bluuebunny/crossref_metadata_2025_split huggingface dataset:
An adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system
Authors: Kasahara Masahiro , Suetsugu Noriyuki , Urano Yuki , Yamamoto Chiaki , Ohmori Mikiya , Takada Yuki , Okuda Shujiro , Nishiyama Tomoaki , Sakayama Hidetoshi , Kohchi Takayuki , Takahashi Fumio 
Published: December 2016

AbstractAdenylyl cyclase (AC), which produces the signalling molecule cAMP, has numerous important cellular functions in diverse organisms from prokaryotes to eukaryotes. Here we report the identification and characterization of an AC gene from the liverwort Marchantia polymorpha. The encoded protein has both a C-terminal AC catalytic domain similar to those of class III ACs and an N-terminal cyclic nucleotide phosphodiesterase (PDE) domain that degrades cyclic nucleotides, thus we designated the gene MpCAPE (COMBINEDAC withPDE). Biochemical analyses of recombinant proteins showed that MpCAPE has both AC and PDE activities. In MpCAPE-promoter-GUS lines, GUS activity was specifically detected in the male sexual organ, the antheridium, suggesting MpCAPE and thus cAMP signalling may be involved in the male reproductive process. CAPE orthologues are distributed only in basal land plants and charophytes that use motile sperm as the male gamete. CAPE is a subclass of class III AC and may be important in male organ and cell development in basal plants.
Mitochondrial Phylogenomics yields Strongly Supported Hypotheses for Ascaridomorph Nematodes
Authors: Liu Guo-Hua , Nadler Steven A. , Liu Shan-Shan , Podolska Magdalena , D’Amelio Stefano , Shao Renfu , Gasser Robin B. , Zhu Xing-Quan 
Published: December 2016

AbstractAscaridomorph nematodes threaten the health of humans and other animals worldwide. Despite their medical, veterinary and economic importance, the identification of species lineages and establishing their phylogenetic relationships have proved difficult in some cases. Many working hypotheses regarding the phylogeny of ascaridomorphs have been based on single-locus data, most typically nuclear ribosomal RNA. Such single-locus hypotheses lack independent corroboration, and for nuclear rRNA typically lack resolution for deep relationships. As an alternative approach, we analyzed the mitochondrial (mt) genomes of anisakids (~14 kb) from different fish hosts in multiple countries, in combination with those of other ascaridomorphs available in the GenBank database. The circular mt genomes range from 13,948-14,019 bp in size and encode 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. Our analysis showed that thePseudoterranova decipienscomplex consists of at least six cryptic species. In contrast, the hypothesis thatContracaecum ogmorhinirepresents a complex of cryptic species is not supported by mt genome data. Our analysis recovered several fundamental and uncontroversial ascaridomorph clades, including the monophyly of superfamilies and families, except for Ascaridiidae, which was consistent with the results based on nuclear rRNA analysis. In conclusion, mt genome analysis provided new insights into the phylogeny and taxonomy of ascaridomorph nematodes.
Broadband and wide-angle RCS reduction using a 2-bit coding ultrathin metasurface at terahertz frequencies
Authors: Liang Lanju , Wei Minggui , Yan Xin , Wei Dequan , Liang Dachuan , Han Jiaguang , Ding Xin , Zhang GaoYa , Yao Jianquan 
Published: December 2016

AbstractA novel broadband and wide-angle 2-bit coding metasurface for radar cross section (RCS) reduction is proposed and characterized at terahertz (THz) frequencies. The ultrathin metasurface is composed of four digital elements based on a metallic double cross line structure. The reflection phase difference of neighboring elements is approximately 90° over a broadband THz frequency. The mechanism of RCS reduction is achieved by optimizing the coding element sequences, which redirects the electromagnetic energies to all directions in broad frequencies. An RCS reduction of less than −10 dB bandwidth from 0.7 THz to 1.3 THz is achieved in the experimental and numerical simulations. The simulation results also show that broadband RCS reduction can be achieved at an incident angle below 60° for TE and TM polarizations under flat and curve coding metasurfaces. These results open a new approach to flexibly control THz waves and may offer widespread applications for novel THz devices.
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia
Authors: Tatlow PJ , Piccolo Stephen R. 
Published: December 2016

AbstractPublic compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began exploring opportunities to work with molecular data in cloud-computing environments. With this approach, it becomes possible for scientists to take their tools to the data and thereby avoid large data transfers. It also becomes feasible to scale computing resources to the needs of a given analysis. We quantified transcript-expression levels for 12,307 RNA-Sequencing samples from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. We used two cloud-based configurations and examined the performance and cost profiles of each configuration. Using preemptible virtual machines, we processed the samples for as little as $0.09 (USD) per sample. As the samples were processed, we collected performance metrics, which helped us track the duration of each processing step and quantified computational resources used at different stages of sample processing. Although the computational demands of reference alignment and expression quantification have decreased considerably, there remains a critical need for researchers to optimize preprocessing steps. We have stored the software, scripts, and processed data in a publicly accessible repository (https://osf.io/gqrz9).
Recombinant Marek’s disease virus type 1 provides full protection against very virulent Marek’s and infectious bursal disease viruses in chickens
Authors: Li Kai , Liu Yongzhen , Liu Changjun , Gao Li , Zhang Yanping , Cui Hongyu , Gao Yulong , Qi Xiaole , Zhong Li , Wang Xiaomei 
Published: December 2016

AbstractMarek’s disease virus (MDV) is a preferred vector in the construction of recombinant vaccines. However, bivalent vaccine based on MDV that confers full protection against both very virulent Marek’s and infectious bursal disease virus (IBDV) infections in chickens has not been produced. Here we developed a system utilizing overlapping fosmid DNAs transfection that rescues an MDV type 1 (MDV1) vaccine strain. Using this system, we inserted the IBDV VP2 gene at MDV1 genome sites UL41, US10 and US2. The VP2 protein was stably expressed in the recombinant MDV-infected cells and self-assembled into IBDV subviral particles. Insertion of the VP2 gene did not affect the replication phenotype of MDV in cell cultures, nor did it increase the virulence of the MDV vaccine strain in chickens. After challenge with very virulent IBDV, r814US2VP2 conferred full protection, whereas r814UL41VP2 and r814US10VP2 provided partial or no protection. All the three recombinant vaccines provided full protection against very virulent MDV challenge in chickens. These results demonstrated that r814US2VP2 could be used as a promising bivalent vaccine against both Marek’s and infectious bursal diseases in chickens.
A structural insight into the negative effects of opioids in analgesia by modulating the TLR4 signaling: An in silico approach
Authors: Shah Masaud , Anwar Muhammad Ayaz , Yesudhas Dhanusha , Krishnan Jayalakshmi , Choi Sangdun 
Published: December 2016

AbstractOpioids are considered the gold standard therapy for pain. However, TLR-dependent negative effects in analgesia have highlighted the complexities in the pharmacodynamics of opioids. While successive studies have reported that morphine and Morphine-3-glucuronide (M3G) activate the TLR4 pathway, the structural details of this mechanism are lacking. Here, we have utilized various computational tools to reveal the structural dynamics of the opioid-bound TLR4/MD2 complex, and have proposed a potential TLR4 activation mechanism. Our results support previous findings, and include the novel insight that the stable binding of morphine and naloxone, but not M3G, in the MD2 cavity, is TLR4 dependent. Morphine interacts with MD2 near its Phe126 loop to induce the active conformation (MD2C); however, this binding is likely reversible, and the complex gains stability upon interaction with TLR4. M3G also induces the MD2Cstate, with both the Phe126 loop and the H1 loop being involved in MD2-M3G complex stability. Remarkably, naloxone, which requires TLR4 interaction for complex stability, switches the conformation of the gating loop to the inactive state (MD2°). Cumulatively, our findings suggest that ligand binding and receptor clustering occur successively in opioid-induced TLR4 signaling, and that MD2 plasticity and pocket hydrophobicity are crucial for the recognition and accommodation of ligands.
Huangqin-tang ameliorates dextran sodium sulphate-induced colitis by regulating intestinal epithelial cell homeostasis, inflammation and immune response
Authors: Zou Ying , Lin Jiantao , Li Wenyang , Wu Zhuguo , He Zhiwei , Huang Guoliang , Wang Jian , Ye Caiguo , Cheng Xiaoyan , Ding Congcong , Zheng Xuebao , Chi Honggang 
Published: December 2016

AbstractHuangqin-tang (HQT) is a traditional Chinese medicine (TCM) formula widely used for the treatment of inflammatory bowel disease in China. However, the molecular mechanisms by which HQT protects the colon are unclear. We studied the protective effects of HQT and the underlying mechanisms in an experimental mouse model and in vitro. In vivo, dextran sodium sulphate (DSS)-induced acute and chronic colitis were significantly ameliorated by HQT as gauged by phenotypic, histopathologic and inflammatory manifestations of the disease. Mechanistically, DSS-induced nuclear factor-κB (NF-κB) signalling was inhibited by HQT. Moreover, HQT-treated mice demonstrated significant changes in cell apoptosis, expression of apoptosis-associated genes such as caspase-3, bax, bcl-2, and intestinal permeability. HQT also increased occluding and zonula occludens-1 (ZO-1), inhibited cell proliferation (Ki67), and increased regulatory T cells numbers, protein expression of Foxp3 and IL-10 in the colonic tissue. In vitro, HQT down-regulated production of pro-inflammatory cytokines and supressed the NF-κB signalling pathway in lipopolysaccharides-induced RAW 264.7 macrophages. Our study suggests that HQT plays a critical role in regulating intestinal epithelial cell homeostasis, inflammation and immune response in colitis and offers novel therapeutic options in the management of inflammatory bowel disease.
Sustained maternal hyperoxygenation improves aortic arch dimensions in fetuses with coarctation
Authors: Zeng Shi , Zhou Jiawei , Peng Qinghai , Deng Wen , Zhang Ming , Zhao Yili , Wang Tao , Zhou Qichang 
Published: December 2016

AbstractThe aim was to investigate the impact of maternal hyperoxygenation (HO) on cardiac dimensions in fetuses with isolated Coarctation (CoA). Fetal echocardiography was performed serially in 48 fetuses with CoA and gestation age matched normal fetues. The Z-scores for the mitral valve (MV), tricuspid valve (TV), aortic valve (AV), ascending aorta (AAo), isthmus, pulmonary valve (PV), main pulmonary artery (MPA), and descending aorta (DAo) were measured and compared among normal fetuses, CoA fetuses with oxygen and CoA fetuses with air. In the group with oxygen, 6 L/min oxygen was administered to the mother using a face mask. Regression analyses were performed to identify potential factors for HO outcome. The left heart dimension Z-scores increased gradually during HO therapy periods, especially at 4 weeks after oxygen therapy (P < 0.05). As for the case group with air, the left heart dimension remained unchanged. The duration of HO was associated with aortic arch Z-scores (adjusted R2 = 0.199, 0.60 for AAO and isthmus, respectively). Sustained maternal middle-flow oxygenation can be safely used to improve left heart dimensions in fetuses with isolated CoA. The duration of HO were associated with treatment outcome. These findings may provide useful information for developing novel treatment strategies.
TracMouse: A computer aided movement analysis script for the mouse inverted horizontal grid test
Authors: Niewiadomski W. , Palasz E. , Skupinska M. , Zylinski M. , Steczkowska M. , Gasiorowska A. , Niewiadomska G. , Riedel G. 
Published: December 2016

AbstractIn rodents, detection and quantification of motor impairments is difficult. The traction test (inverted grid with mice clinging to the underside) currently has no objective rating system. We here developed and validated the semi-automatic MATLAB script TracMouse for unbiased detection of video-recorded movement patterns. High precision videos were analyzed by: (i) principal identification of anatomical paw details frame-by-frame by an experimentally blinded rater; (ii) automatic retrieval of proxies by TracMouse for individual paws. The basic states of Hold and Step were discriminated as duration and frequency, and these principle parameters were converted into static and dynamic endpoints and their discriminating power assessed in a dopaminergic lesion model. Relative to hind paws, forepaws performed ~4 times more steps, they were ~20% longer, and Hold duration was ~5 times shorter in normal C57Bl/6 mice. Thus, forepaw steps were classified as exploratory, hind paw movement as locomotive. Multiple novel features pertaining to paw sequence, step lengths and exploratory touches were accessible through TracMouse and revealed subtle Parkinsonian phenotypes. Novel proxies using TracMouse revealed previously unidentified features of movement and may aid the understanding of (i) brain circuits related to motor planning and execution, and (ii) phenotype detection in experimental models of movement disorders.
Ginsenoside Rg1 attenuates ultraviolet B-induced glucocortisides resistance in keratinocytes via Nrf2/HDAC2 signalling
Authors: Li Jun , Liu Dong , Wu Jinfeng , Zhang Daniel , Cheng Binbin , Zhang Yani , Yin Zifei , Wang Yuan , Du Juan , Ling Changquan 
Published: December 2016

AbstractOxidative stress, which occurs after ultraviolet (UV) radiation, usually results in Glucocorticoid (GC) resistance and the subsequent development of skin inflammation. One approach to protecting the skin against UV radiation is the use of antioxidants. The ginsenoside Rg1 is a novel natural antioxidant isolated from the medicinal plant Panax ginseng C.A. Mey. We demonstrated that UVB exposure exacerbated inflammation and reduced both the level of the glucocorticoid receptor (GR) and the efficacy of dexamethasone (Dex) in human keratinocytes (HaCaT cells). Pretreatment with Rg1 increased the expression of GR and restored Dex responsiveness to inflammation in UVB-irradiated HaCaT cells. Mechanistically, Rg1 rescued UVB-induced HDAC2 degradation. HDAC2 knockdown partially abolished the Rg1-induced up-regulation of GR and the enhancement of GC sensitivity. In addition, Rg1 reduced the production of reactive oxygen species (ROS), which preceded the up-regulation of HDAC2, and consequent sensitization of cells to Dex. Moreover, Rg1 treatment promoted the translocation and activation of Nrf2. Nrf2 knockdown partially abolished the Rg1-induced decrease of ROS production and increase of HDAC2. Rg1 also potentiated the anti-inflammatory effects of Dex in UVB-irradiated mouse skin. In conclusion, we demonstrated that Rg1 attenuated UVB-induced GC insensitivity. Notably, these effects were partially mediated by the Nrf2/HDAC2 pathway.
Effect of hydrothermal pretreatment on the structural changes of alkaline ethanol lignin from wheat straw
Authors: Chen Xue , Li Hanyin , Sun Shaoni , Cao Xuefei , Sun Runcang 
Published: December 2016

AbstractDue to the enormous abundance of lignin and its unique aromatic nature, lignin has great potential for the production of industrially useful fuels, chemicals, and materials. However, the rigid and compact structure of the plant cell walls significantly blocks the separation of lignin. In this study, wheat straw was hydrothermally pretreated at different temperatures (120–200 °C) followed by post-treatment with 70% ethanol containing 1% NaOH to improve the isolation of lignin. Results demonstrated that the content of associated carbohydrates of the lignin fractions was gradually reduced with the increment of the hydrothermal severity. The structure of the lignins changed regularly with the increase of the pretreatment temperature from 120 to 200 °C. In particular, the contents ofβ-O-4′,β-β′,β-5′ linkages and aliphatic OH in the lignins showed a tendency of decrease, while the content of phenolic OH and thermal stability of the lignin fractions increased steadily as the increment of the pretreatment temperature.
Protein knotting through concatenation significantly reduces folding stability
Authors: Hsu Shang-Te Danny 
Published: December 2016

AbstractConcatenation by covalent linkage of two protomers of an intertwined all-helical HP0242 homodimer from Helicobacter pylori results in the first example of an engineered knotted protein. While concatenation does not affect the native structure according to X-ray crystallography, the folding kinetics is substantially slower compared to the parent homodimer. Using NMR hydrogen-deuterium exchange analysis, we showed here that concatenation destabilises significantly the knotted structure in solution, with some regions close to the covalent linkage being destabilised by as much as 5 kcal mol−1. Structural mapping of chemical shift perturbations induced by concatenation revealed a pattern that is similar to the effect induced by concentrated chaotrophic agent. Our results suggested that the design strategy of protein knotting by concatenation may be thermodynamically unfavourable due to covalent constrains imposed on the flexible fraying ends of the template structure, leading to rugged free energy landscape with increased propensity to form off-pathway folding intermediates.
Graphene damage effects on radiation-resistance and configuration of copper–graphene nanocomposite under irradiation: A molecular dynamics study
Authors: Huang Hai , Tang Xiaobin , Chen Feida , Liu Jian , Li Huan , Chen Da 
Published: December 2016

AbstractMetal–graphene nanocomposite is a kind of potential radiation tolerant material. Graphene damage of the composite is inevitable within radiation environments. In this paper, two kinds of copper–graphene nanocomposite (CGNC) systems containing perfect graphene and prefabricated damage graphene, respectively, were adopted to expound the influences of graphene damage on the properties (radiation-resistance and configuration) of CGNC under irradiation by atomistic simulations. In the CGNC containing perfect graphene, the increasing graphene damage induced by the increase of the number of cascades, did not obviously impair the role of copper–graphene interface in keeping the properties of CGNC. In the CGNC containing prefabricated damage graphene, the properties of CGNC would significantly deteriorate once the radius of prefabricated damage exceeds 10 Å, and even stacking fault tetrahedral would occur in the CGNC. The results highlighted that prefabricated graphene damage have greater effects on the change of the properties of CGNC. Therefore, it is very necessary to maintain the structural integrity of graphene for improving the radiation-resistance and configuration of CGNC.
Intraobserver and Interobserver Measurement Variability of the Rib-Vertebral Angle Difference
Authors: Tysklind Robert G. , Myung Karen , Gantsoudes George , Kishan Shyam , Turner Chad , Lee Stella , Wanner Matthew , Sabatino Meagan , Linger Scott , Loder Randall T. 
Published: December 2016

Background:
The rib-vertebral angle (RVAD) differentiates between progressive and resolving infantile idiopathic scoliosis (IIS) curves. Those with a RVAD<20 degrees often resolve without treatment, whereas those >20 degrees often progress and require treatment. The mathematical magnitude of RVAD measurement variability has not been described, and was thus the purpose of this study. It is important to know the reliability of RVAD measurements so as to understand changes that can be attributed to observer error alone.

Purpose:
The purpose of the study was to mathematically determine the intraobserver and interobserver measurement variability of the RVAD difference in IIS.

Methods:
A convenience sample of 50 patients with IIS was selected. The RVAD was measured twice by 7 different observers separated by a minimum of 3 weeks. The 7 different readers chosen to measure the RVAD were 2 orthopaedic residents, 1 pediatric radiologist, and 4 attending pediatric orthopaedic surgeons. The same goniometer was used for all measurements. Intraobserver and interobserver measurement variability was determined using 3 well known used statistical methods.

Results:
The 3 different methods used to determine intraobserver and interobserver variability using 95% prediction/confidence limits gave very similar results. Intraobserver variability was ∼24 degrees and the interobserver variability was ∼23 degrees.

Discussion:
The utility of the RVAD in medical decision-making and counseling of patients with IIS should be approached with caution when used in isolation due to the large measurement variability.

Level of Evidence:
Level 3.
A Whole Exome Study Identifies Novel Candidate Genes for Vertebral Bone Marrow Signal Changes (Modic Changes)
Authors: Kraatari Minna , Skarp Sini , Niinimäki Jaakko , Karppinen Jaro , Männikkö Minna 
Published: December 2016

Study Design.
A family-based study.

Objective.
The aim of this study was to identify rare genetic factors predisposing to Modic changes (MCs).

Summary of Background Data.
Lumbar disc degeneration (LDD) is one of the contributing factors behind low back pain (LBP). Lumbar MC visualized as bone marrow signal intensity changes on magnetic resonance imaging (MRI) represent a specific phenotype of LDD, which has a stronger association with LBP than LDD without MC.

Methods.
The study set consisted of two Finnish families: Family I included seven affected and four unaffected individuals and Family II eight affected and seven unaffected individuals. MCs were evaluated in 26 individuals using MRI. Whole exome sequencing was used to identify alleles cosegregating with MC. Annotate variation was used to carry out functional annotation of alleles and their frequencies were evaluated using 1000Genomes, Sequencing Initiative Suomi (SISu), and the Exome Aggregation Consortium (ExAC) databases.

Results.
We identified predisposing genetic alleles for MC in two Finnish families. In each family, only single allele cosegregated with MC. In Family I, the observed allele was an insertion and deletion in the HSPG2 gene, resulting in a premature termination codon. In Family II, a single nucleotide polymorphism (rs61753465) in the MAML1 gene was identified in all affected family members.

Conclusion.
We have identified two novel candidate genes, MAML1 and HSPG2, associating with MC. These genes are important in cartilage structure and joint cartilage maintenance. Our findings are novel among lumbar spine degenerative phenotypes.

Level of Evidence: N/A