bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding cannabinoids in hair does not prove cannabis consumption
Authors: Moosmann Bjoern , Roth Nadine , Auwärter Volker 
Published: October 2015

AbstractHair analysis for cannabinoids is extensively applied in workplace drug testing and in child protection cases, although valid data on incorporation of the main analytical targets, ∆9-tetrahydrocannabinol (THC) and 11-nor-9-carboxy-THC (THC-COOH), into human hair is widely missing. Furthermore, ∆9-tetrahydrocannabinolic acid A (THCA-A), the biogenetic precursor of THC, is found in the hair of persons who solely handled cannabis material. In the light of the serious consequences of positive test results the mechanisms of drug incorporation into hair urgently need scientific evaluation. Here we show that neither THC nor THCA-A are incorporated into human hair in relevant amounts after systemic uptake. THC-COOH, which is considered an incontestable proof of THC uptake according to the current scientific doctrine, was found in hair, but was also present in older hair segments, which already grew before the oral THC intake and in sebum/sweat samples. Our studies show that all three cannabinoids can be present in hair of non-consuming individuals because of transfer through cannabis consumers, via their hands, their sebum/sweat, or cannabis smoke. This is of concern for e.g. child-custody cases as cannabinoid findings in a child’s hair may be caused by close contact to cannabis consumers rather than by inhalation of side-stream smoke.
Design, Synthesis and Structure-Activity Relationship Optimization of Lycorine Derivatives for HCV Inhibition
Authors: Chen Duozhi , Cai Jieyun , Cheng Junjun , Jing Chenxu , Yin Junlin , Jiang Jiandong , Peng Zonggen , Hao Xiaojiang 
Published: October 2015

AbstractLycorine is reported to be a multifunctional compound. We previously showed that lycorine is an HCV inhibitor with strong activity. Further research on the antivirus mechanism indicated that lycorine does not affect the enzymes that are indispensable to HCV replication but suppresses the expression of Hsc70 in the host cell to limit HCV replication. However, due to the cytotoxicity and apoptosis induction of lycorine, lycorine is unsafe to be a anti-HCV agent for clinical application. As a result of increasing interest, its structure was optimized for the first time and a novel series of lycorine derivatives was synthesized, all of which lost their cytotoxicity to different degrees. Structure-activity analysis of these compounds revealed that disubstitution on the free hydroxyl groups at C1 and C2 and/or degradation of the benzodioxole group would markedly reduce the cytotoxicity. Furthermore, an α, β-unsaturated ketone would improve the HCV inhibitory activity of lycorine. The C3-C4 double bond is crucial to the anti-HCV activity because hydrogenation of this double bond clearly weakened HCV inhibition.
Rhesus monkey model of liver disease reflecting clinical disease progression and hepatic gene expression analysis
Authors: Wang Hong , Tan Tao , Wang Junfeng , Niu Yuyu , Yan Yaping , Guo Xiangyu , Kang Yu , Duan Yanchao , Chang Shaohui , Liao Jianpeng , Si Chenyang , Ji Weizhi , Si Wei 
Published: October 2015

AbstractAlcoholic liver disease (ALD) is a significant public health issue with heavy medical and economic burdens. The aetiology of ALD is not yet completely understood. The development of drugs and therapies for ALD is hampered by a lack of suitable animal models that replicate both the histological and metabolic features of human ALD. Here, we characterize a rhesus monkey model of alcohol-induced liver steatosis and hepatic fibrosis that is compatible with the clinical progression of the biochemistry and pathology in humans with ALD. Microarray analysis of hepatic gene expression was conducted to identify potential molecular signatures of ALD progression. The up-regulation of expression of hepatic genes related to liver steatosis (CPT1A, FASN, LEPR, RXRA, IGFBP1, PPARGC1A and SLC2A4) was detected in our rhesus model, as was the down-regulation of such genes (CYP7A1, HMGCR, GCK and PNPLA3) and the up-regulation of expression of hepatic genes related to liver cancer (E2F1, OPCML, FZD7, IGFBP1 and LEF1). Our results demonstrate that this ALD model reflects the clinical disease progression and hepatic gene expression observed in humans. These findings will be useful for increasing the understanding of ALD pathogenesis and will benefit the development of new therapeutic procedures and pharmacological reagents for treating ALD.
Resting state of the human proton channel dimer in a lipid bilayer
Authors: Li Qufei , Shen Rong , Treger Jeremy S. , Wanderling Sherry S. , Milewski Wieslawa , Siwowska Klaudia , Bezanilla Francisco , Perozo Eduardo 
Published: October 2015

Significance
The human proton channel hHv1 is responsible for the extrusion protons during a series of important physiological events with clinical relevance. Yet, the mechanistic details underlying voltage-dependent gating, ion selectivity, and cooperativity between homodimers remain to be determined. We carried out a structural characterization of hHv1 in a lipid bilayer using spectroscopic methods and revealed a strongly focused electric field across its putative selectivity filter. In combination with computational methods, we showed that the recently determined crystal structure of CiVSD-WT is the best structural template for dimeric hHv1, and constructed a full-length model of dimeric hHv1 with spectroscopic constraints. We proposed an explicit mechanism for hHv1 gating with functional predictions according to the one-click model recently established in CiVSD.
The Incidence of Gastric Adenocarcinoma Among Patients With Gastric Intestinal Metaplasia
Authors: Lee Teng-Yu , Wang Ren-Ching , Lee Yi-Chia , Lin Jaw-Town , Ho Hsiu J. , Hsieh Mu-Chih , Wu Chun-Ying 
Published: October 2015

Background and Aims:
Gastric intestinal metaplasia (IM) has been known as a premalignant condition, but estimates of its cancer risk vary widely. We aimed to analyze cancer risk of gastric IM by a long-term cohort study.

Methods:
We conducted a hospital-based study that included all patients with gastric IM between 1992 and 2010, and the development of gastric adenocarcinoma was evaluated until July 2011. Patients developing gastric cancer ≤180 days after the index diagnosis of IM were excluded. The incidence rate, the cumulative incidence, and the standardized incidence ratio (SIR) of gastric cancer were determined, and hazard ratios (HRs) of risk factors were calculated.

Results:
We identified 7059 patients with a median follow-up duration of 5.1 years, and 81 patients developed gastric adenocarcinoma during the study period. The 5-, 10-, and 15-year cumulative incidences of gastric cancer were 0.9% [95% confidence interval (CI), 0.6-1.1), 2.0% (95% CI, 1.5-2.6), and 3.0% (95% CI, 2.0-4.0), respectively. On multivariate analysis, older age (eg, 75 y and above; HR=7.4; 95% CI, 2.8-19.6), low-grade dysplasia (HR=4.0; 95% CI, 2.1-7.9), and high-grade dysplasia (HR=18.8; 95% CI, 9.0-39.5) were independent risk factors. As compared with the risk in the general population, the SIR of gastric cancer among patients with gastric IM was 2.5 (95% CI, 2.0-3.1). However, the SIR was only 2.0 (95% CI, 1.5-2.6) in the nondysplasia subgroup, but was up to 35.2 (95% CI, 15.2-69.4) in the high-grade dysplasia subgroup.

Conclusions:
Gastric IM is an important risk factor for gastric cancer, but surveillance should be arranged only for those at an especially high risk.
Use of 16S rRNA gene-based sequencing for identification of Oligella urethralis that was misidentified as Fransciella tularensis by an automated system
Authors: Shruthi N. , Dhanalaxmi A. , Rajendran R. 
Published: October 2015

Introduction:

Oligella infections are rare and have been only rarely reported in the literature. This may be due to the misidentification of Oligella as a Moraxella-like organism. To the best of our knowledge, we present what we believe to be the first case report on Oligella urethralis bacteraemia in India.

Case presentation:
A 65-year-old female patient with compromising underlying illness presented with signs and symptoms of bacteraemia. The organism was initially identified as Fransciella tularensis by a bioMérieux colorimetric VITEK 2 Compact GN ID card, but 16S rRNA gene sequencing confirmed the isolate as O. urethralis.

Conclusion:
The case emphasizes the importance of O. urethralis as an emerging opportunistic pathogen. Although automated systems allow accurate and rapid identification of commonly isolated bacterial organisms, they are less likely to correctly identify slow-growing, fastidious, rare or biochemically inert organisms. Therefore, it is good to confirm such isolates with a second method such as 16S sequencing and/or matrix-assisted laser desorption/ionization time-of-flight MS.
Recombination produces coherent bacterial species clusters in both core and accessory genomes
Authors: Marttinen Pekka , Croucher Nicholas J. , Gutmann Michael U. , Corander Jukka , Hanage William P. 
Published: October 2015

Background:
Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be ‘genomically coherent’, even though there is no consensus on how this should be determined.

Results:
We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates.

Conclusions:
The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.
Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila
Authors: Li () Yulong , Armstrong Robin L. , Duronio Robert J. , MacAlpine David M. 
Published: October 2015

ABSTRACTThe methylation state of lysine 20 on histone H4 (H4K20) has been linked to chromatin compaction, transcription, DNA repair and DNA replication. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7. PR-Set7 depletion in mammalian cells results in defective S phase progression and the accumulation of DNA damage, which has been partially attributed to defects in origin selection and activation. However, these studies were limited to only a handful of mammalian origins, and it remains unclear how PR-Set7 and H4K20 methylation impact the replication program on a genomic scale. We employed genetic, cytological, and genomic approaches to better understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication and genome stability inDrosophilacells. We find that deregulation of H4K20 methylation had no impact on origin activation throughout the genome. Instead, depletion of PR-Set7 and loss of H4K20me1 results in the accumulation of DNA damage and an ATR-dependent cell cycle arrest. Coincident with the ATR-dependent cell cycle arrest, we find increased DNA damage that is specifically limited to late replicating regions of theDrosophilagenome, suggesting that PR-Set7-mediated monomethylation of H4K20 is critical for maintaining the genomic integrity of late replicating domains.
3D RNA from evolutionary couplings
Authors: Weinreb Caleb , Gross Torsten , Sander Chris , Marks Debora S. 
Published: October 2015

AbstractNon-protein-coding RNAs are ubiquitous in cell physiology, with a diverse repertoire of known functions. In fact, the majority of the eukaryotic genome does not code for proteins, and thousands of conserved long non-protein-coding RNAs of currently unkown function have been identified. When available, knowledge of their 3D structure is very helpful in elucidating the function of these RNAs. However, despite some outstanding structure elucidation of RNAs using X-ray crystallography, NMR and cryoEM, learning RNA 3D structures remains low-throughput. RNA structure predictionin silicois a promising alternative approach and works well for double-helical stems, but full 3D structure determination requires tertiary contacts outside of secondary structures that are difficult to infer from sequence information. Here, based only on information from RNA multiple sequence alignments, we use a global statistical sequence probability model of co-variation in a pairs of nucleotide positions to detect 3D contacts, in analogy to recently developed breakthrough methods for computational protein folding. In blinded tests on 22 known RNA structures ranging in size from 65 to 1800 nucleotides, the predicted contacts matched physical nucleotide interactions with 65-95% true positive prediction accuracy. Importantly, we infer many long-range tertiary contacts, including non-Watson-Crick interactions, where secondary structure elements assemble in 3D. When used as restraints in molecular dynamics simulations, the inferred contacts improve RNA 3D structure prediction to a coordinate error as low as 6 – 10 Å rmsd deviation in atom positions, with potential for further refinement by molecular dynamics. These contacts include functionally important interactions, such as those that distinguish the active and inactive conformations of four riboswitches. In blind prediction mode, we present evolutionary couplings suitable for folding simulations for 180 RNAs of unknown structure, available athttps://marks.hms.harvard.edu/ev_rna/. We anticipate that this approach can help shed light on the structure and function of non-protein-coding RNAs as well as 3D-structured mRNAs.
Hemodynamic response function in resting brain: disambiguating neural events and autonomic effects
Authors: Wu Guo-Rong , Marinazzo Daniele 
Published: October 2015

AbstractIt has been shown that resting state brain dynamics can be characterized by looking at sparse blood-oxygen-level dependent (BOLD) events, which can be retrieved by point process analysis. Cardiac activity can also induce changes in the BOLD signal, thus affect both the number of these events and the mapping between neural events and BOLD signal, namely the hemodynamic response. To isolate neural activity and autonomic effects, we compare the resting state hemodynamic response retrieved by means of a point process analysis with and without deconvolving the cardiac fluctuations. Brainstem and the surrounding cortical area (such as precuneus, insula etc.) are found to be significantly affected by cardiac pulses. Methodological and physiological implications are then discussed.
Developing collaboration structures for university-industry interaction and innovations
Authors: Mäkimattila Martti , Junell Timo , Rantala Tero 
Published: October 2015

Purpose
– The purpose of this paper is to examine the doing, using, and interacting (DUI) of Universities of Applied Sciences (UAS) while developing intra- and inter-collaboration with industry. It also reviews recent literature related to the roles of absorptive capacity (AC) and social capital (SC) in interaction.

Design/methodology/approach
– A qualitative case research on developing collaborations between UAS and small- and medium-sized enterprises for innovation activities.

Findings
– Prior knowledge and contacts vary in organisations, and interaction should be supported while aiming to maximise benefits of internal and external resources available for innovation. This paper contributes by pointing out the importance of the interconnection of DUI, AC, and SC while developing collaboration.

Originality/value
– This paper describes issues challenging the collaborative innovation activities and directions to focus on structural development to support interaction with parties having different backgrounds, goals, and strengths. The study highlights the importance of knowledge exchange with several universities and firms, and the different learning modes related to innovation.
Workspace calculating and kinematic modelling of a flexible continuum manipulator constructed by steel-wires
Authors: Gao GuoHua , Liu Yue , Wang Hao , Song MingYang , Ren Han 
Published: October 2015

Purpose
– The purpose of this paper is to present a new method to establish a kinematic model for a continuum manipulator, whose end can be controlled to move in a three-dimensional workspace. A continuum manipulator has significant advantages over traditional, rigid manipulators in many applications because of its ability to conform to the environment. Moreover, because of its excellent flexibility, light weight, low energy consumption, low production cost, it has a number of potential applications in areas of earthquake relief, agricultural harvesting, medical facilities and space exploration.

Design/methodology/approach
– This paper uses basic theory of material mechanics to deduct motion equations of the manipulator. Unlike other published papers, the manipulator is not based on segments tactics, but regarded as an integrated flexible system, which simplifies its kinematics modelling and motion controlling. The workspace of the manipulator is analysed by theoretical deducing and simulation modelling. For verification of the presented theory, simulation based on ADAMS software was implemented, while a prototype of the manipulator was developed. Both the software simulation and prototype experiment show that the theoretical analysis in this paper is reasonable. The manipulator can move accurately along the desired trajectories.

Findings
– This paper developed a novel and fully continuous manipulator driven by steel wires. A kinematic model of the manipulator was established. The physical manipulator developed for verifying the kinematic model can effectively track the prescribed trajectory. The presented kinematic model agrees with not only the simulation but also with the experiment.

Research limitations/implications
– The manipulator presented in this paper is constructed by steel wires. It possesses the advantages of structural continuity, high flexibility and low production cost. It can be extensively used in many fields, such as search and rescue robotic systems. The limitation of this research is that the dynamic model of the manipulator is not yet clear, which is one of the directions for future research.

Practical implications
– The manipulator breaks through the limitation of the joint-type or flexible-link-type manipulator, which can also be extensively used in many fields such as search and rescue robotic systems.

Social implications
– The manipulator developed in this paper, currently, is a prototype under the project of “Automatic Picking Manipulator Research”. It possesses a good market value.

Originality/value
– The value of this research is that the manipulator breaks through the limitation of the joint-type or flexible-link-type manipulator and establishes the kinematic model for a fully continuous manipulator by a simple strategy. This is the first study that uses such a strategy for establishing the motion equations of a monolithic continuum manipulator.
A fixed-distance planning algorithm for 6-DOF manipulators
Authors: Gao Mingyu , Chen Da , Yang Yuxiang , He Zhiwei 
Published: October 2015

Purpose– The purpose of this paper is to propose a new trajectory planning algorithm for industrial robots, which can let the robots move through a desired spatial trajectory, avoid colliding with other objects and achieve accurate movements. Trajectory planning algorithms are the soul of motion control of industrial robots. A predefined space trajectory can let the robot move through the desired spatial coordinates, avoid colliding with other objects and achieve accurate movements.Design/methodology/approach– The mathematical expressions of the proposed algorithm are deduced. The speed control, position control and orientation control strategies are realized and verified with simulations, and then implemented on a six degrees of freedom (6-DOF) industrial robot platform.Findings– A fixed-distance trajectory planning algorithm based on Cartesian coordinates was presented. The linear trajectory, circular trajectory, helical trajectory and parabolic trajectory in Cartesian coordinates were implemented on the 6-DOF industrial robot.Originality/value– A simple and efficient algorithm is proposed. Enrich the kind of trajectory which the industrial robot can realize. In addition, the industrial robot can move more concisely, smoothly and precisely.
Volumetric view planning for 3D reconstruction with multiple manipulators
Authors: Li Liangzhi , Xiao Nanfeng 
Published: October 2015

Purpose– This paper aims to propose a new view planning method which can be used to calculate the next-best-view (NBV) for multiple manipulators simultaneously and build an automated three-dimensional (3D) object reconstruction system, which is based on the proposed method and can adapt to various industrial applications.Design/methodology/approach– The entire 3D space is encoded with octree, which marks the voxels with different tags. A set of candidate viewpoints is generated, filtered and evaluated. The viewpoint with the highest score is selected as the NBV.Findings– The proposed method is able to make the multiple manipulators, equipped with “eye-in-hand” RGB-D sensors, work together to accelerate the object reconstruction process.Originality/value– Compared to the existed approaches, the proposed method in this paper is fast, computationally efficient, has low memory cost and can be used in actual industrial productions where the multiple different manipulators exist. And, more notably, a new algorithm is designed to speed up the generation and filtration of the candidate viewpoints, which can guarantee both speed and quality.