bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward accurate tooth segmentation from computed tomography images using a hybrid level set model
Authors: Gan Yangzhou , Xia Zeyang , Xiong Jing , Zhao Qunfei , Hu Ying , Zhang Jianwei 
Published: December 2014

Purpose:A three‐dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images.Methods:The 3D dental CT volumetric images are segmented slice by slice in a two‐dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm3) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state‐of‐the‐art methods.Results:For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm3, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm3, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0.28 ± 0.03 mm, and 1.06 ± 0.40 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the premolar were 37.95 ± 10.13 mm3, 92.45 ± 2.29%, 0.29 ± 0.06 mm, 0.33 ± 0.10 mm, and 1.28 ± 0.72 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the molar were 52.38 ± 17.27 mm3, 94.12 ± 1.38%, 0.30 ± 0.08 mm, 0.35 ± 0.17 mm, and 1.52 ± 0.75 mm, respectively. The computation time of the proposed method for segmenting CBCT images of one subject was 7.25 ± 0.73 min. Compared with two other methods, the proposed method achieves significant improvement in terms of accuracy.Conclusions:The presented tooth segmentation method can be used to segment tooth contours from CT images accurately and efficiently.
Identification of TL-Om1, an Adult T-Cell Leukemia (ATL) Cell Line, as Reference Material for Quantitative PCR for Human T-Lymphotropic Virus 1
Authors: Kuramitsu Madoka , Okuma Kazu , Yamagishi Makoto , Yamochi Tadanori , Firouzi Sanaz , Momose Haruka , Mizukami Takuo , Takizawa Kazuya , Araki Kumiko , Sugamura Kazuo , Yamaguchi Kazunari , Watanabe Toshiki , Hamaguchi Isao 
Published: December 2014

ABSTRACT

Quantitative PCR (qPCR) for human T-lymphotropic virus 1 (HTLV-1) is useful for measuring the amount of integrated HTLV-1 proviral DNA in peripheral blood mononuclear cells. Many laboratories in Japan have developed different HTLV-1 qPCR methods. However, when six independent laboratories analyzed the proviral load of the same samples, there was a 5-fold difference in their results. To standardize HTLV-1 qPCR, preparation of a well-defined reference material is needed. We analyzed the integrated HTLV-1 genome and the internal control (IC) genes of TL-Om1, a cell line derived from adult T-cell leukemia, to confirm its suitability as a reference material for HTLV-1 qPCR. Fluorescent
in situ
hybridization (FISH) showed that HTLV-1 provirus was monoclonally integrated in chromosome 1 at the site of 1p13 in the TL-Om1 genome. HTLV-1 proviral genome was not transferred from TL-Om1 to an uninfected T-cell line, suggesting that the HTLV-1 proviral copy number in TL-Om1 cells is stable. To determine the copy number of HTLV-1 provirus and IC genes in TL-Om1 cells, we used FISH, digital PCR, and qPCR. HTLV-1 copy numbers obtained by these three methods were similar, suggesting that their results were accurate. Also, the ratio of the copy number of HTLV-1 provirus to one of the IC genes, RNase P, was consistent for all three methods. These findings indicate that TL-Om1 cells are an appropriate reference material for HTLV-1 qPCR.
Performance of the Molecular Alere i Influenza A&B Test Compared to That of the Xpert Flu A/B Assay
Authors: Chapin Kimberle C. , Flores-Cortez Estefany J. 
Published: December 2014

ABSTRACT
Data on the performance of rapid molecular point-of-care use platforms for diagnosis of influenza are lacking. We validated nasopharyngeal (NP) flocked specimens in universal transport medium (UTM) and evaluated the clinical sensitivity and specificity of the Alere i influenza A&B test compared to those of the Xpert flu A/B assay. The Alere i influenza A&B test had an overall sensitivity and specificity of 93.8% and 62.5% for influenza A, respectively, and of 91.8% and 53.6% for influenza B, respectively. The poor specificity was due to influenza virus samples determined positive for both type A and B.
Acanthamoeba Encephalitis: Isolation of Genotype T1 in Mycobacterial Liquid Culture Medium
Authors: Azzam Rula , Badenoch Paul R. , Francis Michelle J. , Fernandez Charles , Adamson Penelope J. , Dendle Claire , Woolley Ian , Robson Jenny , Korman Tony M. , Graham Maryza 
Published: December 2014

ABSTRACT

We report a case of
Acanthamoeba
encephalitis diagnosed from an antemortem brain biopsy specimen, where the organism was first isolated in mycobacterial liquid medium and first identified by using a sequence generated by a commercial panfungal sequencing assay. We correlate susceptibility results with clinical outcome.
Accurate Quantification of Episomal HIV-1 Two-Long Terminal Repeat Circles by Use of Optimized DNA Isolation and Droplet Digital PCR
Authors: Malatinkova Eva , Kiselinova Maja , Bonczkowski Pawel , Trypsteen Wim , Messiaen Peter , Vermeire Jolien , Verhasselt Bruno , Vervisch Karen , Vandekerckhove Linos , De Spiegelaere Ward 
Published: December 2014

ABSTRACT
Episomal HIV-1 two-long terminal repeat (2-LTR) circles are considered markers for ongoing viral replication. Two sample processing procedures were compared to accurately quantify 2-LTR in patients by using droplet digital PCR (ddPCR). Here, we show that plasmid isolation with a spiked non-HIV plasmid for normalization enables more accurate 2-LTR quantification than genomic DNA isolation.
Aspergilluscitrinoterreus, a New Species of Section Terrei Isolated from Samples of Patients with Nonhematological Predisposing Conditions
Authors: Guinea Jesús , Sandoval-Denis Marcelo , Escribano Pilar , Peláez Teresa , Guarro Josep , Bouza Emilio 
Published: December 2014

ABSTRACT

The use of molecular identification techniques has revealed an increasing number of new species within
Aspergillus
section
Terrei
. We phenotyped a set of 26 clinical isolates that showed genetic differences from
Aspergillus terreus
sensu stricto
by analyzing sequences from PCR-amplified β-tubulin and calmodulin genes and the internal transcribed spacer region. Since the isolates were phylogenetically and morphologically different from all of the members of
Aspergillus
section
Terrei
, they are described here as a new species,
Aspergillus
citrinoterreus
, so named because it produces a diffusible yellowish pigment in agar.
A. citrinoterreus
isolates were significantly more susceptible to itraconazole, voriconazole, and posaconazole than
A. terreus
sensu stricto
isolates were; in contrast, the amphotericin B MICs for both species were high.
A. citrinoterreus
was found in clinical samples from patients with proven or probable invasive aspergillosis and colonized patients, none of whom had hematological malignancies as predisposing conditions. However, they did have other underlying conditions such as chronic obstructive pulmonary disease, cirrhosis, and cancer or had received a solid organ transplants and presented not only with invasive pulmonary aspergillosis but also with mediastinitis.
A. citrinoterreus
isolates were detected for the first time in 2002. In all cases of invasive aspergillosis,
A. citrinoterreus
was found to be a copathogen, mostly with
A. fumigatus
.
Phosphatidylserine-Specific Phospholipase A1 Involved in Hepatitis C Virus Assembly through NS2 Complex Formation
Authors: Guo Min , Pei Rongjuan , Yang Qi , Cao Huang , Wang Yun , Wu Chunchen , Chen Jizheng , Zhou Yuan , Hu Xue , Lu Mengji , Chen Xinwen 
Published: December 2014

ABSTRACT
Several members of the phospholipase family have been reported to be involved in hepatitis C virus (HCV) replication. Here, we identified another phospholipase, phosphatidylserine-specific phospholipase A1 (PLA1A), as a host factor involved in HCV assembly. PLA1A was upregulated by HCV infection, and PLA1A knockdown significantly reduced J399EM (genotype 2a) HCV propagation at the assembly step but not the entry, RNA replication, and protein translation steps of the life cycle. Protein localization and interaction analysis further revealed a role of PLA1A in the interaction of NS2-E2 and NS2-NS5A, as the formation of the NS2-E2 and NS2-NS5A complexes was weakened in the absence of PLA1A. In addition, PLA1A stabilized the NS2/NS5A dotted structure during infection. These data suggest that PLA1A plays an important role in bridging the membrane-associated NS2-E2 complex and the NS5A-associated replication complex via its interaction with E2, NS2, and NS5A, which leads to a coordinating interaction between the structural and nonstructural proteins and facilitates viral assembly.

IMPORTANCE
Hepatitis C virus (HCV) genomic replication is driven by the replication complex and occurs at the membranous web, while the lipid droplet is the organelle in which virion assembly is initiated. In this study, we identified phosphatidylserine-specific phospholipase A1 (PLA1A), a member of phospholipase A 1 family, as a novel host factor involved in the assembly process of HCV. PLA1A, which is induced by HCV infection at a late infection stage, interacts with HCV E2, NS2, and NS5A proteins and enhances and stabilizes the NS2-E2 and NS2-NS5A complex formation, which is essential for viral assembly. Thus, PLA1A is an important host factor which is involved in the initiation of the viral assembly in close proximity to Core-decorated lipid droplets through bringing together the HCV replication complex and envelope complex.
Objectively measured physical activity in Finnish employees: a cross-sectional study
Authors: Mutikainen Sara , Helander Elina , Pietilä Julia , Korhonen Ilkka , Kujala Urho M 
Published: December 2014

ObjectivesTo objectively measure the amount of intensity-specific physical activity by gender and age with respect to body mass index (BMI) during workdays and days off among Finnish employees.DesignA cross-sectional study.SettingPrimary care occupational healthcare units.ParticipantsA sample of 9554 Finnish employees (4221 men and 5333 women; age range 18–65 years; BMI range 18.5–40 kg/m2) who participated in health assessments related to occupational health promotion.Main outcome measurementsThe amount of moderate-to-vigorous (MVPA) and vigorous (VPA) physical activity (≥3 and ≥6 metabolic equivalents, respectively) was assessed by estimating the minute-to-minute oxygen consumption from the recorded beat-to-beat R-R interval data. The estimation method used heart rate, respiration rate and on/off response information from R-R interval data calibrated by age, gender, height, weight and self-reported physical activity class. The proportion of participants fulfilling the aerobic physical activity recommendation of ≥150 min/week was calculated on the basis of ≥10 min bouts, by multiplying the VPA minutes by 2.ResultsBoth MVPA and VPA were higher among men and during days off, and decreased with increasing age and BMI (p<0.001 for all). Similar results were observed when the probability of having a bout of MVPA or VPA lasting continuously for ≥10 min per measurement day was studied. The total amount of VPA was low among overweight (mean ≤2.6 min/day), obese (mean ≤0.6 min/day) and all women in the age group 51–65 years (mean ≤2.5 min/day) during both types of days. The proportion of participants fulfilling the aerobic physical activity recommendation was highest for normal weight men (65%; 95% CI 62% to 67%) and lowest for obese women (10%; 95% CI 8% to 12%).ConclusionsObjectively measured physical activity is higher among men and during days off, and decreases with increasing age and BMI. The amount of VPA is very low among obese, overweight and older women.
Radiologists’ perspectives about evidence-based medicine and their clinical practice: a semistructured interview study
Authors: Tong Allison , Mahady Suzanne E , Craig Jonathan C , Lau Gabes , Peduto Anthony J , Loy Clement 
Published: December 2014

ObjectivesTo describe radiologist's attitudes and perspectives on evidence-based medicine (EBM) and their practice.DesignFace-to-face semistructured interviews, thematic analysis.Setting24 institutions across six Australian states and New Zealand. Transcripts were imported into HyperRESEARCH software and thematically analysed.Participants25 radiologists.ResultsSix themes were identified: legitimising decisions (validated justification, prioritising patient preferences, reinforcing protocols), optimising outcomes (ensuring patient safety, maximising efficiency), availability of access (requiring immediacy, inadequacy of evidence, time constraints, proximity of peer networks, grasping information dispersion), over-riding pragmatism (perceptibly applicability, preserving the art of medicine, technical demands), limited confidence (conceptual obscurity, reputation-based trust, demands constant practice, suspicion and cynicism), and competing powers (hierarchical conflict, prevailing commercial interests).ConclusionsRadiologists believe EBM can support clinical decision-making for optimal patient outcomes and service efficiency but feel limited in their capacities to assimilate and apply EBM in practice. Improving access to evidence, providing ongoing education and training supplemented with practical tools for appraising evidence; and developing evidence-based guidelines and protocols may enhance feasibility and promote the confidence and skills among radiologists in applying EBM in radiology practice for better patient care.
Improving accessibility of trust guidelines and protocols at the Great Western Hospital, Swindon
Authors: Robertson Ian , Smith Abigail , Tucker Jennifer , Cilia Erica , Chen Kangni , Marion Rose , Nesbitt Julian , Ramcharitar Steve , Cathiavadi Greamspet Mala 
Published: December 2014

AbstractTrust guidelines and policies outline recommendations for the management of common clinical and non-clinical situations, serving to standardise best practice. Prior to this project, there was no consolidated location for these documents. Lack of organisational structure and inadequate search functionality within the trust intranet led to time wasted locating information, acting outside of recognised best practice, and ultimately potentially compromising patient safety.We surveyed 55 junior doctors, 95% of respondents were dependent on guidelines on a daily basis. 20% spending greater than 5 minutes to locate protocols and 38% unable to locate some relevant documents at all. We analysed the time taken for junior doctors to locate six randomly selected protocols. Pre-intervention mean time was 133 seconds (on six occasions doctors were unable to locate the guideline).All trust guidelines and protocols currently available on the intranet were collated, consolidated, and renamed according to content. These were then re-alphabetised and new search terms linked to each document. Existing links were then uploaded and a single web page made available via the trust intranet homepage. The new page was publicised by email, posters and interdepartmental presentations.In our post intervention survey, 97% of respondents were aware of the project and had made use of the page. All protocols were located during re-testing with 90% of those resurveyed stating it was easier to locate protocols. Overall, a reduction in the time and number of clicks required to locate protocols was demonstrated: mean time 16 seconds vs 133 seconds pre-intervention (n=60). 53% of guidelines located in <30s and 86% <2 minutes.
Reducing door to needle time for stroke thrombolysis
Authors: Gill Sumanjit 
Published: December 2014

AbstractBetter outcomes are obtained with stroke thrombolysis the more rapidly it is given, both in terms of the patient's level of functional ability and also mortality. Current UK performance targets (outside London) aim for a time of 45 minutes or less. Thrombolysis pathways involve multidisciplinary working across departmental boundaries as well as senior level decision making. Our system used telemedicine out of hours adding additional complexity to the pathway. The initial planning stages started by auditing current practice and mapping the existing pathway. The figures for door to needle times were held on a database on the stroke unit and collected in detail for the purposes of national reporting.The pathway was mapped by combining personal experience of working within the stroke service with the experiences of the general medical registrars who worked the system out of hours. The initial action was to present this information throughout the hospital at departmental meetings. Opinions were canvassed at these meetings on where the biggest barriers were within the pathway and how we could address them. An awareness campaign was held by advertising over the intranet. An intervention comprising the following elements was introduced over the period of a year: introduction of an ambulance pre-alert, revision of the existing pathway, and education to all those involved in thrombolysis. The cases where particularly long delays were noted were audited in more depth to identify barriers to flow through the system. This was reported in ward meetings for staff to contribute experience and to offer solutions. We went to commissioning group meetings to gain the support of the local ambulance service, and talked to A&E seniors about the project and the ways in which they could help. Median times were calculated from a stroke database.There was a fall in median door to needle time of 65.5 to 49 minutes over a period of 18 months. A complex intervention to improve door to needle time can and did produce good results with a reduction in times to within the London performance standards of care. The efficacy could be improved with an increased staffing level and provision of a formal setting within which to discuss changes and to keep up the momentum of change.
A genome-wide association study of heparin-induced thrombocyto - penia using an electronic medical record
Authors: Karnes Jason H. , Cronin Robert M. , Rollin Jerome , Teumer Alexander , Pouplard Claire , Shaffer Christian M. , Blanquicett Carmelo , Bowton Erica A. , Cowan James D. , Mosley Jonathan D. , Van Driest Sara L. , Weeke Peter E. , Wells Quinn S. , Bakchoul Tamam , Denny Joshua C. , Greinacher Andreas , Gruel Yves , Roden Dan M. 
Published: December 2014

SummaryHeparin-induced thrombocytopenia (HIT) is an unpredictable, potentially catastrophic adverse effect of heparin treatment resulting from an immune response to platelet factor 4 (PF4)/heparin complexes. No genome-wide evaluations have been performed to identify potential genetic influences on HIT. Here, we performed a genome-wide association study (GWAS) and candidate gene study using HIT cases and controls identified using electronic medical records (EMRs) coupled to a DNA biobank and attempted to replicate GWAS associations in an independent cohort. We subsequently investigated influences of GWAS-associated single nucleotide polymorphisms (SNPs) on PF4/heparin antibodies in non-heparin treated individuals. In a recessive model, we observed significant SNP associations (odds ratio [OR] 18.52; 95% confidence interval [CI] 6.33-54.23; p=3.18×10-9) with HIT near the T-Cell Death-Associated Gene 8 (TDAG8). These SNPs are in linkage disequilibrium with a missense TDAG8 SNP. TDAG8 SNPs trended toward an association with HIT in replication analysis (OR 5.71; 0.47-69.22; p=0.17), and the missense SNP was associated with PF4/heparin antibody levels and positive PF4/heparin antibodies in non-heparin treated patients (OR 3.09; 1.14-8.13; p=0.02). In the candidate gene study, SNPs at HLA-DRA were nominally associated with HIT (OR 0.25; 0.15-0.44; p=2.06×10-6). Further study of TDAG8 and HLA-DRA SNPs is warranted to assess their influence on the risk of developing HIT.
Phospholamban as a Crucial Determinant of the Inotropic Response of Human Pluripotent Stem Cell–Derived Ventricular Cardiomyocytes and Engineered 3-Dimensional Tissue Constructs
Authors: Chen Gaopeng , Li Sen , Karakikes Ioannis , Ren Lihuan , Zi-Ying Chow Maggie , Chopra Anant , Keung Wendy , Yan Bin , Chan Camie W.Y. , Costa Kevin D. , Kong Chi-Wing , Hajjar Roger J. , Chen Christopher S. , Li Ronald A. 
Published: December 2014

Background—
Human (h) embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) serve as a potential unlimited ex vivo source of cardiomyocytes (CMs). However, a well-accepted roadblock has been their immature phenotype. hESC/iPSC-derived ventricular (v) CMs and their engineered cardiac microtissues (hvCMTs) similarly displayed positive chronotropic but null inotropic responses to β-adrenergic stimulation. Given that phospholamban (PLB) is robustly present in adult but poorly expressed in hESC/iPSC-vCMs and its defined biological role in β-adrenergic signaling, we investigated the functional consequences of PLB expression in hESC/iPSC-vCMs and hvCMTs.

Methods and Results—

First, we confirmed that PLB protein was differentially expressed in hESC (HES2, H9)- and iPSC-derived and adult vCMs. We then transduced hES2-vCMs with the recombinant adenoviruses (Ad) Ad-PLB or Ad-S16E-PLB to overexpress wild-type PLB or the pseudophosphorylated point–mutated variant, respectively. As anticipated from the inhibitory effect of unphosphorylated PLB on sarco/endoplasmic reticulum Ca
2+
-ATPase, Ad-PLB transduction significantly attenuated electrically evoked Ca
2+
transient amplitude and prolonged the 50% decay time. Importantly, Ad-PLB–transduced hES2-vCMs uniquely responded to isoproterenol. Ad-S16E-PLB–transduced hES2-vCMs displayed an intermediate phenotype. The same trends were observed with H9- and iPSC-vCMs. Directionally, similar results were also seen with Ad-PLB–transduced and Ad-S16E–transduced hvCMTs. However, Ad-PLB altered neither the global transcriptome nor I
Ca,L
, implicating a PLB-specific effect.

Conclusions—
Engineered upregulation of PLB expression in hESC/iPSC-vCMs restores a positive inotropic response to β-adrenergic stimulation. These results not only provide a better mechanistic understanding of the immaturity of hESC/iPSC-vCMs but will also lead to improved disease models and transplantable prototypes with adult-like physiological responses.