bluuebunny/crossref_metadata_2025_split huggingface dataset:
Difference between Chitosan Hydrogels via Alkaline and Acidic Solvent Systems
Authors: Nie Jingyi , Wang Zhengke , Hu Qiaoling 
Published: October 2016

AbstractChitosan (CS) has generated considerable interest for its desirable properties and wide applications. Hydrogel has been proven to be a major and vital form in the applications of CS materials. Among various types of CS hydrogels, physical cross-linked CS hydrogels are popular, because they avoided the potential toxicity and sacrifice of intrinsic properties caused by cross-linking or reinforcements. Alkaline solvent system and acidic solvent system are two important solvent systems for the preparation of physical cross-linked CS hydrogels, and also lay the foundations of CS hydrogel-based materials in many aspects. As members of physical cross-linked CS hydrogels, gel material via alkaline solvent system showed significant differences from that via acidic solvent system, but the reasons behind are still unexplored. In the present work, we studied the difference between CS hydrogel via alkaline system and acidic system, in terms of gelation process, hydrogel structure and mechanical property. In-situ/pseudo in-situ studies were carried out, including fluorescent imaging of gelation process, which provided dynamic visualization. Finally, the reasons behind the differences were explained, accompanied by the discussion about design strategy based on gelation behavior of the two systems.
The impact of reward and punishment on skill learning depends on task demands
Authors: Steel Adam , Silson Edward H. , Stagg Charlotte J. , Baker Chris I. 
Published: October 2016

AbstractReward and punishment motivate behavior, but it is unclear exactly how they impact skill performance and whether the effect varies across skills. The present study investigated the effect of reward and punishment in both a sequencing skill and a motor skill context. Participants trained on either a sequencing skill (serial reaction time task) or a motor skill (force-tracking task). Skill knowledge was tested immediately after training, and again 1 hour, 24–48 hours, and 30 days after training. We found a dissociation of the effects of reward and punishment on the tasks, primarily reflecting the impact of punishment. While punishment improved serial reaction time task performance, it impaired force-tracking task performance. In contrast to prior literature, neither reward nor punishment benefitted memory retention, arguing against the common assumption that reward ubiquitously benefits skill retention. Collectively, these results suggest that punishment impacts skilled behavior more than reward in a complex, task dependent fashion.
Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome
Authors: Mukherjee Souvik , Mitra Rupak , Maitra Arindam , Gupta Satyaranjan , Kumaran Srikala , Chakrabortty Amit , Majumder Partha P. 
Published: October 2016

AbstractThe skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum.
Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS)
Authors: Calderaro Adriana , Arcangeletti Maria Cristina , Rodighiero Isabella , Buttrini Mirko , Montecchini Sara , Vasile Simone Rosita , Medici Maria Cristina , Chezzi Carlo , De Conto Flora 
Published: October 2016

AbstractIn this study matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a reliable identification method for the diagnosis of bacterial and fungal infections, is presented as an innovative tool to investigate the protein profile of cell cultures infected by the most common viruses causing respiratory tract infections in humans. MALDI-TOF MS was applied to the identification of influenza A and B viruses, adenovirus C species, parainfluenza virus types 1, 2 and 3, respiratory syncytial virus, echovirus, cytomegalovirus and metapneumovirus. In this study MALDI-TOF MS was proposed as a model to be applied to the identification of cultivable respiratory viruses using cell culture as a viral proteins enrichment method to the proteome profiling of virus infected and uninfected cell cultures. The reference virus strains and 58 viruses identified from respiratory samples of subjects with respiratory diseases positive for one of the above mentioned viral agents by cell culture were used for the in vitro infection of suitable cell cultures. The isolated viral particles, concentrated by ultracentrifugation, were used for subsequent protein extraction and their spectra profiles were generated by MALDI-TOF MS analysis. The newly created library allowed us to discriminate between uninfected and respiratory virus infected cell cultures.
Targeting inflammasome/IL-1 pathways for cancer immunotherapy
Authors: Guo Beichu , Fu Shunjun , Zhang Jinyu , Liu Bei , Li Zihai 
Published: October 2016

AbstractThe inflammatory microenvironment has been shown to play important roles in various stages of tumor development including initiation, growth, and metastasis. The inflammasome is a critical innate immune pathway for the production of active IL-1β, a potent inflammatory cytokine. Although inflammasomes are essential for host defense against pathogens and contribute to autoimmune diseases, their role in tumor progression remains controversial. Here, our results demonstrate that the inflammasome and IL-1β pathway promoted tumor growth and metastasis in animal and human breast cancer models. We found that tumor progression was associated with the activation of inflammasome and elevated levels of IL-1β at primary and metastatic sites. Mice deficient for inflammasome components exhibited significantly reduced tumor growth and lung metastasis. Furthermore, inflammasome activation promoted the infiltration of myeloid cells such as myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) into tumor microenvironments. Importantly, blocking IL-1R with IL-1R antagonist (IL-Ra) inhibited tumor growth and metastasis accompanied by decreased myeloid cell accumulation. Our results suggest that targeting the inflammasome/IL-1 pathway in tumor microenvironments may provide a novel approach for the treatment of cancer.
Molecular cloning and expression of an encoding galactinol synthase gene (AnGolS1) in seedling of Ammopiptanthus nanus
Authors: Liu YuDong , Zhang Li , Chen LiJing , Ma Hui , Ruan YanYe , Xu Tao , Xu ChuanQiang , He Yi , Qi MingFang 
Published: October 2016

AbstractBased on the galactinol synthase (AnGolS1) fragment sequence from a cold-induced Suppression Subtractive Hybridization (SSH) library derived from Ammopiptanthus nanus (A. nanus) seedlings, AnGolS1 mRNA (including the 5′ UTR and 3′ UTR) (GenBank accession number: GU942748) was isolated and characterized by rapid amplification of cDNA ends polymerase chain reaction (RACE–PCR). A substrate reaction test revealed that AnGolS1 possessed galactinol synthase activity in vitro and could potentially be an early-responsive gene. Furthermore, quantitative real-time PCR (qRT-PCR) indicated that AnGolS1 was responded to cold, salts and drought stresses, however, significantly up-regulated in all origans by low temperatures, especially in plant stems. In addition, the hybridization signals in the fascicular cambium were strongest in all cells under low temperature. Thus, we propose that AnGolS1 plays critical roles in A. nanus low-temperature stress resistance and that fascicular cambium cells could be involved in AnGolS1 mRNA transcription, galactinol transportation and coordination under low-temperature stress.
Bilingual Language Assessment: Contemporary Versus Recommended Practice in American Schools
Authors: Arias Graciela , Friberg Jennifer 
Published: October 2016

Purpose
The purpose of this study was to identify current practices of school-based speech-language pathologists (SLPs) in the United States for bilingual language assessment and compare them to American Speech-Language-Hearing Association (ASHA) best practice guidelines and mandates of the Individuals with Disabilities Education Act (IDEA, 2004).

Method
The study was modeled to replicate portions of Caesar and Kohler's (2007) study and expanded to include a nationally representative sample. A total of 166 respondents completed an electronic survey.

Results
Results indicated that the majority of respondents have performed bilingual language assessments. Furthermore, the most frequently used informal and standardized assessments were identified. SLPs identified supports, and barriers to assessment, as well as their perceptions of graduate preparation.

Conclusion
The findings of this study demonstrated that although SLPs have become more compliant to ASHA and IDEA guidelines, there is room for improvement in terms of adequate training in bilingual language assessment.
First Record of Fibropapillomatosis in a Green Turtle Chelonia mydas from the Baja California Peninsula
Authors: Reséndiz Eduardo , Flores-Ramírez Sergio , Koch Volker , Cordero-Tapia Amaury 
Published: October 2016

Abstract
Fibropapillomatosis (FP) is characterized by multiple fibroepithelial tumors in all parts of the skin and has been reported in sea turtles worldwide. Clinically infected individuals are often emaciated and anemic. In Mexico, however, there are few records of this disease. In this study of green turtles Chelonia mydas in Laguna San Ignacio in Baja California Sur (BCS), we noted one juvenile with multifocal fibropapilloma lesions on the external upper surface of its eyes and hind flippers. Light microscopy revealed hyperkeratosis, epidermal hyperplasia, dermal papillary projections, and fibroblast proliferation. Electron microscopy revealed viral particles. Biopsies of normal skin were done to determine the origin of the turtle through genetic analysis. Its mitochondrial DNA matched that of a haplotype (CMP2) from a Hawaiian green turtle population. Finding FP in a turtle captured in BCS elucidates the need for further monitoring along the west coast of Mexico. Further investigation should include testing tumors to detect and characterize any chelonid herpesviruses and explore any association with FP and other diseases that pose a health risk to other sea turtle species.
Received March 26, 2016; accepted August 3, 2016 Published online October 27, 2016
Xenolog classification
Authors: Darby Charlotte A , Stolzer Maureen , Ropp Patrick J , Barker Daniel , Durand Dannie 
Published: October 2016

Abstract

Motivation
Orthology analysis is a fundamental tool in comparative genomics. Sophisticated methods have been developed to distinguish between orthologs and paralogs and to classify paralogs into subtypes depending on the duplication mechanism and timing, relative to speciation. However, no comparable framework exists for xenologs: gene pairs whose history, since their divergence, includes a horizontal transfer. Further, the diversity of gene pairs that meet this broad definition calls for classification of xenologs with similar properties into subtypes.

Results
We present a xenolog classification that uses phylogenetic reconciliation to assign each pair of genes to a class based on the event responsible for their divergence and the historical association between genes and species. Our classes distinguish between genes related through transfer alone and genes related through duplication and transfer. Further, they separate closely-related genes in distantly-related species from distantly-related genes in closely-related species. We present formal rules that assign gene pairs to specific xenolog classes, given a reconciled gene tree with an arbitrary number of duplications and transfers. These xenology classification rules have been implemented in software and tested on a collection of ∼13 000 prokaryotic gene families. In addition, we present a case study demonstrating the connection between xenolog classification and gene function prediction.

Availability and Implementation
The xenolog classification rules have been implemented in Notung 2.9, a freely available phylogenetic reconciliation software package. http://www.cs.cmu.edu/~durand/Notung. Gene trees are available at http://dx.doi.org/10.7488/ds/1503.

Supplementary information
Supplementary data are available at Bioinformatics online.
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
Authors: Paez-Espino David , Chen I.-Min A. , Palaniappan Krishna , Ratner Anna , Chu Ken , Szeto Ernest , Pillay Manoj , Huang Jinghua , Markowitz Victor M. , Nielsen Torben , Huntemann Marcel , K. Reddy T. B. , Pavlopoulos Georgios A. , Sullivan Matthew B. , Campbell Barbara J. , Chen Feng , McMahon Katherine , Hallam Steve J. , Denef Vincent , Cavicchioli Ricardo , Caffrey Sean M. , Streit Wolfgang R. , Webster John , Handley Kim M. , Salekdeh Ghasem H. , Tsesmetzis Nicolas , Setubal Joao C. , Pope Phillip B. , Liu Wen-Tso , Rivers Adam R. , Ivanova Natalia N. , Kyrpides Nikos C. 
Published: October 2016

AbstractViruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from &gt;6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
Caecilius Statius
Authors: Manuwald Gesine 
Published: October 2016

Caecilius (Statius) (b. c. 230–d. 168/167 bce) was a Roman Republican playwright of fabulae palliatae (“comedies in Greek dress”). Situated in between the two famous representatives Plautus and Terence, of whom complete plays survive, he represents an important stage in the development of Roman palliata comedy. Yet, although he is the best-documented comic playwright among those whose works only survive in fragments and was highly regarded in Antiquity (see Ancient Reception), what remains are just forty-two titles of comedies and almost three hundred (partly incomplete) lines quoted in later writers. In aspects such as metrical variety, use of colorful language or employment of linguistic effects and puns Caecilius Statius seems to have followed the conventions of his predecessors; in other respects, such as choice of themes or engagement with the literary tradition, he looks forward to Terence. Caecilius Statius’s comedies apparently included serious thoughts on moral and social issues, mostly related to the immediate family, the corresponding relationships, and the impact of one’s personal affairs on one’s position in society, but they also provided effective drama. As with other fragmentary playwrights, the remains of Caecilius Statius’s dramas have been overshadowed by the fully extant plays by Plautus and Terence. Therefore, he is regularly mentioned in literary histories and overviews of Roman comedy, especially in the context of attempts at establishing a coherent, evolutionary history of this dramatic genre (see Oxford Bibliographies articles in Classics Latin Drama and Latin Poetry: From the Beginnings through the End of the Republic), but there have been fewer studies specifically devoted to him.
Reconstruction of Alar Nasal Cartilage Defects Using a Tissue Engineering Technique Based on a Combined Use of Autologous Chondrocyte Micrografts and Platelet-rich Plasma: Preliminary Clinical and Instrumental Evaluation
Authors: Gentile Pietro , Scioli Maria G. , Bielli Alessandra , Orlandi Augusto , Cervelli Valerio 
Published: October 2016

Background:Developing cartilage constructs with injectability, appropriate matrix composition, and persistent cartilaginous phenotype remains an enduring challenge in cartilage repair. The combined use of autologous chondrocyte micrografts and platelet-rich plasma (PRP) is an alternative that opens a new era in this field.Methods:At the Department of Plastic and Reconstructive Surgery, University of Rome Tor Vergata, Italy, 11 patients underwent nasal alar reconstruction with chondrocyte micrografts gently poured onto PRP in solid form. A computed tomographic scan control was performed after 12 months. Pearson’s Chi-square test was used to investigate difference in cartilage density between native and newly formed cartilages.Results:The constructs of chondrocyte micrografts–PRP that were subcutaneously injected resulted in a persistent cartilage tissue with appropriate morphology, adequate central nutritional perfusion without central necrosis or ossification, and further augmented nasal dorsum without obvious contraction and deformation.Conclusion:This report demonstrated that chondrocyte micrografts derived from nasal septum poured onto PRP in solid form are useful for cartilage regeneration in patients with external nasal valve collapse.
IMPACT OF VITREORETINAL INTERFACE ARCHITECTURE ON SUCCESSFUL VITREOMACULAR TRACTION RESOLUTION IN EYES SCHEDULED FOR INTRAVITREAL OCRIPLASMIN THERAPY
Authors: Paul Christoph , Heun Christine , Müller Hans H. , Fauser Sascha , Kaymak Hakan , Kazerounian Sara , Sekundo Walter , Mennel Stefan , Meyer Carsten H. , Schmitz-Valckenberg Steffen , Koss Michael J. , Feltgen Nicolas , Bertelmann Thomas 
Published: October 2016

Purpose:
To evaluate the impact of the vitreoretinal interface architecture, in specific the angle between the posterior vitreous cortex and the internal limiting membrane, on vitreomacular traction (VMT) resolution in eyes treated with intravitreally injected ocriplasmin (Jetrea).

Methods:
Retrospective, multicenter cohort study and exploratory data analysis. Spectral domain optical coherence tomography assessments were performed before scheduled ocriplasmin injections. General (age and sex) as well as ocular variables (lens status, presence of epiretinal membrane formations, horizontal diameter of VMT, central retinal thickness, and in particular various prespecified angles between the posterior vitreous cortex and internal limiting membrane) were analyzed to evaluate their impact on successful VMT resolution.

Results:
Fifty-nine eyes of 59 patients were included. Univariate analysis of age (odds ratio [OR]: 0.881; 95% CI: [0.812–0.955]; P = 0.0022) and lens status (OR: 11.03; 95% CI: [2.23–54.57]; P = 0.0033) had a significant impact on successful VMT resolution, whereas sex (OR: 0.668; 95% CI: [0.126–2.065]; P = 0.4906), epiretinal membrane formation (OR: 0.581; 95% CI: [0.168–2.006]; P = 0.3903), horizontal diameter of VMT (OR: 0.99930; 95% CI: [0.99825–1.00035]; P = 0.1886), and central retinal thickness (OR: 0.9985; 95% CI: [0.9934–1.00436]; P = 0.56) failed. The angle at 500 μm apart from the fovea centralis, irrespective if measured nasally (OR: 1.135; 95% CI: [1.013–1.272]; P = 0.0289) or temporally (OR: 1.099; 95% CI: [1.001–1.208]; P = 0.0485), showed a significant correlation with VMT resolution.

Conclusion:
The angle between the posterior vitreous cortex and the internal limiting membrane 500 μm apart from the fovea centralis correlates with VMT resolution and may be a clinically useful marker for selection of patients to be treated with ocriplasmin. This observation needs to be proven in a prospective confirmatory investigation.
Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines
Authors: Babcock Hazen P. , Zhuang Xiaowei 
Published: October 2016

AbstractThe resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2-3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.