bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Location Index Plus Some Maps and no Apologies: Back to Basics on the Development of Links Between Economic Integration and Spatial Concentration of Industries
Authors: Schweizog Robert , Collins Alan 
Published: March 2014

AbstractThe analysis of the location patterns of economic activities in both Europe and the US has been addressed in an extensive literature dependent on increasingly more sophisticated techniques that arguably reframe debate away from the policy questions in focus and towards debate on the complex empirical techniques that seem to be in vogue at any given time. In part this has been a response to some clear shortcomings in the use of simple locational Gini coefficients. It is argued herein that simple index approaches can still retain value if augmented with intuitive reading of some relevant maps. An example of the utility of this approach is provided in relation to the location patterns of four exemplar manufacturing industries in the EU and USA.
A Lagrangian Analysis of the Northern Hemisphere Subtropical Jet
Authors: Martius Olivia 
Published: March 2014

Abstract
This study presents a 5-yr climatology of 7-day back trajectories started from the Northern Hemisphere subtropical jet. These trajectories provide insight into the seasonally and regionally varying angular momentum and potential vorticity characteristics of the air parcels that end up in the subtropical jet. The trajectories reveal preferred pathways of the air parcels that reach the subtropical jet from the tropics and the extratropics and allow estimation of the tropical and extratropical forcing of the subtropical jet.
The back trajectories were calculated 7 days back in time and started every 6 h from December 2005 to November 2010 using the Interim European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-Interim) dataset as a basis. The trajectories were started from the 345-K isentrope in areas where the wind speed exceeded a seasonally varying threshold and where the wind shear was confined to upper levels.
During winter, the South American continent, the Indian Ocean, and the Maritime Continent are preferred areas of ascent into the upper troposphere. From these areas, air parcels follow an anticyclonic pathway into the subtropical jet. During summer, the majority of air parcels ascend over the Himalayas and Southeast Asia.
Angular momentum is overall well conserved for trajectories that reach the subtropical jet from the deep tropics. In winter and spring, the hemispheric-mean angular momentum loss amounts to approximately 6%; in summer, it amounts to approximately 18%; and in fall, it amounts to approximately 13%. This seasonal variability is confirmed using an independent potential vorticity–based method to estimate tropical and extratropical forcing of the subtropical jet.
Structure, Energy, and Parameterization of Inertia–Gravity Waves in Dry and Moist Simulations of a Baroclinic Wave Life Cycle
Authors: Mirzaei Mohammad , Zülicke Christoph , Mohebalhojeh Ali R. , Ahmadi-Givi Farhang , Plougonven Riwal 
Published: March 2014

AbstractThe impact of moisture on inertia–gravity wave generation is assessed for an idealized unstable baroclinic wave using the Weather Research and Forecasting Model (WRF) in a channel on the f plane. The evolution of these waves in a moist simulation is compared with a dry simulation. The centers of action for inertia–gravity wave activity are identified as the equatorward-moving upper-level front and the poleward-progressing upper-level jet–surface front system. Four stratospheric wave packets are found, which are significantly more intense in the moist simulation and have slightly higher frequency. They are characterized by their structure and position during the baroclinic wave life cycle and are related to forcing terms in jet, front, and convection systems.By exploring the time series of mass and energy, it is shown that the release of latent heat leads to a change in enthalpy, an increase in the eddy kinetic energy, and an intensification of the inertia–gravity wave energy. The ratio of the inertia–gravity wave energy to the eddy kinetic energy is estimated to be about 1/200 for the moist simulation, which is 3 times larger than that for the dry simulation. An empirical parameterization scheme for the inertia–gravity wave energy is proposed, based on the fast large-scale ageostrophic flow associated with the jet, front, and convection. The diagnosed stratospheric inertia–gravity wave energy is well captured by this parameterization in six WRF simulations with different moisture and resolutions. The approach used to construct the parameterization may serve as a starting point for state-dependent nonorographic gravity wave drag schemes in general circulation models.
Common tripled fixed point theorems for W-compatible mappings along with the "Equation missing" property in abstract metric spaces
Authors: Wairojjana Nopparat , Sintunavarat Wutiphol , Kumam Poom 
Published: March 2014

Abstract
In this paper, we introduce the concept of common limit in the range property for mappings

F
:
X
×
X
×
X
→
X

and

g
:
X
→
X

, where

(
X
,
d
)

is an abstract metric space, and establish tripled coincidence point and common tripled fixed point theorems by using the common limit in the range property. Our theorems generalize and extend several well-known comparable results in the literature, in particular the results of Aydi et al. (Fixed Point Theory Appl. 2012:134, 2012). Also, we give examples to validate our main results which are not applied by the results in the literature.

MSC:54E40, 47H10, 54E99.
Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles
Authors: Wei Xiaomou , Ai Junmei , Deng Youping , Guan Xin , Johnson David R , Ang Choo Y , Zhang Chaoyang , Perkins Edward J 
Published: March 2014

Abstract

Background
High throughput transcriptomics profiles such as those generated using microarrays have been useful in identifying biomarkers for different classification and toxicity prediction purposes. Here, we investigated the use of microarrays to predict chemical toxicants and their possible mechanisms of action.

Results
In this study, in vitro cultures of primary rat hepatocytes were exposed to 105 chemicals and vehicle controls, representing 14 compound classes. We comprehensively compared various normalization of gene expression profiles, feature selection and classification algorithms for the classification of these 105 chemicals into14 compound classes. We found that normalization had little effect on the averaged classification accuracy. Two support vector machine (SVM) methods, LibSVM and sequential minimal optimization, had better classification performance than other methods. SVM recursive feature selection (SVM-RFE) had the highest overfitting rate when an independent dataset was used for a prediction. Therefore, we developed a new feature selection algorithm called gradient method that had a relatively high training classification as well as prediction accuracy with the lowest overfitting rate of the methods tested. Analysis of biomarkers that distinguished the 14 classes of compounds identified a group of genes principally involved in cell cycle function that were significantly downregulated by metal and inflammatory compounds, but were induced by anti-microbial, cancer related drugs, pesticides, and PXR mediators.

Conclusions
Our results indicate that using microarrays and a supervised machine learning approach to predict chemical toxicants, their potential toxicity and mechanisms of action is practical and efficient. Choosing the right feature and classification algorithms for this multiple category classification and prediction is critical.
Copy number variations among silkworms
Authors: Zhao Qian , Han Min-Jin , Sun Wei , Zhang Ze 
Published: March 2014

Abstract

Background
Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm.

Results
In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals.

Conclusions
An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.
Implications of human genome structural heterogeneity: functionally related genes tend to reside in organizationally similar genomic regions
Authors: Paz Arnon , Frenkel Svetlana , Snir Sagi , Kirzhner Valery , Korol Abraham B 
Published: March 2014

AbstractBackgroundIn an earlier study, we hypothesized that genomic segments with different sequence organization patterns (OPs) might display functional specificity despite their similar GC content. Here we tested this hypothesis by dividing the human genome into 100 kb segments, classifying these segments into five compositional groups according to GC content, and then characterizing each segment within the five groups by oligonucleotide counting (k-mer analysis; also referred to as compositional spectrum analysis, or CSA), to examine the distribution of sequence OPs in the segments. We performed the CSA on the entire DNA, i.e., its coding and non-coding parts the latter being much more abundant in the genome than the former.ResultsWe identified 38 OP-type clusters of segments that differ in their compositional spectrum (CS) organization. Many of the segments that shared the same OP type were enriched with genes related to the same biological processes (developmental, signaling, etc.), components of biochemical complexes, or organelles. Thirteen OP-type clusters showed significant enrichment in genes connected to specific gene-ontology terms. Some of these clusters seemed to reflect certain events during periods of horizontal gene transfer and genome expansion, and subsequent evolution of genomic regions requiring coordinated regulation.ConclusionsThere may be a tendency for genes that are involved in the same biological process, complex or organelle to use the same OP, even at a distance of ~ 100 kb from the genes. Although the intergenic DNA is non-coding, the general pattern of sequence organization (e.g., reflected in over-represented oligonucleotide “words”) may be important and were protected, to some extent, in the course of evolution.
Medical tongue piercing – development and evaluation of a surgical protocol and the perception of procedural discomfort of the participants
Authors: Bentsen Bo , Gaihede Michael , Lontis Romulus , Andreasen Struijk Lotte NS 
Published: March 2014

Abstract

Background
A system providing disabled persons with control of various assistive devices with the tongue has been developed at Aalborg University in Denmark. The system requires an activation unit attached to the tongue with a small piercing. The aim of this study was to establish and evaluate a safe and tolerable procedure for medical tongue piercing and to evaluate the expected and perceived procedural discomfort.

Methods
Four tetraplegic subjects volunteered for the study. A surgical protocol for a safe insertion of a tongue barbell piercing was presented using sterilized instruments and piercing parts. Moreover, post-procedural observations of participant complications such as bleeding, edema, and infection were recorded. Finally, procedural discomforts were monitored by VAS scores of pain, changes in taste and speech as well as problems related to hitting the teeth.

Results
The piercings were all successfully inserted in less than 5 min and the pain level was moderate compared with oral injections. No bleeding, infection, embedding of the piercing, or tooth/gingival injuries were encountered; a moderate edema was found in one case without affecting the speech. In two cases the piercing rod later had to be replaced by a shorter rod, because participants complained that the rod hit their teeth. The replacements prevented further problems. Moreover, loosening of balls was encountered, which could be prevented with the addition of dental glue. No cases of swallowing or aspiration of the piercing parts were recorded.

Conclusions
The procedure proved simple, fast, and safe for insertion of tongue piercings for tetraplegic subjects in a clinical setting. The procedure represented several precautions in order to avoid risks in these susceptible participants with possible co-morbidity. No serious complications were encountered, and the procedure was found tolerable to the participants. The procedure may be used in future studies with tongue piercings being a prerequisite for similar systems, and this may include insertion in an out-patient setting.
Life-threatening cardiac tamponade: a rare complication of acupuncture
Authors: Chun Kook-Jin , Lee Sang-Gwon , Son Bong Soo , Kim Do Hyung 
Published: March 2014

Abstract
Acupuncture as an ancient Chinese treatment has proven effective and is utilized worldwide. Although it is generally believed to be a safe clinical procedure, serious lethal complications including death have been reported. We present a rare case of life-threatening cardiac tamponade due to penetration of an acupuncture needle directly into the right ventricle.
Predictors of durable no evidence of disease status in de novo metastatic inflammatory breast cancer patients treated with neoadjuvant chemotherapy and post-mastectomy radiation
Authors: Takiar Vinita , Akay Catherine L , Stauder Michael C , Tereffe Welela , Alvarez Ricardo H , Hoffman Karen E , Perkins George H , Strom Eric A , Buchholz Thomas A , Ueno Naoto T , Babiera Gildy , Woodward Wendy A 
Published: March 2014

Abstract

Introduction
Definitive locoregional therapy including surgery and post-mastectomy radiation therapy (PMRT) has been offered to select IBC patients with de novo metastatic disease. Herein we examined predictive factors for progression-free survival after comprehensive PMRT radiation +/- locoregional treatment of metastatic sites.

Methods
Charts of T4d, any N, M1 (de novo) patients who completed PMRT to ≥ 50 Gy from 2006–2011 were reviewed. Patients who received doses <50Gy to the primary site, received radiation at another facility or were treated pre-operatively were excluded. The remaining 36 patients formed the study cohort. Progression-free survival post-PMRT (PFSx) was assessed from the last day of radiation. Median dose to primary fields was 51 Gy. Boost doses ranged from 6–16 Gy.

Results
Median age at diagnosis was 54 (range 33–70). Median follow up from primary irradiation completion was 31 months. Sixteen patients were Stage IV NED at last follow-up (IR 37–60 mo). Fifteen patients died of disease. Five patients experienced an in-field recurrence, three of which resulted from local recurrence at the medial edge of the field. Actuarial 5 year locoregional control (LRC) was 86%. Median PFSx was 20 months. All sites of gross disease were treated with radiation in 21/36 patients. Location of metastatic disease had no correlation with PFSx. Estrogen receptor (ER)- patients had shorter 5-yr actuarial PFSx (28% vs. 66%, P = 0.03) and 5 year actuarial OSx (37% vs 71%, P = 0.02). Nine patients (25%) developed a pathological complete response (pCR) after chemotherapy and with a median follow-up of 59 months, 7 remained without evidence of disease.

Conclusions
Despite the poor prognosis associated with metastatic IBC, our data suggest that select patients may be appropriate candidates for locoregional therapy. Patients who achieve a pCR or those with ER + disease have a favorable PFSx. It remains unclear whether all gross disease needs to be addressed with locoregional therapy to provide benefit.
TMEM106B expression is reduced in Alzheimer’s disease brains
Authors: Satoh Jun-ichi , Kino Yoshihiro , Kawana Natsuki , Yamamoto Yoji , Ishida Tsuyoshi , Saito Yuko , Arima Kunimasa 
Published: March 2014

Abstract
Introduction
TMEM106B is a transmembrane glycoprotein of unknown function located within endosome/lysosome compartments expressed ubiquitously in various cell types. Previously, the genome-wide association study (GWAS) identified a significant association of TMEM106B single nucleotide polymorphisms (SNPs) with development of frontotemporal lobar degeneration with ubiquitinated TAR DNA-binding protein-43 (TDP-43)-positive inclusions (FTLD-TDP), particularly in the patients exhibiting the progranulin (PGRN) gene (GRN) mutations. Recent studies indicate that TMEM106B plays a pathological role in various neurodegenerative diseases, including Alzheimer’s disease (AD). However, at present, the precise levels of TMEM106B expression in AD brains remain unknown.

Methods
By quantitative reverse transcription (RT)-PCR (qPCR), western blot and immunohistochemistry, we studied TMEM106B and PGRN expression levels in a series of AD and control brains, including amyotrophic lateral sclerosis, Parkinson’s disease, multiple system atrophy and non-neurological cases.

Results
In AD brains, TMEM106B mRNA and protein levels were significantly reduced, whereas PGRN mRNA levels were elevated, compared with the levels in non-AD brains. In all brains, TMEM106B was expressed in the majority of cortical neurons, hippocampal neurons, and some populations of oligodendrocytes, reactive astrocytes and microglia with the location in the cytoplasm. In AD brains, surviving neurons expressed intense TMEM106B immunoreactivity, while senile plaques, neurofibrillary tangles and the perivascular neuropil, almost devoid of TMEM106B, intensely expressed PGRN.

Conclusions
We found an inverse relationship between TMEM106B (downregulation) and PGRN (upregulation) expression levels in AD brains, suggesting a key role of TMEM106B in the pathological processes of AD.
Bone mass and quality in patients with juvenile idiopathic arthritis: longitudinal evaluation of bone-mass determinants by using dual-energy x-ray absorptiometry, peripheral quantitative computed tomography, and quantitative ultrasonography
Authors: Stagi Stefano , Cavalli Loredana , Signorini Carla , Bertini Federico , Cerinic Marco Matucci , Brandi Maria Luisa , Falcini Fernanda 
Published: March 2014

Abstract
Introduction
Our objective was to evaluate longitudinally the main bone-mass and quality predictors in young juvenile idiopathic arthritis (JIA) patients by using lumbar spine dual-energy X-ray absorptiometry (DXA) scan, radius peripheral quantitative computed tomography (pQCT), and phalangeal quantitative ultrasonography (QUS) at the same time.

Methods
In total, 245 patients (172 females, 73 males; median age, 15.6 years: 148 oligoarticular, 55 polyarticular, 20 systemic, and 22 enthesitis-related-arthritis (ERA) onset) entered the study. Of these, 166 patients were evaluated longitudinally. Data were compared with two age- and sex-matched control groups.

Results
In comparison with controls, JIA patients, but not with ERA, had a reduced spine bone-mineral apparent density (BMAD) standard deviation score (P < 0.001) and musculoskeletal deficits, with significantly lower levels of trabecular bone mineral density (TrabBMD) (P < 0.0001), muscle cross-sectional area (CSA) (P < 0.005), and density-weighted polar section modulus (SSIp) (P < 0.05). In contrast, JIA showed fat CSA significantly higher than controls (P < 0.0001). Finally, JIA patients had a significant reduced amplitude-dependent speed of sound (AD-SoS) (P < 0.001), and QUS z score (P < 0.005).
Longitudinally, we did not find any difference in all JIA patients in comparison with baseline, except for the SSIp value that normalized. Analyzing the treatments, a significant negative correlation among spine BMAD values, TrabBMD, AD-SoS, and systemic and/or intraarticular corticosteroids, and a positive correlation among TNF-α-blocking agents and spine BMAD, TrabBMD, and AD-SoS were observed.

Conclusions
JIA patients have a low bone mass that, after a first increase due to the therapy, does not reach the normal condition over time. The pronounced bone deficits in JIA are greater than would be expected because of reduction in muscle cross-sectional area. Thus, bone alterations in JIA likely represent a mixed defect of bone accrual and lower muscle forces.
Mutation signatures of carcinogen exposure: genome-wide detection and new opportunities for cancer prevention
Authors: Poon Song Ling , McPherson John R , Tan Patrick , Teh Bin Tean , Rozen Steven G 
Published: March 2014

AbstractExposure to environmental mutagens is an important cause of human cancer, and measures to reduce mutagenic and carcinogenic exposures have been highly successful at controlling cancer. Until recently, it has been possible to connect the chemical characteristics of mutagens to actual mutations observed in human tumors only indirectly. Now, next-generation sequencing technology enables us to observe in detail the DNA-sequence-level effects of well-known mutagens, such as ultraviolet radiation and tobacco smoke, as well as endogenous mutagenic processes, such as those involving activated DNA cytidine deaminases (APOBECs). We can also observe the effects of less well-known but potent mutagens, including those recently found to be present in some herbal remedies. Crucially, we can now tease apart the superimposed effects of several mutational exposures and processes and determine which ones occurred during the development of individual tumors. Here, we review advances in detecting these mutation signatures and discuss the implications for surveillance and prevention of cancer. The number of sequenced tumors from diverse cancer types and multiple geographic regions is growing explosively, and the genomes of these tumors will bear the signatures of even more diverse mutagenic exposures. Thus, we envision development of wide-ranging compendia of mutation signatures from tumors and a concerted effort to experimentally elucidate the signatures of a large number of mutagens. This information will be used to link signatures observed in tumors to the exposures responsible for them, which will offer unprecedented opportunities for prevention.