT counterparts, suggesting altered virion composition. When the PA-X gene was mutated in the background of poorly growing PR8 6:2 vaccine reassortant analogues containing the HA and NA segments from H1N1 2009 pandemic viruses or an avian H7N3 strain, HA yield increased up to 2-fold. This suggests that the PR8 PA-X protein may harbour a function unrelated to host cell shut-off and that disruption of the PA-X gene has the potential to improve the HA yield of vaccine viruses.IMPORTANCEInfluenza A virus is a widespread pathogen that affects both man and a variety of animal species, causing regular epidemics and sporadic pandemics with major public health and economic consequences. A better understanding of virus biology is therefore important. The primary control measure is vaccination, which for humans, mostly relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of interest. However, not all reassortants replicate well enough to supply sufficient virus antigen for demand. The significance of our research lies in identifying that mutation of the PA-X gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the pathogenicity of the virus in embryonated eggs.