bluuebunny/crossref_metadata_2025_split huggingface dataset:
Keeping it complicated: Mitochondrial genome plasticity across diplonemids
Authors: Valach Matus , Moreira Sandrine , Hoffmann Steve , Stadler Peter F. , Burger Gertraud 
Published: October 2017

AbstractChromosome rearrangements are important drivers in genome and gene evolution, with implications ranging from speciation to development to disease. In the flagellate Diplonema papillatum (Euglenozoa), mitochondrial genome rearrangements have resulted in nearly hundred chromosomes and a systematic dispersal of gene fragments across the multipartite genome. Maturation into functional RNAs involves separate transcription of gene pieces, joining of precursor RNAs via trans-splicing, and RNA editing by substitution and uridine additions both reconstituting crucial coding sequence. How widespread these unusual features are across diplonemids is unclear. We have analyzed the mitochondrial genomes and transcriptomes of four species from the Diplonema/Rhynchopus clade, revealing a considerable genomic plasticity. Although gene breakpoints, and thus the total number of gene pieces (~80), are essentially conserved across this group, the number of distinct chromosomes varies by a factor of two, with certain chromosomes combining up to eight unrelated gene fragments. Several internal protein-coding gene pieces overlap substantially, resulting, for example, in a stretch of 22 identical amino acids in cytochrome c oxidase subunit 1 and NADH dehydrogenase subunit 5. Finally, the variation of post-transcriptional editing patterns across diplonemids indicates compensation of two adverse trends: rapid sequence evolution and loss of genetic information through unequal chromosome segregation.
Prolonged duration of nonequilibrated Dirac fermions in neutral topological insulators
Authors: Sumida K. , Ishida Y. , Zhu S. , Ye M. , Pertsova A. , Triola C. , Kokh K. A. , Tereshchenko O. E. , Balatsky A. V. , Shin S. , Kimura A. 
Published: October 2017

AbstractTopological insulators (TIs) possess spin-polarized Dirac fermions on their surface but their unique properties are often masked by residual carriers in the bulk. Recently, (Sb1−x
Bi
x
)2Te3 was introduced as a non-metallic TI whose carrier type can be tuned from n to p across the charge neutrality point. By using time- and angle-resolved photoemission spectroscopy, we investigate the ultrafast carrier dynamics in the series of (Sb1−x
Bi
x
)2Te3. The Dirac electronic recovery of ∼10 ps at most in the bulk-metallic regime elongated to >400 ps when the charge neutrality point was approached. The prolonged nonequilibration is attributed to the closeness of the Fermi level to the Dirac point and to the high insulation of the bulk. We also discuss the feasibility of observing excitonic instability of (Sb1−x
Bi
x
)2Te3.
Determining the Quality Factor of Dielectric Ceramic Mixtures with Dielectric Constants in the Microwave Frequency Range
Authors: Chen Hetuo , Fu Xuewen , An Qi , Tang Bin , Zhang Shuren , Yang Hao , Long Yin , Harfouche Mark , Wang Huolei , Li Yingxiang 
Published: October 2017

AbstractMicrowave dielectric ceramic materials are extensively utilized in microwave applications because of their high dielectric constants and quality factors. These applications also require ceramics of zero temperature coefficients at the resonant frequency (τ
f
), which can be realized through mixing a ceramic that one is interested in with another ceramic with −τ
f
, or by performing the ionic substitution. With the mixing/ionic substitution, it is indispensable to compute the quality factors precisely. Previous study indicates that the quality factor depends on the grain size, porosity, internal strain, structure, phase evolution, and conductivity etc. Here we derive a quality factor formula based on the definition, which works very well for multiphase composites, single phase solid solutions, and equivalent ionic substituted single phase materials. Our formula calculation and fits to the previous experimental results demonstrate that the quality factor of the ceramic mixtures strongly depend on the dielectric constants and the dielectric constant variation index. Our results suggest that the impacts from grain size, porosity, and internal strain etc. can be summarized to the dielectric constant or dielectric constant variation index, which is of great importance for future design of high performance microwave dielectric ceramics.
Unravelling pathways downstream Sox6 induction in K562 erythroid cells by proteomic analysis
Authors: Barbarani Gloria , Ronchi Antonella , Ruoppolo Margherita , Santorelli Lucia , Steinfelder Robert , Elangovan Sudharshan , Fugazza Cristina , Caterino Marianna 
Published: October 2017

AbstractThe Sox6 transcription factor is crucial for terminal maturation of definitive red blood cells. Sox6-null mouse fetuses present misshapen and nucleated erythrocytes, due to impaired actin assembly and cytoskeleton stability. These defects are accompanied with a reduced survival of Sox6−/− red blood cells, resulting in a compensated anemia. Sox6-overexpression in K562 cells and in human primary ex vivo erythroid cultures enhances erythroid differentiation and leads to hemoglobinization, the hallmark of erythroid maturation. To obtain an overview on processes downstream to Sox6 expression, we performed a differential proteomic analysis on human erythroid K562 cells overexpressing Sox6. Sox6-overexpression induces dysregulation of 64 proteins, involved in cytoskeleton remodeling and in protein synthesis, folding and trafficking, key processes for erythroid maturation. Moreover, 43 out of 64 genes encoding for differentially expressed proteins contain within their proximal regulatory regions sites that are bound by SOX6 according to ENCODE ChIP-seq datasets and are possible direct SOX6 targets. SAR1B, one of the most induced proteins upon Sox6 overexpression, shares a conserved regulatory module, composed by a double SOX6 binding site and a GATA1 consensus, with the adjacent SEC24 A gene. Since both genes encode for COPII components, this element could concur to the coordinated expression of these proteins during erythropoiesis.
Improved performance of the artus Mycobacterium tuberculosis RG PCR kit in a low incidence setting: a retrospective monocentric study
Authors: Kohlmorgen Britta , Elias Johannes , Schoen Christoph 
Published: October 2017

AbstractTuberculosis (TB) and the spread of Mycobacterium tuberculosis complex (MTBC) strains resistant against rifampin (RIF) and isoniazid (INH) pose a serious threat to global health. However, rapid and reliable MTBC detection along with RIF/INH susceptibility testing are challenging in low prevalence countries due to the higher rate of false positives. Here, we provide the first performance data for the artus MTBC PCR assay in a low prevalence setting. We analyze 1323 respiratory and 311 non-respiratory samples with the artus MTBC PCR assay as well as by mycobacterial culture and microscopy. We propose retesting of specimens in duplicate and consideration of a determined cycle-threshold value cut-off greater than 34, as this significantly increases accuracy, specificity, and negative predictive value without affecting sensitivity. Furthermore, we tested fourteen MTBC positive samples with the GenoType MTBDRplus test and demonstrate that using an identical DNA extraction protocol for both assays does not impair downstream genotypic testing for RIF and INH susceptibility. In conclusion, our procedure optimizes the use of the artus MTB assay with workload efficient methods in a low incidence setting. Combining the modified artus MTB with the GenoType MTBDRplus assays allows rapid and accurate detection of MTBC and RIF/INH resistance.
Reducing the critical particle diameter in (highly) asymmetric sieve-based lateral displacement devices
Authors: Dijkshoorn J. P. , Schutyser M. A. I. , Sebris M. , Boom R. M. , Wagterveld R. M. 
Published: October 2017

AbstractDeterministic lateral displacement technology was originally developed in the realm of microfluidics, but has potential for larger scale separation as well. In our previous studies, we proposed a sieve-based lateral displacement device inspired on the principle of deterministic lateral displacement. The advantages of this new device is that it gives a lower pressure drop, lower risk of particle accumulation, higher throughput and is simpler to manufacture. However, until now this device has only been investigated for its separation of large particles of around 785 µm diameter. To separate smaller particles, we investigate several design parameters for their influence on the critical particle diameter. In a dimensionless evaluation, device designs with different geometry and dimensions were compared. It was found that sieve-based lateral displacement devices are able to displace particles due to the crucial role of the flow profile, despite of their unusual and asymmetric design. These results demonstrate the possibility to actively steer the velocity profile in order to reduce the critical diameter in deterministic lateral displacement devices, which makes this separation principle more accessible for large-scale, high throughput applications.
UPS-indel: a Universal Positioning System for Indels
Authors: Hasan Mohammad Shabbir , Wu Xiaowei , Watson Layne T. , Zhang Liqing 
Published: October 2017

AbstractStoring biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare different indel calling results. UPS-indel identifies 15% redundant indels in dbSNP, 29% in COSMIC coding, and 13% in COSMIC noncoding datasets across all human chromosomes, higher than previously reported. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to state-of-the-art approaches for indel call set comparison demonstrates its clear superiority in finding common indels among call sets. UPS-indel is theoretically proven to find all equivalent indels, and thus exhaustive.
Combining 18F-FDG positron emission tomography with Up-to-seven criteria for selecting suitable liver transplant patients with advanced hepatocellular carcinoma
Authors: Kornberg Arno , Witt Ulrike , Schernhammer Martina , Kornberg Jennifer , Ceyhan Gueralp O. , Mueller Katharina , Friess Helmut , Thrum Katharina 
Published: October 2017

AbstractThe Up-to-seven (UTS) criteria (sum of tumor size and number not exceeding 7) for indicating liver transplantation (LT) in hepatocellular carcinoma (HCC) were originally based on explant pathology features and absence of microvascular invasion (MVI). 18F-fludeoxyglucose (18F-FDG) positron emission tomography (PET) was shown to indicate the risk of MVI and tumor recurrence. The aim of this study was to analyze the prognostic significance of the clinical UTS criteria when being combined with PET-status of the tumor. Data of 116 liver transplant patients were subject to retrospective analysis. Five-year recurrence-free survival (RFS) rates in patients meeting (n = 85) and exceeding (n = 21) the radiographic UTS criteria were 81% and 55.1%, respectively (p = 0.014). In the UTS In subset, RFS was significantly better in PET-negative (94.9%) than in PET-positive patients (48.3%; p < 0.001). In the UTS Out subset, 5-year RFS rates were 87.1% and 19% in patients with non- 18F-FDG-avid and 18F-FDG-avid tumors (p < 0.001), respectively. Positive PET-status was identified as the only independent clinical predictor of tumor recurrence in beyond UTS patients (Hazard ratio [HR] 19.25; p < 0.001). Combining radiographic UTS criteria with FDG-PET may safely expand the HCC selection criteria for LT.
Quantitative label-free single cell tracking in 3D biomimetic matrices
Authors: Sapudom Jiranuwat , Waschke Johannes , Franke Katja , Hlawitschka Mario , Pompe Tilo 
Published: October 2017

AbstractLive cell imaging enables an observation of cell behavior over a period of time and is a growing field in modern cell biology. Quantitative analysis of the spatio-temporal dynamics of heterogeneous cell populations in three-dimensional (3D) microenvironments contributes a better understanding of cell-cell and cell-matrix interactions for many biomedical questions of physiological and pathological processes. However, current live cell imaging and analysis techniques are frequently limited by non-physiological 2D settings. Furthermore, they often rely on cell labelling by fluorescent dyes or expression of fluorescent proteins to enhance contrast of cells, which frequently affects cell viability and behavior of cells. In this work, we present a quantitative, label-free 3D single cell tracking technique using standard bright-field microscopy and affordable computational resources for data analysis. We demonstrate the efficacy of the automated method by studying migratory behavior of a large number of primary human macrophages over long time periods of several days in a biomimetic 3D microenvironment. The new technology provides a highly affordable platform for long-term studies of single cell behavior in 3D settings with minimal cell manipulation and can be implemented for various studies regarding cell-matrix interactions, cell-cell interactions as well as drug screening platform for primary and heterogeneous cell populations.
Removal of cationic and anionic heavy metals from water by 1D and 2D-carbon structures decorated with magnetic nanoparticles
Authors: Santhosh Chella , Nivetha Ravi , Kollu Pratap , Srivastava Varsha , Sillanpää Mika , Grace Andrews Nirmala , Bhatnagar Amit 
Published: October 2017

AbstractIn this study, cobalt ferrites (C) decorated onto 2D material (porous graphene (PG)) and 1D material (carbon nanofibers (CNF)), denoted as PG-C and CNF-C nanocomposites, respectively, were synthesized using solvothermal process. The prepared nanocomposites were studied as magnetic adsorbents for the removal of lead (cationic) and chromium(VI) (anionic) metal ions. The structural and chemical analysis of synthesized nanocomposites was conducted using different characterization techniques including Brunauer–Emmett–Teller (BET) analysis, field emission-scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FTIR), high resolution-transmission electron microscopy (HR-TEM), vibrating sample magnetometer (VSM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). Batch mode adsorption studies were conducted with the prepared nanocomposites to examine their maximum adsorption potential for lead and chromate ions. Performance parameters (time, pH, adsorbent dosage and initial ion concentrations) effecting the adsorption capacity of the nanocomposites were optimized. Different kinetic and isotherm models were examined to elucidate the adsorption process. Synthesized nanocomposites exhibited significant potential for the studied metal ions that can be further examined at pilot scale for the removal of metal ions from contaminated water.
Terahertz beam switching by electrical control of graphene-enabled tunable metasurface
Authors: Zhang Yin , Feng Yijun , Zhao Junming , Jiang Tian , Zhu Bo 
Published: October 2017

AbstractControlling the terahertz wave, especially the dynamical and full control of terahertz wavefront, is highly demanded due to the increasing development of practical devices and application systems. Recently considerable efforts have been made to fill the ‘terahertz gap’ with the help of artificial metamaterial or metasurface incorporated with graphene material. Here, we propose a scheme to design tunable metasurface consisting of metallic patch array on a grounded polymer substrate embedded with graphene layers to electrically control the electromagnetic beam reflection at terahertz frequency. By adjusting geometric dimension of the patch elements, 360 degree reflection phase range may be achieved, thus abrupt phase shifts can be introduced along the metasurface for tailoring the reflected wavefront. Moreover, the reflective phase gradient over the metasurface can be switched between 90 and 360 degree by controlling the Fermi energy of the embedded graphene through voltage biasing, hence dynamically switching the reflective beam directions. Numerical simulations demonstrate that either single beam or dual beam dynamically switching between normal and oblique reflection angles can be well attained at working frequency. The proposed approach will bring much freedom in the design of beam manipulation devices and may be applied to terahertz radiation control.
Deregulated expression and activity of Farnesyl Diphosphate Synthase (FDPS) in Glioblastoma
Authors: Abate Mario , Laezza Chiara , Pisanti Simona , Torelli Giovanni , Seneca Vincenzo , Catapano Giuseppe , Montella Francesco , Ranieri Roberta , Notarnicola Maria , Gazzerro Patrizia , Bifulco Maurizio , Ciaglia Elena 
Published: October 2017

AbstractGlioblastoma (GBM), the most aggressive brain cancer, is highly dependent on the mevalonate (MVA) pathway for the synthesis of lipid moieties critical for cell proliferation but the function and regulation of key intermediate enzymes like farnesyl-diphosphate synthase (FDPS), up to now, remained unknown. A deregulated expression and activity of FDPS was the central research idea of the present study. FDPS mRNA, protein and enzyme activity were analyzed in a cohort of stage III-IV glioma patients (N = 49) and primary derived cells. FDPS silencing helped to clarify its function in the maintenance of malignant phenotype. Interestingly, compared to tumor-free peripheral (TFB) brain and normal human astrocytes (NHA), FDPS protein expression and enzyme activity were detected at high degree in tumor mass where a correlation with canonical oncogenic signaling pathways such as STAT3, ERK and AKT was also documented. Further, FDPS knockdown in U87 and GBM primary cells but not in NHA, enhanced apoptosis. With the effort to develop a more refined map of the connectivity between signal transduction pathways and metabolic networks in cancer FDPS as a new candidate metabolic oncogene in glioblastoma, might suggest to further target MVA pathway as valid therapeutic tool.
Effects of crop load on distribution and utilization of 13C and 15N and fruit quality for dwarf apple trees
Authors: Ding Ning , Chen Qian , Zhu Zhanling , Peng Ling , Ge Shunfeng , Jiang Yuanmao 
Published: October 2017

AbstractIn order to define the effects of fruit crop load on the distribution and utilization of carbon and nitrogen in dwarf apple trees, we conducted three crop load levels (High-crop load, 6 fruits per trunk cross-sectional area (cm2, TCA)), Medium-crop load (4 fruits cm−2 TCA), Low-crop load (2 fruits cm−2 TCA)) in 2014 and 2015. The results indicated that the 15N derived from fertilizer (Ndff) values of fruits decreased with the reduction of crop load, but the Ndff values of annual branches, leaves and roots increased. The plant 15N-urea utilization rates on Medium and Low-crop load were 1.12–1.35 times higher than the High-crop load. With the reduction of crop load, the distribution rate of 13C and 15N in fruits was gradually reduced, but in contrast, the distribution of 13C and 15N gradually increased in annual branches, leaves and roots. Compared with High-crop load, the Medium and Low-crop load significantly improved fruit quality p < 0.05. Hence, controlling fruit load effectively regulated the distribution of carbon and nitrogen in plants, improved the nitrogen utilization rate and fruit quality. The appropriate crop load level for mature M.26 interstocks apple orchards was deemed to be 4.0 fruits cm−2 TCA.
Caffeine affects autonomic control of heart rate and blood pressure recovery after aerobic exercise in young adults: a crossover study
Authors: Gonzaga Luana Almeida , Vanderlei Luiz Carlos Marques , Gomes Rayana Loch , Valenti Vitor Engrácia 
Published: October 2017

AbstractThe post-exercise recovery period is associated with changes in autonomic modulation, which can promote an intercurrent-favorable environment. Caffeine has the ability to release catecholamines, but its effects after exercises is little explored. The present study aims to evaluate the acute effects of caffeine on the autonomic control and cardiorespiratory parameters after moderate intensity aerobic exercise. 32 young males (23,59 ± 3,45 years) were submitted to two protocols: Placebo and Caffeine, consisting of 15 minutes of rest, 30 minutes of exercise on a treadmill to 60% on VO2peak, followed by 60 minutes of recovery. Heart rate variability indices and cardiorespiratory parameters were determined at different times during the protocols. The RMSSD and SD1 indices recovered faster in placebo (p < 0.05). The systolic blood pressure differences were found from the 1st to the 5th minute of recovery with the caffeine protocol and from the 1st and 3rd minute with the placebo, whereas, for diastolic blood pressure, significant differences (p < 0.0001) were observed only for the caffeine protocol at the 1st and 3rd minutes of recovery. Caffeine was shown to be capable of delaying parasympathetic recovery but did not influence the behavior of the respiratory rate, oxygen saturation or frequency-domain HRV indices.
The RBM14/CoAA-interacting, long intergenic non-coding RNA Paral1 regulates adipogenesis and coactivates the nuclear receptor PPARγ
Authors: Firmin François F. , Oger Frederik , Gheeraert Céline , Dubois-Chevalier Julie , Vercoutter-Edouart Anne-Sophie , Alzaid Fawaz , Mazuy Claire , Dehondt Hélène , Alexandre Jeremy , Derudas Bruno , Dhalluin Quentin , Ploton Maheul , Berthier Alexandre , Woitrain Eloise , Lefebvre Tony , Venteclef Nicolas , Pattou François , Staels Bart , Eeckhoute Jérôme , Lefebvre Philippe 
Published: October 2017

AbstractAdipocyte differentiation and function relies on a network of transcription factors, which is disrupted in obesity-associated low grade, chronic inflammation leading to adipose tissue dysfunction. In this context, there is a need for a thorough understanding of the transcriptional regulatory network involved in adipose tissue pathophysiology. Recent advances in the functional annotation of the genome has highlighted the role of non-coding RNAs in cellular differentiation processes in coordination with transcription factors. Using an unbiased genome-wide approach, we identified and characterized a novel long intergenic non-coding RNA (lincRNA) strongly induced during adipocyte differentiation. This lincRNA favors adipocyte differentiation and coactivates the master adipogenic regulator peroxisome proliferator-activated receptor gamma (PPARγ) through interaction with the paraspeckle component and hnRNP-like RNA binding protein 14 (RBM14/NCoAA), and was therefore called PPARγ-activator RBM14-associated lncRNA (Paral1). Paral1 expression is restricted to adipocytes and decreased in humans with increasing body mass index. A decreased expression was also observed in diet-induced or genetic mouse models of obesity and this down-regulation was mimicked in vitro by TNF treatment. In conclusion, we have identified a novel component of the adipogenic transcriptional regulatory network defining the lincRNA Paral1 as an obesity-sensitive regulator of adipocyte differentiation and function.