bluuebunny/crossref_metadata_2025_split huggingface dataset:
Death Due to Pulmonary Alveolar Proteinosis
Authors: Altaf Emran , Mitchel Erik K. , Berry Chris , Hossain Altaf 
Published: November 2016

Abstract
Presented are 2 cases of death from pulmonary alveolar proteinosis (PAP). Within the past 2 years, there have been 2 cases of rare nonneoplastic lung disease that consists of the filling of the alveoli of the lung by a periodic acid–Schiff stain-positive lipoproteinaceous material. This condition bears a certain resemblance to interstitial lung disease and/or Pneumocystitis jirovecci infection of the lungs. The presented cases were clinically diagnosed as interstitial lung disease. In the first case presented, the decedent was admitted to hospital with diagnosis of pneumonia but died in hospital despite observation and treatment. Autopsy examination revealed that instead of an infection, there was amorphous granular eosinophilic proteinaceous fluid in irregular clumps, with scattered foamy macrophages and cholesterol clefts and cracks in the lung alveoli. The second case was suspected of electrocution. There were no findings pointing to or against the possibility of electrocution, whereas the alveoli and terminal bronchioles were filled with amorphous granular eosinophilic lipoproteinaceous substance. The alveolar structure was well preserved, and the interstitium had no or mild chronic inflammatory cells. In both cases, the lipoproteinaceous material stained deep pink with periodic acid–Schiff stain. The gross and microscopic examination in the second case also signified pulmonary alveolar proteinosis.
The following report describes 2 cases of this uncommon disorder, with cause of death confirmed by postmortem examination.
Integration of EEG Into Psychiatric Practice: A Step Toward Precision Medicine for Autism Spectrum Disorder
Authors: Swatzyna Ronald J. , Tarnow Jay D. , Turner Robert P. , Roark Alexandra J. , MacInerney Erin K. , Kozlowski Gerald P. 
Published: November 2016

Introduction:
Data from an EEG is not commonly used by psychiatrists to plan treatment and medication. However, EEG abnormalities such as isolated epileptiform discharges are found to be more prevalent in psychiatric patients, particularly those diagnosed with autism spectrum disorder (ASD). Most medications prescribed for ASD lower seizure threshold and increase side effects. Therefore, it may be prudent to order an EEG for ASD cases, especially those categorized as refractory.

Methods:
The data set was obtained from a multidisciplinary practice that treats a wide variety of neuroatypical children and adolescent refractory patients. This study investigated 140 nonepileptic subjects diagnosed with ASD, aged 4 to 25 years. Visual inspection of the EEG was performed to search for paroxysmal, focal, or lateralizing patterns.

Results:
Of the 140 subjects, the EEG data identified 36% with isolated epileptiform discharges. The χ2 analysis found no significant difference between genders among the three age groups. Findings indicated a high prevalence of isolated epileptiform discharges among individuals with ASD.

Conclusions:
Our results find that compared with the healthy population, a large number of patients with ASD have isolated epileptiform discharges despite never having a seizure. Our findings support the use of EEG in children, adolescents, and young adults with ASD, regardless of gender or age. This is particularly true for those who exhibit aggressive behaviors or those who have failed previous medication attempts with stimulants, antidepressants, and/or antipsychotics.
Neuronal components of evaluating the human origin of abstract shapes
Authors: Goldberg Hagar , Hart Yuval , Mayo Avraham E , Alon Uri , Malach Rafael 
Published: November 2016

AbstractCommunication through visual symbols is a key aspect of human culture. However, to what extent can people distinguish between human-origin and artificial symbols, and the neuronal mechanisms underlying this process are not clear. Using fMRI we contrasted brain activity during presentation of human-created abstract shapes and random-algorithm created shapes, both sharing similar low level features.We found that participants correctly identified most shapes ashumanorrandom. The lateral occipital complex (LOC) was the main brain region showing preference to human-made shapes, independently of task. Furthermore, LOC activity was parametrically correlated to beauty and familiarity scores of the shapes (rated following the scan). Finally, a model classifier based only on LOC activity showed human level accuracy at discriminating between human-made and randomly-made shapes.Our results highlight the sensitivity of the human brain to social and cultural cues, and point to high-order object areas as central nodes underlying this capacity.
Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
Authors: Montefiori Lindsey , Hernandez Liana , Zhang Zijie , Gilad Yoav , Ober Carole , Crawford Gregory , Nobrega Marcelo , Sakabe Noboru Jo 
Published: November 2016

AbstractATAC-seq is a high-throughput sequencing technique that aims at identifying DNA sequences located in open chromatin. Depending on the cell type, ATAC-seq may yield a high number of mitochondrial sequencing reads (~20-80% of the reads). As the regions of open chromatin of interest are usually located in the nuclear genome, mitochondrial reads are typically discarded from the analysis. To decrease wasted sequencing, we performed targeted cleavage of mitochondrial DNA using CRISPR/Cas9 and 100 mtDNA-specific guide RNAs. We also tested a modified ATAC-seq protocol that does not include detergent in the cell lysis buffer. Both treatments resulted in considerable reduction of mitochondrial reads (1.7 and 3-fold, respectively). The removal of detergent, however, resulted in increased background and fewer peaks identified. The highest number of peaks and highest quality data was obtained by preparing samples with the original ATAC-seq protocol (using detergent) and treating them with anti-mitochondrial guide RNAs and Cas9. This strategy could lead to considerable cost reduction and improved peak calling when performing ATAC-seq on a moderate to large number of samples and in cell types that contain a large amount of mitochondria.
In vivoimaging of coral tissue and skeleton with optical coherence tomography
Authors: Wangpraseurt Daniel , Wentzel Camilla , Jacques Steven L. , Wagner Michael , Kuhl Michael 
Published: November 2016

AbstractOptical coherence tomography (OCT) is a non-invasive three-dimensional imaging technique with micrometer resolution allowing microstructural characterization of tissuesin vivoand in real time. We present the first application of OCT forin vivoimaging of tissue and skeleton structure of intact living corals spanning a variety of morphologies and tissue thickness. OCT visualized different coral tissue layers (e.g. endoderm vs ectoderm), special structures such as mesenterial filaments and skeletal cavities, as well as mucus release from living corals. We also developed a new approach for non-invasive imaging and quantification of chromatophores containing green fluorescent protein (GFP)-like host pigment granules in coral tissue. The chromatophore system is hyper-reflective and can thus be imaged with good optical contrast in OCT, enabling quantification of chromatophore size, distribution and abundance. Because of its rapid imaging speed, OCT can also be used to quantify coral tissue movement showing that maximal linear contraction velocity was ~120 μm per second upon high light stimulation. Based on OCT imaging of tissue expansion and contraction, we made first estimates of dynamic changes in the coral tissue surface area, which varied by a factor of 2 between the contracted and expanded state of the coralPocillopora damicornis. We conclude that OCT is an excellent novel tool forin vivotomographic imaging of corals that can reveal tissue and skeleton organization as well as quantify dynamic changes in tissue structure and coral surface area non-invasively and at high spatio-temporal resolution.
Raoult’s law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments
Authors: Bowler Michael G. , Bowler David R. , Bowler Matthew W. 
Published: November 2016

AbstractThe humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, which often leads to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals on a beamline have led to this technique being increasingly adopted, as experiments become easier and more reproducible. Matching the relative humidity to the mother liquor is the first step to allow the stable mounting of a crystal. In previous work, we measured the equilibrium relative humidity for a range of concentrations of the most commonly used precipitants and showed how this related to Raoult’s law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between measured values and those predicted by theory could not be explained. Here, we have used a more precise humidity control device to determine equilibrium relative humidity points. The new results are in agreement with Raoult’s law. We also present a simple argument in statistical mechanics demonstrating that the saturated vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult’s Law. The same argument can be extended to the case where solvent and solute molecules are of different size, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding samples.SynopsisThe equilibrium relative humidity values for a number of the most commonly used precipitants in biological macromolecule crystallisation have been measured using a new humidity control device. A simple argument in statistical mechanics demonstrates that the saturated vapour pressure of a solvent is proportional to its mole fraction in an ideal solution (Raoult’s Law). The same argument can be extended to the case where solvent and solute molecules are of different size.
Mycoplasma Faucium and Breast Cancer
Authors: Mitin V. , Tumanova L. , Botnariuc N. 
Published: November 2016

AbstractViruses and bacteria are the cause of a large number of different human diseases. It is believed that some of them may even contribute to the development of cancer. The present work is dedicated to the identification of mycoplasmas in patients with breast cancer. Mycoplasmas may participate in the development of several human diseases including chronic fatigue syndrome, acquired immunodeficiency syndrome, atypical pneumonia, etc. Moreover, there is a reason to believe that mycoplasma can participate in the development of cancer, leukemia and lymphoma.DNA samples from blood, saliva and tumor tissues of the Oncology Institute of Moldova patients diagnosed with breast cancer were analyzed. Mycoplasma testing was performed using nested PCR method. ForMycoplasma spp. detection, we used primers from the region of the 16S-23S RNA genes. The identification ofMycoplasma faucium,Mycoplasma salivariumandMycoplasma oralewas performed by nested PCR with primers for RNA polymerase beta subunit gene corresponding to mycoplasma.M.fauciumandM.salivariuswas found in saliva at about 100%, andM.orale at a frequency of about 50%. OnlyM.fauciumwas found with the frequency of about 60% in the tissue of the patients. Moreover, a fairly high rate of detection of mycoplasma is observed both in the cases when primers for RNA polymerase gene and primers for 16S-23S RNA were used.We foundM.fauciumin tumor tissues of patients diagnosed with breast cancer. It is known that mycoplasmas are able to stimulate the synthesis of certain cytokines, which act as mitogenes on the cell. We assume that M.faucium can stimulate the mitogenes synthesis in breast tissues (e.g., cytokines) which, in turn, stimulate cell division and thus participate in the initiation of breast cancer.
The Impact of Lethal Recessive Alleles on Bottlenecks with Implications for Conservation Genetics
Authors: Campbell R. B. 
Published: November 2016

AbstractWhen a bottleneck occurs, lethal recessive alleles from the ancestral population provide a genetic load. The purging of lethal recessive mutations may prolong the bottleneck, or even cause the population to become extinct. But the purging is of short duration, it will be over before near neutral deleterious alleles accumulate. Lethal recessive alleles from the parental population and near neutral deleterious mutations which occur during a bottleneck are temporally separated threats to the survival of a population. Breeding individuals from a large population into a small endangered population will provide the benefit of viable alleles to replace near neutral deleterious alleles but also the cost of lethal recessive mutations from the large population.
Flagellar synchronization is a simple alternative to cell cycle synchronization for ciliary and flagellar studies
Authors: Dutta Soumita , Avasthi Prachee 
Published: November 2016

AbstractThe unicellular green alga,Chlamydomonas reinhardtii, is an ideal model organism for studies of ciliary function and assembly. In assays for biological and biochemical effects of various factors on flagellar structure and function, synchronous culture is advantageous for minimizing variability. Here, we have characterized a method in which 100% synchronization is achieved with respect to flagellar length but not with respect to the cell cycle. The method requires inducing flagellar regeneration by amputation of the entire cell population and limiting regeneration time, which results in a maximally homogeneous distribution of flagellar length at three hours post-amputation. We find that time-limiting new protein synthesis during flagellar synchronization limits variability in the unassembled pool of limiting flagellar protein and variability in flagellar length without scaling the cell volume range. We also find that long and short flagella mutants that regenerate normally require longer and shorter synchronization times, respectively. By minimizing flagellar length variability using a simple method requiring only hours and no changes in media, flagellar synchronization facilitates the detection of small changes in flagellar length resulting from both chemical and genetic perturbations inChlamydomonas. This method increases our ability to probe the basic biology of ciliary size regulation and related disease etiologies.
Cross-laboratory analysis of brain cell type transcriptomes with applications to interpretation of bulk tissue data
Authors: Mancarci B. Ogan , Toker Lilah , Tripathy Shreejoy J , Li Brenna , Rocco Brad , Sibille Etienne , Pavlidis Paul 
Published: November 2016

AbstractEstablishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cell type microarray and single cell RNA-sequencing studies. We used these data to identify cell type-specific marker genes, discovering a substantial number of novel markers, many of which we validated using computational and experimental approaches. We further demonstrate that summarized expression of marker gene sets in bulk tissue data can be used to estimate the relative cell type abundance across samples. To facilitate use of this expanding resource, we provide a user-friendly web interface atNeuroexpresso.org.Significance StatementCell type markers are powerful tools in the study of the nervous system that help reveal properties of cell types and acquire additional information from large scale expression experiments. Despite their usefulness in the field, known marker genes for brain cell types are few in number. We present NeuroExpresso, a database of brain cell type specific gene expression profiles, and demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. The database will prove itself as a useful resource for researchers aiming to reveal novel properties of the cell types and aid both laboratory and computational scientists to unravel the cell type specific components of brain disorders.
Seismic risk management of a large public facilities portfolio: a New Zealand case study
Authors: Walsh Kevin Quinn , Jafarzadeh Reza , Short Nicola M. , Ingham Jason M. 
Published: November 2016

Purpose
The purpose of this article is to assist facilities asset managers who are dealing with regulatory environments pertaining to earthquakes and buildings. These professionals can learn a great deal from the successes and short-comings of a case study programme from the Auckland Council Property Department (ACPD), which manages the public facilities portfolio for the largest local administrative region in New Zealand in both population and landmass.

Design/methodology/approach
ACPD has initiated its response to New Zealand’s earthquake mitigation mandates by identifying buildings most at risk to an earthquake in its large and varied portfolio through the use of a rapid building evaluation programme strategically targeted to vulnerable building types with consequential attributes, including service type, number of occupants, floor area and geographic location.

Findings
ACPD was able to rapidly cull down its portfolio of approximately 3,500 buildings to just over 100 “high-exposure” buildings in urgent need of evaluation, set priorities for future evaluations, estimate needed operational and capital expenditures for long-term planning and provide useful information to more general facilities management decision-making processes.

Originality/value
A number of major cities around the world in areas of high seismicity have enacted ordinances mandating seismic retrofitting. However, much of the existing guiding literature regarding earthquake-related portfolio evaluations and costs pertains to specific scenarios involving real or hypothetical earthquakes. This case study, in contrast, details the approach taken by a public portfolio owner responding to legal mandates and attempting to quantify and reduce its life-safety risk exposure across a large portfolio as efficiently as possible using readily available information, a rapid building evaluation programme and best-practice predictive models for consulting and construction work.
Symmetry reductions and rational non-traveling wave solutions for the (2+1)-D Ablowitz-Kaup-Newell-Segur equation
Authors: Kang Xiao-rong , Daquan Xian 
Published: November 2016

Purpose
The purpose of this paper is to find out some new rational non-traveling wave solutions and to study localized structures for (2+1)-dimensional Ablowitz-Kaup-Newell-Segur (AKNS) equation.

Design/methodology/approach
Along with some special transformations, the Lie group method and the rational function method are applied to the (2+1)-dimensional AKNS equation.

Findings
Some new non-traveling wave solutions are obtained, including generalized rational solutions with two arbitrary functions of time variable.

Research limitations/implications
As a typical nonlinear evolution equation, some dynamical behaviors are also discussed.

Originality/value
With the help of the Lie group method, special transformations and the rational function method, new non-traveling wave solutions are derived for the AKNS equation by Maple software. These results are much useful for investigating some new localized structures and the interaction of waves in high-dimensional models, and enrich dynamical features of solutions for the higher dimensional systems.
Magnetohydrodynamic time-dependent computational natural convection flow, heat and mass transfer in inclined semi-circular enclosures
Authors: Rahman M.M. , Öztop Hakan F. , Saidur R. , Naim A.G. , Al-Salem Khaled S. , Ibrahim Talaat A. 
Published: November 2016

Purpose
The purpose of this paper is to make a numerical analysis on unsteady analysis of natural convection heat and mass transfer to obtain flow field, temperature distribution, and concentration distribution.

Design/methodology/approach
A finite element method is applied to solve governing equations of natural convection in curvilinear-shaped system for different parameters as thermal Rayleigh numbers (103=RaT=106), inclination angle (0°=φ=60°) and Hartmann numbers (0=Ha=100).

Findings
Both magnetic field and inclination angle can be used as control parameter on heat and mass transfer. Flow strength decreases almost 100 percent between Ha=0 and Ha=100 on behalf of the higher values of thermal Rayleigh number.

Originality/value
The originality of this work is to application of magnetic field on time-dependent natural convection flow, heat and mass transfer for curvilinear geometry.
Mapping the gendered ecosystem
Authors: Aidis Ruta , Weeks Julie 
Published: November 2016

PurposeThere is a growing understanding that gender-blind business support measures do not assist women’s enterprise development to the extent that they assist its male equivalent. Focusing efforts specifically on women’s enterprise development, and measuring the impact of those efforts, is paramount. This paper aims to assess the evolution of two indices that analyze high-impact female entrepreneurship development: the Gender-Global Entrepreneurship and Development Index (GEDI) and the 2015 Global Women Entrepreneur Leaders Scorecard. Both utilize data from reliable data sources, yet are limited by the quality and availability of sex-disaggregated data. However, they differ in terms of variable choice, methodology and results.Design/methodology/approachIn this paper, the authors assess the evolution of two indices that analyze high-impact female entrepreneurship development. High-impact female entrepreneurship is defined as firms headed by women that are market-expanding, export-oriented and innovative. The assessment is focused on two new indices, the 2013 and 2014 Gender-GEDI and, the newly created measurement tool, the 2015 Global Women Entrepreneur Leaders Scorecard.FindingsBoth indices rely on existing data from reliable, internationally recognized data sets, yet are limited by the sex-disaggregated data that are currently available. However, they differ in terms of variable choice, methodology and results.Originality/valueThere is an increasing need by researchers and policy makers alike to consolidate existing data to better understand the existing barriers for women entrepreneurs and to be able to benchmark change. This paper assesses two indices that provide insights into the conditions for high-impact women entrepreneurs in a country comparative way.