bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects
Authors: Giacomin Paul , Zakrzewski Martha , Croese John , Su Xiaopei , Sotillo Javier , McCann Leisa , Navarro Severine , Mitreva Makedonka , Krause Lutz , Loukas Alex , Cantacessi Cinzia 
Published: September 2015

AbstractThe intestinal microbiota plays a critical role in the development of the immune system. Recent investigations have highlighted the potential of helminth therapy for treating a range of inflammatory disorders, including celiac disease (CeD); however, the mechanisms by which helminths modulate the immune response of the human host and ameliorate CeD pathology are unknown. In this study, we investigated the potential role of alterations in the human gut microbiota in helminth-mediated suppression of an inflammatory disease. We assessed the qualitative and quantitative changes in the microbiota of human volunteers with CeD prior to and following infection with human hookworms and following challenge with escalating doses of dietary gluten. Experimental hookworm infection of the trial subjects resulted in maintenance of the composition of the intestinal flora, even after a moderate gluten challenge. Notably, we observed a significant increase in microbial species richness over the course of the trial, which could represent a potential mechanism by which hookworms can regulate gluten-induced inflammation and maintain intestinal immune homeostasis.
A field experiment with elevated atmospheric CO2-mediated changes to C4 crop-herbivore interactions
Authors: Xie Haicui , Liu Kaiqiang , Sun Dandan , Wang Zhenying , Lu Xin , He Kanglai 
Published: September 2015

AbstractThe effects of elevated CO2 (E-CO2) on maize and Asian corn borer (ACB), Ostrinia furnacalis, in open-top chambers were studied. The plants were infested with ACB and exposed to ambient and elevated (550 and 750 μl/l) CO2. E-CO2 increased the plant height and kernel number per ear. The plants had lower nitrogen contents and higher TNC: N ratios under E-CO2 than at ambient CO2. The response of plant height to E-CO2 was significantly dampened in plants with ACB infestation. However, the weight gain of the survivors declined in plants grown under E-CO2. Moreover, the plant damage caused by ACB was not different among the treatments. Overwintering larvae developed under E-CO2 had a lower supercooling point than those developed under ambient CO2. The results indicated that there was a positive effect of E-CO2 on the accumulation of maize biomass, i.e., the “air-fertilizer” effect, which led to a nutritional deficiency in the plants. The fitness-related parameters of ACB were adversely affected by the CO2-mediated decreased in plant nutritional quality and ACB might alter its food consumption to compensate for these changes. Larval damage to maize under E-CO2 appears to be offset by this “air-fertilizer” effect, with reductions in larval fitness.
RTB Lectin: a novel receptor-independent delivery system for lysosomal enzyme replacement therapies
Authors: Acosta Walter , Ayala Jorge , Dolan Maureen C. , Cramer Carole L. 
Published: September 2015

AbstractEnzyme replacement therapies have revolutionized patient treatment for multiple rare lysosomal storage diseases but show limited effectiveness for addressing pathologies in “hard-to-treat” organs and tissues including brain and bone. Here we investigate the plant lectin RTB as a novel carrier for human lysosomal enzymes. RTB enters mammalian cells by multiple mechanisms including both adsorptive-mediated and receptor-mediated endocytosis and thus provides access to a broader array of organs and cells. Fusion proteins comprised of RTB and human α-L-iduronidase, the corrective enzyme for Mucopolysaccharidosis type I, were produced using a tobacco-based expression system. Fusion products retained both lectin selectivity and enzyme activity, were efficiently endocytosed into human fibroblasts and corrected the disease phenotype of mucopolysaccharidosis patient fibroblasts in vitro. RTB-mediated delivery was independent of high-mannose and mannose-6-phosphate receptors, which are exploited for delivery of currently approved lysosomal enzyme therapeutics. Thus, the RTB carrier may support distinct in vivo pharmacodynamics with potential to address hard-to-treat tissues.
Mesoporous TiO2 Yolk-Shell Microspheres for Dye-sensitized Solar Cells with a High Efficiency Exceeding 11%
Authors: Li Zhao-Qian , Chen Wang-Chao , Guo Fu-Ling , Mo Li-E , Hu Lin-Hua , Dai Song-Yuan 
Published: September 2015

AbstractYolk-shell TiO2 microspheres were synthesized via a one-pot template-free solvothermal method building on the aldol condensation reaction of acetylacetone. This unique structure shows superior light scattering ability resulting in power conversion efficiency as high as 11%. This work provided a new synthesis system for TiO2 microspheres from solid to hollow and a novel material platform for high performance solar cells.
A moment from before 365 Ma frozen in time and space
Authors: Błażejowski Błażej , Gieszcz Piotr , Brett Carlton E. , Binkowski Marcin 
Published: September 2015

AbstractThis study presents a detailed analysis of an exceptionally well-preserved articulated specimen of the trilobite Trimerocephalus from the Late Devonian of the Holy Cross Mountains in Poland. X-ray microtomography reveals the oldest direct evidence for a moulting episode known from the fossil record. The process of moulting as well as associated features observed in the investigated specimen are interpreted by comparison with extinct and extant Xiphosurida arthropods, which survived global P/T extinction and are among the closest extant relatives of trilobites. A very special moment frozen in time and space millions years ago provides rare insights into the behavior and physiology of these long-extinct arthropods.
Pain modulation effect of breathing-controlled electrical stimulation (BreEStim) is not likely to be mediated by deep and fast voluntary breathing
Authors: Hu Huijing , Li Shengai , Li Sheng 
Published: September 2015

AbstractVoluntary breathing-controlled electrical stimulation (BreEStim), a novel non-invasive and non-pharmacological treatment protocol for neuropathic pain management, was reported to selectively reduce the affective component of pain possibly by increasing pain threshold. The underlying mechanisms involved in the analgesic effect of BreEStim were considered to result from combination of multiple internal pain coping mechanisms triggered during BreEStim. Findings from our recent studies have excluded possible roles of acupuncture and aversiveness and habituation of painful electrical stimulation in mediating the analgesia effect of BreEStim. To further investigate the possible role of voluntary breathing during BreEStim, the effectiveness of fast and deep voluntary breathing-only and BreEStim on experimentally induced pain was compared in healthy human subjects. Results showed no change in electrical pain threshold after Breathing-only, but a significant increase in electrical pain threshold after BreEStim. There was no statistically significant change in other thresholds after Breathing-only and BreEStim. The findings suggest that the analgesic effect of BreEStim is not likely attributed to fast and deep voluntary breathing. Possible mechanisms are discussed.
Positive regulation of the Shewanella oneidensis OmpS38, a major porin facilitating anaerobic respiration, by Crp and Fur
Authors: Gao Tong , Ju Lili , Yin Jianhua , Gao Haichun 
Published: September 2015

AbstractMajor porins are among the most abundant proteins embedded in the outer membrane (OM) of Gram-negative bacteria, playing crucial roles in maintenance of membrane structural integrity and OM permeability. Although many OM proteins (especially c-type cytochromes) in Shewanella oneidensis, a research model for respiratory versatility, have been extensively studied, physiological significance of major porins remains largely unexplored. In this study, we show that OmpS38 and OmpA are two major porins, neither of which is responsive to changes in osmolarity or contributes to the intrinsic resistance to β-lactam antibiotics. However, OmpS38 but not OmpA is largely involved in respiration of non-oxygen electron acceptors. We then provide evidence that expression of ompS38 is transcribed from two promoters, the major of which is favored under anaerobic conditions while the other appears constitutive. The major promoter is under the direct control of Crp, the master regulator dictating respiration. As a result, the increase in the level of OmpS38 correlates with an elevated activity in Crp under anaerobic conditions. In addition, we show that the activity of the major promoter is also affected by Fur, presumably indirectly, the transcription factor for iron-dependent gene expression.
Replication of Leaf Surface Structures for Light Harvesting
Authors: Huang Zhongjia , Yang Sai , Zhang Hui , Zhang Meng , Cao Wei 
Published: September 2015

AbstractAs one of the most important hosts of natural light harvesting, foliage normally has complicated surface structures to capture solar radiances. Bio-mimicking leaf surface structures can provide novel designs of covers in photovoltaic systems. In this article, we reported on replicating leaf surface structures on poly-(methyl methacrylate) polymers to prompt harvesting efficiencies. Prepared via a double transfer process, the polymers were found to have high optical transparencies and transmission hazes, with both values exceeding 80% in some species. Benefiting from optical properties and wrinkled surfaces, the biomimetic polymers brought up to 17% gains to photovoltaic efficiencies. Through Monte-Carlo simulations of light transport, ultrahigh haze values and low reflections were attributed to lightwave guidance schemes lead by the nano- and micro-morphologies which are inherited from master leaves. Thus, leaf surface bio-mimicking can be considered as a strategic direction to design covers of light harvesting systems.
Online Sentence Reading in People With Aphasia: Evidence From Eye Tracking
Authors: Knilans Jessica , DeDe Gayle 
Published: September 2015

Purpose
There is a lot of evidence that people with aphasia have more difficulty understanding structurally complex sentences (e.g., object clefts) than simpler sentences (subject clefts). However, subject clefts also occur more frequently in English than object clefts. Thus, it is possible that both structural complexity and frequency affect how people with aphasia understand these structures.

Method
Nine people with aphasia and 8 age-matched controls participated in the study. The stimuli consisted of 24 object cleft and 24 subject cleft sentences. The task was eye tracking during reading, which permits a more fine-grained analysis of reading performance than measures such as self-paced reading.

Results
As expected, controls had longer reading times for critical regions in object cleft sentences compared with subject cleft sentences. People with aphasia showed the predicted effects of structural frequency. Effects of structural complexity in people with aphasia did not emerge on their first pass through the sentence but were observed when they were rereading critical regions of complex sentences.

Conclusions
People with aphasia are sensitive to both structural complexity and structural frequency when reading. However, people with aphasia may use different reading strategies than controls when confronted with relatively infrequent and complex sentence structures.
Verbal Description of Concrete Objects: A Method for Assessing Semantic Circumlocution in Persons With Aphasia
Authors: Antonucci Sharon M. , MacWilliam Colleen 
Published: September 2015

Purpose
We investigated from a theoretically motivated perspective what information differentiated sufficient from insufficient descriptions of objects provided by persons with aphasia.

Method
Twenty-one adults with aphasia consequent to single left-hemisphere stroke verbally described 9 living and 9 nonliving objects. Responses were scored for accuracy (i.e., sufficiency) and tallied for type and quantity of semantic feature information provided. Main effects and interactions were identified using repeated measures analyses of variance, with significant findings followed up with planned comparisons.

Results
Differences between correct and incorrect descriptions were identified with respect to both feature type and feature distinctiveness for living and nonliving items, in particular highlighting the importance of distinctive features in descriptions of both domains.

Conclusions
These findings add to the relatively small body of literature investigating semantic feature processing in adults with aphasia. This is a critical gap to close when considered in light of the preponderance of semantically based treatments for word-retrieval impairment in stroke-aphasia. Our findings provide preliminary support for the notion that semantically guided treatments for word-retrieval impairment in stroke-aphasia may be geared toward increasing specificity of semantic circumlocution to increase semantic self-cueing and to improve communication of information to conversation partners.
Parent Telegraphic Speech Use and Spoken Language in Preschoolers With ASD
Authors: Venker Courtney E. , Bolt Daniel M. , Meyer Allison , Sindberg Heidi , Ellis Weismer Susan , Tager-Flusberg Helen 
Published: September 2015

PurposeThere is considerable controversy regarding whether to use telegraphic or grammatical input when speaking to young children with language delays, including children with autism spectrum disorder (ASD). This study examined telegraphic speech use in parents of preschoolers with ASD and associations with children's spoken language 1 year later.MethodParent–child dyads (n= 55) participated when children were, on average, 3 (Time 1) and 4 years old (Time 2). The rate at which parents omitted obligatory determiners was derived from transcripts of parent–child play sessions; measures of children's spoken language were obtained from these same transcripts.ResultsTelegraphic speech use varied substantially across parents. Higher rates of parent determiner omissions at Time 1 were significantly associated with lower lexical diversity in children's spoken language at Time 2, even when controlling for children's baseline lexical diversity and nonverbal IQ. Findings from path analyses supported the directionality of effects assumed in our regression analyses, although these results should be interpreted with caution due to the limited sample size.ConclusionsTelegraphic input may have a negative impact on language development in young children with ASD. Future experimental research is needed to directly investigate how telegraphic input affects children's language learning and processing.
Variability and Diagnostic Accuracy of Speech Intelligibility Scores in Children
Authors: Hustad Katherine C. , Oakes Ashley , Allison Kristen 
Published: September 2015

Purpose
We examined variability of speech intelligibility scores and how well intelligibility scores predicted group membership among 5-year-old children with speech motor impairment (SMI) secondary to cerebral palsy and an age-matched group of typically developing (TD) children.

Method

Speech samples varying in length from 1–4 words were elicited from 24 children with cerebral palsy (mean age 60.50 months) and 20 TD children (mean age 60.33 months). Two hundred twenty adult listeners made orthographic transcriptions of speech samples (
n
= 5 per child).

Results
Variability associated with listeners made a significant contribution to explaining the variance in intelligibility scores for TD and SMI children, but the magnitude was greater for TD children. Intelligibility scores differentiated very well between children who have SMI and TD children when intelligibility was at or below approximately 75% and above approximately 85%.

Conclusions
Intelligibility seems to be a useful clinical tool for differentiating between TD children and children with SMI at 5 years of age; however, there is considerable variability within and between listeners, highlighting the need for more than one listener per child to ensure validity of an intelligibility measure.
Vertical‐cavity surface‐emitting lasers with birefringence splitting above 250 GHz
Authors: Pusch T. , Lindemann M. , Gerhardt N.C. , Hofmann M.R. , Michalzik R. 
Published: September 2015

Using the elasto‐optic effect, increase of the frequency difference between the two orthogonally polarised modes, the so‐called birefringence splitting, in standard single‐mode oxide‐confined AlGaAs‐based vertical‐cavity surface‐emitting lasers is achieved to values beyond 250 GHz. A large birefringence is required for the generation of ultra‐fast polarisation oscillations for potential future high‐speed communication applications.
ICT: isotope correction toolbox
Authors: Jungreuthmayer Christian , Neubauer Stefan , Mairinger Teresa , Zanghellini Jürgen , Hann Stephan 
Published: September 2015

Abstract
Summary: Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences—in particular for complex isotopic systems—is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms.
Availability and implementation: Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/
Contact: {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at}
Supplementary information: Supplementary data are available at Bioinformatics online.
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
Authors: Leggett Richard M. , Heavens Darren , Caccamo Mario , Clark Matthew D. , Davey Robert P. 
Published: September 2015

Abstract
Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving.
Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.
Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK.
Contact: richard.leggett@tgac.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Expression of Malic Enzymes in Sebaceous Lesions
Authors: Su Ting-Fu , Gao Hong-Wei 
Published: September 2015

Abstract:
Malic enzymes (MEs) are involved in fatty acid biosynthesis and lipid accumulation, and their expression in sebocytes and sebaceous lesions has not been investigated. The aims of this study were to examine ME1 and ME2 expression in normal skin and sebaceous lesions. A total of 68 cases including 5 specimens of normal skin, 12 facial lesions showing sebaceous hyperplasia, 18 sebaceous adenomas, 10 sebaceomas, 13 steatocystomas, and 10 sebaceous carcinomas were examined for the expression of ME1 and ME2. All benign and malignant sebaceous lesions showed ME1+(vesicular) in clear cells and ME2+(granular) in nonclear cells, respectively. ME1−/ME2+ phenotype is seen in basal sebocytes, basal keratinocytes, sweat glands, and outer root sheath cells and hence not specific. This study demonstrates that ME1+(vesicular)/ME2+(granular) expression phenotype may have a potential to be a valuable marker for sebaceous differentiation. It is necessary to perform large-scale studies including skin tumors with a clear cell morphology that may mimic sebaceous differentiation.
A pathway-centric view of spatial proximity in the 3D nucleome across cell lines
Authors: Karathia Hiren , Kingsford Carl , Girvan Michelle , Hannenhalli Sridhar 
Published: September 2015

AbstractSpatial organization of the genome is critical for condition-specific gene expression. Previous studies have shown that functionally related genes tend to be spatially proximal. However, these studies have not been extended to multiple human cell types, and the extent to which context-specific spatial proximity of a pathway is related to its context-specific activity is not known. We report the first pathway-centric analyses of spatial proximity in six human cell lines. We find that spatial proximity of genes in a pathway tends to be context-specific, in a manner consistent with the pathway’s context-specific expression and function; housekeeping genes are ubiquitously proximal to each other, and cancer-related pathways such as p53 signaling are uniquely proximal in hESC. Intriguingly, we find a correlation between the spatial proximity of genes and interactions of their protein products, even after accounting for the propensity of co-pathway proteins to interact. Related pathways are also often spatially proximal to one another, and housekeeping genes tend to be proximal to several other pathways suggesting their coordinating role. Further, the spatially proximal genes in a pathway tend to be the drivers of the pathway activity and are enriched for transcription, splicing and transport functions. Overall, our analyses reveal a pathway-centric organization of the 3D nucleome whereby functionally related and interacting genes, particularly the initial drivers of pathway activity, but also genes across multiple related pathways, are in spatial proximity in a context-specific way. Our results provide further insights into the role of differential spatial organization in cell type-specific pathway activity.