bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer
Authors: Li Na , McInerny Simone , Zethoven Magnus , Cheasley Dane , Lim Belle W X , Rowley Simone M , Devereux Lisa , Grewal Norah , Ahmadloo Somayeh , Byrne David , Lee Jue Er Amanda , Li Jason , Fox Stephen B , John Thomas , Antill Yoland , Gorringe Kylie L , James Paul A , Campbell Ian G 
Published: April 2019

Abstract

Background
Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer.

Methods
RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation.

Results
A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P&lt; .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P &lt;. 001) or triple-negative cancer (P &lt; .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency.

Conclusions
This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
Intensity-modulated radiotherapy for cervical esophageal squamous cell carcinoma without hypopharyngeal invasion: dose distribution and clinical outcome
Authors: Ishida Yuichi , Sakanaka Katsuyuki , Fujii Kota , Itasaka Satoshi , Mizowaki Takashi 
Published: April 2019

AbstractHypopharyngeal invasion would be a key finding in determining the extent of the irradiation fields in patients with cervical esophageal squamous cell carcinoma (CESCC). This study aimed to investigate the clinical outcomes of chemoradiotherapy using simultaneous integrated boost intensity-modulated radiotherapy (SIB-IMRT) omitting upper cervical lymph nodal irradiation in CESCC without hypopharyngeal invasion, and the dosimetric superiority of SIB-IMRT to 3D conformal radiotherapy (3DCRT). We retrospectively identified 21 CESCC patients without hypopharyngeal invasion [clinical Stage I/II/III/IV (M1LYM); 3/6/5/7] (UICC-TNM 7th edition) who underwent chemoradiotherapy using SIB-IMRT between 2009 and 2015. SIB-IMRT delivered 60 Gy to each primary tumor and the metastatic lymph nodes, and 48 Gy to elective lymph nodal regions, including Levels III and IV of the neck, supraclavicular, and upper mediastinal lymphatic regions, in 30 fractions. The overall survival rate, locoregional control rate, and initial recurrence site were evaluated. 3DCRT plans were created to perform dosimetric comparisons with SIB-IMRT. At a median follow-up of 64.5 months, the 5-year locoregional control and overall survival rates were 66.7% and 53.4%, respectively. Disease progressed in eight patients: all were locoregional progressions and no patients developed distant progression including upper cervical lymph nodal regions as initial recurrence sites. The planning study showed SIB-IMRT improved target coverage without compromising the dose to the organs at risk, compared with 3DCRT. In conclusion, omitting the elective nodal irradiation of the upper cervical lymph nodes was probably reasonable for CESCC patients without hypopharyngeal invasion. Locoregional progression remained the major progression site in this population.
The O star hinterland of the Galactic starburst, NGC 3603
Authors: Drew J E , Monguió M , Wright N J 
Published: April 2019

ABSTRACT
The very bright and compact massive young cluster, NGC 3603, has been cited as an example of a starburst in the Milky Way and compared with the much-studied R136/30 Doradus region in the Large Magellanic Cloud. Here we build on the discovery by Mohr-Smith et al. of a large number of reddened O stars around this cluster. We construct a list of 288 candidate O stars with proper motions (PMs), in a region of sky spanning 1.5 × 1.5 deg2 centred on NGC 3603, by cross-matching the Mohr-Smith et al. catalogue with Gaia DR2. This provides the basis for a first comprehensive examination of the PMs of these massive stars in the halo of NGC 3603, relative to the much better studied central region. We identify up to 11 likely O star ejections – 8 of which would have been ejected between 0.60 and 0.95 Myr ago (supporting the age of ∼1 Myr that has been attributed to the bright cluster centre). Seven candidate ejections are arranged in a partial ring to the south of the cluster core spanning radii of 9–18 arcmin (18–36 pc if the cluster is 7 kpc away). We also show that the cluster has a halo of a further ∼100 O stars extending to a radius of at least 5 arcmin, adding to the picture of NGC 3603 as a scaled down version of the R136/30 Dor region.
Is There a Need for a 6-Month Postradiosurgery Magnetic Resonance Imaging in the Treatment of Vestibular Schwannoma?
Authors: Perry Avital , Graffeo Christopher S , Carlstrom Lucas P , Hughes Joshua D , Peris-Celda Maria , Cray Nealey M , Pollock Bruce E , Link Michael J 
Published: April 2019

Abstract

BACKGROUND
Stereotactic radiosurgery (SRS) is a common treatment modality for vestibular schwannoma (VS), with a role in primary and recurrent/progressive algorithms. At our institution, routine magnetic resonance imaging (MRI) is obtained at 6 and 12 mo following SRS for VS.

OBJECTIVE
To analyze the safety and financial impact of eliminating the 6-mo post-SRS MRI in asymptomatic VS patients.

METHODS
A prospectively maintained SRS database was retrospectively reviewed for VS patients with 1 yr of post-treatment follow-up, 2005 to 2015. Decisions at 6-mo MRI were binarily categorized as routine follow-up vs clinical action—defined as a clinical visit, additional imaging, or an operation as a direct result of the 6-mo study.

RESULTS
A total of 296 patients met screening criteria, of whom 53 were excluded for incomplete follow-up and 8 for NF-2. Nine were reimaged prior to 6 mo due to clinical symptoms. Routine 6-mo post-SRS MRI was completed by 226 patients (76% of screened cohort), following from which zero instances of clinical action occurred. When scaled using national insurance database-derived financials—which estimated the mean per-study charge for MRI of the brain with and without contrast at $1767—the potential annualized national charge reduction was approximated as $1 611 504.

CONCLUSION
For clinically stable VS, 6-mo post-SRS MRI does not contribute significantly to management. We recommend omitting routine MRI before 12 mo, in patients without new or progressive neurological symptoms. If extrapolated nationally to the more than 100 active SRS centers, thousands of patients would be spared an inconvenient, nonindicated study, and national savings in health care dollars would be on the order of millions annually.
Clinical Outcomes of Stereotactic Radiosurgery for Cerebral Arteriovenous Malformations in Pediatric Patients: Systematic Review and Meta-Analysis
Authors: Börcek Alp Özgün , Çeltikçi Emrah , Aksoğan Yiğit , Rousseau Matthew John 
Published: April 2019

Abstract

BACKGROUND
Arteriovenous malformations (AVMs) in pediatric patients exhibit remarkable differences in terms of management and outcomes. Owing to a paucity of relevant data pertaining to AVMs in pediatric patients, special interest and investigation are required for an improved understanding of the available evidence by clinicians.

OBJECTIVE
To determine the clinical outcomes of single-session stereotactic radiosurgery (SRS) for AVMs in pediatric patients.

METHODS
A systematic literature review was performed to identify studies that reported the outcomes of SRS for AVMs in pediatric patients. Data pertaining to variables such as obliteration rate, post-SRS new hemorrhage rate, post-SRS new neurological deficit rate, and mortality rate were extracted and analyzed using meta-analysis techniques.

RESULTS
Based on pooled data from 20 studies with 1212 patients, single-session SRS resulted in complete obliteration in 65.9% (95% confidence interval [CI], 60.5%-71.1%; I2 = 66.5%) patients. Overall complication rate (including new hemorrhage, new neurodeficit, and mortality) was 8.0% (95% CI, 5.1%-11.5%; I2 = 66.4%). Post-SRS new neurological deficit rate was 3.1% (95% CI, 1.3%-5.4%; I2 = 59.7%), and post-SRS hemorrhage rate was 4.2% (95% CI, 2.5%-6.3%; I2 = 42.7%). There was no significant difference between studies disaggregated by treatment method (Gamma Knife [Elekta AB] vs other), treatment year (before year 2000 vs after year 2000), median AVM volume reported (≥3 vs <3 cm3), median dose reported (≥20 vs <20 Gy), or follow-up period (≥36 vs <36 mo).

CONCLUSION
Single-SRS is a safe treatment alternative that achieves high obliteration rates and acceptable complication rates for AVMs in pediatric patients.
IMPACT ON ABSORBED DOSE RATE IN AIR IN KANTO REGION BY FUKUSHIMA DAIICHI NUCLEAR POWER PLANT ACCIDENT
Authors: Inoue K , Arai M , Tsuruoka H , Saito K , Fujisawa M , Nakazawa S , Veerasamy N , Fukushi M 
Published: April 2019

Abstract
Absorbed dose rates in air were measured for the whole area of the Kanto region in 2015, 2016 and 2017 (n = 31 147). The mean absorbed dose rates in air for each prefecture measured by car-borne surveys were from 44 to 67 nGy h−1 (13–289 nGy h−1). The absorbed dose rate in air from artificial radionuclides (134Cs + 137Cs) measured by fixed-point observation (n = 507) was from 1 to 14 nGy h−1 (0–105 nGy h−1), and meaning that the contribution ratios of 134Cs and 137Cs were 3–22%. The deposited location of artificial radionuclides was less than 1000 m from ground level and depended on the topography, wind direction and precipitation field.
NATURAL RADIONUCLIDES IN AGRICULTURAL PLANTS FROM NORTHERN THAILAND
Authors: Kritsananuwat R , Kranrod C , Chanyotha S , Ploykrathok T , Sriploy P 
Published: April 2019

Abstract
Thailand is predominantly an agricultural country. The Northern Region occupies the second largest cultivated land area in the country. To establish baseline data for future environmental monitoring, seventy-nine plant samples including vegetables, fruits and tobaccos and their relevant soils were collected from the major plantation zones of Northern Thailand. Activity concentrations of natural radionuclides in the samples were determined using gamma-ray spectrometry technique. The median activity concentrations of 226Ra and 228Ra in the soil samples were higher than worldwide value, while as those of 40K were comparable with worldwide value. There was a large variation and non-uniform distribution in the soil samples. The activity concentrations of 226Ra, 228Ra and 40K in the plant samples varied widely within plants and between species and were very low compared to their relevant soils. A decreasing trend of their activity concentration has been observed in the order leaf > stem > rhizome/root (as found in galangal); and leaf > stalk/stem (as found in lemongrass).
INTERCOMPARISON EXPERIMENT AND UNCERTAINTY ANALYSIS OF THREE MEASUREMENT METHODS FOR RADON PROGENY AT NIM
Authors: Wang Yunxiang , Zhang Lei , Yang Zhijie , Guo Qiuju , Liang Juncheng 
Published: April 2019

Abstract
An intercomparison experiment of three radon progeny measurement methods, based on alpha spectrometry (Kerr method), alpha–beta spectrometry and liquid scintillation counter (LSC method), was carried out in the standard radon chamber at NIM. Both the consistency and the uncertainty analysis of three different methods were studied in detail. Results show that, at the EEC level of 4000 Bq/m3, the uncertainties of the alpha–beta spectrometry, LSC method and Kerr method were 3.78%, 6.41% and 9.46%, respectively, which are mainly contributed by detection efficiency uncertainty, measuring time uncertainty and counting statistical uncertainty in sequence. The comparison results at different concentration levels show that the measurement values of three methods are consistent within the error range of 3%. The alpha–beta spectrometry can be used as a reference standard method to achieve the simultaneous measurement of RaA, RaB, RaC concentrations and EEC in the radon chamber.
Rhinovirus 2A is the predominant protease responsible for instigating the early block to gene expression encountered in infected cells
Authors: Smart David , Filippi Irene , Smalley Benjamin , Davies Donna , McCormick Christopher J. 
Published: April 2019

AbstractHuman rhinoviruses express 2 cysteine proteases, 2A and 3C, that are responsible for viral polyprotein processing. Both proteases also suppress host gene expression by inhibiting mRNA transcription, nuclear export and cap-dependent translation. However, the relative contribution that each makes in achieving this goal remains unclear. In this study we have compared both the combined and individual ability of the 2 proteases to shut downin cellulogene expression using a novel dynamic reporter system. Our findings show that 2A inhibits host gene expression much more rapidly than 3C. By comparing the activities of a representative set of proteases from the three different Human Rhinovirus (HRV) species, we also find variation in the speed at which host gene expression is suppressed. Our work highlights the key role that 2A plays in early suppression of the infected host cell response and shows that this can be influenced by natural variation in the activity of this enzyme.
Nanoaperture fabrication via colloidal lithography for single molecule fluorescence imaging
Authors: Jamiolkowski Ryan M. , Chen Kevin Y , Fiorenza Shane A. , Tate Alyssa M. , Pfeil Shawn H. , Goldman Yale E. 
Published: April 2019

AbstractIn single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100-300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.
IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis
Authors: Chen Yun-Ching , Suresh Abhilash , Underbayev Chingiz , Sun Clare , Singh Komudi , Seifuddin Fayaz , Wiestner Adrian , Pirooznia Mehdi 
Published: April 2019

AbstractIn single-cell RNA-seq analysis, clustering cells into groups and differentiating cell groups by marker genes are two separate steps for investigating cell identity. However, results in clustering greatly affect the ability to differentiate between cell groups. We develop IKAP – an algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets, we demonstrate IKAP improves identification of major cell types and facilitates cell ontology curation.
dropClust2: An R package for resource efficient analysis of large scale single cell RNA-Seq data
Authors: Sinha Debajyoti , Sinha Pradyumn , Saha Ritwik , Bandyopadhyay Sanghamitra , Sengupta Debarka 
Published: April 2019

ABSTRACTDropClust leverages Locality Sensitive Hashing (LSH) to speed up clustering of large scale single cell expression data. It makes ingenious use of structure persevering sampling and modality based principal component selection to rescue minor cell types. Existing implementation of dropClust involves interfacing with multiple programming languagesviz. R, python and C, hindering seamless installation and portability. Here we present dropClust2, a complete R package that’s not only fast but also minimally resource intensive. DropClust2 features a novel batch effect removal algorithm that allows integrative analysis of single cell RNA-seq (scRNA-seq) datasets.Availability and implementationdropClust2 is freely available athttps://debsinha.shinyapps.io/dropClust/as an online web service and athttps://github.com/debsin/dropClustas an R package.
Establishing insect community composition using metabarcoding of soil samples, and preservative ethanol and homogenate from Malaise trap catches: surprising inconsistencies between methods
Authors: Marquina Daniel , Esparza-Salas Rodrigo , Roslin Tomas , Ronquist Fredrik 
Published: April 2019

AbstractDNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several alternative approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different sampling methods – homogenized Malaise trap samples (homogenate), preservative ethanol from the same samples, and soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is quite distinct from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol, with some exceptions that could be related to taxon-specific traits. For soil samples, highly degenerate COI primers pick up large amounts of non-target DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in MOTU content was found between the trap and the soil samples. Our results demonstrate that no metabarcoding approach is all-comprehensive in itself. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.
What, if anything, is the true neurophysiological significance of “rotational dynamics”?
Authors: Lebedev Mikhail A. , Ossadtchi Alexei , Mill Nil Adell , Armengol Urpí Núria , Cervera Maria R. , Nicolelis Miguel A.L. 
Published: April 2019

AbstractBack in 2012, Churchland and his colleagues proposed that “rotational dynamics”, uncovered through linear transformations of multidimensional neuronal data, represent a fundamental type of neuronal population processing in a variety of organisms, from the isolated leech central nervous system to the primate motor cortex. Here, we evaluated this claim using Churchland’s own data and simple simulations of neuronal responses. We observed that rotational patterns occurred in neuronal populations when (1) there was a temporal shift in peak firing rates exhibited by individual neurons, and (2) the temporal sequence of peak rates remained consistent across different experimental conditions. Provided that such a temporal order of peak firing rates existed, rotational patterns could be easily obtained using a rather arbitrary computer simulation of neural activity; modeling of any realistic properties of motor cortical responses was not needed. Additionally, arbitrary traces, such as Lissajous curves, could be easily obtained from Churchland’s data with multiple linear regression. While these observations suggest that temporal sequences of neuronal responses could be visualized as rotations with various methods, we express doubt about Churchland et al.’s exaggerated assessment that such rotations are related to “an unexpected yet surprisingly simple structure in the population response”, which “explains many of the confusing features of individual neural responses.” Instead, we argue that their approach provides little, if any, insight on the underlying neuronal mechanisms employed by neuronal ensembles to encode motor behaviors in any species.
Characterizing macroinvertebrate community composition and abundance in freshwater tidal wetlands of the Sacramento-San Joaquin Delta
Authors: Hartman Rosemary , Sherman Stacy , Contreras Dave , Furler Alison , Kok Ryan 
Published: April 2019

AbstractRestored tidal wetlands may provide important food web support for at-risk fish species in the Sacramento-San Joaquin Delta (Delta) of California, including Delta Smelt (Hypomesus transpacificus) and Chinook Salmon (Oncorhynchus tshawytscha). Since many tidal wetland restoration projects are planned or have recently been constructed in the Delta, understanding the diversity and variability of wetland invertebrates that are fish prey items is of increasing importance. During this study, two different invertebrate sampling techniques were tested (leaf packs and sweep nets) in four habitat types within three different wetland sites to evaluate which sampling technique provided the most reliable metric of invertebrate abundance and community composition. Sweep nets provided a better measure of fish food availability than leaf packs and were better able to differentiate between habitat types. Generalized linear models showed submerged and floating vegetation had higher abundance and species richness than channel habitats or emergent vegetation. Permutational multivariate analysis of variance showed significantly different communities of invertebrates in different habitat types and in different wetlands, and point-biserial correlation coefficients found a greater number of mobile taxa associated with sweep nets. There were more taxa associated with vegetated habitats than channel habitats, and one region had more taxa associated with it than the other two regions. These results suggest that restoration sites that contain multiple habitat types may enhance fish invertebrate prey diversity and resilience. However, the effect of habitat diversity must be monitored as restoration sites develop to assess actual benefits to at-risk fish species.