bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of Storage Temperature for Retention of Undifferentiated Cell Character of Cultured Human Epidermal Cell Sheets
Authors: Jackson Catherine J. , Reppe Sjur , Eidet Jon R. , Eide Lars , Tønseth Kim A. , Bergersen Linda H. , Dartt Darlene A. , Griffith May , Utheim Tor P. 
Published: August 2017

AbstractCultured epidermal cell sheets (CES) containing undifferentiated cells are useful for treating skin burns and have potential for regenerative treatment of other types of epithelial injuries. The undifferentiated phenotype is therefore important for success in both applications. This study aimed to optimize a method for one-week storage of CES for their widespread distribution and use in regenerative medicine. The effect of storage temperatures 4 °C, 8 °C, 12 °C, 16 °C, and 24 °C on CES was evaluated. Analyses included assessment of viability, mitochondrial reactive oxygen species (ROS), membrane damage, mitochondrial DNA (mtDNA) integrity, morphology, phenotype and cytokine secretion into storage buffer. Lowest cell viability was seen at 4 °C. Compared to non-stored cells, ABCG2 expression increased between temperatures 8–16 °C. At 24 °C, reduced ABCG2 expression coincided with increased mitochondrial ROS, as well as increased differentiation, cell death and mtDNA damage. P63, C/EBPδ, CK10 and involucrin fluorescence combined with morphology observations supported retention of undifferentiated cell phenotype at 12 °C, transition to differentiation at 16 °C, and increased differentiation at 24 °C. Several cytokines relevant to healing were upregulated during storage. Importantly, cells stored at 12 °C showed similar viability and undifferentiated phenotype as the non-stored control suggesting that this temperature may be ideal for storage of CES.
Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community
Authors: Pennington Marcus J. , Rothman Jason A. , Jones Michael B. , McFrederick Quinn S. , Gan Jay , Trumble John T. 
Published: August 2017

AbstractDrought, rising temperatures, and expanding human populations are increasing water demands. Many countries are extending potable water supplies by irrigating crops with wastewater. Unfortunately, wastewater contains biologically active, long-lived pharmaceuticals, even after treatment. Run-off from farms and wastewater treatment plant overflows contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on a cosmopolitan saprophagous insect, Megaselia scalaris (Diptera: Phoridae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Female flies showed no oviposition preference for treated or untreated diets. Larvae exposed to caffeine in diets showed increased mortality, and larvae fed antibiotics and hormones showed signs of slowed development, especially in females. The normal sex ratio observed in M. scalaris from control diets was affected by exposure to caffeine and pharmaceutical mixture treatments. There was an overall effect of treatment on the flies’ microbial communities; notably, caffeine fed insects displayed higher microbial variability. Eight bacterial families accounted for approximately 95% of the total microbes in diet and insects. Our results suggest that CECs at environmentally relevant concentrations can affect the biology and microbial communities of an insect of ecological and medical importance.
Localized iron accumulation precedes nucleation and growth of magnetite crystals in magnetotactic bacteria
Authors: Werckmann Jacques , Cypriano Jefferson , Lefèvre Christopher T. , Dembelé Kassiogé , Ersen Ovidiu , Bazylinski Dennis A. , Lins Ulysses , Farina Marcos 
Published: August 2017

AbstractMany magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles that originate from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here we address the question: can iron transported inside MTB for the production of magnetite crystals be spatially mapped using electron microscopy? Cultured and uncultured MTB from brackish and freshwater lagoons were studied using analytical transmission electron microscopy in an attempt to answer this question. Scanning transmission electron microscopy was used at sub-nanometric resolution to determine the distribution of elements by implementing high sensitivity energy dispersive X-ray (EDS) mapping and electron energy loss spectroscopy (EELS). EDS mapping showed that magnetosomes are enmeshed in a magnetosomal matrix in which iron accumulates close to the magnetosome forming a continuous layer visually appearing as a corona. EELS, obtained at high spatial resolution, confirmed that iron was present close to and inside the lipid bilayer magnetosome membrane. This study provides important clues to magnetite formation in MTB through the discovery of a mechanism where iron ions accumulate prior to magnetite biomineralization.
Toxicological effects of patulin mycotoxin on the mammalian system: an overview
Authors: Pal Saurabh , Singh Neha , Ansari Kausar Mahmood 
Published: August 2017

Abstract
The mycotoxin PAT (4-hydroxy-4H-furo[3,2c]pyran-2[6H]-one) is a secondary metabolic product of molds such as Penicillium, Aspergillus, and Byssochlamys species. PAT is a common contaminant of fruit and vegetable based products, most notably apples. Despite PAT's original discovery as an antibiotic, it has come under heavy scrutiny for its potential to impart negative health effects. Studies investigating these health effects have proved its toxic potential. PAT occurrence in the food commodities poses a serious threat and necessitates novel and cost-effective mitigation methods to remove it from food products. It also creates a demand to improve handling and food processing techniques. With this being the case, several studies have been devoted to understanding the key biological and chemical attributes of PAT. While past research has elucidated a great deal, PAT contamination continues to be a challenge for the food industry. Here, we review its influence within the mammalian system, including its regulation, incidences of experimental evidence of PAT toxicity, its interaction with intracellular components, and the effects of PAT induced systemic toxicity on vital organs. Finally, key areas where future PAT research should focus to best control the PAT contamination problem within the food industry have been addressed.
Positionierungskissen in der ATP-G
Authors: Bartels Friedhilde , Eckardt Claudia 
Published: August 2017

Zusammenfassung
Basismaterial Positionierungskissen Was dem Arzt die Medikamente und Instrumente, sind für Pflegende, den Patienten oder Bewohner das
Material zur passenden Positionierung. Der Patient soll in seinen Ressourcen unterstützt werden. Die Entwicklung geht hin zu neuen
Materialien.
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment
Authors: Rapakoulia Trisevgeni , Gao Xin , Huang Yi , de Hoon Michiel , Okada-Hatakeyama Mariko , Suzuki Harukazu , Arner Erik 
Published: August 2017

Abstract

Motivation
Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations.

Results
We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens.

Availability and implementation
The CAGE sequence data used in this study is available in the DDBJ Sequence Read Archive (http://trace.ddbj.nig.ac.jp/index_e.html), accession number DRP001113.

Supplementary information
Supplementary data are available at Bioinformatics online.
MIRMMR: binary classification of microsatellite instability using methylation and mutations
Authors: Foltz Steven M , Liang Wen-Wei , Xie Mingchao , Ding Li 
Published: August 2017

Abstract

Summary
MIRMMR predicts microsatellite instability status in cancer samples using methylation and mutation information, in contrast to existing methods that rely on observed microsatellites. Additionally, MIRMMR highlights those genetic alterations contributing to microsatellite instability.

Availability and implementation
Source code is freely available at https://github.com/ding-lab/MIRMMR under the MIT license, implemented in R and supported on Unix/OS X operating systems.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improving protein fold recognition by extracting fold-specific features from predicted residue–residue contacts
Authors: Zhu Jianwei , Zhang Haicang , Li Shuai Cheng , Wang Chao , Kong Lupeng , Sun Shiwei , Zheng Wei-Mou , Bu Dongbo 
Published: August 2017

Abstract

Motivation
Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue–residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge.

Results
In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue–residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent performance improvement, indicating robustness of our approach. Furthermore, bi-clustering results of the extracted features are compatible with fold hierarchy of proteins, implying that these features are fold-specific. Together, these results suggest that the features extracted from predicted contacts are orthogonal to alignment-related features, and the combination of them could greatly facilitate fold recognition at superfamily/fold levels and template-based prediction of protein structures.

Availability and implementation
Source code of DeepFR is freely available through https://github.com/zhujianwei31415/deepfr, and a web server is available through http://protein.ict.ac.cn/deepfr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Career Progression Expectations and Aspirations of Female Police Officers in England and Wales
Authors: Boag-Munroe Fran 
Published: August 2017

AbstractThe Peelian principle that ‘the police are the public, and the public are the police’ remains a central tenet of the ‘policing by consent’ model of policing. However, the police in England and Wales are currently not gender-representative, most notably at the highest ranks. Using a sample of 21,490 officers in England and Wales between the ranks of Constable and Chief Inspector we addressed two questions to help better understand female officers’ career progression: the extent to which female officers saw hierarchical rank progression, first as realistic and second as desirable. Compared with male officers, and controlling for covariates, female constables were less likely to expect or desire progression to higher ranks, in particular Superintending and Chief Officer ranks. Gender differences in both expectation and aspiration regarding hierarchical rank progression were more limited amongst supervisory ranks. The implications of these findings for achieving a gender-representative police service are discussed.
Multimodal Study of Resting-State Functional Connectivity Networks using EEG electrodes position as seed
Authors: Rojas Gonzalo M. , Alvarez Carolina , Montoya Carlos , de la Iglesia-Vayá María , Cisternas Jaime , Gálvez Marcelo 
Published: August 2017

AbstractElectroencephalography (EEG) is the standard diagnosis method for a wide variety of diseases such as epilepsy, sleep disorders, encephalopathies, and coma, among others. Resting-state functional magnetic resonance (rs-fMRI) is currently a technique used in research in both healthy individuals as well as patients. EEG and fMRI are procedures used to obtain direct and indirect measurements of brain neural activity: EEG measures the electrical activity of the brain using electrodes placed on the scalp, and fMRI detects the changes in blood oxygenation that occur in response to neural activity. EEG has a high temporal resolution and low spatial resolution, while fMRI has high spatial resolution and low temporal resolution. Thus, the combination of EEG with rs-fMRI using different methods could be very useful for research and clinical applications. In this article, we describe and show the results of a new methodology for processing rs-fMRI using seeds positioned according to the 10-10 EEG standard. We analyze the functional connectivity and adjacency matrices obtained using 65 seeds based on 10-10 EEG scheme and 21 seeds based on 10-20 EEG. Connectivity networks are created using each 10-20 EEG seeds and are analyzed by comparisons to the seven networks that have been found in recent studies. The proposed method captures high correlation between contralateral seeds, ipsilateral and contralateral occipital seeds, and some in the frontal lobe.
Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing
Authors: Alamri Ahmad M. , Liu Xuefeng , Blancato Jan K. , Haddad Bassem R. , Wang Weisheng , Zhong Xiaogang , Choudhary Sujata , Krawczyk Ewa , Kallakury Bhaskar V. , Davidson Bruce J. , Furth Priscilla A. 
Published: August 2017

AbstractRestricted availability of cell and animal models is a rate-limiting step for investigation of salivary gland neoplasm pathophysiology and therapeutic response. Conditionally reprogrammed cell (CRC) technology enables establishment of primary epithelial cell cultures from patient material. This study tested a translational workflow for acquisition, expansion and testing of CRC-derived primary cultures of salivary gland neoplasms from patients presenting to an academic surgical practice. Results showed cultured cells were sufficient for epithelial cell-specific transcriptome characterization to detect candidate therapeutic pathways and fusion genes in addition to screening for cancer-risk-associated single nucleotide polymorphisms (SNPs) and driver gene mutations through exome sequencing. Focused study of primary cultures of a low-grade mucoepidermoid carcinoma demonstrated Amphiregulin-Mechanistic Target of Rapamycin-AKT/Protein kinase B (AKT) pathway activation, identified through bioinformatics and subsequently confirmed as present in primary tissue and preserved through different secondary 2D and 3D culture media and xenografts. Candidate therapeutic testing showed that the allosteric AKT inhibitor MK2206 reproducibly inhibited cell survival across different culture formats. In contrast, the cells appeared resistant to the adenosine triphosphate competitive AKT inhibitor GSK690693. Procedures employed here illustrate an approach for reproducibly obtaining material for pathophysiological studies of salivary gland neoplasms, and other less common epithelial cancer types, that can be executed without compromising pathological examination of patient specimens. The approach permits combined genetic and cell-based physiological and therapeutic investigations in addition to more traditional pathologic studies and can be used to build sustainable bio-banks for future inquiries.
The fallacy of identification by neutralization in the light of cytopathology nonproducing enterovirus strains
Authors: Adewumi Moses Olubusuyi , Faleye Temitope Oluwasegun Cephas , Adeniji Johnson Adekunle 
Published: August 2017

ABSTRACTWe describe the characterization of an enterovirus isolate recovered from untreated raw sewage in Ibadan, southwest Nigeria in 2010. The isolate was neutralized by specific antisera and consequently identified as Echovirus 7 (E7). Subsequent molecular characterization showed the isolate to be a mixture of E7 and Coxsackievirus A24 (CV-A24) thereby suggesting the CV-A24 strain to be non-cytopathology producing. Further molecular analysis suggested that the CV-A24 might have recombined with a Sabin poliovirus 2 (PV2) in its non-structural region. This is the first description of a Nigerian CV-A24 strain.
Open‐top chambers for temperature manipulation in taller‐stature plant communities
Authors: Welshofer Kileigh B. , Zarnetske Phoebe L. , Lany Nina K. , Thompson Luke A.E. 
Published: August 2017

Abstract

Open‐top chambers simulate global warming by passively increasing air temperatures in field experiments. They are commonly used in low‐stature alpine and arctic ecosystems, but rarely in taller‐stature plant communities because of their limited height.

We present a modified International Tundra Experiment (ITEX) chamber design for year‐round outdoor use in warming taller‐stature plant communities up to 1.5 m tall. We report a full year of results for the chambers' effects on air and soil temperature, relative humidity, and soil moisture in a northern hardwood forest clearing and a southern early successional grassland site located in Michigan, USA. Detailed construction plans are also provided.

The chambers elevated daytime air temperatures at 1 m height by 1.8°C above ambient levels, on average over an entire year, at both the northern and southern site. The chambers did not affect relative humidity at either site. The chambers did not alter average soil temperature or moisture at the northern site and reduced soil temperatures and soil moisture at the southern site. The chambers increased variability in soil freeze/thaw cycles at both sites.

The chambers achieved predicted levels of warming for mid‐century (2046–2065) scenarios consistent with the majority of representative concentration pathways in the International Panel on Climate Change Fifth Assessment Report, with minimal experimental artefact. This design is a valuable tool for examining the effects of in situ warming on understudied taller‐stature plant communities and creates the opportunity to expand future comparisons across a diversity of systems.
Predicting Short‐term Risk of Arrhythmia among Patients With Syncope: The Canadian Syncope Arrhythmia Risk Score
Authors: Thiruganasambandamoorthy Venkatesh , Stiell Ian G. , Sivilotti Marco L. A. , Rowe Brian H. , Mukarram Muhammad , Arcot Kirtana , Kwong Kenneth , McRae Andrew D. , Wells George A. , Taljaard Monica 
Published: August 2017

AbstractBackgroundSyncope can be caused by serious occult arrhythmias not evident during initial emergency department (ED) evaluation. We sought to develop a risk tool for predicting 30‐day arrhythmia or death after ED disposition.MethodsWe conducted a multicenter prospective cohort study at six tertiary care EDs and included adults (≥16 years) with syncope. We collected standardized variables from clinical evaluation and investigations including electrocardiogram and troponin at index presentation. Adjudicated outcomes included death or arrhythmias including procedural interventions for arrhythmia within 30 days. We used multivariable logistic regression to derive the prediction model and bootstrapping for interval validation to estimate shrinkage and optimism.ResultsA total of 5,010 patients (mean ± SD age = 53.4 ± 23.0 years, 54.8% females, and 9.5% hospitalized) were enrolled with 106 (2.1%) patients suffering 30‐day arrhythmia/death after ED disposition. We examined 39 variables and eight were included in the final model: lack of vasovagal predisposition, heart disease, any ED systolic blood pressure < 90 or > 180 mm Hg, troponin (>99th percentile), QRS duration > 130 msec, QTc interval > 480 msec, and ED diagnosis of cardiac/vasovagal syncope (optimism corrected C‐statistic 0.90 [95% CI = 0.87–0.93]; Hosmer‐Lemeshow p = 0.08). The Canadian Syncope Arrhythmia Risk Score had a risk ranging from 0.2% to 74.5% for scores of –2 to 8. At a threshold score of ≥0, the sensitivity was 97.1% (95% CI = 91.6%–99.4%) and specificity was 53.4% (95% CI = 52.0%–54.9%).ConclusionsThe Canadian Syncope Arrhythmia Risk Score can improve patient safety by identification of those at risk for arrhythmias and aid in acute management decisions. Once validated, the score can identify low‐risk patients who will require no further investigations.