bluuebunny/crossref_metadata_2025_split huggingface dataset:
RP Implementation: Specimen Management
Authors: Graybill‐D'Ercole Patricia 
Published: November 2014

AbstractEffective specimen management in the perioperative setting is essential for accurate patient diagnosis and intervention. AORN's “Recommended practices for specimen management” provides guidance to help perioperative nurses, in collaboration with a multidisciplinary team, implement a specimen management process that includes a needs assessment, site identification, collection and handling, transfer from the sterile field, containment, specimen identification and labeling, preservation, transport, disposition, and documentation. Accurate specimen management requires effective multidisciplinary communication and an awareness of the potential opportunities for error. Specimens discussed in the recommended practices document include breast cancer specimens, amputated digits and limbs to be reattached, forensic and radioactive specimens, and explanted medical devices and orthopedic hardware. The recommendations are applicable to both hospital and ambulatory settings.
Possible levetiracetam induced encephalopathy presenting as electrical status epilepticus: An unknown occurrence
Authors: Mahale Rohan , Mehta Anish , Javali Mahendra , Sharma Suryanarayana , Madhusudhan Byadaralli , Srinivasa Rangasetty 
Published: November 2014

AbstractLevetiracetam is a novel, broad spectrum anti-epileptic drug with proven efficacy in generalized as well as focal onset seizures. It has renal elimination with no hepatic metabolism. Levetiracetam induced encephalopathy is rarely reported in literature. Triphasic waves in the electroencephalogram are seen in toxic-metabolic encephalopathies of various aetiology like hepatic encephalopathy, uraemia. We report a patient who was on levetiracetam for acute symptomatic seizures and developed encephalopathy with electroencephalogram showing generalised triphasic waves. These triphasic waves disappeared with intravenous lorazepam but without clinical improvement in sensorium. The electroencephalographic abnormality appeared as electrical status epilepticus which got normalised on discontinuation of levetiracetam. This is the first report of levetiracetam induced encephalopathy presenting as electrical status epilepticus and also depicts electroencephalographic correlate of levetiracetam induced encephalopathy.
Investigations on contribution of glial inwardly‐rectifying K+ current to membrane potential and ion flux: An experimental and theoretical study
Authors: Wu Sheng‐Nan , Huang Yan‐Ming , Kao Ching‐An , Chen Bing‐Shuo , Lo Yi‐Ching 
Published: November 2014

AbstractThe inwardly rectifying K+ current [IK(IR)] allows large inward K+ currents at potentials negative to K+ equilibrium potential (EK) and it becomes small outward K+ currents at those positive to EK. How changes of such currents enriched in glial cells can influence the functions of glial cell, neurons, or both is not clearly defined, although mutations of Kir4.1 channels have been demonstrated to cause serious neurological disorders. In this study, we identified the presence of IK(IR) in human glioma cells (U373 and U87 cells). The amplitude of IK(IR) in U373 cells was subject to inhibition by amitriptyline, arecoline, or BaCl2. The activity of inwardly rectifying K+ channels was also clearly detected, and single‐channel conductance of these channels was calculated to be around 23 pS. Moreover, based on a simulation model derived from neuron–glial interaction mediated by ion flux, we further found out that incorporation of glial IK(IR) conductance into the model can significantly contribute to regulation of extracellular K+ concentrations and glial resting potential, particularly during high‐frequency stimulation. Glial cells and neurons can mutually modulate their expression of ion channels through K+ ions released into the extracellular space. It is thus anticipated that glial IK(IR) may be a potential target utilized to influence the activity of neuronal and glial cells as well as their interaction.
Implication of Boron Isotope Geochemistry for the Pedogenic Environments in Loess and Paleosol Sequences of Central China
Authors: Wei Hai-Zhen , Lei Fang , Jiang Shao-Yong , Lu Hua-Yu , Xiao Ying-Kai , Zhang Han-Zhi , Sun Xue-Feng 
Published: November 2014

AbstractWe investigated the boron isotopic composition in loess–paleosol sequences in five different profiles in the Chinese Loess Plateau. Three possible boron sources are identified: atmospheric input, carbonates, and weathered silicate rocks. Variations of [Sr], [B], δ11B and the magnetic susceptibility correlate well with the pedogenetic intensity in three out of the five studied profiles, where pedogenesis under a cold–dry climate indicates lower δ11B, lower [B], lower magnetic susceptibility and higher [Sr] values. Exceptions to the variations between the δ11B and other known proxies were observed in arenaceous soils and the Red Clay sequence: the former suggested that vertical redistribution probably occurred with the boron migration, and the latter indicated an unknown mechanism of susceptibility enhancement. A better correlation between the δ11B and magnetic susceptibility and the quantitative estimation of boron budget from each source confirms the influence of paleoenvironmental changes on boron geochemical cycle. Significant positive correlations in Sr/Ca vs. B/Ca and Mg/Ca vs. B/Ca reflect consistent enrichment behavior of those mobile elements into calcium carbonate. The preliminary results imply that boron isotopic compositions in soils can be a potential geochemical proxy to reconstruct the paleoenvironmental changes in loess–paleosol sequences.
Treatment of early episode in patients with schizophrenia: the role of long acting antipsychotics
Authors: Heres S. , Lambert M. , Vauth R. 
Published: November 2014

AbstractThe use of long-acting injectable antipsychotics (LAIs) in schizophrenia is usually restricted to patients in long-term treatment, who prefer them to oral antipsychotics, and to patients with multiple relapses who have a history of non-adherence. However, preliminary evidence from patients in the early phases of the disease suggest that second generation LAIs may be superior to second generation oral medications with regard to the control of negative symptoms and psychosocial functioning. Moreover, several studies have found that psychiatrists are generally reluctant to prescribe LAI antipsychotics and under-estimate their acceptability by patients. Key elements to take into account when offering a LAI in the early course of schizophrenia should include their potential superiority in allowing early detection of non-adherence and in reducing the number of rehospitalisations and relapses.
Verification of the Spectral Classification of Stars Using the Hipparcos Catalogue
Authors: Deb D. , Chakraborty P. 
Published: November 2014

AbstractThe spectral classifications of the stars from spectral data have been corrected from time to time and new spectral and luminosity classes have been assigned. Identifying stars with wrong spectral and luminosity classification has been a stupendous task from the huge catalogue of stars. In this work we describe a simple statistical technique to identify stars with wrong spectral and luminosity classification. We make use of the Hipparcos catalogue which has the most accurate measurement of the distance d of the stars. A comparison is made between the absolute V magnitudes MV computed using the observed V magnitude mV and d, with the standard absolute magnitude MV0 assigned to a spectral and luminosity classification for a large number of stars (with d < 100 pc). As expected, for most of the stars the difference between MV and MV0 lies within the range ±2 mag, due to the intrinsic nature of each star ignored in this generalisation. A systematic error analysis is made of all the observable used in the computation. Therefore to identify stars which we suspect to be wrongly classified, we look for abnormal deviation in |MV – MV0| ≥5. The location of these stars with respect to the galactic plain and interstellar extinction is also investigated to rule out effects due to variations in the interstellar extinction. From our results we see that some of the stars were indeed wrongly classified and have recently been reclassified (SIMBAD). The reclassification drastically reduces the |MV – MV0| deviation. The other stars in the list which have not yet been reclassified need to be spectroscopically investigated and classified again.
Effects of Rhodiola on production, health and gut development of broilers reared at high altitude in Tibet
Authors: Li Long , Wang Honghui , Zhao Xin 
Published: November 2014

AbstractRhodiola has long been used as a traditional medicine to increase resistance to physical stress in humans in Tibet. The current study was designed to investigate whether Rhodiola crenulata (R. crenulata) could alleviate the negative effects of hypoxia on broiler chickens reared in Tibet Plateau. The effect of supplementing crushed roots of R. crenulata on production performance, health and intestinal morphology in commercial male broilers was investigated. Dietary treatments included CTL (basal diet), Low-R (basal diet + 0.5% R. crenulata) and High-R (basal diet + 1.5% R. crenulata). In comparison with broilers fed the control diet, Low-R had no effect on production performance while High-R significantly decreased average daily feed intake at d14, 28 and 42, body weight at d28 and 42 and gut development. Ascites induced mortality did not differ among treatments. Nevertheless Low-R significantly reduced non-ascites induced mortality and total mortality compared with broilers fed CTL and High-R diets. Broilers fed the High-R diet had significantly increased blood red blood cell counts and hemoglobin levels at 28d compared with other treatments. Our results suggest that supplementation with Rhodiola might reduce the effects of hypoxia on broilers and consequently decrease mortality rate.
Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients
Authors: Wang Conan K. , Northfield Susan E. , Colless Barbara , Chaousis Stephanie , Hamernig Ingrid , Lohman Rink-Jan , Nielsen Daniel S. , Schroeder Christina I. , Liras Spiros , Price David A. , Fairlie David P. , Craik David J. 
Published: November 2014

Significance
Peptides are valuable leads for drug development, offering advantages over other molecular classes. Specifically, they can bind potently and selectively to drug targets, including protein–protein interactions that are too challenging for small-molecule therapeutics. However, peptides are poor drugs because of their low in vivo stability and poor oral bioavailability. We propose a strategy for improving the oral bioavailability of peptides by identifying appropriate amides for chemical modification using temperature coefficients measured by NMR. The modified peptides have improved solvation properties, making them more membrane permeable. This approach for identifying sites for modification is a rapid method for guiding peptide drug design.
Polyharmonic maps of order 𝑘 with finite 𝐿^{𝑝} k-energy into Euclidean spaces
Authors: Maeta Shun 
Published: November 2014

We consider polyharmonic maps

ϕ
:
(
M
,
g
)
→

E

n

\phi :(M,g)\rightarrow \mathbb {E}^n

of order

k
k

from a complete Riemannian manifold into the Euclidean space and let

p
p

be a real constant satisfying

2
≤
p
>
∞

2\leq p>\infty

.

(
i
)

(i)

If

∫
M

|

W

k
−
1

|

p

d

v
g

>
∞

\int _M|W^{k-1}|^{p}dv_g>\infty

and

∫
M

|

∇
¯

W

k
−
2

|

2

d

v
g

>
∞
,

\int _M|\overline \nabla W^{k-2}|^2dv_g>\infty ,

then

ϕ
\phi

is a polyharmonic map of order

k
−
1

k-1

.

(
i
i
)

(ii)

If

∫
M

|

W

k
−
1

|

p

d

v
g

>
∞

\int _M|W^{k-1}|^{p}dv_g>\infty

and

Vol

(
M
,
g
)
=
∞

\textrm {Vol}(M,g)=\infty

, then

ϕ
\phi

is a polyharmonic map of order

k
−
1

k-1

. Here,

W
s

=

Δ
¯

s
−
1

τ
(
ϕ
)

(
s
=
1
,
2
,
⋯
)

W^s=\overline \Delta ^{s-1}\tau (\phi )\ (s=1,2,\cdots )

and

W
0

=
ϕ

W^0=\phi

. As a corollary, we give an affirmative partial answer to the generalized Chen conjecture.
Multi-scaling limits for relativistic diffusion equations with random initial data
Authors: Liu Gi-Ren , Shieh Narn-Rueih 
Published: November 2014

Let

u
(
t
,

x

)
,

t
>
0
,

x

∈

R

n

,

u(t,\mathbf {x}),\ t>0,\ \mathbf {x}\in \mathbb {R}^{n},

be the spatial-temporal random field arising from the solution of a relativistic diffusion equation with the spatial-fractional parameter

α
∈
(
0
,
2
)

\alpha \in (0,2)

and the mass parameter

m

>
0

\mathfrak {m}> 0

, subject to a random initial condition

u
(
0
,

x

)

u(0,\mathbf {x})

which is characterized as a subordinated Gaussian field. In this article, we study the large-scale and the small-scale limits for the suitable space-time re-scalings of the solution field

u
(
t
,

x

)

u(t,\mathbf {x})

. Both the Gaussian and the non-Gaussian limit theorems are discussed. The small-scale scaling involves not only scaling on

u
(
t
,

x

)

u(t,\mathbf {x})

but also re-scaling the initial data; this is a new type result for the literature. Moreover, in the two scalings the parameter

α
∈
(
0
,
2
)

\alpha \in (0,2)

and the parameter

m

>
0

\mathfrak {m}> 0

play distinct roles for the scaling and the limiting procedures.
Farmland Protection and Agricultural Land Values at the Urban‐Rural Fringe: British Columbia's Agricultural Land Reserve
Authors: Eagle Alison J. , Eagle David E. , Stobbe Tracy E. , van Kooten G. Cornelis 
Published: November 2014

AbstractFarmland conservation policies typically use zoning and differentiated taxes to prevent urban development of farmland, but little is known about the effectiveness of these policies. This study adds to current knowledge by examining the impact of British Columbia's Agricultural Land Reserve (ALR), established in 1973, which severely restricts subdivision and nonagricultural uses for more than 4.7 million hectares of farmland. To determine the extent to which the ALR preserves farmland by reducing or removing the development option, a multilevel hedonic pricing model is used to estimate the impact of land use, geographic, and zoning characteristics on farmland value near the capital city of Victoria on Vancouver Island. Using sales data from 1974 through 2008, the model demonstrates a changing ALR impact over time that varies considerably by improved and unimproved land types. In 2008, landowners paid 19% less for the typical improved farmland parcel within the ALR versus that outside it. This suggests that would‐be developers expect permanency in the zoning law, and prefer non‐ALR zoned land. However, ALR land that is unimproved has a premium of 55%, suggesting that this land is more valuable for agriculture than for development. Farmland located closer to the city or the commuting highway commands a premium if it has a residence on it, with a residence also explaining why smaller agricultural properties sell at higher prices. However, it appears that zoning by itself is insufficient to protect farmland; other policies likely need to be implemented in conjunction with zoning to protect agricultural land.
Molecular principles of human virus protein–protein interactions
Authors: Halehalli Rachita Ramachandra , Nagarajaram Hampapathalu Adimurthy 
Published: November 2014

Abstract
Motivation: Viruses, from the human protein–protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. However, not much is known about the general characteristic features of the human proteins interacting with viral proteins (referred to as hVIPs) as well as the motifs and domains utilized by human-virus protein–protein interactions (referred to as Hu-Vir PPIs).
Results: Our study has revealed that hVIPs are mostly disordered proteins, whereas viral proteins are mostly ordered proteins. Protein disorder in viral proteins and hVIPs varies from one subcellular location to another. In any given viral-human PPI pair, at least one of the two proteins is structurally disordered suggesting that disorder associated conformational flexibility as one of the characteristic features of virus–host interaction. Further analyses reveal that hVIPs are (i) slowly evolving proteins, (ii) associated with high centrality scores in human-PPI network, (iii) involved in multiple pathways, (iv) enriched in eukaryotic linear motifs (ELMs) associated with protein modification, degradation and regulatory processes, (v) associated with high number of splice variants and (vi) expressed abundantly across multiple tissues. These aforementioned findings suggest that conformational flexibility, spatial diversity, abundance and slow evolution are the characteristic features of the human proteins targeted by viral proteins. Hu-Vir PPIs are mostly mediated via domain–motif interactions (DMIs) where viral proteins employ motifs that mimic host ELMs to bind to domains in human proteins. DMIs are shared among viruses belonging to different families indicating a possible convergent evolution of these motifs to help viruses to adopt common strategies to subvert host cellular pathways.
Availability and implementation: Hu-Vir PPI data, DDI and DMI data for human–virus PPI can be downloaded from http://cdfd.org.in/labpages/computational_biology_datasets.html.
Contact: han@cdfd.org.in
Supplementary information: Supplementary data are available at Bioinformatics online.
NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei
Authors: Poulet Axel , Arganda-Carreras Ignacio , Legland David , Probst Aline V. , Andrey Philippe , Tatout Christophe 
Published: November 2014

Abstract
Summary: NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.
Availability and implementation: Dataset of nuclei is available at https://www.gred-clermont.fr/media/WorkDirectory.zip. NucleusJ is available at http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start.
Contact: philippe.andrey@versailles.inra.fr and christophe.tatout@univ-bpclermont.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development
Authors: Chen Haifen , Guo Jing , Mishra Shital K. , Robson Paul , Niranjan Mahesan , Zheng Jie 
Published: November 2014

Abstract
Motivation: Transcriptional regulatory networks controlling cell fate decisions in mammalian embryonic development remain elusive despite a long time of research. The recent emergence of single-cell RNA profiling technology raises hope for new discovery. Although experimental works have obtained intriguing insights into the mouse early development, a holistic and systematic view is still missing. Mathematical models of cell fates tend to be concept-based, not designed to learn from real data. To elucidate the regulatory mechanisms behind cell fate decisions, it is highly desirable to synthesize the data-driven and knowledge-driven modeling approaches.
Results: We propose a novel method that integrates the structure of a cell lineage tree with transcriptional patterns from single-cell data. This method adopts probabilistic Boolean network (PBN) for network modeling, and genetic algorithm as search strategy. Guided by the ‘directionality’ of cell development along branches of the cell lineage tree, our method is able to accurately infer the regulatory circuits from single-cell gene expression data, in a holistic way. Applied on the single-cell transcriptional data of mouse preimplantation development, our algorithm outperforms conventional methods of network inference. Given the network topology, our method can also identify the operational interactions in the gene regulatory network (GRN), corresponding to specific cell fate determination. This is one of the first attempts to infer GRNs from single-cell transcriptional data, incorporating dynamics of cell development along a cell lineage tree.
Availability and implementation: Implementation of our algorithm is available from the authors upon request.
Contact: zhengjie@ntu.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data
Authors: Liu Zhenqiu , Sun Fengzhu , Braun Jonathan , McGovern Dermot P.B. , Piantadosi Steven 
Published: November 2014

Abstract
Motivation: Identifying disease associated taxa and constructing networks for bacteria interactions are two important tasks usually studied separately. In reality, differentiation of disease associated taxa and correlation among taxa may affect each other. One genus can be differentiated because it is highly correlated with another highly differentiated one. In addition, network structures may vary under different clinical conditions. Permutation tests are commonly used to detect differences between networks in distinct phenotypes, and they are time-consuming.
Results: In this manuscript, we propose a multilevel regularized regression method to simultaneously identify taxa and construct networks. We also extend the framework to allow construction of a common network and differentiated network together. An efficient algorithm with dual formulation is developed to deal with the large-scale n ≪ m problem with a large number of taxa (m) and a small number of samples (n) efficiently. The proposed method is regularized with a general Lp (p∈[0,2]) penalty and models the effects of taxa abundance differentiation and correlation jointly. We demonstrate that it can identify both true and biologically significant genera and network structures.
Availability and implementation: Software MLRR in MATLAB is available at http://biostatistics.csmc.edu/mlrr/.
Contact: liuzx@cshs.org
Supplementary information: Supplementary data are available at Bioinformatics online.