bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knee loading reduces MMP13 activity in the mouse cartilage
Authors: Hamamura Kazunori , Zhang Ping , Zhao Liming , Shim Joon W , Chen Andy , Dodge Todd R , Wan Qiaoqiao , Shih Han , Na Sungsoo , Lin Chien-Chi , Sun Hui Bin , Yokota Hiroki 
Published: November 2013

AbstractBackgroundModerate loads with knee loading enhance bone formation, but its effects on the maintenance of the knee are not well understood. In this study, we examined the effects of knee loading on the activity of matrix metalloproteinase13 (MMP13) and evaluated the role of p38 MAPK and Rac1 GTPase in the regulation of MMP13.MethodsKnee loading (0.5–3 N for 5 min) was applied to the right knee of surgically-induced osteoarthritis (OA) mice as well as normal (non-OA) mice, and MMP13 activity in the femoral cartilage was examined. The sham-loaded knee was used as a non-loading control. We also employed primary non-OA and OA human chondrocytes as well as C28/I2 chondrocyte cells, and examined MMP13 activity and molecular signaling in response to shear at 2–20 dyn/cm2.ResultsDaily knee loading at 1 N for 2 weeks suppressed cartilage destruction in the knee of OA mice. Induction of OA elevated MMP13 activity and knee loading at 1 N suppressed this elevation. MMP13 activity was also increased in primary OA chondrocytes, and this increase was attenuated by applying shear at 10 dyn/cm2. Load-driven reduction in MMP13 was associated with a decrease in the phosphorylation level of p38 MAPK (p-p38) and NFκB (p-NFκB). Molecular imaging using a fluorescence resonance energy transfer (FRET) technique showed that Rac1 activity was reduced by shear at 10 dyn/cm2and elevated by it at 20 dyn/cm2. Silencing Rac1 GTPase significantly reduced MMP13 expression and p-p38 but not p-NFκB. Transfection of a constitutively active Rac1 GTPase mutant increased MMP13 activity, while a dominant negative mutant decreased it.ConclusionsKnee loading reduces MMP13 activity at least in part through Rac1-mediated p38 MAPK signaling. This study suggests the possibility of knee loading as a therapy not only for strengthening bone but also preventing tissue degradation of the femoral cartilage.
Cytokine response to pregnancy-associated recrudescence of Plasmodium berghei infection in mice with pre-existing immunity to malaria
Authors: Megnekou Rosette , Staalsoe Trine , Hviid Lars 
Published: November 2013

AbstractBackgroundDuring childhood, residents of areas with stable transmission ofPlasmodium falciparumparasites acquire substantial protective immunity to malaria, and adults therefore rarely experience clinical disease episodes. However, susceptibility to infection reappears in pregnant women, particularly primigravidae. This is due to appearance of antigenic parasite variants that are restricted to pregnancy. Variant-specific immunity also governs pregnancy-associated recrudescence ofPlasmodium bergheiinfection in pregnant mice. Pregnancy-related changes in the plasma cytokine levels of mice with immunity acquired prior to first pregnancy have not been studied in detail previously, and were the topic of the present study.MethodsA multiplexed bead assay was used to measure plasma levels of IL-5, IL-10, IL-12, IL-13, IFN-γ and TNF in BALB/c mice immunized againstP. bergheiK173 by repeated infection and drug cure before the first pregnancy. The association between cytokine levels on the one hand and parasitaemia and haemoglobin levels on the other, in mice that had never been pregnant or were pregnant for the first, second or third time were evaluated by Mann–Whitney test and Spearman rank-order correlation analysis.ResultsPregnancyper sedid not further increase the already high cytokine levels in mice previously immunized by repeated infection and drug cure. Levels of all the cytokines except IL-10 were correlated with each other, and with parasitaemia and haemoglobin levels. Furthermore, levels of all cytokines were positively correlated with parity, except IL-10, which was negatively correlated with parity. High levels of IL-10 and low levels of the other cytokines were associated with poor pregnancy outcome.ConclusionsHigh levels of IL-10 and low levels of the other cytokines were associated with poor pregnancy outcome in this mouse model of placental malaria. Since the model replicates key parasitological and immunological features of placentalP. falciparummalaria, it underpins its usefulness in immunology and pathogenesis studies of this important cause of mother/child morbidity in endemic areas.
Small-area and compact CMOS emulator circuit for CMOS/nanoscale memristor co-design
Authors: Shin SangHak , Choi Jun-Myung , Cho Seongik , Min Kyeong-Sik 
Published: November 2013

Abstract
In this paper, a CMOS emulator circuit that can reproduce nanoscale memristive behavior is proposed. The proposed emulator circuit can mimic the pinched hysteresis loops of nanoscale memristor memory's current-voltage relationship without using any resistor array, complicated circuit blocks, etc. that may occupy very large layout area. Instead of using a resistor array, other complicated circuit blocks, etc., the proposed emulator circuit can describe the nanoscale memristor's current-voltage relationship using a simple voltage-controlled resistor, where its resistance can be programmed by the stored voltage at the state variable capacitor. Comparing the layout area between the previous emulator circuit and the proposed one, the layout area of the proposed emulator circuit is estimated to be 32 times smaller than the previous emulator circuit. The proposed CMOS emulator circuit of nanoscale memristor memory will be very useful in developing hybrid circuits of CMOS/nanoscale memristor memory.
Dynamic voltage and frequency scaling scheme for an adaptive LDPC decoder using SNR estimation
Authors: Ahn Youngho , Park Joo-yul , Chung Ki-Seok 
Published: November 2013

Abstract
In this paper, we propose a low-power adaptive low-density parity check (LDPC) decoder that utilizes dynamic voltage and frequency scaling to reduce power consumption. Most existing adaptive LDPC decoders have focused only on the decoding performance based on the signal-to-noise ratio (SNR) estimation. However, significant idle power is consumed when the decoder awaits the next frame after processing a frame. In mobile communication standards such as China Mobile Multimedia Broadcasting and Digital Video Broadcasting Satellite Second Generation, adaptive coding and modulation has been adopted. Thus, it is possible to reduce the power consumption efficiently by using the SNR estimation. In this paper, we apply a customized frequency selection scheme and a variable voltage generation scheme to an adaptive LDPC decoder to reduce the dynamic power consumption. The proposed schemes result in a reduction of 44% in the energy consumption of an LDPC decoder implemented using 0.18-μm complementary metal-oxide-semiconductor technology.
Path2Models: large-scale generation of computational models from biochemical pathway maps
Authors: Büchel Finja , Rodriguez Nicolas , Swainston Neil , Wrzodek Clemens , Czauderna Tobias , Keller Roland , Mittag Florian , Schubert Michael , Glont Mihai , Golebiewski Martin , van Iersel Martijn , Keating Sarah , Rall Matthias , Wybrow Michael , Hermjakob Henning , Hucka Michael , Kell Douglas B , Müller Wolfgang , Mendes Pedro , Zell Andreas , Chaouiya Claudine , Saez-Rodriguez Julio , Schreiber Falk , Laibe Camille , Dräger Andreas , Le Novère Nicolas 
Published: November 2013

Abstract

Background
Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.

Results
To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps.

Conclusions
To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
Inter and intra‐rater repeatability of the scoring of foot pain drawings
Authors: Chatterton Benjamin D , Muller Sara , Thomas Martin J , Menz Hylton B , Rome Keith , Roddy Edward 
Published: November 2013

AbstractBackgroundFoot pain drawings (manikins) are commonly used to describe foot pain location in self‐report health surveys. Respondents shade the manikin where they experience pain. The manikin is then scored via a transparent overlay that divides the drawings into areas. In large population based studies they are often scored by multiple raters. A difference in how different raters score manikins (inter‐rater repeatability), or in how an individual rater scores manikins over time (intra‐rater repeatability) can therefore affect data quality. This study aimed to assess inter‐ and intra‐rater repeatability of scoring of the foot manikin.MethodsA random sample was generated of 50 respondents to a large population based survey of adults aged 50 years and older who experienced foot pain and completed a foot manikin. Manikins were initially scored by any one of six administrative staff (Rating 1). These manikins were re‐scored by a second rater (Rating 2). The second rater then re‐scored the manikins one week later (Rating 3). The following scores were compared: Rating 1 versus Rating 2 (inter‐rater repeatability), and Rating 2 versus Rating 3 (intra‐rater repeatability). A novel set of clinically relevant foot pain regions made up of one or more individual areas on the foot manikin were developed, and assessed for inter‐ and intra‐rater repeatability.ResultsScoring agreement of 100% (all 50 manikins) was seen in 69% (40 out of 58) of individual areas for inter‐rater scoring (range 94 to 100%), and 81% (47 out of 58) of areas for intra‐rater scoring (range 96 to 100%). All areas had a kappa value of ≥0.70 for inter‐ and intra‐rater scoring. Scoring agreement of 100% was seen in 50% (10 out of 20) of pain regions for inter‐rater scoring (range 96 to 100%), and 95% (19 out of 20) of regions for intra‐rater scoring (range 98 to 100%). All regions had a kappa value of >0.70 for inter‐ and intra‐rater scoring.ConclusionsIndividual and multiple raters can reliably score the foot pain manikin. In addition, our proposed regions may be used to reliably classify different patterns of foot pain using the foot manikin.
PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans
Authors: Pavelitz Thomas , Gray Lucas T , Padilla Stephanie L , Bailey Arnold D , Weiner Alan M 
Published: November 2013

Abstract

Background
piggyBac domain (PGBD) transposons are found in organisms ranging from fungi to humans. Three domesticated piggyBac elements have been described. In the ciliates Paramecium tetraurelia and Tetrahymena thermophila, homologs known as piggyMacs excise internal eliminated sequences from germline micronuclear DNA during regeneration of the new somatic macronucleus. In primates, a PGBD3 element inserted into the Cockayne syndrome group B (CSB) gene over 43 Mya serves as an alternative 3′ terminal exon, enabling the CSB gene to generate both full length CSB and a conserved CSB-PGBD3 fusion protein that joins an N-terminal CSB domain to the C-terminal transposase domain.

Results
We describe a fourth domesticated piggyBac element called PGBD5. We show that i) PGBD5 was first domesticated in the common ancestor of the cephalochordate Branchiostoma floridae (aka lancelet or amphioxus) and vertebrates, and is conserved in all vertebrates including lamprey but cannot be found in more basal urochordates, hemichordates, or echinoderms; ii) the lancelet, lamprey, and human PGBD5 genes are syntenic and orthologous; iii) no potentially mobile ancestral PGBD5 elements can be identified in other more deeply rooted organisms; iv) although derived from an IS4-related transposase of the RNase H clan, PGBD5 protein is unlikely to retain enzymatic activity because the catalytic DDD(D) motif is not conserved; v) PGBD5 is preferentially expressed in certain granule cell lineages of the brain and in the central nervous system based on available mouse and human in situ hybridization data, and the tissue-specificity of documented mammalian EST and mRNA clones; vi) the human PGBD5 promoter and gene region is rich in bound regulatory factors including the neuron-restrictive silencer factors NRSF/REST and CoREST, as well as SIN3, KAP1, STAT3, and CTCF; and vii) despite preferential localization within the nucleus, PGBD5 protein is unlikely to bind DNA or chromatin as neither DNase I digestion nor high salt extraction release PGBD5 from fractionated mouse brain nuclei.

Conclusions
We speculate that the neural-specific PGBD5 transposase was domesticated >500 My after cephalochordates and vertebrates split from urochordates, and that PGBD5 may have played a role in the evolution of a primitive deuterostome neural network into a centralized nervous system.
Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation
Authors: Price Katherine E , Hampton Thomas H , Gifford Alex H , Dolben Emily L , Hogan Deborah A , Morrison Hilary G , Sogin Mitchell L , O’Toole George A 
Published: November 2013

Abstract

Background
Cystic fibrosis (CF) is caused by inherited mutations in the cystic fibrosis transmembrane conductance regulator gene and results in a lung environment that is highly conducive to polymicrobial infection. Over a lifetime, decreasing bacterial diversity and the presence of Pseudomonas aeruginosa in the lung are correlated with worsening lung disease. However, to date, no change in community diversity, overall microbial load or individual microbes has been shown to correlate with the onset of an acute exacerbation in CF patients. We followed 17 adult CF patients throughout the course of clinical exacerbation, treatment and recovery, using deep sequencing and quantitative PCR to characterize spontaneously expectorated sputum samples

Results
We identified approximately 170 bacterial genera, 12 of which accounted for over 90% of the total bacterial load across all patient samples. Genera abundant in any single patient sample tended to be detectable in most samples. We found that clinical stages could not be distinguished by absolute Pseudomonas aeruginosa load, absolute total bacterial load or the relative abundance of any individual genus detected, or community diversity. Instead, we found that the microbial structure of each patient’s sputum microbiome was distinct and resilient to exacerbation and antibiotic treatment.

Conclusion
Consistent with previously reported sputum microbiome studies we found that total and relative abundance of genera at the population level were remarkably stable for individual patients regardless of clinical status. Patient-by-patient analysis of diversity and relative abundance of each individual genus revealed a complex microbial landscape and highlighted the difficulty of identifying a universal microbial signature of exacerbation. Overall, at the genus level, we find no evidence of a microbial signature of clinical stage.
New measurement criteria for studying alcohol drinking and relapse in rodents
Authors: Villarín Pildaín Lilian , Vengeliene Valentina , Matthäus Franziska 
Published: November 2013

Abstract
Purpose
Relapse to alcohol use is considered as one of the central features distinguishing dependence from controlled alcohol consumption. Relapse-like drinking in rodents is a transient episode of heavy drinking that follows a period of abstinence. This behaviour is called the alcohol deprivation effect (ADE). Not all animals develop behavioural changes that resemble relapse-like drinking behaviour. The purpose of our study was to develop a generalized quantitative criterion by which animals could be separated into two groups depending on their behaviour during a relapse-like situation (ADE vs. no-ADE).

Methods
An automated drinkometer system was used for data collection. This system measures fluid consumption by means of high-precision sensors attached to the drinking bottles in the home cage of the rat. We used a four bottle free choice paradigm with water 5, 10, and 20% ethanol solutions. For data analysis we developed a new measure of alcohol intake that quantifies net alcohol intake in relation to net consumption of water. This new measure is called water-penalized net ethanol intake.

Results
The new measure is more robust than commonly used measurements, such as alcohol preference and intake. It allows the comparison of alcohol intake between different groups of animals and different setups using an arbitrary number of bottles. Based on this new measure we developed a method to automatically select the threshold for the presence of ADE in individual animals.

Conclusions
Separating animals by their behavior during relapse-like situation could be used as one of the criteria for identification of alcohol addicted and non-addicted rats. A classification into presenting ADE or not is also essential to test the effectiveness of newly developed therapeutic drugs.
Development of foundation year 1 psychiatry posts: implications
for practice
Authors: Steele Rachel , Beattie Sharon 
Published: November 2013

SummaryMost literature discussing the introduction of foundation year 1 (F1)
psychiatry posts has focused on recruitment. However, for F1 posts to offer
a valuable learning experience and a potential recruitment boost,
psychiatrists and employing organisations should be aware of general issues
arising in the first postgraduate year. These include the inherently
stressful student-to-doctor transition, the need for bespoke induction
programmes for new graduates, F1 doctors' specific needs for support,
supervision and peer support, and the centrality of the relationship with
the consultant supervisor to the new doctor. Understanding these themes will
enable psychiatrists and mental health organisations to offer better F1
psychiatry experiences, which may boost recruitment and could maximise the
opportunities for F1 doctors to develop skills and qualities that will be of
value in their future careers, whatever specialty they end up working
in.
Flight of ideas – death of a definition: a discussion on phenomenology
Authors: Jeyasingam Neil 
Published: November 2013

SummaryPhenomenology provides the foundations on which the functions of modern psychiatry stand. It also provides a common language for the assessment of patients, and for the education of the next generation of psychiatrists. However, phenomenology is not anchored in independent clinicopathological correlates, and therefore it is vulnerable to subtle alterations over time. This article briefly discusses some concepts regarding phenomenology and attempts to comment on the various definitions available under the common descriptor termed ‘flight of ideas'. It is asserted that without appropriate monitoring and teaching of these basic descriptors and recognising the value of historical observations, serious inconsistencies will continue to arise in clinical theory and practice, which may prove difficult to rectify.
Insights into Protein Allostery in the CsoR/RcnR Family of Transcriptional Repressors
Authors: Higgins Khadine A , Giedroc David 
Published: November 2013

Abstract
CsoR/RcnR transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. Individual members of this large family of repressors coordinate Cu(I) or Ni(II)/Co(II) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. Here we highlight recent insights into the functional diversity of this fascinating family of repressors.
Investors� Own Human Capital and Its Effect on Innovation Projects Realization
Authors: �����������  , Vorfolomeev Boris 
Published: November 2013

The goal of this paper is to study the investors� own human capital and how
it effects its contribution to the success of innovation projects implementation
in Russia. It is already proven and recognized by foreign researchers
that for the first-time entrepreneurs such factors, as the investor�s knowledge,
skills, experience and business connections year by year are becoming
more and more significant, than the amount of potential project funding.
Based on the review and analysis of recently published foreign studies on
investors� own human capital, the author puts forward a number of hypotheses
and explores the Russian market accordingly. As a result the author
compares the role of investors who manage projects in the developed (US
and European) markets with that of investors managing projects in the
emerging (Russian) market.
FEATURES OF NEW-GENERATION STANDARTS AS TO NURTURNIG HEALTHY LIFESTYLE AMONG SCHOOL-AGED CHILDREN
Authors: ��������  , Zvezdina Marina 
Published: November 2013

The article discusses the national policy aimed at maintaining, enhancing
and building-up health of the rising generation through engraining habits of healthy
lifestyle during the schooldays. The school is considered to be the most sustainable
social institution and efficient conductor of the national policy in the field of health.
The author compares how Educational standards of the 1st and 2nd generations deal
with the goal of cultivating ideas of healthy lifestyle among students. Special emphasis
is made on fundamental differences in targets and performance requirements for
education at primary, secondary and senior school. The role of certain subjects in
nurturing the culture of healthy lifestyle is highlighted.
Educational standards are analyzed with respect to current trends, observed both
in this country and abroad, concerning the role of school education in upbringing
healthy generation. The main trends are: shift from the tradition of public healthcare to
caring about health of individuals and the recognition of lifestyle as the leading factor
of individual�s health. Hence the declared objective of school education is to nurture
the culture of healthy lifestyle among students. The author mentions two fundamental
ideas for boosting education in the field of health: to make education more individually-,
axiologically- and culturally-oriented and also to enhance its pragmatic aspect.
Such subjects as physical training and FFI play the leading role in implementing these
ideas at all levels of education, while the subject of �Surrounding World� is crucial
for the primary school education, and Biology � for secondary and senior school.
The 2nd generation educational standards, the author argues, tend to integrate educational
goals of different subjects, e.g., physical training and FFI, in order to implement
systems-and-activity approach in education.