bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined CT radiomics of primary tumor and metastatic lymph nodes improves prediction of loco-regional control in head and neck cancer
Authors: Bogowicz Marta , Tanadini-Lang Stephanie , Guckenberger Matthias , Riesterer Oliver 
Published: October 2019

AbstractLoco-regional control (LRC) is a major clinical endpoint after definitive radiochemotherapy (RCT) of head and neck cancer (HNC). Radiomics has been shown a promising biomarker in cancer research, however closer related to primary tumor control than composite endpoints. Radiomics studies often focus on the analysis of primary tumor (PT). We hypothesize that the combination of PT and lymph nodes (LN) radiomics better predicts LRC in HNC treated with RCT. Radiomics analysis was performed in CT images of 128 patients using Z-Rad implementation (training n = 77, validation n = 51). 285 features were extracted from PT and involved LN. Features were preselected with the maximum relevance minimum redundancy method and the multivariate Cox model was trained using least absolute shrinkage and selection operator. The mixed model was based on the combination of PT and LN radiomics, whereas the PT model included only the PT features. The mixed model showed significantly higher performance than the PT model (p < 0.01), c-index of 0.67 and 0.63, respectively; and better risk group stratification. The clinical nodal status was not a significant predictor in the combination with PT radiomics. This study shows that the LRC can be better predicted by expansion of radiomics analysis with LN features.
Pluronic gel-based burrowing assay for rapid assessment of neuromuscular health in C. elegans
Authors: Lesanpezeshki Leila , Hewitt Jennifer E. , Laranjeiro Ricardo , Antebi Adam , Driscoll Monica , Szewczyk Nathaniel J. , Blawzdziewicz Jerzy , Lacerda Carla M. R. , Vanapalli Siva A. 
Published: October 2019

AbstractWhole-organism phenotypic assays are central to the assessment of neuromuscular function and health in model organisms such as the nematode C. elegans. In this study, we report a new assay format for engaging C. elegans in burrowing that enables rapid assessment of nematode neuromuscular health. In contrast to agar environments that pose specific drawbacks for characterization of C. elegans burrowing ability, here we use the optically transparent and biocompatible Pluronic F-127 gel that transitions from liquid to gel at room temperature, enabling convenient and safe handling of animals. The burrowing assay methodology involves loading animals at the bottom of well plates, casting a liquid-phase of Pluronic on top that solidifies via a modest temperature upshift, enticing animals to reach the surface via chemotaxis to food, and quantifying the relative success animals have in reaching the chemoattractant. We study the influence of Pluronic concentration, gel height and chemoattractant choice to optimize assay performance. To demonstrate the simplicity of the assay workflow and versatility, we show its novel application in multiple areas including (i) evaluating muscle mutants with defects in dense bodies and/or M-lines (pfn-3, atn-1, uig-1, dyc-1, zyx-1, unc-95 and tln-1), (ii) tuning assay conditions to reveal changes in the mutant gei-8, (iii) sorting of fast burrowers in a genetically-uniform wild-type population for later quantitation of their distinct muscle gene expression, and (iv) testing proteotoxic animal models of Huntington and Parkinson’s disease. Results from our studies show that stimulating animals to navigate in a dense environment that offers mechanical resistance to three-dimensional locomotion challenges the neuromuscular system in a manner distinct from standard crawling and thrashing assays. Our simple and high throughput burrowing assay can provide insight into molecular mechanisms for maintenance of neuromuscular health and facilitate screening for therapeutic targets.
Gene and lncRNA co-expression network analysis reveals novel ceRNA network for triple-negative breast cancer
Authors: Le Kehao , Guo Hui , Zhang Qiulei , Huang Xiaojuan , Xu Ming , Huang Ziwei , Yi Pengfei 
Published: October 2019

AbstractBreast cancer is the most frequently diagnosed malignancy among women, and triple-negative breast cancer (TNBC) is a highly aggressive subtype. Increasing evidence has shown that lncRNAs are involved in tumor growth, cell-cycle, and apoptosis through interactions with miRNAs or mRNAs. However, there is still limited data on ceRNAs involved in the molecular mechanisms underlying TNBC. In this study, we applied the weighted gene co-expression network analysis to the existing microarray mRNA and lncRNA expression data obtained from the breast tissues of TNBC patients to find the hub genes and lncRNAs involved in TNBC. Functional enrichment was performed on the module that correlated with Ki-67 status the most (Turquoise module). The hub genes in the Turquoise module were found to be associated with DNA repair, cell proliferation, and the p53 signaling pathway. We performed co-expression analysis of the protein-coding and lncRNA hub genes in the Turquoise module. Analysis of the RNA-seq data obtained from The Cancer Genome Atlas database revealed that the protein-coding genes and lncRNAs that were co-expressed were also differentially expressed in the TNBC tissues compared with the normal mammary tissues. On the basis of establishing the ceRNA network, two mRNAs (RAD51AP1 and TYMS) were found to be correlated with overall survival in TNBC. These results suggest that TNBC-specific mRNA and lncRNAs may participate in a complex ceRNA network, which represents a potential therapeutic target for the treatment of TNBC.
Orientation analysis of pentacene molecules in organic field-effect transistor devices using polarization-dependent Raman spectroscopy
Authors: Bhardwaj Bishwajeet Singh , Sugiyama Takeshi , Namba Naoko , Umakoshi Takayuki , Uemura Takafumi , Sekitani Tsuyoshi , Verma Prabhat 
Published: October 2019

AbstractPentacene, an organic molecule, is a promising material for high-performance field effect transistors due to its high charge carrier mobility in comparison to usual semiconductors. However, the charge carrier mobility is strongly dependent on the molecular orientation of pentacene in the active layer of the device, which is hard to investigate using standard techniques in a real device. Raman scattering, on the other hand, is a high-resolution technique that is sensitive to the molecular orientation. In this work, we investigated the orientation distribution of pentacene molecules in actual transistor devices by polarization-dependent Raman spectroscopy and correlated these results with the performance of the device. This study can be utilized to understand the distribution of molecular orientation of pentacene in various electronic devices and thus would help in further improving their performances.
Magnetic oxygen stored in quasi-1D form within BaAl2O4 lattice
Authors: Vrankić Martina , Šarić Ankica , Bosnar Sanja , Pajić Damir , Dragović Jure , Altomare Angela , Falcicchio Aurelia , Popović Jasminka , Jurić Marijana , Petravić Mladen , Badovinac Ivana Jelovica , Dražić Goran 
Published: October 2019

AbstractInorganic materials that enable a link between the storage and release of molecular oxygen offer a fertile ground in continuous quest for the applications that can potentially reduce energy consumption and thus minimize adverse effects on the environment. Herein, we address reversible intake/release of an oxygen within the BaAl2O4 material as evidenced by unexpected magnetic ordering. Magnetic measurements unveil that an oxygen is stored in the form of condensed matter, creating a kind of low dimensional, chain-like assembly within the tunnels of BaAl2O4 structure. We demonstrate that oxygen is adsorbed simply by staying in air, at ambient conditions, and released relatively quickly by staying in the He or other gas atmosphere of several millibars pressure even at 300 K.
Structural and In Vitro Functional Analyses of Novel Plant-Produced Anti-Human PD1 Antibody
Authors: Rattanapisit Kaewta , Phakham Tanapati , Buranapraditkun Supranee , Siriwattananon Konlavat , Boonkrai Chatikorn , Pisitkun Trairak , Hirankarn Nattiya , Strasser Richard , Abe Yoshito , Phoolcharoen Waranyoo 
Published: October 2019

AbstractImmunotherapy has emerged as a promising and effective treatment for cancer. The frequently used immunotherapy agents are immune checkpoint inhibitors, such as antibodies specific to PD1, PD-L1, or CTLA-4. However, these drugs are highly expensive, and most people in the world cannot access the treatment. The development of recombinant protein production platforms that are cost-effective, scalable, and safe is needed. Plant platforms are attractive because of their low production cost, speed, scalability, lack of human and animal pathogens, and post-translational modifications that enable them to produce effective monoclonal antibodies. In this study, an anti-PD1 IgG4 monoclonal antibody (mAb) was transiently produced in Nicotiana benthamiana leaves. The plant-produced anti-PD1 mAb was compared to the commercial nivolumab produced in CHO cells. Our results showed that both antibodies have similar protein structures, and the N-glycans on the plant-produced antibody lacks plant-specific structures. The PD1 binding affinity of the plant-produced and commercial nivolumab, determined by two different techniques, that is, enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR), are also comparable. Plant-produced nivolumab binds to human PD1 protein with high affinity and specificity, blocks the PD-1/PD-L1 interaction, and enhances T cell function, comparable to commercial nivolumab. These results confirmed that plant-produced anti-PD1 antibody has the potential to be effective agent for cancer immunotherapy.
School environment associates with lung function and autonomic nervous system activity in children: a cross-sectional study
Authors: Paciência Inês , Rufo João Cavaleiro , Silva Diana , Martins Carla , Mendes Francisca , Rama Tiago , Rodolfo Ana , Madureira Joana , Delgado Luís , de Oliveira Fernandes Eduardo , Padrão Patrícia , Moreira Pedro , Severo Milton , Pina Maria Fátima , Teixeira João Paulo , Barros Henrique , Ruokolainen Lasse , Haahtela Tari , Moreira André 
Published: October 2019

AbstractChildren are in contact with local environments, which may affect respiratory symptoms and allergic sensitization. We aimed to assess the effect of the environment and the walkability surrounding schools on lung function, airway inflammation and autonomic nervous system activity. Data on 701 children from 20 primary schools were analysed. Lung function, airway inflammation and pH from exhaled breath condensate were measured. Pupillometry was performed to evaluate autonomic activity. Land use composition and walkability index were quantified within a 500 m buffer zone around schools. The proportion of effects explained by the school environment was measured by mixed-effect models. We found that green school areas tended to be associated with higher lung volumes (FVC, FEV1 and FEF25–75%) compared with built areas. FVC was significantly lower in-built than in green areas. After adjustment, the school environment explained 23%, 34% and 99.9% of the school effect on FVC, FEV1, and FEF25–75%, respectively. The walkability of school neighbourhoods was negatively associated with both pupil constriction amplitude and redilatation time, explaining −16% to 18% of parasympathetic and 8% to 29% of sympathetic activity. Our findings suggest that the environment surrounding schools has an effect on the lung function of its students. This effect may be partially mediated by the autonomic nervous system.
Highly Sensitive and Full Range Detectable Humidity Sensor using PEDOT:PSS, Methyl Red and Graphene Oxide Materials
Authors: Hassan Gul , Sajid Memoon , Choi Changhwan 
Published: October 2019

AbstractSingle transducer with humidity sensing materials has limitations in both range and sensitivity, which cannot be used to detect the full range of humidity with consistent sensitivity. To enlarge range and improve sensitivity in the all range relative humidity (RH), we propose a highly sensitive and full range detectable humidity sensor based on multiple inter-digital transducer (IDT) electrodes connected in series with poly(3,4-ethylenedioxythiophene) doped poly (styrene sulfonate) anions (PEDOT: PSS), C15H15N3O2 (Methyl Red), and graphene oxide (GO) thin films as the active sensing materials. The humidity sensor with single active material has a limit in the detecting ranges, where the GO, PEDOT: PSS, and Methyl Red materials have sensing responses of 0 to 78% RH, 30 to 75% RH, and 25 to 100% RH, respectively. However, a humidity sensor using combined three active materials can respond to much wider range of RH with high sensitivity, where the IDTs and the active regions were prepared using ink-jet printing and spin coating, respectively. This proposed sensor can detect a full range of 0% RH to 100% RH. The response and recovery times are 1 sec and 3.5 sec, respectively. Our single sensing device using multiple IDTs connected different active materials in series can overcome the limitations of single transducer based sensor for the high performance sensor applications.
Improved lyophilization conditions for long-term storage of bacteriophages
Authors: Manohar Prasanth , Ramesh Nachimuthu 
Published: October 2019

AbstractPhage therapy is one of the promising alternatives to combat the increasing problem of antibiotic resistance. Lyophilization is used for the preparation of pharmaceutical products to improve their stability in long-term storage. The aim of this study was to improve the stability of lyophilized bacteriophages using different excipients. Three lytic bacteriophages Escherichia phage ECP311, Klebsiella phage KPP235 and Enterobacter phage ELP140 were subjected to lyophilization using six different excipients: glucose, sucrose, gelatin, mannitol, polyethylene glycol and sorbitol. The lyophilized phages were stored at 4 °C and 37 °C and rehydrated using biological saline to test their viability at 5 months interval up to 20 months. The results showed that the use of sucrose, gelatin and their combination was beneficial in maintaining the viability of phages post-lyophilization. When lyophilized phages were stored at 4 °C, their viability was maintained up to 20 months, but at 37 °C there was a reduction in activity after 10 months. This is one of the few studies to report the lyophilization of phage cocktails to have viability for up to 10 months. Our study identified promising lyophilization excipients to effectively lyophilize bacteriophages for pharmaceutical applications and long-term storage.
Western Aphasia Battery–Revised Profiles in Primary Progressive Aphasia and Primary Progressive Apraxia of Speech
Authors: Clark Heather M. , Utianski Rene L. , Duffy Joseph R. , Strand Edythe A. , Botha Hugo , Josephs Keith A. , Whitwell Jennifer L. 
Published: October 2019

Purpose

The primary aim was to examine the utility of the Western Aphasia Battery–Revised (WAB-R;
Kertesz, 2007
) for classifying variants of primary progressive aphasia (PPA). Traditional WAB-R metrics of Aphasia Quotient (AQ), subtest scores, WAB-R classification, and several novel metrics were examined. A secondary aim was to examine these same WAB-R metrics in individuals with primary progressive apraxia of speech (PPAOS).

Method
A retrospective analysis of WAB-R records from 169 participants enrolled in a study of neurodegenerative speech and language disorders was conducted. PPA/PPAOS classification was determined by consensus review of speech, language, and cognitive profiles. Scores on each of the WAB-R subtests were obtained to derive AQ, WAB-R aphasia profile, and 3 ratios reflecting relative performance on subtests.

Results
Mean AQ was significantly higher in the PPAOS group compared to all PPA variants except primary fluent aphasia. AQ above the normal cutoff was observed for 20% of participants with PPA. Significant main effects of group were noted for each of the subtests. Follow-up comparisons most frequently discriminated PPAOS, primary agrammatic aphasia (PAA), and logopenic progressive aphasia. Primary fluent aphasia and semantic dementia (SD) subtest scores were less distinctive, with the exception of Naming for SD, which was significantly lower than for PAA and PPAOS. When the WAB-R AQ detected aphasia, a classification of anomic aphasia was most frequently observed; this pattern held true for each of the PPA variants. The mean Information Content:Naming ratio was highest for SD, and the mean Comprehension:Fluency ratio was highest for PAA.

Conclusions
In the current study, AQ underestimated the presence of PPA and WAB-R classification did not distinguish among PPA classification determined by consensus. Performance on individual subtests and relative performance across subtests demonstrated inconsistent alignment with PPA classification. We conclude the WAB-R in isolation is inadequate to detect or characterize PPA. We instead suggest utilizing the WAB-R as 1 component of a comprehensive language and motor speech assessment when PPA is suspected.
Vocal Communication With Canonical Syllables Predicts Later Expressive Language Skills in Preschool-Aged Children With Autism Spectrum Disorder
Authors: McDaniel Jena , Woynaroski Tiffany , Keceli-Kaysili Bahar , Watson Linda R. , Yoder Paul 
Published: October 2019

Purpose
We examined associations between vocal communication with canonical syllables and expressive language and then examined 2 potential alternative explanations for such associations.

Method

Specifically, we tested whether the associations remained when excluding canonical syllables in identifiable words and controlling for the number of communication acts. Participants included 68 preverbal or low verbal children with autism spectrum disorder (
M
age
= 35.26 months).

Results

Vocal communication with canonical syllables and expressive language were concurrently and longitudinally associated with moderate to strong (
R
2
s = .13–.70) and significant (
p
s < .001) effect sizes. Even when excluding spoken words from the vocal predictor and controlling for the number of communication acts, vocal communication with canonical syllables predicted expressive language.

Conclusions
The findings provide increased support for measuring vocal communication with canonical syllables and for examining a causal relation between vocal communication with canonical syllables and expressive language in children with ASD who are preverbal or low verbal. In future studies, it may be unnecessary to eliminate identifiable words when measuring vocal communication in this population. Following replication, vocal communication with canonical syllables may be considered when making intervention- planning decisions.
Experimental characterization of modal noise in multimode fibers for astronomical spectrometers
Authors: Oliva E. , Rainer M. , Tozzi A. , Sanna N. , Iuzzolino M. , Brucalassi A. 
Published: October 2019

Context. High resolution spectroscopy at high signal-to-noise ratios (S/Ns) is one the key techniques of the quantitative study of the atmospheres of extrasolar planets. Observations at near-infrared wavelengths with fiber-fed spectrographs coupled to extremely large telescopes are particularly important to tackle the ultimate goal of detecting biosignatures in rocky planets.
Aims. To achieve high S/Ns in fiber-fed spectrogrpahs, the systematic noise effects introduced by the fibers must be properly understood and mitigated. In this paper we concentrate on the effects of modal noise in multimode fibers.
Methods. Starting from our puzzling on-sky experience with the GIANO-TNG spectrometer we set up an infrared high resolution spectrometer in our laboratory and used this instrument to characterize the modal noise generated in fibers of different types (circular and octagonal) and sizes. Our experiment includes two conventional scrambling systems for fibers: a mechanical agitator and an optical double scrambler.
Results. We find that the strength of the modal noise primarily depends on how the fiber is illuminated. It dramatically increases when the fiber is under-illuminated, either in the near field or in the far field. The modal noise is similar in circular and octagonal fibers. The Fourier spectrum of the noise decreases exponentially with frequency; i.e., the modal noise is not white but favors broad spectral features. Using the optical double scrambler has no effect on modal noise. The mechanical agitator has effects that vary between different types of fibers and input illuminations. In some cases this agitator has virtually no effect. In other cases, it mitigates the modal noise, but flattens the noise spectrum in Fourier space; i.e., the mechanical agitator preferentially filters the broad spectral features.
Conclusions. Our results show that modal noise is frustratingly insensitive to the use of octagonal fibers and optical double scramblers; i.e., the conventional systems used to improve the performances of spectrographs fed via unevenly illuminated fibers. Fiber agitation may help in some cases, but its effect has to be verified on a case-by-case basis. More generally, our results indicate that the design of the fiber link feeding a spectrograph should be coupled with laboratory measurements that reproduce, as closely as possible, the conditions expected at the telescope.
Austrian Pinot blanc wines: Typicity, wine styles and the influence of different oenological decisions on the volatile profile of wines
Authors: Philipp C. , Sari S. , Eder P. , Patzl-Fischerleitner E. , Eder R. 
Published: October 2019

Pinot blanc is found in all wine regions of Austria. However, it plays an economically subordinate role compared to the most important white grape variety, Grüner Veltliner. The concept of wine typicity and terroir is that the geographical origin and oenological practices, along with the grape variety, make an important contribution to the final expression of the finished wine. The purpose of this study was to discuss different styles of Austrian Pinot blanc wines and to discuss the various wine production decisions in terms of wine stylistics and aromatic profile. 131 commercial Austrian wine samples of the Pinot blanc variety of the 2015 to 2017 vintages were collected and the manufacturer's practices were determined by means of a questionnaire related to the wine styles. Using various GC-SIM-MS methods, more than 100 essential volatile substances were quantified. A trained panel, an expert panel and consumers evaluated the wines based on typicity and quality. 15 typical wines were then assessed on a sensory basis by means of predetermined aroma and wine styles. The four Austrian Pinot blanc wine styles previously discussed and presented by the same authors (citrus (1st style), green apple and green pear (2nd style), ripe yellow apple, quince, cooked pear, bread and honey notes (3rd style), as well as intensive oak notes (4th style)) were able to be partially reproduced by the trained panel. The following three wine styles could be better understood by the consumers: fresh fruity (style A), complex aroma with or without moderate wood (style B) and lots of wood aroma (style C). These styles (A–C) were able to withstand a sensory examination and a discriminant analysis by substance. An oenological guideline could help the producers to achieve the respective style. Austria's wine-growing area is probably too small and the importance of the Pinot blanc variety for the individual areas still too low to support the terroir concept for this grape variety.