bluuebunny/crossref_metadata_2025_split huggingface dataset:
An investigation of the low-ΔV near-Earth asteroids (341843) 2008 EV5 and (52381) 1993 HA
Authors: Perna D. , Popescu M. , Monteiro F. , Lantz C. , Lazzaro D. , Merlin F. 
Published: October 2016

Context. The Asteroid Redirect Mission (ARM) under development by NASA is being planned to collect a multi-meter boulder from a near-Earth asteroid (NEA), and to bring it to the cis-lunar space in the mid-2020’s for future study and exploitation by a crewed mission. The MarcoPolo-M5 project is being proposed in 2016 for the M5 mission opportunity by ESA, to bring back to Earth a sample from a very primitive D-type NEA. As D-types are very rare within the NEA population, considerable effort is still in progress to characterize easily accessible targets with unknown surface composition, in order to discover further asteroids that belong to this taxonomic group.
Aims. We aim to further characterize the physical properties of two optimal targets for sample return space missions, the low-ΔV NEAs (341843) 2008 EV5 and (52381) 1993 HA. The asteroid 2008 EV5 is the baseline target of ARM, but only one spectrum of this object exists in the literature. The asteroid 1993 HA is a very favourable target for a space mission based on its dynamical properties: here we intend to assess if it is a suitable target for MarcoPolo-M5.
Methods. We obtained visible spectroscopy of 2008 EV5 with the FORS2 instrument at ESO-VLT (Paranal, Chile), at different rotational phases. We also obtained visible and near-infrared spectroscopy of 1993 HA, using the EFOSC2 and SOfI instruments at ESO-NTT (La Silla, Chile). Visible photometry of 1993 HA was carried out within the IMPACTON project at the Observatório Astronômico do Sertão de Itaparica (Itacuruba, Brazil).
Results. Our new observations are in agreement with the C-type classification of 2008 EV5, which is a requirement for the ARM mission. We obtained five visible spectra which do not show any variability within the limits of noise, suggesting a homogeneous surface. We obtained the first ever spectroscopic dataset (~0.4–1.6 μm) for 1993 HA, finding a featureless, red-sloped behaviour typical of D-types (a T or X classification is also possible, with decreasing confidence). We also found that the synodic rotation period of 1993 HA is 4.107 ± 0.002 h, a value that is optimal for the execution of a sample return mission. The derived lightcurve also suggests an elongated shape (axis ratio a/b ≥ 1.71). At this stage 1993 HA does indeed seem to be the most favourable target for MarcoPolo-M5, though future observations are necessary to study it further.
A study on a dental device for the prevention of mucosal dose enhancement caused by backscatter radiation from dental alloy during external beam radiotherapy
Authors: Katsura Kouji , Utsunomiya Satoru , Abe Eisuke , Sakai Hironori , Kushima Naotaka , Tanabe Satoshi , Yamada Takumi , Hayakawa Takahide , Yamanoi Yoshihiko , Kimura Syuhei , Wada Shinichi , Aoyama Hidefumi , Hayashi Takafumi 
Published: October 2016

Abstract
The changes in dose distribution caused by backscatter radiation from a common commercial dental alloy (Au–Ag–Pd dental alloy; DA) were investigated to identify the optimal material and thicknesses of a dental device (DD) for effective prevention of mucositis. To this end, 1 cm3 of DA was irradiated with a 6-MV X-ray beam (100 MU) in a field size of 10 × 10 cm2 using a Novalis TX linear accelerator. Ethylene vinyl acetate copolymer, polyolefin elastomer, and polyethylene terephthalate (PET) were selected as DD materials. The depth dose along the central axis was determined with respect to the presence/absence of DA and DDs at thicknesses of 1–10 mm using a parallel-plate ionization chamber. The dose in the absence of DDs showed the lowest value at a distance of 5 mm from the DA surface and gradually increased with distance between the measurement point and the DA surface for distances of ≥5 mm. Except for PET, no significant difference between the DA dose curves for the presence and absence of DDs was observed. In the dose curve, PET showed a slightly higher dose for DA with DD than for DA without DD for thicknesses of ≥4 mm. The findings herein suggest that the optimal DD material for preventing local dose enhancement of the mucosa caused by DA backscatter radiation should have a relatively low atomic number and physical density and that optimal DD thickness should be chosen considering backscatter radiation and percentage depth dose.
Insurance Status and Hospital Payer Mix Are Linked With Variation in Metastatic Site Resection in Patients With Advanced Colorectal Cancers
Authors: Healy Mark A. , Pradarelli Jason C. , Krell Robert W. , Regenbogen Scott E. , Suwanabol Pasithorn A. 
Published: October 2016

BACKGROUND:
Despite substantially improved survival with metastatic site resection in colorectal cancers, uptake of aggressive surgical approaches remains low among certain patients. It is unknown whether financial determinants of care, such as insurance status, play a role in this treatment gap.

OBJECTIVE:
We sought to evaluate the effect of insurance status on metastasectomy in patients with advanced colorectal cancers.

DESIGN:
This was a retrospective cohort study.

SETTINGS:
Using the National Cancer Data Base Participant User File, incident cases of colorectal cancer metastatic to the lung and/or liver with diagnosis from 2010 to 2013 were identified.

PATIENTS:
We identified 42,300 patients in our cohort with a mean age 64 years.

MAIN OUTCOME MEASURES:
Controlling for patient, tumor, and hospital characteristics, hierarchical regression was used to examine associations between hospital payer mix and metastatic site resection. Metastatic site resection occurred in 12.3% of all patients.

RESULTS:
Adjusting for patient and hospital fixed effects, we found that patients who were uninsured or on Medicaid were 38% less likely to undergo metastasectomy (OR = 0.62 (95% CI, 0.56–0.66)). Patients in hospitals with staff treating a high percentage of uninsured patients or patients with Medicaid were less likely to undergo metastasectomy, even after controlling for individual patient insurance status.

LIMITATIONS:
The study was limited by its retrospective design and the granularity and accuracy of the National Cancer Data Base.

CONCLUSIONS:
Differences in insurance status and hospital payer mix are associated with differences in rates of metastatic site resection in patients with colorectal cancer that is metastatic to the lung and/or liver. There is a need for improved access to metastatic site resection for individual patients who are uninsured or who have Medicaid insurance, as well as for all patients who seek care at hospitals treating a large proportion of patients who are uninsured or on Medicaid. Remedies for individual patients could include improved access to private insurance through employment or individual plans or improved reimbursement from Medicaid for this procedure. Strategies for patients at low-performing hospitals include selective referral to centers that perform mestastectomy more frequently when appropriate.
A Novel Reticular Dermal Graft Leverages Architectural and Biological Properties to Support Wound Repair
Authors: Dasgupta Anouska , Orgill Dennis , Galiano Robert D. , Zelen Charles M. , Huang Yen-Chen , Chnari Evangelia , Li William W. 
Published: October 2016

Background:
Acellular dermal matrices (ADMs) are frequently used in reconstructive surgery and as scaffolds to treat chronic wounds. The 3-dimensional architecture and extracellular matrix provide structural and signaling cues for repair and remodeling. However, most ADMs are not uniformly porous, which can lead to heterogeneous host engraftment. In this study, we hypothesized that a novel human reticular ADM (HR-ADM; AlloPatch Pliable, Musculoskeletal Transplant Foundation, Edison, N.J.) when aseptically processed would have a more open uniform structure with retention of biological components known to facilitate wound healing.

Methods:
The reticular and papillary layers were compared through histology and scanning electron microscopy. Biomechanical properties were assessed through tensile testing. The impact of aseptic processing was evaluated by comparing unprocessed with processed reticular grafts. In vitro cell culture on fibroblasts and endothelial cells were performed to showcase functional cell activities on HR-ADMs.

Results:
Aseptically processed HR-ADMs have an open, interconnected uniform scaffold with preserved collagens, elastin, glycosaminoglycans, and hyaluronic acid. HR-ADMs had significantly lower ultimate tensile strength and Young’s modulus versus the papillary layer, with a higher percentage elongation at break, providing graft flexibility. These preserved biological components facilitated fibroblast and endothelial cell attachment, cell infiltration, and new matrix synthesis (collagen IV, fibronectin, von Willebrand factor), which support granulation and angiogenic activities.

Conclusions:
The novel HR-ADMs provide an open, interconnected scaffold with native dermal mechanical and biological properties. Furthermore, aseptic processing retains key extracellular matrix elements in an organized framework and supports functional activities of fibroblasts and endothelial cells.
King's Variceal Prediction Score
Authors: Witters Peter , Hughes Dominic , Karthikeyan Palaniswamy , Ramakrishna Somashekara , Davenport Mark , Dhawan Anil , Grammatikopoulos Tassos 
Published: October 2016

ABSTRACTBackground and Aims:Variceal haemorrhage can be a life‐threatening complication of chronic liver disease in children. There is limited evidence about the optimal prophylactic management and selection criteria of children who will benefit from upper gastrointestinal endoscopy.Methods:Children presenting in our centre with suspected portal hypertension or gastrointestinal bleeding and undergoing their first oesophagogastroduodenoscopy between 2005 and 2012 were included. Clinical, biochemical, and radiological data were collected. A separate validation cohort from May 2013 to October 2014 was obtained.Results:Data on 124 treatment‐naïve patients were collected; 50% had biliary atresia. Thirty‐five (28%) children presented with gastrointestinal bleeding and overall 79 (64%) had clinically significant (grade II–III) varices. Clinical prediction rule, aspartate aminotransferase‐platelet ratio index, and varices prediction rule had at optimal cut‐off sensitivity and specificity of 76% and 59%, 60% and 55%, and 80% and 59%, respectively. Logistic regression yielded a new prediction rule of (3 × albumin ([g/dL]) − (2 − equivalent adult spleen size [cm]). This King's variceal prediction score had a favourable areas under the curve of 0.772 (0.677–0.867) compared to clinical prediction rule 0.732 (0.632–0.832). At the optimal cut‐off of 76 this yielded a sensitivity and specificity of 72% and 73% and a positive and negative predictive value of 82% and 60%, respectively. In the validation cohort areas under the curve was 0.818 (0.654–0.995) with sensitivity and specificity of 78% and 73%, respectively.Conclusions:Our new prediction score may be a useful tool in the selection of children with clinically significant varices eligible for a screening endoscopy.
Determining the role of inflammation in the selection of JAK2 mutant cells in myeloproliferative neoplasms
Authors: Zhang Jie , Fleischman Angela , Wodarz Dominik , Komarova Natalia L. 
Published: October 2016

AbstractMyeloproliferative neoplasm (MPN) is a hematologic malignancy characterized by the clonal outgrowth of hematopoietic cells with a somatically acquired mutation most commonly in JAK2 (JAK2V617F). This mutation endows upon myeloid progenitors cytokine independent growth and consequently leads to excessive production of myeloid lineage cells. It has been previously suggested that inflammation may play a role in the clonal evolution of JAK2V617Fmutants. In particular, it is possible that one or more cellular kinetic parameters of hematopoietic stem cells (HSCs) are affected by inflammation, such as division or death rates of cells, and the probability of HSC differentiation. This suggests a mechanism that can steer the outcome of the cellular competition in favor of the mutants, initiating the disease. In this paper we create a number of mathematical evolutionary models, from very abstract to more concrete, that describe cellular competition in the context of inflammation. It is possible to build a model axiomatically, where only very general assumptions are imposed on the modeling components and no arbitrary (and generally unknown) functional forms are used, and still generate a set of testable predictions. In particular, we show that, if HSC death is negligible, the evolutionary advantage of mutant cells can only be conferred by an increase in differentiation probability of HSCs in the presence of inflammation, and if death plays a significant role in the dynamics, an additional mechanism may be an increase of HSC’s division-to-death ratio in the presence of inflammation. Further, we show that in the presence of inflammation, the wild type cell population is predicted to shrink under inflammation (even in the absence of mutants). Finally, it turns out that if only the differentiation probability is affected by the inflammation, then the resulting steady state population of wild type cells will contain a relatively smaller percentage of HSCs under inflammation. If the division-to-death rate is also affected, then the percentage of HSCs under inflammation can either decrease or increase, depending on other parameters.
Adaptive Somatic Mutations Calls with Deep Learning and Semi-Simulated Data
Authors: Torracinta Remi , Mesnard Laurent , Levine Susan , Shaknovich Rita , Hanson Maureen , Levine Susan 
Published: October 2016

ABSTRACTA number of approaches have been developed to call somatic variation in high-throughput sequencing data. Here, we present an adaptive approach to calling somatic variations. Our approach trains a deep feed-forward neural network with semi-simulated data. Semi-simulated datasets are constructed by planting somatic mutations in real datasets where no mutations are expected. Using semi-simulated data makes it possible to train the models with millions of training examples, a usual requirement for successfully training deep learning models. We initially focus on calling variations in RNA-Seq data. We derive semi-simulated datasets from real RNA-Seq data, which offer a good representation of the data the models will be applied to. We test the models on independent semi-simulated data as well as pure simulations. On independent semi-simulated data, models achieve an AUC of 0.973. When tested on semi-simulated exome DNA datasets, we find that the models trained on RNA-Seq data remain predictive (sens 0.4 & spec 0.9 at cutoff of P > = 0.9), albeit with lower overall performance (AUC=0.737). Interestingly, while the models generalize across assay, training on RNA-Seq data lowers the confidence for a group of mutations. Haloplex exome specific training was also performed, demonstrating that the approach can produce probabilistic models tuned for specific assays and protocols. We found that the method adapts to the characteristics of experimental protocol. We further illustrate these points by training a model for a trio somatic experimental design when germline DNA of both parents is available in addition to data about the individual. These models are distributed with Goby (http://goby.campagnelab.org).
Growth-Altering Microbial Interactions Are Highly Sensitive to Environmental Context
Authors: Liu Angela , Archer Anne , Biggs Matthew B. , Papin Jason A. 
Published: October 2016

AbstractMicrobial interactions are ubiquitous in nature, and equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed highly dynamic and responsive to environmental context.
Unsupervised feature selection for interpretable classification in behavioral assessment of children
Authors: Jiménez Fernando , Jódar Rosalia , Martín Maria del Pilar , Sánchez Gracia , Sciavicco Guido 
Published: October 2016

AbstractIn this paper, we consider a data set taken from the administration of the Behavior Assessment System for Children test to 157 subjects, and we approach the problem of clustering and classify the subjects in an interpretable fashion. Because the Behavior Assessment System for Children test is originally composed of 149 questions (152 in the particular version used for this experiment), we first propose a feature selection wrapper model composed by a multi‐objective evolutionary algorithm, the iterative clustering method expectation–maximization, and the classifier C4.5 for the unsupervised feature selection towards the classification of the data with two objectives: maximizing the likelihood of the clustering model and maximizing the accuracy of the obtained classifier. We propose a methodology to integrate feature selection for unsupervised classification, model evaluation, decision‐making (to choose the most satisfactory model according to ana posterioriprocess in a multi‐objective context), and testing. The selected data set that is the result of this process, where each instance is labeled with its class, is then used for supervised learning via both C4.5 and a novel evolutionary computation‐based fuzzy classifier to obtain interpretable rules. We discuss and compare the behavior of two different evolutionary algorithms (ENORA (Evolutionary NOn‐dominated Radial slots based Algorithm) and NSGA‐II (Non‐dominated Sorted Genetic Algorithm)) at different levels: as search strategies for feature selection, as search strategies for fuzzy classification, and in terms of quality of the results. It turns out that ENORA behaves better in terms of quality of the result in the feature selection phase (obtaining a selection that shows higher accuracy under C4.5 after cross‐validation), and again in the fuzzy classification phase, from both points of view: hypervolume evolution and interpretability of results. During the entire process, the solutions are validated by the psychologists who collected the data.
Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism
Authors: Nguyen Ngoc-Phuong-Thao , Linder Sonja , Flitsch Stefanie K. , Schiel-Bengelsdorf Bettina , Dürre Peter , Soucaille Philippe 
Published: October 2016

ABSTRACT

An operon comprising two genes,
CA_P0037
and
CA_P0036
, that encode proteins of unknown function that were previously shown to be highly expressed in acidogenic cells and repressed in solventogenic and alcohologenic cells is located on the pSOL1 megaplasmid of
Clostridium acetobutylicum
upstream of
adhE2
. A
CA_P0037
::
int
(
189/190s
) mutant in which an intron was inserted at position 189/190 in the sense strand of
CA_P0037
was successfully generated by the Targetron technique. The resultant mutant showed significantly different metabolic flux patterns in acidogenic (producing mainly lactate, butyrate, and butanol) and alcohologenic (producing mainly butyrate, acetate, and lactate) chemostat cultures but not in solventogenic or batch cultures. Transcriptomic investigation of the
CA_P0037
::
int
(
189/190s
) mutant showed that inactivation of
CA_P0037
significantly affected the expression of more than 258 genes under acidogenic conditions. Surprisingly, genes belonging to the Fur regulon, involved in iron transport (
CA_C1029-CA_C1032
), or coding for the main flavodoxin (
CA_C0587
) were the most significantly expressed genes under all conditions, whereas
fur
(coding for the ferric uptake regulator) gene expression remained unchanged. Furthermore, most of the genes of the Rex regulon, such as the
adhE2
and
ldhA
genes, and of the PerR regulon, such as
rbr3A-rbr3B
and
dfx
, were overexpressed in the mutant. In addition, the whole
CA_P0037-CA_P0036
operon was highly expressed under all conditions in the
CA_P0037
::
int
(
189/190s
) mutant, suggesting a self-regulated expression mechanism. Cap0037 was shown to bind to the
CA_P0037-CA_P0036
operon,
sol
operon, and
adc
promoters, and the binding sites were determined by DNA footprinting. Finally, a putative Cap0037 regulon was generated using a bioinformatic approach
.

IMPORTANCE
Clostridium acetobutylicum
is well-known for its ability to produce solvents, especially
n
-butanol. Understanding the regulatory network of
C. acetobutylicum
will be crucial for further engineering to obtain a strain capable of producing
n
-butanol at high yield and selectivity. This study has discovered that the Cap0037 protein is a novel regulator of
C. acetobutylicum
that drastically affects metabolism under both acidogenic and alcohologenic fermentation conditions. This is pioneering work for further determining the regulatory mechanism of Cap0037 in
C. acetobutylicum
and studying the role of proteins homologous to Cap0037 in other members of the phylum
Firmicutes
.