bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective
Authors: Cvijovic Marija , Höfer Thomas , Aćimović Jure , Alberghina Lilia , Almaas Eivind , Besozzi Daniela , Blomberg Anders , Bretschneider Till , Cascante Marta , Collin Olivier , de Atauri Pedro , Depner Cornelia , Dickinson Robert , Dobrzynski Maciej , Fleck Christian , Garcia-Ojalvo Jordi , Gonze Didier , Hahn Jens , Hess Heide Marie , Hollmann Susanne , Krantz Marcus , Kummer Ursula , Lundh Torbjörn , Martial Gifta , dos Santos Vítor Martins , Mauer-Oberthür Angela , Regierer Babette , Skene Barbara , Stalidzans Egils , Stelling Jörg , Teusink Bas , Workman Christopher T , Hohmann Stefan 
Published: May 2016

AbstractSystems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student’s ability to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development.
Smaller grafts do not imply early recurrence in recipients transplanted for hepatocellular carcinoma: A Chinese experience
Authors: Hu Zhenhua , Zhong Xun , Zhou Jie , Xiang Jie , Li Zhiwei , Zhang Min , Wu Jian , Jiang Wenshi , Zheng Shusen 
Published: May 2016

AbstractLiver graft size has long been a critical issue in adult-to-adult living donor liver transplantation (LDLT). We analyzed China Liver Transplant Registry data (January 2007–December 2009), identifying 295 patients who underwent LDLT for hepatocellular carcinoma (HCC). The recipients were divided into two groups: A, graft-to-recipient body weight ratio (GRWR) ≤ 0.8% (n = 56); B, GRWR > 0.8% (n = 239). We evaluated donor, recipient, and operative factors and analyzed survival outcome and the risk factors affecting overall and recurrence survival. As a result, the overall survival rates of group B were significantly higher than that of group A (p = 0.009); the corresponding tumor-free survival rates did not differ significantly (p = 0.133). The overall survival rates among the 151 recipients who met the Hangzhou criteria did not differ significantly (p = 0.953), nor did the corresponding tumor-free survival rates (p = 0.893). Multivariate analysis determined that GRWR was a significant risk factor for poor survival but not for early recurrence. In conclusion, small grafts may predict poorer survival outcome but do not indicate earlier HCC recurrence in recipients transplanted for HCC, and survival outcome with smaller grafts is merely acceptable in selected recipients.
Modification of Ni-Rich FCG NMC and NCA Cathodes by Atomic Layer Deposition: Preventing Surface Phase Transitions for High-Voltage Lithium-Ion Batteries
Authors: Mohanty Debasish , Dahlberg Kevin , King David M. , David Lamuel A. , Sefat Athena S. , Wood David L. , Daniel Claus , Dhar Subhash , Mahajan Vishal , Lee Myongjai , Albano Fabio 
Published: May 2016

AbstractThe energy density of current lithium-ion batteries (LIBs) based on layered LiMO2 cathodes (M = Ni, Mn, Co: NMC; M = Ni, Co, Al: NCA) needs to be improved significantly in order to compete with internal combustion engines and allow for widespread implementation of electric vehicles (EVs). In this report, we show that atomic layer deposition (ALD) of titania (TiO2) and alumina (Al2O3) on Ni-rich FCG NMC and NCA active material particles could substantially improve LIB performance and allow for increased upper cutoff voltage (UCV) during charging, which delivers significantly increased specific energy utilization. Our results show that Al2O3 coating improved the NMC cycling performance by 40% and the NCA cycling performance by 34% at 1 C/−1 C with respectively 4.35 V and 4.4 V UCV in 2 Ah pouch cells. High resolution TEM/SAED structural characterization revealed that Al2O3 coatings prevented surface-initiated layered-to-spinel phase transitions in coated materials which were prevalent in uncoated materials. EIS confirmed that Al2O3-coated materials had significantly lower increase in the charge transfer component of impedance during cycling. The ability to mitigate degradation mechanisms for Ni-rich NMC and NCA illustrated in this report provides insight into a method to enable the performance of high-voltage LIBs.
Budding of Tiger Frog Virus (an Iridovirus) from HepG2 Cells via Three Ways Recruits the ESCRT Pathway
Authors: Mi Shu , Qin Xiao-Wei , Lin Yi-Fan , He Jian , Chen Nan-Nan , Liu Chang , Weng Shao-Ping , He Jian-Guo , Guo Chang-Jun 
Published: May 2016

AbstractThe cellular endosomal sorting complex required for transport (ESCRT) pathway is a multifunctional pathway involved in cell physiological activities. While the majority of RNA viruses bearing L-domains are known to hijack the ESCRT pathway to complete the budding process, the budding of large and complex enveloped DNA viruses, especially iridoviruses, has been rarely investigated. In the present study, we use the tiger frog virus (TFV) as a model to investigate whether iridoviruses are released from host cells through the ESCRT pathway. Inhibition of class E proteins and auxiliary proteins (VPS4A, VPS4B, Tsg101, Alix, and Nedd4.1) reduces extracellular virion production, which preliminarily indicates that the ESCRT pathway is involved in TFV release. The respective interactions of TFV VP031L, VP065L, VP093L with Alix, Tsg101, Nedd4 suggest the underlying molecular mechanism by which TFV gets access to the ESCRT pathway. Co-depletion of Alix, Tsg101, and Nedd4.1 induces a significant reduction in extracellular virion production, which implies the functional redundancy of host factors in TFV budding. Those results are first observation that iridovirus gains access to ESCRT pathway through three ways of interactions between viral proteins and host proteins. Our study provides a better understanding of the budding mechanism of enveloped DNA viruses.
Epigenetic inactivation of the CpG demethylase TET1 as a DNA methylation feedback loop in human cancers
Authors: Li Lili , Li Chen , Mao Haitao , Du Zhenfang , Chan Wai Yee , Murray Paul , Luo Bing , Chan Anthony TC , Mok Tony SK , Chan Francis KL , Ambinder Richard F , Tao Qian 
Published: May 2016

AbstractPromoter CpG methylation is a fundamental regulatory process of gene expression. TET proteins are active CpG demethylases converting 5-methylcytosine to 5-hydroxymethylcytosine, with loss of 5 hmC as an epigenetic hallmark of cancers, indicating critical roles of TET proteins in epigenetic tumorigenesis. Through analysis of tumor methylomes, we discovered TET1 as a methylated target, and further confirmed its frequent downregulation/methylation in cell lines and primary tumors of multiple carcinomas and lymphomas, including nasopharyngeal, esophageal, gastric, colorectal, renal, breast and cervical carcinomas, as well as non-Hodgkin, Hodgkin and nasal natural killer/T-cell lymphomas, although all three TET family genes are ubiquitously expressed in normal tissues. Ectopic expression of TET1 catalytic domain suppressed colony formation and induced apoptosis of tumor cells of multiple tissue types, supporting its role as a broad bona fide tumor suppressor. Furthermore, TET1 catalytic domain possessed demethylase activity in cancer cells, being able to inhibit the CpG methylation of tumor suppressor gene (TSG) promoters and reactivate their expression, such as SLIT2, ZNF382 and HOXA9. As only infrequent mutations of TET1 have been reported, compared to TET2, epigenetic silencing therefore appears to be the dominant mechanism for TET1 inactivation in cancers, which also forms a feedback loop of CpG methylation during tumorigenesis.
Enhancing synchronization stability in a multi-area power grid
Authors: Wang Bing , Suzuki Hideyuki , Aihara Kazuyuki 
Published: May 2016

AbstractMaintaining a synchronous state of generators is of central importance to the normal operation of power grids, in which many networks are generally interconnected. In order to understand the condition under which the stability can be optimized, it is important to relate network stability with feedback control strategies as well as network structure. Here, we present a stability analysis on a multi-area power grid by relating it with several control strategies and topological design of network structure. We clarify the minimal feedback gain in the self-feedback control, and build the optimal communication network for the local and global control strategies. Finally, we consider relationship between the interconnection pattern and the synchronization stability; by optimizing the network interlinks, the obtained network shows better synchronization stability than the original network does, in particular, at a high power demand. Our analysis shows that interlinks between spatially distant nodes will improve the synchronization stability. The results seem unfeasible to be implemented in real systems but provide a potential guide for the design of stable power systems.
SALM5 trans-synaptically interacts with LAR-RPTPs in a splicing-dependent manner to regulate synapse development
Authors: Choi Yeonsoo , Nam Jungyong , Whitcomb Daniel J. , Song Yoo Sung , Kim Doyoun , Jeon Sangmin , Um Ji Won , Lee Seong-Gyu , Woo Jooyeon , Kwon Seok-Kyu , Li Yan , Mah Won , Kim Ho Min , Ko Jaewon , Cho Kwangwook , Kim Eunjoon 
Published: May 2016

AbstractSynaptogenic adhesion molecules play critical roles in synapse formation. SALM5/Lrfn5, a SALM/Lrfn family adhesion molecule implicated in autism spectrum disorders (ASDs) and schizophrenia, induces presynaptic differentiation in contacting axons, but its presynaptic ligand remains unknown. We found that SALM5 interacts with the Ig domains of LAR family receptor protein tyrosine phosphatases (LAR-RPTPs; LAR, PTPδ, and PTPσ). These interactions are strongly inhibited by the splice insert B in the Ig domain region of LAR-RPTPs, and mediate SALM5-dependent presynaptic differentiation in contacting axons. In addition, SALM5 regulates AMPA receptor-mediated synaptic transmission through mechanisms involving the interaction of postsynaptic SALM5 with presynaptic LAR-RPTPs. These results suggest that postsynaptic SALM5 promotes synapse development by trans-synaptically interacting with presynaptic LAR-RPTPs and is important for the regulation of excitatory synaptic strength.
An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)
Authors: Peng Wenzhu , Xu Jian , Zhang Yan , Feng Jianxin , Dong Chuanju , Jiang Likun , Feng Jingyan , Chen Baohua , Gong Yiwen , Chen Lin , Xu Peng 
Published: May 2016

AbstractHigh density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.
Label-free nonlinear optical microscopy detects early markers for osteogenic differentiation of human stem cells
Authors: Hofemeier Arne D. , Hachmeister Henning , Pilger Christian , Schürmann Matthias , Greiner Johannes F. W. , Nolte Lena , Sudhoff Holger , Kaltschmidt Christian , Huser Thomas , Kaltschmidt Barbara 
Published: May 2016

AbstractTissue engineering by stem cell differentiation is a novel treatment option for bone regeneration. Most approaches for the detection of osteogenic differentiation are invasive or destructive and not compatible with live cell analysis. Here, non-destructive and label-free approaches of Raman spectroscopy, coherent anti-Stokes Raman scattering (CARS) and second harmonic generation (SHG) microscopy were used to detect and image osteogenic differentiation of human neural crest-derived inferior turbinate stem cells (ITSCs). Combined CARS and SHG microscopy was able to detect markers of osteogenesis within 14 days after osteogenic induction. This process increased during continued differentiation. Furthermore, Raman spectroscopy showed significant increases of the PO43− symmetric stretch vibrations at 959 cm−1 assigned to calcium hydroxyapatite between days 14 and 21. Additionally, CARS microscopy was able to image calcium hydroxyapatite deposits within 14 days following osteogenic induction, which was confirmed by Alizarin Red-Staining and RT- PCR. Taken together, the multimodal label-free analysis methods Raman spectroscopy, CARS and SHG microscopy can monitor osteogenic differentiation of adult human stem cells into osteoblasts with high sensitivity and spatial resolution in three dimensions. Our findings suggest a great potential of these optical detection methods for clinical applications including in vivo observation of bone tissue–implant-interfaces or disease diagnosis.
The Magea gene cluster regulates male germ cell apoptosis without affecting the fertility in mice
Authors: Hou Siyuan , Xian Li , Shi Peiliang , Li Chaojun , Lin Zhaoyu , Gao Xiang 
Published: May 2016

AbstractWhile apoptosis is essential for male germ cell development, improper activation of apoptosis in the testis can affect spermatogenesis and cause reproduction defects. Members of the MAGE-A (melanoma antigen family A) gene family are frequently clustered in mammalian genomes and are exclusively expressed in the testes of normal animals but abnormally activated in a wide variety of cancers. We investigated the potential roles of these genes in spermatogenesis by generating a mouse model with a 210-kb genomic deletion encompassing six members of the Magea gene cluster (Magea1, Magea2, Magea3, Magea5, Magea6 and Magea8). Male mice carrying the deletion displayed smaller testes from 2 months old with a marked increase in apoptotic germ cells in the first wave of spermatogenesis. Furthermore, we found that Magea genes prevented stress-induced spermatogenic apoptosis after N-ethyl-N-nitrosourea (ENU) treatment during the adult stage. Mechanistically, deletion of the Magea gene cluster resulted in a dramatic increase in apoptotic germ cells, predominantly spermatocytes, with activation of p53 and induction of Bax in the testes. These observations demonstrate that the Magea genes are crucial in maintaining normal testicular size and protecting germ cells from excessive apoptosis under genotoxic stress.
Long-term results of anterior cervical corpectomy and fusion with nano-hydroxyapatite/polyamide 66 strut for cervical spondylotic myelopathy
Authors: Zhang Yuan , Deng Xu , Jiang Dianming , Luo Xiaoji , Tang Ke , Zhao Zenghui , Zhong Weiyang , Lei Tao , Quan Zhengxue 
Published: May 2016

AbstractTo assess the long-term clinical and radiographic outcomes of anterior cervical corpectomy and fusion (ACCF) with a neotype nano-hydroxyapatite/polyamide 66 (n-HA/PA66) strut in the treatment of cervical spondylotic myelopathy (CSM). Fifty patients with CSM who underwent 1- or 2-level ACCF with n-HA/PA66 struts were retrospectively investigated. With a mean follow-up of 79.6 months, the overall mean JOA score, VAS and cervical alignment were improved significantly. At last follow-up, the fusion rate was 98% and the subsidence rate of the n-HA/PA66 strut was 8%. The “radiolucent gap” at the interface between the n-HA/PA66 strut and the vertebra was further noted to evaluate the osteoconductivity and osseointegration of the strut and the incidence of it was 62% at the last follow-up. Three patients suffered symptomatic adjacent segment degeneration (ASD). No significant difference was detected in the outcomes between 1- and 2-level corpectomy at follow-ups. In conclusion, the satisfactory outcomes in this study indicated that the n-HA/PA66 strut was an effective graft for cervical reconstruction. Moreover, the osteoconductivity and osseointegration of the strut is still need to be optimized for future clinical application owing to the notably presence of “radiolucent gap” in present study.
Use of recombinant porcine β-defensin 2 as a medicated feed additive for weaned piglets
Authors: Peng Zixin , Wang Anru , Xie Linqi , Song Weiping , Wang Jie , Yin Zhe , Zhou Dongsheng , Li Fengqin 
Published: May 2016

AbstractPost-weaning diarrhoea (PWD) in piglets is associated with colonization of the intestine with bacterial pathogens. In this study, we evaluated the use of recombinant porcine β-defensin 2 (rpBD2) as a medicated feed additive for weaned piglets. The crude extract from the culture supernatant of rpBD2-expressing Pichia pastoris was used as a medicated feed additive for weaned piglets. Dietary treatments included a positive control (basal diet + antibiotics, designated PC) and three different rpBD2 treatments without antibiotics (basal diet supplemented with 1, 5, or 15 g of crude rpBD2/kg basal diet, designated 1PD, 5PD and 15PD, respectively). Of all the treatments, 5PD had the greatest impact on the weaned piglets. It increased their body weight, average daily weight gain, average daily feed intake and intestinal villus height in the duodenum and jejunum and reduced the incidence of PWD. The diversity of the cecal digesta and mucosa microflora was compared between the weaned piglets in the PC and 5PD groups. Piglets treated with 5PD had lower diversity indices and fewer bacterial pathogens in their cecal digesta and mucosa than the PC group. Our results demonstrate that crude rpBD2 could provide an alternative to the traditional antibiotic feed additives given to weaned piglets.
P-wave Variability and Atrial Fibrillation
Authors: Censi Federica , Corazza Ivan , Reggiani Elisa , Calcagnini Giovanni , Mattei Eugenio , Triventi Michele , Boriani Giuseppe 
Published: May 2016

AbstractThe analysis of P-wave template has been widely used to extract indices of Atrial Fibrillation (AF) risk stratification. The aim of this paper was to assess the potential of the analysis of the P-wave variability over time in patients suffering from atrial fibrillation. P-wave features extracted from P-wave template together with novel indices of P-wave variability have been estimated in a population of patients suffering from persistent AF and compared to those extracted from control subjects. We quantify the P-wave variability over time using three algorithms and we extracted three novel indices: one based on the cross-correlation coefficients among the P-waves (Cross-Correlation Index, CCI), one associated to variation in amplitude of the P-waves (Amplitude Dispersion Index, ADI), one sensible to the phase shift among P-waves (Warping Index, WI). The control group resulted to be characterized by shorter P-wave duration and by a less amount of fragmentation and variability, respect to AF patients. The parameter CCI shows the highest sensitivity (97.3%) and a good specificity (95%).
The decisive role of free water in determining homogenous ice nucleation behavior of aqueous solutions
Authors: Wang Qiang , Zhao Lishan , Li Chenxi , Cao Zexian 
Published: May 2016

AbstractIt is a challenging issue to quantitatively characterize how the solute and pressure affect the homogeneous ice nucleation in a supercooled solution. By measuring the glass transition behavior of solutions, a universal feature of water-content dependence of glass transition temperature is recognized, which can be used to quantify hydration water in solutions. The amount of free water can then be determined for water-rich solutions, whose mass fraction, Xf, is found to serve as a universal relevant parameter for characterizing the homogeneous ice nucleation temperature, the meting temperature of primary ice and even the water activity of solutions of electrolytes and smaller organic molecules. Moreover, the effects of hydrated solute and pressure on ice nucleation is comparable and the pressure, when properly scaled, can be incorporated into the universal parameter Xf. These results help establish the decisive role of free water in determining ice nucleation and other relevant properties of aqueous solutions.
Chloroplast FBPase and SBPase are thioredoxin-linked enzymes with similar architecture but different evolutionary histories
Authors: Gütle Desirée D. , Roret Thomas , Müller Stefanie J. , Couturier Jérémy , Lemaire Stéphane D. , Hecker Arnaud , Dhalleine Tiphaine , Buchanan Bob B. , Reski Ralf , Einsle Oliver , Jacquot Jean-Pierre 
Published: May 2016

Significance
We demonstrate that, although the two phosphatases of the Calvin–Benson cycle of photosynthesis [sedoheptulose-1,7-bisphosphatase (SBPase) and fructose-1,6-bisphosphatase (FBPase)] share extensive structural homology, their redox-regulatory disulfides are incorporated in strikingly different positions, in agreement with an independent evolutionary origin of each enzyme. This article compares in detail the structures of the enzymes together with their regulatory and catalytic properties as well as their phylogenies. Significantly, the substrate binding site of SBPase is larger than that of FBPase, thus allowing it to accommodate both seven- and six-carbon sugar phosphate substrates, whereas FBPase is active only with the latter. The data suggest that SBPase is of archaeal origin, whereas FBPase is descended from bacteria.