bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of females with Chlamydia trachomatis infections attending a sexually transmissible infection clinic in Singapore in 2010
Authors: Low Lynette C. M. , Tan Feng Ling G. , Chan Ellen , Chio Martin , Chan Roy , Sen Priya
Published: September 2013

Background
Chlamydia (Chlamydia trachomatis) is the most commonly diagnosed sexually transmissible infection (STI) in Singapore, with rising incidence. Method: Random sampling was performed on all chlamydia-positive samples collected from female patients who attended a women’s clinic from January 2010 to December 2010. Some 250 electronic medical records were analysed. Population demographics, sexual histories, symptoms, diagnostic methods and management were recorded. Results: One hundred and forty-two (56.8%) patients were under 25 years of age. The predominant race diagnosed with Chlamydia cervicitis were Chinese (116 cases, 46.4%) followed by 86 (34.4%) Malays and 20 (8%) Filipinos. Sixty-three (25.2%) were skilled workers and (47) 18.8% were students. Professionals and office workers together formed 68 (27.2%) of the patients. Some 248 (99.2%) patients were heterosexual and 2 (0.8%) patients were bisexual; 229 (91.6%) patients had regular partners, 18 (7.2%) had casual partners and 3 (1.2%) had both. Concurrency prevalence accounted for 49 cases (19.6%) and condom use was less common. Patients were generally asymptomatic, with 114 (45.5%) presenting with symptoms. One hundred and eight (43.2%) patients had 2–5 sexual partners in their lifetime. Patients with a termination made up 12% of our cohort. This episode of infection was the first diagnosis of an STI for 198 (79.2%) patients; 24 (9.6%) of patients had been previously diagnosed with chlamydia. Conclusion: Chlamydia infection was most prevalent in skilled workers and their regular partners with heterosexual practices under 25 years old. Most patients had 2–5 sexual partners and did not use condoms consistently or at all.
Stabilization of mutant BRCA1 protein confers PARP inhibitor and platinum resistance
Authors: Johnson Neil , Johnson Shawn F. , Yao Wei , Li Yu-Chen , Choi Young-Eun , Bernhardy Andrea J. , Wang Yifan , Capelletti Marzia , Sarosiek Kristopher A. , Moreau Lisa A. , Chowdhury Dipanjan , Wickramanayake Anneka , Harrell Maria I. , Liu Joyce F. , D’Andrea Alan D. , Miron Alexander , Swisher Elizabeth M. , Shapiro Geoffrey I.
Published: October 2013

Significance

Poly(ADP-ribose) polymerase (PARP) inhibitors have produced responses in homologous recombination (HR) repair-deficient cancers, such as those with a mutated breast cancer 1, early onset (
BRCA1
) gene. We have delineated a two-event mechanism of acquired resistance by using a
BRCA1
BRCA C-terminal (BRCT) domain-mutated breast cancer cell line, involving heat shock protein (HSP)90-mediated stabilization of the mutant protein coupled with tumor protein p53 binding protein 1 (
TP53BP1
) gene mutation, which together restore DNA end resection and RAD51 filament formation, critical steps in HR. Similar events may occur in primary
BRCA1
-mutated ovarian cancers as cells develop resistance to platinum. The data demonstrate that, even though BRCA1 BRCT domain mutant proteins cannot promote DNA end resection, they retain partial function and can contribute to RAD51 loading and HR. Finally, HSP90 inhibition may prove useful for resensitizing resistant
BRCA1
-mutant cancer cells to drug treatment.
Quantitative apical membrane proteomics reveals vasopressin-induced actin dynamics in collecting duct cells
Authors: Loo Chin-San , Chen Cheng-Wei , Wang Po-Jen , Chen Pei-Yu , Lin Shu-Yu , Khoo Kay-Hooi , Fenton Robert A. , Knepper Mark A. , Yu Ming-Jiun
Published: October 2013

Significance

Vasopressin is a peptide hormone that regulates renal water excretion to maintain whole-body water balance. It does so by regulating trafficking of a molecular water channel, aquaporin-2, to and from the plasma membrane of collecting duct cells. This study uses two state-of-the-art methods (protein mass spectrometry of affinity-isolated apical plasma membrane proteins and live-cell imaging of actin dynamics) to uncover the central role of the actin dynamics in the trafficking of aquaporin-2–containing vesicles. The results coupled with prior data produce a model in which vasopressin signaling triggers actin accumulation near the tight junction and concomitant depletion of actin from the central regions of the apical plasma membrane, thereby providing access of aquaporin-2–containing vesicles to the apical plasma membrane.
Receptive field focus of visual area V4 neurons determines responses to illusory surfaces
Authors: Cox Michele A. , Schmid Michael C. , Peters Andrew J. , Saunders Richard C. , Leopold David A. , Maier Alexander
Published: October 2013

Significance

Visual information is often fragmented, such as when objects block each other from view, and our brain must actively deduce missing parts of an image to perceive key features of the world. This study asks whether neurons in cortical area V4 can infer the presence of an object’s surface when visual clues are limited. Indeed, our experiments reveal that certain V4 neurons enhance their responses to an array of stimuli only when they are configured to give rise to an illusory surface. Intriguingly, this effect exhibited unexpected spatial precision relative to the inducing components of the illusion. These findings provide important clues about how the brain overcomes a fundamental challenge of vision.
Users of secondary school‐based counselling services and specialist CAMHS in Wales: A comparison study
Authors: Jackson Charlie , Pybis Joanne , Cooper Mick , Hill Andy , Cromarty Karen , Rogers Jack
Published: October 2013

Background: The increasing prevalence of mental health issues in young people has contributed to a rise in the provision of school‐based counselling services in the UK. Between 2008/09 and 2010/11, data were collected from users of secondary school‐based counselling services in Wales. Aims: To identify the characteristics of users of school‐based counselling services in Wales – including demographics, referral pathways, presenting issues, and predominant issues – and how they compare to users of specialist CAMHS in Wales and Welsh secondary school pupils in general. Method: Data were collected on 10,687 episodes of counselling. School counsellors completed a client record sheet after each counselling episode and submitted these to their Local Authority. Collated results were then compared to matched data from Welsh specialist CAMHS and Welsh secondary schools data. Results/findings: A typical user of a secondary school‐based counselling service in Wales was female, of white ethnicity, and from the ‘middle’ school years. There was a marked under‐representation of users from BME backgrounds. Users were most often referred by school staff, and the most common presenting issues were family‐related, anger, and behaviour‐related. Conclusions: There was a higher proportion of females accessing school‐based counselling services than males. This was in direct contrast to data from specialist CAMHS and possible explanations for this are discussed. The under‐representation of BME populations suggested that there were some equality issues associated with accessing these services. Implications for practice: Future research should explore equality issues associated with young people from BME backgrounds accessing intervention services.
Analysis of the local organization and dynamics of cellular actin networks
Authors: Luo Weiwei , Yu Cheng-han , Lieu Zi Zhao , Allard Jun , Mogilner Alex , Sheetz Michael P. , Bershadsky Alexander D.
Published: September 2013

A ctin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm.
Recruitment of folliculin to lysosomes supports the amino acid–dependent activation of Rag GTPases
Authors: Petit Constance S. , Roczniak-Ferguson Agnes , Ferguson Shawn M.
Published: September 2013

Birt-Hogg-Dubé syndrome, a human disease characterized by fibrofolliculomas (hair follicle tumors) as well as a strong predisposition toward the development of pneumothorax, pulmonary cysts, and renal carcinoma, arises from loss-of-function mutations in the folliculin (FLCN) gene. In this study, we show that FLCN regulates lysosome function by promoting the mTORC1-dependent phosphorylation and cytoplasmic sequestration of transcription factor EB (TFEB). Our results indicate that FLCN is specifically required for the amino acid–stimulated recruitment of mTORC1 to lysosomes by Rag GTPases. We further demonstrated that FLCN itself was selectively recruited to the surface of lysosomes after amino acid depletion and directly bound to RagA via its GTPase domain. FLCN-interacting protein 1 (FNIP1) promotes both the lysosome recruitment and Rag interactions of FLCN. These new findings define the lysosome as a site of action for FLCN and indicate a critical role for FLCN in the amino acid–dependent activation of mTOR via its direct interaction with the RagA/B GTPases.
PLP helps the mother centrosome stay mum
Authors: Short Ben
Published: September 2013

Protein aids centrosome segregation by limiting centrosome activity in neural stem cells.
Michael Sixt: Love the way they move
Authors: Sedwick Caitlin
Published: September 2013

Sixt studies the mechanisms of leukocyte locomotion.
Quantification of Na+,K+ pumps and their transport rate in skeletal muscle: Functional significance
Authors: Clausen Torben
Published: September 2013

During excitation, muscle cells gain Na+ and lose K+, leading to a rise in extracellular K+ ([K+]o), depolarization, and loss of excitability. Recent studies support the idea that these events are important causes of muscle fatigue and that full use of the Na+,K+-ATPase (also known as the Na+,K+ pump) is often essential for adequate clearance of extracellular K+. As a result of their electrogenic action, Na+,K+ pumps also help reverse depolarization arising during excitation, hyperkalemia, and anoxia, or from cell damage resulting from exercise, rhabdomyolysis, or muscle diseases. The ability to evaluate Na+,K+-pump function and the capacity of the Na+,K+ pumps to fill these needs require quantification of the total content of Na+,K+ pumps in skeletal muscle. Inhibition of Na+,K+-pump activity, or a decrease in their content, reduces muscle contractility. Conversely, stimulation of the Na+,K+-pump transport rate or increasing the content of Na+,K+ pumps enhances muscle excitability and contractility. Measurements of [3H]ouabain binding to skeletal muscle in vivo or in vitro have enabled the reproducible quantification of the total content of Na+,K+ pumps in molar units in various animal species, and in both healthy people and individuals with various diseases. In contrast, measurements of 3-O-methylfluorescein phosphatase activity associated with the Na+,K+-ATPase may show inconsistent results. Measurements of Na+ and K+ fluxes in intact isolated muscles show that, after Na+ loading or intense excitation, all the Na+,K+ pumps are functional, allowing calculation of the maximum Na+,K+-pumping capacity, expressed in molar units/g muscle/min. The activity and content of Na+,K+ pumps are regulated by exercise, inactivity, K+ deficiency, fasting, age, and several hormones and pharmaceuticals. Studies on the α-subunit isoforms of the Na+,K+-ATPase have detected a relative increase in their number in response to exercise and the glucocorticoid dexamethasone but have not involved their quantification in molar units. Determination of ATPase activity in homogenates and plasma membranes obtained from muscle has shown ouabain-suppressible stimulatory effects of Na+ and K+.
MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples
Authors: Liebner David A. , Huang Kun , Parvin Jeffrey D.
Published: October 2013

Background: One of the significant obstacles in the development of clinically relevant microarray-derived biomarkers and classifiers is tissue heterogeneity. Physical cell separation techniques, such as cell sorting and laser-capture microdissection, can enrich samples for cell types of interest, but are costly, labor intensive and can limit investigation of important interactions between different cell types.

Results: We developed a new computational approach, called microarray microdissection with analysis of differences (MMAD), which performs microdissection in silico. Notably, MMAD (i) allows for simultaneous estimation of cell fractions and gene expression profiles of contributing cell types, (ii) adjusts for microarray normalization bias, (iii) uses the corrected Akaike information criterion during model optimization to minimize overfitting and (iv) provides mechanisms for comparing gene expression and cell fractions between samples in different classes. Computational microdissection of simulated and experimental tissue mixture datasets showed tight correlations between predicted and measured gene expression of pure tissues as well as tight correlations between reported and estimated cell fraction for each of the individual cell types. In simulation studies, MMAD showed superior ability to detect differentially expressed genes in mixed tissue samples when compared with standard metrics, including both significance analysis of microarrays and cell type-specific significance analysis of microarrays.

Conclusions: We have developed a new computational tool called MMAD, which is capable of performing robust tissue microdissection in silico, and which can improve the detection of differentially expressed genes. MMAD software as implemented in MATLAB is publically available for download at http://sourceforge.net/projects/mmad/.

Contact:  david.liebner@gmail.com

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Differential reproductive responses to stress reveal the role of life-history strategies within a species
Authors: Schultner J. , Kitaysky A. S. , Gabrielsen G. W. , Hatch S. A. , Bech C.
Published: October 2013

Life-history strategies describe that ‘slow’- in contrast to ‘fast’-living species allocate resources cautiously towards reproduction to enhance survival. Recent evidence suggests that variation in strategies exists not only among species but also among populations of the same species. Here, we examined the effect of experimentally induced stress on resource allocation of breeding seabirds in two populations with contrasting life-history strategies: slow-living Pacific and fast-living Atlantic black-legged kittiwakes. We tested the hypothesis that reproductive responses in kittiwakes under stress reflect their life-history strategies. We predicted that in response to stress, Pacific kittiwakes reduce investment in reproduction compared with Atlantic kittiwakes. We exposed chick-rearing kittiwakes to a short-term (3-day) period of increased exogenous corticosterone (CORT), a hormone that is released during food shortages. We examined changes in baseline CORT levels, parental care and effects on offspring. We found that kittiwakes from the two populations invested differently in offspring when facing stress. In response to elevated CORT, Pacific kittiwakes reduced nest attendance and deserted offspring more readily than Atlantic kittiwakes. We observed lower chick growth, a higher stress response in offspring and lower reproductive success in response to CORT implantation in Pacific kittiwakes, whereas the opposite occurred in the Atlantic. Our findings support the hypothesis that life-history strategies predict short-term responses of individuals to stress within a species. We conclude that behaviour and physiology under stress are consistent with trade-off priorities as predicted by life-history theory. We encourage future studies to consider the pivotal role of life-history strategies when interpreting inter-population differences of animal responses to stressful environmental events.
Giardia duodenalis typing from stools: a comparison of three approaches to extracting DNA, and validation of a probe-based real-time PCR typing assay
Authors: Elwin K. , Fairclough H. V. , Hadfield S. J. , Chalmers R. M.
Published: October 2013

A weighted, multi-attribute approach was used to compare three methods for direct extraction of Giardia duodenalis DNA from 15 microscopy-positive stools: (1) a QIAamp spin-column method for stools including a 10 min incubation at 95 °C, (2) method 1 preceded by five freeze–thaw cycles and (3) bead beating with guanidine thiocyanate using a FastPrep-28 machine followed by liquid-phase silica purification of DNA. The attributes compared included DNA yield measured using a new triose phosphate isomerase (tpi) gene probe-based real-time PCR, also described here. All three methods shared 100 % PCR positivity, while the bead-beating method provided the highest G. duodenalis DNA yield (P<0.01). However, when other weighted attributes, including biocontainment, resources and technical requirements, were also considered, spin-column extraction with prior freeze–thaw treatment (method 2) was deemed the most desirable and was selected for use. The tpi real-time PCR typing assay was designed to discriminate between the main human infectious assemblages of G. duodenalis (A and B) and was evaluated initially using standard isolates. Validation using microscopy-positive stools from 78 clinical giardiasis cases revealed 100 % typability; 20 (26 %) samples contained assemblage A, 56 (72 %) assemblage B and two (3 %) assemblages A and B. While the epidemiological significance of assemblage distribution will be revealed as more isolates are typed and analysed with patient demographic and exposure data, the utility of this assay and its ready application in our laboratory workflow and result turnaround margins is already evident.
Exogenous Gibberellins Induce Wheat Spike Development under Short Days Only in the Presence of VERNALIZATION1
Authors: Pearce Stephen , Vanzetti Leonardo S. , Dubcovsky Jorge
Published: October 2013

The activation of the meristem identity gene VERNALIZATION1 (VRN1) is a critical regulatory point in wheat (Triticum spp.) flowering. In photoperiod-sensitive wheat varieties, VRN1 is expressed only under long days (LDs), but mutants carrying deletions in a regulatory element in its promoter show VRN1 transcription and early spike development under short days (SDs). However, complete spike development is delayed until plants are transferred to LDs, indicating the existence of an additional regulatory mechanism dependent on LDs. We show here that exogenous gibberellin (GA) application accelerates spike development under SDs, but only in wheat lines expressing VRN1. The simultaneous presence of GA and VRN1 results in the up-regulation of the floral meristem identity genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY, whereas inhibition of GA biosynthesis with paclobutrazol precludes the LD induction of these two genes. The inductive role of GA on wheat flowering is further supported by the up-regulation of GA biosynthetic genes in the apices of plants transferred from SDs to LDs and in photoperiod-insensitive and transgenic wheat plants with increased FLOWERING LOCUS T transcription under SDs. The up-regulation of GA biosynthetic genes was not observed in the leaves of the same genetic stocks. Based on these observations, we propose a model in which FLOWERING LOCUS T is up-regulated in the leaves under LDs and is then transported to the shoot apical meristem, where it simultaneously induces the expression of VRN1 and GA biosynthetic genes, which are both required for the up-regulation of the early floral meristem genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY and the timely development of the wheat spike.
Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western‐Mediterranean Harpactocrates (Araneae, Dysderidae) spiders
Authors: Bidegaray‐Batista Leticia , Ferrández Miguel Á. , Arnedo Miquel A.
Published: September 2013

Past climatic shifts have played a major role in generating and shaping biodiversity. Quaternary glacial cycles are the better known examples of dramatic climatic changes endured by ecosystems in temperate regions. Although still a matter of debate, some authors suggest that glaciations promoted speciation. Here we investigate the effect of past climatic changes on the diversification of the ground‐dwelling spider genus Harpactocrates, distributed across the major mountain ranges of the western Mediterranean. Concatenated and species‐tree analyses of multiple mitochondrial and nuclear loci, combined with the use of fossil and biogeographic calibration points, reveal a Miocene origin of most nominal species, but also unravel several cryptic lineages tracing back to the Pleistocene. We hypothesize that the Miocene Climatic Transition triggered major extinction events in the genus but also promoted its subsequent diversification. Under this scenario, the Iberian mountains acted as an island‐like system, providing shelter to Harpactocrates lineages during the climate shifts and favouring isolation between mountain ranges. Quaternary glacial cycles contributed further to the diversification of the group by isolating lineages in peripheral refugia within mountain ranges. In addition, we recovered some unique biogeographic patterns, such as the colonization of the Alps and the Apennines from the Iberian Peninsula.
On the Use of Auxiliary and Paradata for Dealing With Non‐sampling Errors in Household Surveys
Authors: Zhang Li‐Chun , Thomsen Ib , Kleven Øyvin
Published: October 2013

Dans cet article, nous considérons l'utilisation de paradonnées pour traiter la non‐réponse et les erreurs de mesure dans les enquêtes auprès des ménages. Trois propriétés fondamentales sont mises en évidence: l'amélioration des taux de réponses, l'ajustement statistique et l'analyse du biais. Nous portons une attention particulière à plusieurs aspects durant les différentes phases de la production statistique à partir de la collecte des données, en passant par l'analyse des données et la manière de sélectionner et d'utiliser l'information auxiliaire disponible et les paradonnées. Les données de registres administratifs fournissent la source d'information auxiliaire pertinente la plus riche et s'ajoutent aux données collectées par les enquêtes et recensements antérieurs. Comme il est important de les utiliser efficacement pour traiter les erreurs qui ne sont pas dues à l'échantillonnage, on doit faire tous les efforts possibles pour augmenter leur disponibilité dans le système statistique et, en même temps, pour développer des méthodes statistiques efficaces qui permettent de mettre à profit l'intégration de données de sources différentes.
Objective Bayes Factors for Inequality Constrained Hypotheses
Authors: Hoijtink Herbert
Published: October 2013

Ce travail présente un facteur Bayésien pour la comparaison entre une hypothèse d'intérêt définie par des inégalités et son complément d'une part, l'hypothèse non contrainte d'autre part. Des ensembles équivalents d'hypothèses forment la base d'une quantification de la complexité d'une hypothèse d'intérêt. Nous montrons qu'une distribution a priori peut tre choisie de façon que l'un des termes composant le facteur Bayésien représente cette quantification. L'autre terme constitue une mesure de la qualité de l'adéquation à cette hypothèse. Si un a priori vague est utilisé, cette mesure d'adéquation est essentiellement déterminée par les observations. Le résultat est un facteur Bayésien objectif.
Advances in Joint Modelling: A Review of Recent Developments with Application to the Survival of End Stage Renal Disease Patients
Authors: McCrink Lisa M. , Marshall Adele H. , Cairns Karen J.
Published: October 2013

L'approche mixte, pour la modélisation des processus de survie et des processus longitudinaux, connait de nos jours un succès grandissant, en particulier lorsqu';il existe une interdépendance entre ceux‐ci. Réputés pour leur efficacité, les modèles mixtes sont moins biaisés par rapport aux méthodes classiques naïves, d'où une littérature abondante sur le sujet. L'objet de cette étude est de présenter une revue de la littérature récente sur les modèles mixtes, en l'occurrence ceux utilisés pour l'estimation du temps d'échec dans les processus de survie. Nous présenterons une analyse détaillée de la gamme de modèles de survie utilisés pour la construction des modèles mixtes. Une attention particulière sera accordée aux progrès récents dans le développement des logiciels dédiés à la construction de ces modéles. Une illustration sur l'utilisation des progiciels JM et JoineR, développés dans l'environnement R, sera présentée pour le cas de l'analyse de survie des patients souffrant d'insuffisance rénale en phase terminale. Finalement, nous concluons avec une discussion sur plusieurs pistes de recherche potentielles dans le domaine.
Statistical Disclosure Risk: Separating Potential and Harm
Authors: Skinner Chris
Published: October 2013

Les agences statistiques ont à coeur la mise au point de procédés permettant l'accès à leurs données dans le respect de la confidentialité de ces dernières. Bien que les méthodes d'évaluation du risque de divulgation soient désormais bien établies dans la littérature statistique, l'intégration de ces méthodes à la pratique des instituts sur des bases scientifiques se révèle encore difficile. Cet article vise à examiner, tout en le clarifiant, le rôle de la statistique dans les fondements conceptuels de l'évaluation du risque de divulgation dans le cadre des activités des instituts. Ce risque comporte deux composantes: la mesure de la possibilité d'une réelle divulgation, et le dommage potentiellement associéà celle‐ci. Nous développons l'idée que la statistique est bien adaptée à l'évaluation de la première de ces deux composantes, et proposons un cadre pour une telle évaluation. Nous soutenons que le comportement liéà une éventuelle intrusion malveillante peut être considéré indépendamment de ce cadre pourvu qu'il soit tenu compte de façon appropriée de la nature des tentatives d'attaques dans la définition du potentiel de divulgation.
Traceable Regressions
Authors: Wermuth Nanny
Published: October 2013

Dans cet article, nous définitions et étudions le concept de traçabilité des régressions et l'appliquer á quelques exemples. Régressions traçables sont des séquences de distributions conditionnelles dans les réponses individuelles ou conjointes pour lesquelles un graphe correspondant capte non seulement une structure indépendance, mais représente, en outre, dépendances conditionnelles qui permettent le traçage des voies de la dépendance. Nous donnons les propriétés nécessaires pour transformer ces graphes et des critères graphiques de décider si un chemin dans le graphe induit une dépendance. Les contraintes beaucoup plus fortes sur les distributions qui sont fidèles á un graphe sont comparés á ceux nécessaires pour les régressions traçables.
Viscosity and Friction Factor of Aluminum Oxide–Water Nanofluid Flow in Circular Tubes
Authors: Tang Clement C. , Tiwari Sanjib , Cox Matthew W.
Published: September 2013

Experiments have been conducted to characterize the viscosity and friction factor of aluminum oxide (Al2O3) nanoparticle dispersions at 6 vol. % in water. Rheological characterization of the Al2O3 nanofluid has shown that it exhibits a Newtonian fluid behavior for the shear rate range of 6 to 122 s−1 at temperatures between 6 and 75 °C. Friction factor results of the nanofluid flowing through circular tubes of 1 m in length with different inner tube diameters (2.97 and 4.45 mm) were experimentally measured in the laminar and the onset of transition regions. The experimental results from this study indicate that, when the nanofluid properties are properly characterized, the friction factors of the Al2O3 nanofluid are largely in agreement with classical friction factor theory for single-phase flow. An early transition to turbulent flow is observed for the nanofluid flow at a Reynolds number of approximately 1500, when compared with water flow where transition occurs at the textbook Reynolds number of roughly 2300.
Study on Lateral Earth Pressure Coefficient at Rest for Frozen Soils
Authors: Yao Xiaoliang , Qi Jilin , Yu Fan
Published: September 2013

The lateral earth pressure coefficient at rest, K0, is an important parameter in geotechnical engineering. There have been many studies for unfrozen soils; however, this is not the case for frozen soils, which impedes reasonable calculation concerning cold regions engineering. This paper introduces a novel triaxial apparatus for frozen soils with reference to that for unfrozen soils. The device is capable of performing experiments on frozen soil samples with K0 status under precisely controlled negative temperature. Two soils along the Qinghai-Tibetan highway are taken as study objects. K0 experiments are carried out with the apparatus and K0 is obtained under different testing conditions. It is found that temperature is a dominant factor in influencing K0 of frozen soils, while stress state and soil type should also be taken into account.
An Experimental Study of Passive and Active Heat Transfer Enhancement in Microchannels
Authors: Wang Yingying , Peles Yoav
Published: September 2013

An experimental study on single-phase heat transfer and fluid flow downstream a single microscale pillar in a microchannel was conducted. A secondary jet flow was issued from slits formed along the pillar. A comparison of the thermal performances of a plain microchannel, a microchannel with a pillar, and a microchannel with a jet issued from a pillar was performed to elucidate the merits of this heat transfer enhancement technique. It was found that the presence of a pillar upstream the heater enhanced the heat transfer; the addition of jet flow issued from a pillar further enhanced the heat transfer. At a Reynolds number of 730, an improvement of spatially averaged Nusselt number of 80% was achieved due to the combined effect of the pillar and the jet compared with the corresponding plain channel. Micro particle image velocimetry (μPIV) measurements provided planar velocity fields at two planes along the channel height, and allowed flow structure visualization. Turbulent kinetic energy (TKE) was used to measure flow mixing and to quantify the hydrodynamic effect of the jet. It was shown that the TKE is closely related to the Nusselt number.
Determination of the Thermal Conductivity in Adobe With Several Models
Authors: Mosquera P. , Cañas I. , Cid-Falceto J. , Marcos F.
Published: September 2013

The thermal conductivity of the earth materials conditions their ability as thermal isolator and its heating capacity, which has a direct impact on the energy consumption of the buildings built with these materials. Two original mathematical models have been developed (models MA-1 and MA-2) to calculate the effective thermal conductivity (λE) of adobes and their results have been compared with other models already known for other materials and with experimental measures done on adobes. The model MA-1 starts from the electric analogy of the transmission of heat in series and in parallel. The model MA-2 is obtained with a regression curve from experimental and literature values of λE in adobes. The λE in adobes has been measured by the thermal needle probe (TNP) procedure using 10 min as the measuring time. For dry adobes, with average environmental conditions of 19 °C and 41% of relative moisture, the values of λE measured were 0.80 W/(m·K) ± 10%. For natural hygroscopic moisture of 1.67% in the same environmental conditions, a λE of 0.90 W/(m·K) ± 10% was measured. Only five of the 18 models analyzed adjust to the values experimentally measured, and their precision depends on the values of λ of the components, which are obtained from the literature. Of the proposed models, the MA-1 fits for the values of the dry and wet material and with some determined values of the literature. The model MA-2 fits in all cases since it does not depend on the values of the literature but on the density of the material and its moisture content.
Thermal Modeling of Ultraviolet Nanoimprint Lithography
Authors: Patel Bhavik C. , Jain Ankur
Published: September 2013

Nanoimprint lithography (NIL) is a promising nanomanufacturing technology that offers an alternative to traditional photolithography for manufacturing next-generation semiconductor devices. This technology involves coating an ultraviolet (UV)-curable monomer layer on the substrate and then imprinting it with a template containing topography corresponding to the desired substrate features. While the template is close to contact with the substrate, the monomer is cured by UV exposure. This results in definition of desired features on the substrate. While NIL has the potential of defining very small feature sizes, thermal management of this process is critical for ensuring accuracy. Heat generation in the monomer layer due to UV absorption needs to be managed and dissipated in order to avoid thermal expansion mismatch and consequent misalignment between the template and wafer. In addition, thermal dissipation must occur in a timeframe that does not adversely affect the required lithography throughout. This paper develops a numerical simulation model of the nanoimprinting process and utilizes the model to study the effect of various geometrical parameters on the accuracy and throughput of the process. The effect of the UV power characteristics on heat dissipation and consequently on misalignment due to thermal expansion is studied. Results indicate that the thermal expansion mismatch due to commonly used UV exposure parameters may be minimized by utilizing a lower exposure power for longer time. A transient model enables a study of the effect of die imprint sequencing on the overall temperature rise during the process. Results indicate a critical trade-off between minimizing temperature rise on one hand, and maximizing system-level throughput on the other. By identifying and quantifying this trade-off, this work contributes to development of error-free nanoimprint lithography for future technology nodes.
Coriolis Effects on the Flow Field Inside a Rotating Triangular Channel for Leading Edge Cooling
Authors: Pascotto Matteo , Armellini Alessandro , Mucignat Claudio , Casarsa Luca
Published: September 2013

The flow field inside a rotating smooth radial channel with a triangular shaped cross section is investigated. Test conditions resemble those pertaining to the passages used for the internal cooling of the gas turbine blade's leading edge. Heat transfer data are also available from the literature on the same geometry and at comparable working conditions and have been profitably used for a combined aerothermal analysis. The model consists of a straight smooth channel with an equilateral triangle cross section. The rotation axis is aligned with one of the triangle bisectors. Two dimensional particle image velocimetry (PIV) and stereo-PIV were used in order to characterize the inlet flow (in static conditions) and the rotation-induced secondary flow in the channel cross section at Re = 20,000, Ro = 0.2 and Re = 10,000, Ro = 0.4. A wider range of working conditions (Re = 10,000–40,000, Ro = 0.2–0.6) was explored by means of Reynolds averaged Navier–Stokes (RANS) simulations carefully validated by the available PIV data. The turbulence was modeled by means of the shear stress transport (SST) model with a hybrid near-wall treatment. The results show that the rotation-induced flow structure is rather complicated and show relevant differences compared to the flow models that have been considered thus far. Indeed, the secondary flow turned out to be characterized by the presence of two or more vortex cells, depending on channel location and Ro number. No separation or reattachment of these structures is found on the channel walls but they have been observed at the channel apexes. The stream-wise velocity distribution shows a velocity peak close to the lower apex and the overall flow structure does not reach a steady configuration along the channel length. This evolution is fastened (in space) if the rotation number is increased while changes of the Re number have no effect. Finally, due to the understanding of the flow mechanisms associated with rotation, it was possible to provide a precise justification of the channel thermal behavior.
Numerical Analysis of Flow in a Transonic Compressor With a Single Circumferential Casing Groove: Influence of Groove Location and Depth on Flow Instability
Authors: Sakuma Yasunori , Watanabe Toshinori , Himeno Takehiro , Kato Dai , Murooka Takeshi , Shuto Yukari
Published: September 2013

The effect of circumferential single grooved casing treatment on the stability enhancement of NASA Rotor 37 has been examined with computational fluid dynamics analysis. Stall inception mechanism of Rotor 37 is presented first with principal focus on the tip leakage flow behavior, passage blockage, and the vortical flow structures. Detailed observation showed that the combined interaction of the stagnated flow of tip leakage vortex breakdown and the jetlike leakage flow from the midchord region leads to the blade tip-initiated stall inception. The result of numerical parametric study is then demonstrated to show the effect of varying the axial location and the depth of a circumferential single groove. The evaluation based on stall margin improvement showed a higher potential of deeper grooves in stability enhancement, and the optimal position for the groove to be located was indicated to exist near the leading edge of the blade.
Synchronization of Slowly Rotating Nonidentically Driven Pendula
Authors: Lazarek Mateusz , Nielaczny Michal , Czolczynski Krzysztof , Kapitaniak Tomasz
Published: September 2013

We study the synchronization of two rotating pendula mounted on a horizontal beam, which can roll on the parallel surface. The pendula are forced to rotate by different driving torques. It has been shown that after a transient two different types of synchronization between the pendula can be observed. The approximate analytical methods allow us to derive the synchronization conditions and explain the observed types of synchronous configurations. The energy balance in the system allows us to show how the energy is transferred between the pendula via the oscillating beam.
Distributed Operational Space Formulation of Serial Manipulators
Authors: Bhalerao Kishor D. , Critchley James , Oetomo Denny , Featherstone Roy , Khatib Oussama
Published: September 2013

This paper presents a new parallel algorithm for the operational space dynamics of unconstrained serial manipulators, which outperforms contemporary sequential and parallel algorithms in the presence of two or more processors. The method employs a hybrid divide and conquer algorithm (DCA) multibody methodology which brings together the best features of the DCA and fast sequential techniques. The method achieves a logarithmic time complexity (O(log(n)) in the number of degrees of freedom (n) for computing the operational space inertia (Λe) of a serial manipulator in presence of O(n) processors. The paper also addresses the efficient sequential and parallel computation of the dynamically consistent generalized inverse (J¯e) of the task Jacobian, the associated null space projection matrix (Ne), and the joint actuator forces (τnull) which only affect the manipulator posture. The sequential algorithms for computing J¯e, Ne, and τnull are of O(n), O(n2), and O(n) computational complexity, respectively, while the corresponding parallel algorithms are of O(log(n)), O(n), and O(log(n)) time complexity in the presence of O(n) processors.
In-situ plasma cleaning of samples to remove hydrocarbon and/or polydimethylsiloxane prior to ToF-SIMS analysis
Authors: Smentkowski Vincent S. , Moore C. A.
Published: October 2013

The surface of many real-life samples that are generated in an industrial research laboratory is often contaminated with adsorbed layers of hydrocarbons and/or silicones [in particular, polydimethylsiloxane (PDMS)]. These surface contaminants can attenuate or mask underlying species of interest, inhibiting or compromising accurate analysis. While samples can be sputter cleaned in order to remove surface contaminants, this approach is not ideal as sputtering may alter the chemistry of the surface of interest. In this manuscript, the authors report that an air-based remote plasma cleaning of samples in the load lock of a commercially available time of flight secondary ion mass spectroscopy (ToF-SIMS) instrument can remove both hydrocarbons and PDMS from the outer surface of three different samples that were submitted for surface analysis by ToF-SIMS.
High-Throughput Methods for Combinatorial Drug Discovery
Authors: Sun Xiaochen , Vilar Santiago , Tatonetti Nicholas P.
Published: October 2013

Combinatorial drug discovery will rely on new approaches to analyzing highly dimensional data resources.
Ordered Kinetochore Assembly in the Human-Pathogenic Basidiomycetous Yeast Cryptococcus neoformans
Authors: Kozubowski Lukasz , Yadav Vikas , Chatterjee Gautam , Sridhar Shreyas , Yamaguchi Masashi , Kawamoto Susumu , Bose Indrani , Heitman Joseph , Sanyal Kaustuv
Published: October 2013

Kinetochores facilitate interaction between chromosomes and the spindle apparatus. The formation of a metazoan trilayered kinetochore is an ordered event in which inner, middle, and outer layers assemble during disassembly of the nuclear envelope during mitosis. The existence of a similar strong correlation between kinetochore assembly and nuclear envelope breakdown in unicellular eukaryotes is unclear. Studies in the hemiascomycetous budding yeasts
Saccharomyces cerevisiae
and
Candida albicans
suggest that an ordered kinetochore assembly may not be evolutionarily conserved. Here, we utilized high-resolution time-lapse microscopy to analyze the localization patterns of a series of putative kinetochore proteins in the basidiomycetous budding yeast
Cryptococcus neoformans
, a human pathogen. Strikingly, similar to most metazoa but atypical of yeasts, the centromeres are not clustered but positioned adjacent to the nuclear envelope in premitotic
C. neoformans
cells. The centromeres gradually coalesce to a single cluster as cells progress toward mitosis. The mitotic clustering of centromeres seems to be dependent on the integrity of the mitotic spindle. To study the dynamics of the nuclear envelope, we followed the localization of two marker proteins, Ndc1 and Nup107. Fluorescence microscopy of the nuclear envelope and components of the kinetochore, along with ultrastructure analysis by transmission electron microscopy, reveal that in
C. neoformans
, the kinetochore assembles in an ordered manner prior to mitosis in concert with a partial opening of the nuclear envelope. Taken together, the results of this study demonstrate that kinetochore dynamics in
C. neoformans
is reminiscent of that of metazoans and shed new light on the evolution of mitosis in eukaryotes.

IMPORTANCE
Successful propagation of genetic material in progeny is essential for the survival of any organism. A proper kinetochore-microtubule interaction is crucial for high-fidelity chromosome segregation. An error in this process can lead to loss or gain of chromosomes, a common feature of most solid cancers. Several proteins assemble on centromere DNA to form a kinetochore. However, significant differences in the process of kinetochore assembly exist between unicellular yeasts and multicellular metaozoa. Here, we examined the key events that lead to formation of a proper kinetochore in a basidiomycetous budding yeast,
Cryptococcus neoformans
. We found that, during the progression of the cell cycle, nonclustered centromeres gradually clustered and kinetochores assembled in an ordered manner concomitant with partial opening of the nuclear envelope in this organism. These events have higher similarity to mitotic events of metazoans than to those previously described in other yeasts.
Uterine duplicity without communication between both hemiuteri and cervicovaginal atresia: importance of a thorough diagnosis before treatment
Authors: Martínez-Escoriza Juan Carlos , Palacios-Marqués Ana , Oliva-García Ana Belén , Ballester-Galiana Hortensia
Published: September 2013

The study described diagnostic and therapeutic processes for an exceptional congenital female genital anomaly involving a 15-year-old girl with progressive dysmenorrhoea and intense abdominal pain, and analyses pathogenesis of embryological anomalies associated with uterine duplicity (UD). Diagnostic methodology is analysed; treatment is described; and recommendations are provided. For the study of anomalies such as UD, we recommend the use of an ultrasound, vaginoscopy, MRI and laparoscopy imaging. Keeping in mind that hemihysterectomy should only be performed in cases with endometriosis or other unusual circumstances, surgical treatment should be avoided. A complete study based on gynaecological examination and ultrasound should be performed in adolescents with severe and progressive dysmenorrhoea. Based on the findings, imaging tests such as MRI and, if necessary, laparoscopy coinciding with menstruation, should be conducted before opting for surgical treatment.
Staged interventional and surgical management for complex low birthweight tetralogy of Fallot: another imperfect but legitimate strategy
Authors: Connolly Georgia May , Armstrong Catherine , Caputo Massimo , Morgan Gareth J
Published: September 2013

Management of spelling low weight infants with complex tetralogy of Fallot is often fraught. We present a 2.8-kg infant with DiGeorge syndrome and spelling tetralogy with non-confluent pulmonary arteries, the left pulmonary artery being supplied by an aberrant ductus arteriosus from the left common carotid artery. We performed stenting of the outflow tract and the ductus to allow this patient to achieve a successful elective surgical correction.
Eosinophilic enteritis: a rare cause of diarrhoea
Authors: Lladó Ana , Oliveira João , Silva Pedro , Pinheiro Sofia
Published: September 2013

We report a case of a healthy young man presenting with 1-week history of diarrhoea, acute abdominal pain and weight loss. Laboratory investigation showed very high peripheral eosinophils levels. After exclusion of the other causes of eosinophilia, a histological bowel sample analysis revealed marked eosinophilic infiltration of a small bowel mucosal layer which confirmed the suspicion of eosinophilic enteritis. Unlike most of the described cases, this patient did not require any specific treatment. Eosinophilic gastroenteritis is a rare and heterogeneous disease that is probably underdiagnosed in clinical practice because it requires a high degree of suspicion and an endoscopic biopsy for definite diagnosis.