bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Probabilistic Bulk Model of Coupled Mixed Layer and Convection. Part II: Shallow Convection Case
Authors: Gentine Pierre , Betts Alan K. , Lintner Benjamin R. , Findell Kirsten L. , van Heerwaarden Chiel C. , D’Andrea Fabio 
Published: January 2013

Abstract
The probabilistic bulk convection model (PBCM) developed in a companion paper is here extended to shallow nonprecipitating convection. The PBCM unifies the clear-sky and shallow convection boundary layer regimes by obtaining mixed-layer growth, cloud fraction, and convective inhibition from a single parameterization based on physical principles. The evolution of the shallow convection PBCM is based on the statistical distribution of the surface thermodynamic state of convective plumes.
The entrainment velocity of the mixed layer is related to the mass flux of the updrafts overshooting the dry inversion capping the mixed layer. The updrafts overcoming the convective inhibition generate active cloud-base mass flux, which is the boundary condition for the shallow cumulus scheme. The subcloud-layer entrainment velocity is directly coupled to the cloud-base mass flux through the distribution of vertical velocity and fractional cover of the updrafts.
Comparisons of the PBCM against large-eddy simulations from the Barbados Oceanographic and Meteorological Experiment (BOMEX) and from the Southern Great Plains Atmospheric Radiation Measurement Program (ARM) facility demonstrate good agreement in terms of thermodynamic structure, cloud-base mass flux, and cloud top.
The equilibrium between the cloud-base mass flux and rate of growth of the mixed layer determines the equilibrium convective inhibition and cloud cover. This process is an important new insight on the coupling between the mixed-layer and cumulus dynamics. Given its relative simplicity and transparency, the PBCM represents a powerful tool for developing process-based understanding and intuition about the physical processes involved in boundary layer–convection interactions, as well as a test bed for diagnosing and validating shallow convection parameterizations.
Factors Influencing the Development and Maintenance of Nocturnal Heavy-Rain-Producing Convective Systems in a Storm-Scale Ensemble
Authors: Schumacher Russ S. , Clark Adam J. , Xue Ming , Kong Fanyou 
Published: January 2013

Abstract
From 9 to 11 June 2010, a mesoscale convective vortex (MCV) was associated with several periods of heavy rainfall that led to flash flooding. During the overnight hours, mesoscale convective systems (MCSs) developed that moved slowly and produced heavy rainfall over small areas in south-central Texas on 9 June, north Texas on 10 June, and western Arkansas on 11 June. In this study, forecasts of this event from the Center for the Analysis and Prediction of Storms' Storm-Scale Ensemble Forecast system are examined. This ensemble, with 26 members at 4-km horizontal grid spacing, included a few members that very accurately predicted the development, maintenance, and evolution of the heavy-rain-producing MCSs, along with a majority of members that had substantial errors in their precipitation forecasts. The processes favorable for the initiation, organization, and maintenance of these heavy-rain-producing MCSs are diagnosed by comparing ensemble members with accurate and inaccurate forecasts. Even within a synoptic environment known to be conducive to extreme local rainfall, there was considerable spread in the ensemble's rainfall predictions. Because all ensemble members included an anomalously moist environment, the precipitation predictions were insensitive to the atmospheric moisture. However, the development of heavy precipitation overnight was very sensitive to the intensity and evolution of convection the previous day. Convective influences on the strength of the MCV and its associated dome of cold air at low levels determined whether subsequent deep convection was initiated and maintained. In all, this ensemble provides quantitative and qualitative information about the mesoscale processes that are most favorable (or unfavorable) for localized extreme rainfall.
Varus External Rotation Stress Test for Radiographic Detection of Deep Deltoid Ligament Disruption With and Without Syndesmotic Disruption
Authors: Femino John E. , Vaseenon Tanawat , Phistkul Phinit , Tochigi Yuki , Anderson Donald D. , Amendola Annunziato 
Published: January 2013

Background: External rotation stress is used intraoperatively for diagnosing medial ankle and syndesmotic instability in rotational ankle fractures after reduction and fixation of the fibula. However, external rotation includes hindfoot, midfoot, and ankle motion. The purpose of this study was to determine the effect of hindfoot positioning when using the external rotation stress test. Isolated deep deltoid ligament (DDL) instability and combined DDL and syndesmotic instability were modeled. An intact fibula was used as a surrogate for an anatomically fixed fibula fracture. Methods: Six cadaver specimens with full-length tib-fib articulations were used. Specimens were fixed into a Taylor Spatial Frame (Smith&Nephew, Memphis, TN) with 4 to 5 points of fixation in the tibia and the foot. Specimens were mounted in ankle and foot neutral position. Metal markers were placed at the medial gutter and syndesmosis. Anteroposterior (AP) and mortise radiographs were obtained in 3 positions: neutral hindfoot, valgus external rotation stress, and varus external rotation stress. For both valgus and varus external rotation stress, the frame was loosened and stressed to a hard end point and then locked. Three modes were studied: intact ligaments, DDL transected, and DDL+ syndesmosis transected. Digital radiographs were used to measure the displacement of the markers. Results: The varus external rotation stress test demonstrated significant widening of the medial gutter in specimens with isolated DDL instability, in both AP ( P = .01) and mortise ( P = .02) views. Both maneuvers demonstrated significant medial gutter widening with combined DDL and syndesmosis disruption ( P ≤ .01), although the varus external rotation stress test produced nearly twice as much displacement (10.7 vs 5.4 mm). Syndesmotic widening was not significant with either maneuver. Conclusions: Varus external rotation stress was more effective than valgus external rotation stress in demonstrating displacement of markers at the medial gutter and on AP and mortise radiographs for both DDL and DDL with syndesmotic instability. Clinical Relevance: These findings may lead to improved clinical detection of rotational ankle instability from combined DDL and syndesmotic disruption, which may affect decision making for using syndesmotic fixation when using intraoperative stress fluoroscopy images. Occult DDL instability may be underdiagnosed, and this may affect future directions of the treatment of rotational ankle fractures and severe sprains.
Reconstruction of phyletic trees by global alignment of multiple metabolic networks
Authors: Ma Cheng-Yu , Lin Shu-Hsi , Lee Chi-Ching , Tang Chuan Yi , Berger Bonnie , Liao Chung-Shou 
Published: January 2013

Abstract

Background
In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.

Results
We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis.

Conclusions
We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.
Human CD3γ, but not CD3δ, haploinsufficiency differentially impairs γδ versus αβ surface TCR expression
Authors: Muñoz-Ruiz Miguel , Pérez-Flores Verónica , Garcillán Beatriz , Guardo Alberto C , Mazariegos Marina S , Takada Hidetoshi , Allende Luis M , Kilic Sara S , Sanal Ozden , Roifman Chaim M , López-Granados Eduardo , Recio María J , Martínez-Naves Eduardo , Fernández-Malavé Edgar , Regueiro José R 
Published: January 2013

AbstractBackgroundThe T cell antigen receptors (TCR) of αβ and γδ T lymphocytes are believed to assemble in a similar fashion in humans. Firstly, αβ or γδ TCR chains incorporate a CD3δε dimer, then a CD3γε dimer and finally a ζζ homodimer, resulting in TCR complexes with the same CD3 dimer stoichiometry. Partial reduction in the expression of the highly homologous CD3γ and CD3δ proteins would thus be expected to have a similar impact in the assembly and surface expression of both TCR isotypes. To test this hypothesis, we compared the surface TCR expression of primary αβ and γδ T cells from healthy donors carrying a single null or leaky mutation inCD3G(γ+/−) orCD3D(δ+/−, δ+/leaky) with that of normal controls.ResultsAlthough the partial reduction in the intracellular availability of CD3γ or CD3δ proteins was comparable as a consequence of the mutations, surface TCR expression measured with anti-CD3ε antibodies was significantly more decreased in γδ than in αβ T lymphocytes in CD3γ+/−individuals, whereas CD3δ+/−and CD3δ+/leakydonors showed a similar decrease of surface TCR in both T cell lineages. Therefore, surface γδ TCR expression was more dependent on available CD3γ than surface αβ TCR expression.ConclusionsThe results support the existence of differential structural constraints in the two human TCR isotypes regarding the incorporation of CD3γε and CD3δε dimers, as revealed by their discordant surface expression behaviour when confronted with reduced amounts of CD3γ, but not of the homologous CD3δ chain. A modified version of the prevailing TCR assembly model is proposed to accommodate these new data.
A computational method using multiresolution for volumetric data integration
Authors: Akinlar Mehmet Ali , Kurulay Muhammet , Secer Aydin , Celenk Mehmet 
Published: January 2013

Abstract
In this paper, we present a new method for integration of 3-D medical data by utilizing the advantages of 3-D multiresolution analysis and techniques of variational calculus. We first express the data integration problem as a variational optimal control problem where we express the displacement field in terms of wavelet expansions and, secondly, we write the components of the displacement field in terms of wavelet coefficients. We solve this optimization problem with a blockwise descent algorithm. We demonstrate the registration of 3-D brain MR images in the size of

257
×
257
×
65

as an application of the present method. Experimental results indicate that the method can integrate 3-D MR images better than only variational or only wavelet-based methods.

MSC: 68U10, 65D18, 65J05, 97N40.
Enzymatic lignocellulose hydrolysis: Improved cellulase productivity by insoluble solids recycling
Authors: Weiss Noah , Börjesson Johan , Pedersen Lars Saaby , Meyer Anne S 
Published: January 2013

Abstract

Background
It is necessary to develop efficient methods to produce renewable fuels from lignocellulosic biomass. One of the main challenges to the industrialization of lignocellulose conversion processes is the large amount of cellulase enzymes used for the hydrolysis of cellulose. One method for decreasing the amount of enzyme used is to recycle the enzymes. In this study, the recycle of enzymes associated with the insoluble solid fraction after the enzymatic hydrolysis of cellulose was investigated for pretreated corn stover under a variety of recycling conditions.

Results
It was found that a significant amount of cellulase activity could be recovered by recycling the insoluble biomass fraction, and the enzyme dosage could be decreased by 30% to achieve the same glucose yields under the most favorable conditions. Enzyme productivity (g glucose produced/g enzyme applied) increased between 30 and 50% by the recycling, depending on the reaction conditions. While increasing the amount of solids recycled increased process performance, the methods applicability was limited by its positive correlation with increasing total solids concentrations, reaction volumes, and lignin content of the insoluble residue. However, increasing amounts of lignin rich residue during the recycle did not negatively impact glucose yields.

Conclusions
To take advantage of this effect, the amount of solids recycled should be maximized, based on a given processes ability to deal with higher solids concentrations and volumes. Recycling of enzymes by recycling the insoluble solids fraction was thus shown to be an effective method to decrease enzyme usage, and research should be continued for its industrial application.
Live cell imaging techniques to study T cell trafficking across the blood-brain barrier in vitro and in vivo
Authors: Coisne Caroline , Lyck Ruth , Engelhardt Britta 
Published: January 2013

Abstract

Background
The central nervous system (CNS) is an immunologically privileged site to which access for circulating immune cells is tightly controlled by the endothelial blood–brain barrier (BBB) located in CNS microvessels. Under physiological conditions immune cell migration across the BBB is low. However, in neuroinflammatory diseases such as multiple sclerosis, many immune cells can cross the BBB and cause neurological symptoms. Extravasation of circulating immune cells is a multi-step process that is regulated by the sequential interaction of different adhesion and signaling molecules on the immune cells and on the endothelium. The specialized barrier characteristics of the BBB, therefore, imply the existence of unique mechanisms for immune cell migration across the BBB.

Methods and design
An in vitro mouse BBB model maintaining physiological barrier characteristics in a flow chamber and combined with high magnification live cell imaging, has been established. This model enables the molecular mechanisms involved in the multi-step extravasation of T cells across the in vitro BBB, to be defined with high-throughput analyses. Subsequently these mechanisms have been verified in vivo using a limited number of experimental animals and a spinal cord window surgical technique. The window enables live observation of the dynamic interaction between T cells and spinal cord microvessels under physiological and pathological conditions using real time epifluorescence intravital imaging. These in vitro and in vivo live cell imaging methods have shown that the BBB endothelium possesses unique and specialized mechanisms involved in the multi-step T cell migration across this endothelial barrier under physiological flow. The initial T cell interaction with the endothelium is either mediated by T cell capture or by T cell rolling. Arrest follows, and then T cells polarize and especially CD4+ T cells crawl over long distances against the direction of flow to find the rare sites permissive for diapedesis through the endothelium.

Discussion
The sequential use of in vitro and in vivo live cell imaging of T cells interacting with the BBB allows us to delineate the kinetics and molecular determinants involved in multistep extravasation of encephalitogenic T cells across the BBB.
Phenomenologic analysis of healthcare worker perceptions of intensive care unit diaries
Authors: Perier Antoine , Revah-Levy Anne , Bruel Cédric , Cousin Nathalie , Angeli Stéphanie , Brochon Sandie , Philippart François , Max Adeline , Gregoire Charles , Misset Benoit , Garrouste-Orgeas Maité 
Published: January 2013

Abstract
Introduction
Studies have reported associations between diaries kept for intensive care unit (ICU) patients and long-term quality-of-life and psychological outcomes in patients and their relatives. Little was known about perceptions of healthcare workers reading and writing in the diaries. We investigated healthcare worker perceptions the better to understand their opinions and responses to reading and writing in the diaries.

Methods
We used a phenomenologic approach to conduct a qualitative study of 36 semistructured interviews in a medical-surgical ICU in a 460-bed tertiary hospital.

Results
Two domains of perception were assessed: reading and writing in the diaries. These two domains led to four main themes in the ICU workers' perceptions: suffering of the families; using the diary as a source of information for families but also as generating difficulties in writing bad news; determining the optimal interpersonal distance with the patient and relatives; and using the diary as a tool for constructing a narrative of the patient's ICU stay.

Conclusions
The ICU workers thought that the diary was beneficial in communicating the suffering of families while providing comfort and helping to build the patient's ICU narrative. They reported strong emotions related to the diaries and a perception of intruding into the patients' and families' privacy when reading the diaries. Fear of strong emotional investment may adversely affect the ability of ICU workers to perform their duties optimally. ICU workers are in favor of ICU diaries, but activation by the diaries of emotions among younger ICU workers may require specific support.
Metallothionein-protein interactions
Authors: Atrian Sílvia , Capdevila Mercè 
Published: January 2013

AbstractMetallothioneins (MTs) are a family of universal, small proteins, sharing a high cysteine content and an optimal capacity for metal ion coordination. They take part in a plethora of metal ion-related events (from detoxification to homeostasis, storage, and delivery), in a wide range of stress responses, and in different pathological processes (tumorigenesis, neurodegeneration, and inflammation). The information on both intracellular and extracellular interactions of MTs with other proteins is here comprehensively reviewed. In mammalian kidney, MT1/MT2 interact with megalin and related receptors, and with the transporter transthyretin. Most of the mammalian MT partners identified concern interactions with central nervous system (mainly brain) proteins, both through physical contact or metal exchange reactions. Physical interactions mainly involve neuronal secretion multimers. Regarding metal swap events, brain MT3 appears to control the metal ion load in peptides whose aggregation leads to neurodegenerative disorders, such as Aβ peptide, α-synuclein, and prion proteins (Alzheimer’s and Parkinson’s diseases, and spongiform encephalopathies, respectively). Interaction with ferritin and bovine serum albumin are also documented. The intercourse of MTs with zinc-dependent enzymes and transcription factors is capable to activate/deactivate them, thus conferring MTs the role of metabolic and gene expression regulators. As some of these proteins are involved in cell cycle and proliferation control (p53, nuclear factor κB, and PKCμ), they are considered in the context of oncogenesis and tumor progression. Only one non-mammalian MT interaction, involving Drosophila MtnA and MtnB major isoforms and peroxiredoxins, has been reported. The prospective use for biomedical applications of the MT-interaction information is finally discussed.
Long-term stability of laboratory tests and practical implications for quality management
Authors: Van Houcke Sofie K. , Stepman Hedwig C.M. , Thienpont Linda M. , Fiers Tom , Stove Veronique , Couck Pedro , Anckaert Ellen , Gorus Frans 
Published: January 2013

Abstract

Background: Long-term stability of analytical performance is required for adequate patient management. We investigated the use of patient data to document test stability, and the relevance of observed instabilities on a surrogate medical outcome. We used multiyear patient and internal quality control (IQC) data from two laboratories for tests to monitor chronic kidney and thyroid disease.

Methods: We plotted moving means of the 50th percentiles of stratified patient data and of the daily IQC means. We evaluated observed instabilities based on goals inferred from the analytes’ biological variation and investigated their effect on classification of results against reference intervals.

Results: Patient and IQC data generally matched well, except for analytes, for which other than analytical variation sources prevailed. Analytical instabilities were predominantly due to reagent/calibrator lot changes, however, for immunoassays also to within-lot instabilities, urging frequent recalibrations. The relevance of biased results on medical decisions ranged from negligible to very pronounced, indicating the need for assessment of analytical performance in relation to quality goals inferred from biological variation.

Conclusions: Patient percentiles offer great potential to assess/monitor the medium- to long-term analytical stability of a test within certain constraints. Differences in analytical quality between assays can significantly affect medical outcome.
Strichartz estimates for partially periodic solutions to Schrödinger equations in 4d$4d$ and applications
Authors: Herr Sebastian , Tataru Daniel , Tzvetkov Nikolay 
Published: January 2013

Abstract.

We consider the energy critical nonlinear Schrödinger equation on
periodic domains of the form

ℝ
m

×

𝕋

4
-
m

$\mathbb {R}^m\times \mathbb {T}^{4-m}$

with

m
=
0
,
1
,
2
,
3

$m =
0,1,2,3$

. Assuming that a certain L4
Strichartz estimate holds
for solutions to the corresponding linear Schrödinger equation, we
prove that the nonlinear problem is locally well-posed in the energy
space. Then we verify that the L4
estimate holds if

m
=
2
,
3

$m=2,3$

.
Motivational stage of change in young patients undergoing day treatment for eating disorders
Authors: Bustin Lisa A. , Lane-Loney Susan E. , Hollenbeak Christopher S. , Ornstein Rollyn M. 
Published: January 2013

Abstract
Background: The objective was to determine whether motivation to change is significantly altered over the course of partial hospitalization in children and adolescents with eating disorders (EDs).
Method: This study was a retrospective chart review of 30 sets of adolescents and their parents who completed the Motivational Stage of Change for Adolescents Recovering from an Eating Disorder (MSCARED) at both intake and discharge from partial hospitalization. The main outcome variables included change in stage of change (SOC) for patients and their parents. Secondary outcomes included correlations between SOC and other baseline variables, as well as changes in SOC and psychological test scores.
Results: The SOC was significantly higher at discharge than at intake in both the patients and parents, but the two groups were not in agreement at discharge. The change in the SOC was correlated with change in Children’s Eating Attitudes Test scores. Assessment of decisional balance showed correlations with SOC. Age, change in weight, and psychiatric diagnoses did not correlate with initial SOC.
Conclusion: The MSCARED may be a useful tool for monitoring young ED patients’ psychological improvements with day treatment. Initial SOC is not predictive of treatment outcomes.