bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunable Ampere phase plate for low dose imaging of biomolecular complexes
Authors: Tavabi Amir H. , Beleggia Marco , Migunov Vadim , Savenko Alexey , Öktem Ozan , Dunin-Borkowski Rafal E. , Pozzi Giulio 
Published: March 2018

AbstractA novel device that can be used as a tunable support-free phase plate for transmission electron microscopy of weakly scattering specimens is described. The device relies on the generation of a controlled phase shift by the magnetic field of a segment of current-carrying wire that is oriented parallel or antiparallel to the electron beam. The validity of the concept is established using both experimental electron holographic measurements and a theoretical model based on Ampere’s law. Computer simulations are used to illustrate the resulting contrast enhancement for studies of biological cells and macromolecules.
Filamentous Virus-based Assembly: Their Oriented Structures and Thermal Diffusivity
Authors: Sawada Toshiki , Murata Yuta , Marubayashi Hironori , Nojima Shuichi , Morikawa Junko , Serizawa Takeshi 
Published: March 2018

AbstractOrganic polymers are generally regarded as thermal insulators because amorphous arrangement of molecular chains reduces the mean free path of heat-conducting phonons. However, recent studies indicated that single chains of polymers with highly oriented structures could have high thermal conductivity than bulk polymers because stretched polymer chains effectively conduct phonons through polymeric covalent bonds. Here, we demonstrated the possibility of non-covalent virus assembly prepared by simple flow-induced methods toward high thermal conductive polymeric materials. Films with high thermal diffusivity composed of non-covalent bond-based assemblies of liquid crystalline filamentous viruses were prepared using a simple flow-induced orientation method. Structural and thermal characterization demonstrated that highly oriented structures of the viruses in the film were attributed to the high thermal diffusivity. Our results will open attractive opportunities for biomolecular-based thermally conductive soft materials even though the assemblies are based on non-covalent bonds.
Transcriptome Profiles Reveal the Crucial Roles of Hormone and Sugar in the Bud Dormancy of Prunus mume
Authors: Zhang Zhiyong , Zhuo XiaoKang , Zhao Kai , Zheng Tangchun , Han Yu , Yuan Cunquan , Zhang Qixiang 
Published: March 2018

AbstractBud dormancy transition is a vital developmental process for perennial plant survival. The process is precisely regulated by diverse endogenous genetic factors and environmental cues, but the mechanisms are not yet fully understood. Prunus mume is an ideal crop for bud dormancy analysis because of its early spring-flowering characteristics and small sequenced genome. Here, we analyzed the transcriptome profiles at the three endodormancy stages and natural flush stage using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism have been observed, and α-amylases, Glucan Hydrolase Family 17 and diphosphate-glycosyltransferase family might play crucial roles in the interactions between hormones and sugars. The following hypothetical model for understanding the molecular mechanism of bud dormancy in Prunus mume is proposed: low temperatures exposure induces the significant up-regulation of eight C-repeat binding factor genes, which directly promotes all six dormancy-associated MADS-box genes, resulting in dormancy establishment. The prolonged cold and/or subsequently increasing temperature then decreases the expression levels of these two gene families, which alleviates the inhibition of FLOWERING LOCUS T and reopens the growth-promoting pathway, resulting in dormancy release and the initiation of the bud break process.
Extracting quasi-steady Lagrangian transport patterns from the ocean circulation: An application to the Gulf of Mexico
Authors: Duran R. , Beron-Vera F. J. , Olascoaga M. J. 
Published: March 2018

AbstractWe construct a climatology of Lagrangian coherent structures (LCSs)—the concealed skeleton that shapes transport—with a twelve-year-long data-assimilative simulation of the sea-surface circulation in the Gulf of Mexico (GoM). Computed as time-mean Cauchy–Green strain tensorlines of the climatological velocity, the climatological LCSs (cLCSs) unveil recurrent Lagrangian circulation patterns. The cLCSs strongly constrain the ensemble-mean Lagrangian circulation of the instantaneous model velocity, showing that a climatological velocity can preserve meaningful transport information. The quasi-steady transport patterns revealed by the cLCSs agree well with aspects of the GoM circulation described in several previous observational and numerical studies. For example, the cLCSs identify regions of persistent isolation, and suggest that coastal regions previously identified as high-risk for pollution impact are regions of maximal attraction. We also show that cLCSs are remarkably accurate at identifying transport patterns observed during the Deepwater Horizon and Ixtoc oil spills, and during the Grand LAgrangian Deployment (GLAD) experiment. Thus it is shown that computing cLCSs is an efficient and meaningful way of synthesizing vast amounts of Lagrangian information. The cLCS method confirms previous GoM studies, and contributes to our understanding by revealing the persistent nature of the dynamics and kinematics treated therein.
Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls
Authors: Kovanda Anja , Leonardis Lea , Zidar Janez , Koritnik Blaž , Dolenc-Groselj Leja , Ristic Kovacic Stanislava , Curk Tomaž , Rogelj Boris 
Published: March 2018

AbstractAmyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown. Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls. The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS. Furthermore, the identified miRNAs are predicted to target proteins that are involved in both normal processes and various muscle disorders and indicate muscle tissue is undergoing active reinnervation/compensatory attempts thus providing targets for further research and therapy development in ALS.
Spindle cell sarcoma: a SEER population-based analysis
Authors: Feng Lei , Wang Meng , Yibulayin Feiluore , Zhang Hao , Yang Yin-Long , Ren Fei , Wushou Alimujiang 
Published: March 2018

AbstractDue to the substantial limitation of study population, Spindle cell sarcoma (SCS) was unexplored comprehensively. In this study, we investigated the clinical characteristics and disease specific prognostic factors of SCS. 3299 SCS cases were identified and extracted from Surveillance, Epidemiology, and End Results (SEER) database (1973–2017). White people account for 79.1% with median age of 57 years without predominance in any gender. Significant disease specific survival (DSS) and overall survival (OS) were found differentiated in age, T stage, N stage, M stage, AJCC stage, SEER historic stage, tumor locations, surgery, and pathologic grade. In the multivariate Cox analysis, the age >64 years (for DSS, P < 0.001 and for OS, P < 0.001; Reference age ≤64 years), AJCC stage III (for DSS, P = 0.006 and for OS, P = 0.04; Reference: AJCC stage I), and non-surgical treatment (for DSS, P < 0.001 and for OS, P < 0.001; Reference: surgery) were independently associated with worse DSS and OS. In brief, our study demonstrated that SCS mostly found in white people at fifth to seventh decades of life without gender predilection. The patient’s age, AJCC stage, tumor location and surgery were independent prognostic indicators for both DSS and OS of SCS.
Frequency of Esophageal Eosinophilia in a Pediatric Population from Central Brazil
Authors: Strozzi Daniel , Botacin Marco Aurélio Silveira , Mekdessi Marilia Adriano , Salustiano Luciana Ximenes , Silva Pedro H. de Paula , Minasi Lysa Bernardes , Segundo Gesmar Rodrigues Silva , Cruz Aparecido Divino da 
Published: March 2018

AbstractHere we report a retrospective cross-sectional study on Esophageal eosinophilia (EsEo) frequency in Brazil, for 2, 425 pediatric patients with symptoms associated with gastroesophageal diseases in 2012. EsEo is defined by ≥15 eosinophils per high power field (400x) and confirmed through histological analyses of esophageal biopsies. Overall, 126 patients had EsEo equating to a frequency of 5.2%. There was a significant difference between the endoscopic features of patients with EsEo, where 10.7% had erosive esophagitis, 3.0% had non-erosive esophagitis and 1% showed normal esophageal mucosa. According to the interaction of the variables in the Classification and Regression Tree Analysis, most patients diagnosed with EsEo were older males with erosive esophagitis. On the other hand, the lowest frequency of EsEo was found among younger females with non-erosive esophagitis/normal mucosa. Environmental conditions, including climate variation and changes, were observed in association with EsEo, supporting a potential role for environmental factors in its pathogenesis. There was an inverse correlation between the number of EsEo, rainfall and humidity. EsEo is a relatively frequent finding in the pediatric population of Brazil with symptoms of gastroesophageal diseases. Both clinical and histological examinations of patients are important for a reliable diagnostic of EsEo cases and to patient care.
Towards Millimeter-wavelength: Transmission-Mode Fresnel-Zone Plate Lens Antennas using Plastic Material Porosity Control in Homogeneous Medium
Authors: Pourahmadazar Javad , Denidni Tayeb A. 
Published: March 2018

AbstractWe present two transmission-mode dielectric Fresnel-Zone Plate Lens (FZPL) antennas for use within the V-band spectrum. The proposed FZPs are realized via pure plastic material using two different additive manufacturing processes. The proposed FZP lenses are designed with half (λ/2) and quarter (λ/4) phase correction rings at 60-GHz with 30λ0 diameter, where λ0 is the free-space wavelength. The permittivity effect for lens sub-zones is controlled by material porosity in cube-shaped structures. The 3D printed zone plate lenses are built using additive manufacturing plastic materials with a thickness of λ0 and constant relative permittivities equal to 2.76 and 3.6. Different types of antenna with cosn-like radiation patterns as lens illuminators are analyzed on the vertical plane of the flat lenses to have a high efficiency over the considered operating band. Simulations and experimental measurements show a reasonably close match, therefore allowing for a reliable predictability.
Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Authors: Koudijs Karel K. M. , Terwisscha van Scheltinga Anton G. T. , Böhringer Stefan , Schimmel Kirsten J. M. , Guchelaar Henk-Jan 
Published: March 2018

AbstractReversal of cancer gene expression is predictive of therapeutic potential and can be used to find new indications for existing drugs (drug repositioning). Gene expression reversal potential is currently calculated, in almost all studies, by pre-aggregating all tumour samples into a single group signature or a limited number of molecular subtype signatures. Here, we investigate whether drug repositioning based on individual tumour sample gene expression signatures outperforms the use of tumour group and subtype signatures. The tumour signatures were created using 534 tumour samples and 72 matched normal samples from 530 clear cell renal cell carcinoma (ccRCC) patients. More than 20,000 drug signatures were extracted from the CMAP and LINCS databases. We show that negative enrichment of individual tumour samples correlated (Spearman’s rho = 0.15) much better with the amount of differentially expressed genes in drug signatures than with the tumour group signature (Rho = 0.08) and the 4 tumour subtype signatures (Rho 0.036-0.11). Targeted drugs used against ccRCC, such as sirolimus and temsirolimus, which could not be identified with the pre-aggregated tumour signatures could be recovered using individual sample analysis. Thus, drug repositioning can be personalized by taking into account the gene expression profile of the individual’s tumour sample.
Neuronal differentiation induces SNORD115 expression and is accompanied by post-transcriptional changes of serotonin receptor 2c mRNA
Authors: Bratkovič Tomaž , Modic Miha , Camargo Ortega Germán , Drukker Micha , Rogelj Boris 
Published: March 2018

AbstractThe serotonin neurotransmitter system is widespread in the brain and implicated in modulation of neuronal responses to other neurotransmitters. Among 14 serotonin receptor subtypes, 5-HT2cR plays a pivotal role in controlling neuronal network excitability. Serotonergic activity conveyed through receptor 5-HT2cR is regulated post-transcriptionally via two mechanisms, alternative splicing and A-to-I RNA editing. Brain-specific small nucleolar RNA SNORD115 harbours a phylogenetically conserved 18-nucleotide antisense element with perfect complementarity to the region of 5ht2c primary transcript that undergoes post-transcriptional changes. Previous 5ht2c minigene studies have implicated SNORD115 in fine-tuning of both post-transcriptional events. We monitored post-transcriptional changes of endogenous 5ht2c transcripts during neuronal differentiation. Both SNORD115 and 5ht2c were upregulated upon neuronal commitment. We detected increased 5ht2c alternative exon Vb inclusion already at the stage of neuronal progenitors, and more extensive A-to-I editing of non-targeted sites A and B compared to adjacent adenosines at sites E, C and D throughout differentiation. As the extent of editing is known to positively correlate with exon Vb usage while it reduces receptor functionality, our data support the model where SNORD115 directly promotes alternative exon inclusion without the requirement for conversion of key adenosines to inosines, thereby favouring production of full-length receptor isoforms with higher potency.
Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies
Authors: Panek Marina , Čipčić Paljetak Hana , Barešić Anja , Perić Mihaela , Matijašić Mario , Lojkić Ivana , Vranešić Bender Darija , Krznarić Željko , Verbanac Donatella 
Published: March 2018

AbstractThe information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for collection and storage of faecal samples (native and OMNIgene.GUT system) and bacterial DNA extraction (MP Biomedicals, QIAGEN and MO BIO kits), using two NGS platforms for 16S rRNA gene sequencing (Ilumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of faecal samples although favouring Sutterella genus. MP provided superior DNA yield and quality, MO BIO depleted Gram positive organisms while using QIAGEN with OMNIgene.GUT resulted in greatest variability compared to other two kits. MiSeq and IT platforms in their supplier recommended setups provided comparable reproducibility of donor faecal microbiota. The differences included higher diversity observed with MiSeq and increased capacity of MiSeq to detect Akkermansia muciniphila, [Odoribacteraceae], Erysipelotrichaceae and Ruminococcaceae (primarily Faecalibacterium prausnitzii). The results of our study could assist the investigators using NGS technologies to make informed decisions on appropriate tools for their experimental pipelines.
A wide-band bio-chip for real-time optical detection of bioelectromagnetic interactions with cells
Authors: Merla Caterina , Liberti Micaela , Marracino Paolo , Muscat Adeline , Azan Antoine , Apollonio Francesca , Mir Lluis M. 
Published: March 2018

AbstractThe analytical and numerical design, implementation, and experimental validation of a new grounded closed coplanar waveguide for wide-band electromagnetic exposures of cells and their optical detection in real-time is reported. The realized device fulfills high-quality requirements for novel bioelectromagnetic experiments, involving elevated temporal and spatial resolutions. Excellent performances in terms of matching bandwidth (less than −10 dB up to at least 3 GHz), emission (below 1 × 10−6 W/m2) and efficiency (around 1) have been obtained as revealed by both numerical simulations and experimental measurements. A low spatial electric field inhomogeneity (coefficient of variation of around 10 %) has been achieved within the cell solutions filling the polydimethylsiloxane reservoir of the conceived device. This original bio-chip based on the grounded closed coplanar waveguide concept opens new possibilities for the development of controlled experiments combining electromagnetic exposures and sophisticated imaging using optical spectroscopic techniques.
Propensity Score-Matched Analysis on the Association Between Pregnancy Infections and Adverse Birth Outcomes in Rural Northwestern China
Authors: Guo Leqian , Qu Pengfei , Zhang Ruo , Zhao Doudou , Wang Hongli , Liu Rong , Mi Baibing , Yan Hong , Dang Shaonong 
Published: March 2018

AbstractThe purpose of this study is to examine the relationship between infections and birth outcomes in pregnant Chinese women by using propensity score (PS) matching. The data used here was from a large population-based cross-sectional epidemiological survey on birth defects in Shaanxi province, Northwest China. The babies born during 2010–2013 and their mothers were selected with a stratified multistage sampling method. We used PS-matched (1:1) analysis to match participants with infections to participants without infections. Of 22916 rural participants, the overall prevalence of infection was about 39.96%. 5381 pairs were matched. We observed increased risks of birth defects with infections, respiratory infections and genitourinary infections during the pregnancy (OR, 1.59; 95% CI: 1.21–2.08; OR, 1.44; 95% CI: 1.10–1.87; OR, 3.11; 95% CI: 1.75–5.54). There was also a significant increase of low birth weight associated with respiratory infections (1.13(1.01–1.27)). The association of birth defect with the infection could be relatively stable but the effect could be mediated by some important factors such as mother’s age, education level and economic level. The infection during pregnancy is common in Chinese women and might increase the risk of offspring birth defects and low birth weight, especially in younger, lower education, poor pregnant women.
Data-based Decision Rules to Personalize Depression Follow-up
Authors: Lin Ying , Huang Shuai , Simon Gregory E. , Liu Shan 
Published: March 2018

AbstractDepression is a common mental illness with complex and heterogeneous progression dynamics. Risk grouping of depression treatment population based on their longitudinal patterns has the potential to enable cost-effective monitoring policy design. This paper establishes a rule-based method to identify a set of risk predictive patterns from person-level longitudinal disease measurements by integrating the data transformation, rule discovery and rule evaluation. We further extend the identified rules to create rule-based monitoring strategies to adaptively monitor individuals with different disease severities. We applied the rule-based method on an electronic health record (EHR) dataset of depression treatment population containing person-level longitudinal Patient Health Questionnaire (PHQ)-9 scores for assessing depression severity. 12 risk predictive rules are identified, and the rule-based prognostic model based on identified rules enables more accurate prediction of disease severity than other prognostic models including RuleFit, logistic regression and Support Vector Machine. Two rule-based monitoring strategies outperform the latest PHQ-9 based monitoring strategy by providing higher sensitivity and specificity. The rule-based method can lead to a better understanding of disease dynamics, achieving more accurate prognostics of disease progressions, personalizing follow-up intervals, and designing cost-effective monitoring of patients in clinical practice.
Whey protein lowers systolic blood pressure and Ca-caseinate reduces serum TAG after a high-fat meal in mildly hypertensive adults
Authors: Fekete Ágnes A. , Giromini Carlotta , Chatzidiakou Yianna , Givens D. Ian , Lovegrove Julie A. 
Published: March 2018

AbstractEpidemiological studies show an inverse association between dairy consumption and blood pressure (BP) but there are few data on the postprandial effects of milk proteins. This study examined their effects, compared to maltodextrin, on postprandial BP and other CVD risk markers in volunteers with mild and pre-hypertension over an 8 h period. In this double-blinded, randomised, cross-over, controlled study 27 adults ingested a high-fat, isoenergetic breakfast and lunch with 28 g whey protein, 28 g Ca-caseinate or 27 g maltodextrin. Whey protein reduced systolic BP compared with Ca-caseinate (−15.2 ± 13.6 mmHg) and maltodextrin (−23.4 ± 10.5 mmHg) up to 5 h post-ingestion. There was an improvement in arterial stiffness after whey protein compared with maltodextrin (incremental Area Under the Curve- iAUC0–8h: +14.4 ± 6.2%). Despite similar glucose levels after both whey protein and Ca-caseinate, whey protein induced a higher insulin response than Ca-caseinate (iAUC0–8h: +219.5 ± 54.6 pmol/L). Ca-caseinate induced less suppression of non-esterified fatty acids than whey protein (iAUC0–5h: −58.9 ± 135.5 μmol/L) and maltodextrin (iAUC0–5h: −106.9 ± 89.4 μmol/L) and induced a smaller postprandial triacylglycerol response than whey protein (iAUC0–8h: −1.68 ± 0.6 mmol/L). Milk proteins co-ingestion with high-fat meals may have the potential to maintain or improve CVD risk factors.