bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and validation of the RiceWrist-S exoskeleton for robotic rehabilitation after incomplete spinal cord injury
Authors: Pehlivan Ali Utku , Sergi Fabrizio , Erwin Andrew , Yozbatiran Nuray , Francisco Gerard E. , O'Malley Marcia K. 
Published: June 2014

SUMMARYRobotic devices are well-suited to provide high intensity upper limb therapy in order to induce plasticity and facilitate recovery from brain and spinal cord injury. In order to realise gains in functional independence, devices that target the distal joints of the arm are necessary. Further, the robotic device must exhibit key dynamic properties that enable both high dynamic transparency for assessment, and implementation of novel interaction control modes that significantly engage the participant. In this paper, we present the kinematic design, dynamical characterization, and clinical validation of the RiceWrist-S, a serial robotic mechanism that facilitates rehabilitation of the forearm in pronation-supination, and of the wrist in flexion-extension and radial-ulnar deviation. The RiceWrist-Grip, a grip force sensing handle, is shown to provide grip force measurements that correlate well with those acquired from a hand dynamometer. Clinical validation via a single case study of incomplete spinal cord injury rehabilitation for an individual with injury at the C3-5 level showed moderate gains in clinical outcome measures. Robotic measures of movement smoothness also captured gains, supporting our hypothesis that intensive upper limb rehabilitation with the RiceWrist-S would show beneficial outcomes.
Performance analysis and parameter optimization of an inner spiral in-pipe robot
Authors: Liang Liang , Peng Hui , Chen Bai , Tang Yong , Chen Sun , Xu Yan 
Published: June 2014

SUMMARYA novel micro in-pipe robot using an internally threaded profile for propulsion is proposed in this paper, and the dynamic model of the robot in the turbulent liquid pipeline is established, and the computational fluid dynamics method is used to solve the influence of environmental parameters and operating parameters on the robotic performance. By the orthogonal experimental optimization method, the optimal inner spiral structural parametrical combination is obtained. According to the working principle of the inner spiral robot, an inner spiral driving device is designed and fabricated, and the running experiment in the pipeline full of 201 methyl silicone oil verifies the feasibility of the proposed robot. Adopting the pulsating blood flow function as the inlet condition, in a pulsating period, the robotic performance is numerically analyzed.
Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states inOrbicella faveolata
Authors: Closek Collin J , Sunagawa Shinichi , DeSalvo Michael K , Piceno Yvette M , DeSantis Todd Z , Brodie Eoin L , Weber Michele X , Voolstra Christian R , Andersen Gary L , Medina Mónica 
Published: June 2014

AbstractCoral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.
Nitrogen stress response and stringent response are coupled in Escherichia coli
Authors: Brown Daniel R. , Barton Geraint , Pan Zhensheng , Buck Martin , Wigneshweraraj Sivaramesh 
Published: June 2014

AbstractAssimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC. In addition, nitrogen-starved E. coli cells synthesize a signal molecule, guanosine tetraphosphate (ppGpp), which serves as an effector molecule of many processes including transcription to initiate global physiological changes, collectively termed the stringent response. The regulatory mechanisms leading to elevated ppGpp levels during nutritional stresses remain elusive. Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation. The results reveal that NtrC couples these two major bacterial stress responses to manage conditions of nitrogen limitation, and provide novel mechanistic insights into how a specific nutritional stress leads to elevating ppGpp levels in bacteria.
Layer Anti-Ferromagnetism on Bilayer Honeycomb Lattice
Authors: Tao Hong-Shuai , Chen Yao-Hua , Lin Heng-Fu , Liu Hai-Di , Liu Wu-Ming 
Published: June 2014

AbstractBilayer honeycomb lattice, with inter-layer tunneling energy, has a parabolic dispersion relation and the inter-layer hopping can cause the charge imbalance between two sublattices. Here, we investigate the metal-insulator and magnetic phase transitions on the strongly correlated bilayer honeycomb lattice by cellular dynamical mean-field theory combined with continuous time quantum Monte Carlo method. The procedures of magnetic spontaneous symmetry breaking on dimer and non-dimer sites are different, causing a novel phase transition between normal anti-ferromagnet and layer anti-ferromagnet. The whole phase diagrams about the magnetism, temperature, interaction and inter-layer hopping are obtained. Finally, we propose an experimental protocol to observe these phenomena in future optical lattice experiments.
Facile strain analysis of largely bending films by a surface-labelled grating method
Authors: Akamatsu Norihisa , Tashiro Wataru , Saito Keisuke , Mamiya Jun-ichi , Kinoshita Motoi , Ikeda Tomiki , Takeya Jun , Fujikawa Shigenori , Priimagi Arri , Shishido Atsushi 
Published: June 2014

AbstractMechanical properties of flexible films, for example surface strain of largely bending films, are key to design of stretchable electronic devices, wearable biointegrated devices and soft microactuators/robots. However, existing methods are mainly based on strain-gauge measurements that require miniaturized array sensors, lead wires and complicated calibrations. Here we introduce a facile method, based on surface-labelled gratings, for two-dimensional evaluation of surface strains in largely bending films. With this technique, we demonstrate that soft-matter mechanics can be distinct from the mechanics of hard materials. In particular, liquid-crystalline elastomers may undergo unconventional bending in three dimensions, in which both the inner and outer surfaces of the bending film are compressed. We also show that this method can be applied to amorphous elastomeric films, which highlights the general importance of this new mechanical evaluation tool in designing soft-matter-based electronic/photonic as well as biointegrated materials.
Elucidation of the preferred routes of C8-vinyl reduction in chlorophyll and bacteriochlorophyll biosynthesis
Authors: Canniffe Daniel P. , Chidgey Jack W. , Hunter C. Neil 
Published: June 2014

Most of the chlorophylls and bacteriochlorophylls utilized for light harvesting by phototrophic organisms carry an ethyl group at the C8 position of the molecule, the product of a C8-vinyl reductase acting on a chlorophyll/bacteriochlorophyll biosynthetic precursor. Two unrelated classes of C8-vinyl reductase are known to exist, BciA and BciB, found in the purple phototroph Rhodobacter sphaeroides and the cyanobacterium Synechocystis sp. PCC6803 respectively. We constructed strains of each bacterium with the native C8-vinyl reductase swapped for the other class of the enzyme, and combined these replacements with a series of deletions of the native bch and chl genes. In vivo data indicate that the preferred substrates for both classes of the enzyme is C8-vinyl chlorophyllide, with C8-vinyl protochlorophyllide reduced only under conditions in which this pigment accumulates as a result of perturbed formation of chlorophyllide.
Development of Spatial Release From Masking in Mandarin-Speaking Children With Normal Hearing
Authors: Yuen Kevin C. P. , Yuan Meng 
Published: June 2014

Purpose
This study investigated the development of spatial release from masking in children using closed-set Mandarin disyllabic words and monosyllabic words carrying lexical tones as test stimuli and speech spectrum–weighted noise as a masker.

Method
Twenty-six children ages 4–9 years and 12 adults, all with normal hearing, participated in speech recognition tests under 2 conditions: (a) speech and noise spatially mixed and presented from the front (NF), and (b) speech presented from the front with noise spatially separated and presented from the side (NS) with different signal-to-noise ratios (SNRs). Performance-SNR psychometric functions were obtained that generated the SNR for a 50% correct score (SNR-50%) as the outcome measure.

Results
In the child participants, SNR-50% improved with age in NS but not NF. The difference in SNR-50% between NS and NF—the spatial release from masking (SRM)—increased with age with an average improvement of 0.1–0.15 dB per month.

Conclusions
SRM has a long developmental time, at least up to 9 years of age, which is significantly longer than some previous developmental studies have suggested. The child participants had not yet reached the adult SRM performance level. SRM is a potential clinical measure to reflect the maturation of spatial auditory processing.
Murine Joubert syndrome reveals Hedgehog signaling defects as a potential therapeutic target for nephronophthisis
Authors: Hynes Ann Marie , Giles Rachel H. , Srivastava Shalabh , Eley Lorraine , Whitehead Jennifer , Danilenko Marina , Raman Shreya , Slaats Gisela G. , Colville John G. , Ajzenberg Henry , Kroes Hester Y. , Thelwall Peter E. , Simmons Nicholas L. , Miles Colin G. , Sayer John A. 
Published: June 2014

Significance
The molecular mechanisms underlying the juvenile onset cystic kidney disease nephronophthisis, remain incompletely understood. Our mutant mouse model identifies abnormal Hedgehog signaling as the primary lesion in nephronophthisis, although currently the perceived knowledge is that aberrant wingless-int signaling is responsible. Primary kidney collecting duct cells isolated from mutant mice with nephronophthisis are morphologically and functionally rescued when Hedgehog signaling is stimulated. This finding was replicated in ex vivo cultured urine-derived renal epithelial cells from a patient with Joubert syndrome and nephronophthisis. Understanding the initial molecular mechanisms of nephronophthisis is a significant advancement of the wider field of ciliopathies and identifies Hedgehog signaling as a potential therapeutic target for these conditions.
Stem cell differentiation as a many-body problem
Authors: Zhang Bin , Wolynes Peter G. 
Published: June 2014

Significance
A molecular understanding of stem cell differentiation requires the study of gene regulatory network dynamics that includes the statistics of synthesizing transcription factors, their degradation, and their binding to the DNA. Brute force simulation for complex large realistic networks can be computationally challenging. Here we develop a sound approximation method built upon theories originating from quantum statistical mechanics to study the network for embryonic stem cell development. Mechanistic insight is provided on the role of the master regulator Nanog in safeguarding stem cell pluripotency. We also demonstrate the significant influence of DNA-binding kinetics, an aspect that often has been overlooked, on the transition rate between gene network steady states.
Effectiveness of Screening Hospital Admissions to Detect Asymptomatic Carriers of Clostridium difficile: A Modeling Evaluation
Authors: Lanzas Cristina , Dubberke Erik R. 
Published: June 2014

ObjectiveBoth asymptomatic and symptomatic Clostridium difficile carriers contribute to new colonizations and infections within a hospital, but current control strategies focus only on preventing transmission from symptomatic carriers. Our objective was to evaluate the potential effectiveness of methods targeting asymptomatic carriers to control C. difficile colonization and infection (CDI) rates in a hospital ward: screening patients at admission to detect asymptomatic C. difficile carriers and placing positive patients into contact precautions.MethodsWe developed an agent-based transmission model for C. difficile that incorporates screening and contact precautions for asymptomatic carriers in a hospital ward. We simulated scenarios that vary according to screening test characteristics, colonization prevalence, and type of strain present at admission.ResultsIn our baseline scenario, on average, 42% of CDI cases were community-onset cases. Within the hospital-onset (HO) cases, approximately half were patients admitted as asymptomatic carriers who became symptomatic in the ward. On average, testing for asymptomatic carriers reduced the number of new colonizations and HO-CDI cases by 40%–50% and 10%–25%, respectively, compared with the baseline scenario. Test sensitivity, turnaround time, colonization prevalence at admission, and strain type had significant effects on testing efficacy.ConclusionsTesting for asymptomatic carriers at admission may reduce both the number of new colonizations and HO-CDI cases. Additional reductions could be achieved by preventing disease in patients who are admitted as asymptomatic carriers and developed CDI during the hospital stay.
Correcting for link loss in causal network inference caused by regulator interference
Authors: Wang Ying , Penfold Christopher A. , Hodgson David A. , Gifford Miriam L. , Burroughs Nigel J. 
Published: June 2014

AbstractMotivation: There are a number of algorithms to infer causal regulatory networks from time series (gene expression) data. Here we analyse the phenomena of regulator interference, where regulators with similar dynamics mutually suppress both the probability of regulating a target and the associated link strength; for instance, interference between two identical strong regulators reduces link probabilities by ∼50%.Results: We construct a robust method to define an interference-corrected causal network based on an analysis of the conditional link probabilities that recovers links lost through interference. On a large real network ( Streptomyces coelicolor , phosphate depletion), we demonstrate that significant interference can occur between regulators with a correlation as low as 0.865, losing an estimated 34% of links by interference. However, levels of interference cannot be predicted from the correlation between regulators alone and are data specific. Validating against known networks, we show that high numbers of functional links are lost by regulator interference. Performance against other methods on DREAM4 data is excellent.Availability and implementation : The method is implemented in R and is publicly available as the NIACS package at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software .Contact: N.J.Burroughs@warwick.ac.ukSupplementary information: Supplementary materials are available at Bioinformatics online.
Benthos distribution modelling and its relevance for marine ecosystem management
Authors: Reiss Henning , Birchenough Silvana , Borja Angel , Buhl-Mortensen Lene , Craeymeersch Johan , Dannheim Jennifer , Darr Alexander , Galparsoro Ibon , Gogina Mayya , Neumann Hermann , Populus Jacques , Rengstorf Anna M. , Valle Mireia , van Hoey Gert , Zettler Michael L. , Degraer Steven 
Published: June 2014

AbstractMarine benthic ecosystems are difficult to monitor and assess, which is in contrast to modern ecosystem-based management requiring detailed information at all important ecological and anthropogenic impact levels. Ecosystem management needs to ensure a sustainable exploitation of marine resources as well as the protection of sensitive habitats, taking account of potential multiple-use conﬂicts and impacts over large spatial scales. The urgent need for large-scale spatial data on benthic species and communities resulted in an increasing application of distribution modelling (DM). The use of DM techniques enables to employ full spatial coverage data of environmental variables to predict benthic spatial distribution patterns. Especially, statistical DMs have opened new possibilities for ecosystem management applications, since they are straightforward and the outputs are easy to interpret and communicate. Mechanistic modelling techniques, targeting the fundamental niche of species, and Bayesian belief networks are the most promising to further improve DM performance in the marine realm. There are many actual and potential management applications of DMs in the marine benthic environment, these are (i) early warning systems for species invasion and pest control, (ii) to assess distribution probabilities of species to be protected, (iii) uses in monitoring design and spatial management frameworks (e.g. MPA designations), and (iv) establishing long-term ecosystem management measures (accounting for future climate-driven changes in the ecosystem). It is important to acknowledge also the limitations associated with DM applications in a marine management context as well as considering new areas for future DM developments. The knowledge of explanatory variables, for example, setting the basis for DM, will continue to be further developed: this includes both the abiotic (natural and anthropogenic) and the more pressing biotic (e.g. species interactions) aspects of the ecosystem. While the response variables on the other hand are often focused on species presence and some work undertaken on species abundances, it is equally important to consider, e.g. biological traits or benthic ecosystem functions in DM applications. Tools such as DMs are suitable to forecast the possible effects of climate change on benthic species distribution patterns and hence could help to steer present-day ecosystem management.
Visible-wavelength spectroscopy of subkilometer-sized near-Earth asteroids with a low delta-v
Authors: Kuroda Daisuke , Ishiguro Masateru , Takato Naruhisa , Hasegawa Sunao , Abe Masanao , Tsuda Yuichi , Sugita Seiji , Usui Fumihiko , Hattori Takashi , Iwata Ikuru , Imanishi Masatoshi , Terada Hiroshi , Choi Young-Jun , Watanabe Sei-ichiro , Yoshikawa Makoto 
Published: June 2014

Abstract
This paper provides a unique data set representing the taxonomic type of near-Earth asteroids (NEAs) accessible by available spacecraft. The research on NEAs has entered upon a new phase, thanks to sample-return space explorations together with state-of-the-art large ground-based telescopes. We made observations of 13 asteroids with the Subaru, GEMINI-North, GEMINI-South, and Okayama 188 cm telescopes. Twelve of them have low delta-v orbits with the potential to be investigated by manned/unmanned spacecraft. Also, ten subkilometer-sized bodies are included among them, and are one of remarkable characteristics in terms of their evolutionary scenario. We have found that eleven asteroids are classified as S-complex, and one asteroid as the V-type. Most S-complex asteroids (eight out of eleven, ∼ 70%) have spectra similar to subgroups of Q- or Sq-type, suggesting that these objects are less matured by space weathering. We discuss the dominance of S-complex asteroids based on previous research.
The natverse: a versatile computational toolbox to combine and analyse neuroanatomical data
Authors: Bates Alexander S. , Manton James D. , Jagannathan Sridhar R. , Costa Marta , Schlegel Philipp , Rohlfing Torsten , Jefferis Gregory S. X. E. 
Published: June 2014

AbstractTo analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation, clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison of morphology and connectivity across many neurons after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community.
Beyond library size: a field guide to NGS normalization
Authors: Aleksic Jelena , Carl Sarah , Frye Michaela 
Published: June 2014

AbstractBackground:Next generation sequencing (NGS) is a widely used technology in both basic research and clinical settings and it will continue to have a major impact on biomedical sciences. However, the use of incorrect normalization methods can lead to systematic biases and spurious results, making the selection of an appropriate normalization strategy a crucial and often overlooked part of NGS analysis.Results:We present a basic introduction to the currently available normalization methods for differential expression and ChIP-seq applications, along with best use recommendations for different experimental techniques and datasets.We demonstrate that the choice of normalization technique can have a significant impact on the number of genes called as differentially expressed in an RNA-seq experiment or peaks called in a ChIP-seq experiment.Conclusions:The choice of the most adequate normalization method depends on both the distribution of signal in the dataset and the intended downstream applications. Depending on the design and purpose of the study, appropriate bias correction should also be considered.