bluuebunny/crossref_metadata_2025_split huggingface dataset:
The performance of transient elastography compared to clinical acumen and routine tests – what is the incremental diagnostic value?
Authors: Dolman Grace E. , Nieboer Daan , Steyerberg Ewout W. , Harris Scott , Ferguson Amanda , Zaitoun Abed M. , Ryder Stephen D. , James Martin W. , Aithal Guruprasad P. , Guha Indra Neil 
Published: October 2012

AbstractBackground/AimsThere is substantial evidence suggesting transient elastography (TE) is a useful tool in assessing liver fibrosis. We aimed to determine whether TE has incremental diagnostic value over clinical acumen and routinely available tests.MethodsWe performed a retrospective study of 130 patients to assess the ability of hepatologists to predict severity of fibrosis using clinical acumen; clinical acumen with routine tests; and elastography in patients with chronic liver disease. The incremental diagnostic benefit was assessed using the area under the ROC curve (AUC) and the Net Reclassification Index (NRI).ResultsUsing universally available tests, including clinical acumen, the AUCs for detection of cirrhosis ranged from 0.70 to 0.80 for the four hepatologists. Elastography led to statistically non‐significant improvements in AUC statistics (range 0.83–0.89; P > 0.01). The detection of significant fibrosis using clinical acumen and routine tests was less accurate, with AUCs of 0.52–0.59. Elastography had incremental diagnostic value (AUC performance range 0.76–0.82; P < 0.01). The NRI indicated that 39–58% were correctly reclassified using elastography, especially with respect to sensitivity.ConclusionsOur study suggests that the diagnostic value of clinical acumen and routine tests is acceptable for detection of cirrhosis, but not significant fibrosis. Elastography detects significant fibrosis or cirrhosis with acceptable accuracy and offered incremental diagnostic value in detecting significant fibrosis, but not cirrhosis. These findings have implications for determining the diagnostic value of tests over and above routine clinical assessment, which will aid incorporation of novel tests into clinical algorithms.
Lack of Methylation in the Upstream Region of Human Papillomavirus Type 6 from Aerodigestive Tract Papillomas
Authors: Ure Agustín Enrique , Forslund Ola 
Published: October 2012

ABSTRACT
Methylation of the high-risk human papillomavirus type 16 (HPV16) upstream regulatory region (URR) has been described, but whether methylation is present among low-risk HPVs is unknown. The methylation status of the HPV6 URR was analyzed in papillomas from the upper aerodigestive tract of six adult patients. All CpGs in the URR were unmethylated, from both basal/intermediate and superficial cells, suggesting that methylation is not involved in the regulation of transcription from the HPV6 URR, regardless of epithelial differentiation.
Severe Acute Respiratory Syndrome Coronavirus Protein nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation
Authors: Lokugamage Kumari G. , Narayanan Krishna , Huang Cheng , Makino Shinji 
Published: October 2012

ABSTRACT
Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 1 (nsp1) binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. nsp1 inhibits the translation of cap-dependent and internal ribosome entry site (IRES)-driven mRNAs, including SARS coronavirus mRNAs, hepatitis C virus (HCV), and cricket paralysis virus (CrPV) IRES-driven mRNAs that are resistant to nsp1-induced RNA cleavage. We used an nsp1 mutant, nsp1-CD, lacking the RNA cleavage function, to delineate the mechanism of nsp1-mediated translation inhibition and identify the translation step(s) targeted by nsp1. nsp1 and nsp1-CD had identical inhibitory effects on mRNA templates that are resistant to nsp1-induced RNA cleavage, implying the validity of using nsp1-CD to dissect the translation inhibition function of nsp1. We provide evidence for a novel mode of action of nsp1. nsp1 inhibited the translation initiation step by targeting at least two separate stages: 48S initiation complex formation and the steps involved in the formation of the 80S initiation complex from the 48S complex. nsp1 had a differential, mRNA template-dependent, inhibitory effect on 48S and 80S initiation complex formation. nsp1 inhibited different steps of translation initiation on CrPV and HCV IRES, both of which initiate translation via an IRES-40S binary complex intermediate; nsp1 inhibited binary complex formation on CrPV IRES and 48S complex formation on HCV IRES. Collectively, the data revealed that nsp1 inhibited translation by exerting its effect on multiple stages of translation initiation, depending on the mechanism of initiation operating on the mRNA template.
Acid-Activated Structural Reorganization of the Rift Valley Fever Virus Gc Fusion Protein
Authors: de Boer S. M. , Kortekaas J. , Spel L. , Rottier P. J. M. , Moormann R. J. M. , Bosch B. J. 
Published: October 2012

ABSTRACT
The entry of the enveloped Rift Valley fever virus (RVFV) into its host cell is mediated by the viral glycoproteins Gn and Gc. We investigated the RVFV entry process and, in particular, its pH-dependent activation mechanism using our recently developed nonspreading-RVFV-particle system. Entry of the virus into the host cell was efficiently inhibited by lysosomotropic agents that prevent endosomal acidification and by compounds that interfere with dynamin- and clathrin-dependent endocytosis. Exposure of plasma membrane-bound virions to an acidic pH (<pH 6) equivalent to the pH of late endolysosomal compartments allowed the virus to bypass the endosomal route of infection. Acid exposure of virions in the absence of target membranes triggered the class II-like Gc fusion protein to form extremely stable oligomers that were resistant to SDS and temperature dissociation and concomitantly compromised virus infectivity. By targeted mutagenesis of conserved histidines in Gn and Gc, we demonstrated that mutation of a single histidine (H857) in Gc completely abrogated virus entry, as well as acid-induced Gc oligomerization. In conclusion, our data suggest that after endocytic uptake, RVFV traffics to the acidic late endolysosomal compartments, where histidine protonation drives the reorganization of the Gc fusion protein that leads to membrane fusion.
Interaction of the Hepatitis B Spliced Protein with Cathepsin B Promotes Hepatoma Cell Migration and Invasion
Authors: Chen Wan-Nan , Chen Jin-Yan , Jiao Bo-Yan , Lin Wan-Song , Wu Yun-Li , Liu Ling-Ling , Lin Xu 
Published: October 2012

ABSTRACT

Hepatitis B spliced protein (HBSP) is involved in the pathogenicity and/or persistence of hepatitis B virus (HBV). Chronic HBV infection is one of the most important risk factors for the development of hepatocellular carcinoma (HCC). However, whether or not HBSP contributes to the progression of HBV-associated HCC remains unknown. This study reports that overexpression of HBSP in human hepatoma cells increased cell invasion and motility. Conversely, small interfering RNA (siRNA)-mediated knockdown of HBSP expression inhibited migration and invasion. By glutathione
S
-transferase (GST) pulldown, coimmunoprecipitation, and a mammalian two-hybrid assay, HBSP was found to directly interact with cathepsin B (CTSB). Similar to HBSP knockdown, knocking down CTSB also reduced cell migration and invasion. Furthermore, the HBSP-overexpressing hepatoma cells were shown to have increased expression and activity of matrix metalloproteinase-9 (MMP-9) and urokinase-type plasminogen activator (uPA), and overexpression of HBSP significantly enhanced tumor-induced vascularization of endothelial cells. In contrast, knockdown of either HBSP or CTSB by siRNA resulted in inhibition of the two proteolytic enzymes and of the
in vitro
angiogenesis. Expression of HBSP in the hepatoma cells appeared to activate the mitogen-activated protein kinase (MAPK) and Akt signaling pathway, as evidenced by increases in phosphorylation of p38, Jun N-terminal protein kinase (JNK), extracellular signal-regulated kinase (ERK), and Akt. Taken together, these findings imply that interaction of HBSP with CTSB may promote hepatoma cell motility and invasion and highlight new molecular mechanisms for HBSP-induced HCC progression that involve the secretion and activation of proteolytic enzymes, increased tumor-induced angiogenesis, and activation of the MAPK/Akt signaling, thereby leading to the aggressiveness of hepatoma cells.
Quality improvement initiative: enhanced communication of newly identified, suspected GI malignancies with direct critical results messaging to surgical specialist
Authors: Browning Travis , Kasper Jared , Rofsky Neil M , Camp Geoffrey , Mang John , Yopp Adam , Peshock Ronald 
Published: October 2012

PurposeTo improve timely evaluation and management of newly identified, suspected, gastrointestinal (GI) malignancies discovered on radiologic imaging at a safety-net hospital through direct critical results messaging to surgical specialists.Materials and MethodsTo address delays in evaluating patients for suspected GI malignancies identified on imaging, an enhanced workflow was created--electronically routed critical results messaging to the ordering provider was supplemented with parallel messaging to the surgical oncology clinic. Messaging data obtained for 10 months pre and post intervention were compared. Using chart reviews, time intervals were recorded to assess the impact on (1) being seen by a specialist, (2) completing a diagnostic workup and (3) initiating definitive management.ResultsSignificant improvements were achieved: (1) patients seen by a specialist increased from 45.9% to 98.0% (p<0.001), with median time decreasing from 35 to 7 days (p<0.001); (2) patients completing a diagnostic workup increased from 77.1% to 93.9% (p<0.05), with median time decreasing from 44 to 18 days (p<0.001); (3) patients with initiation of definitive management increased from 72.1% to 89.8% (p<0.05), with median time decreasing from 62 to 35 days (p<0.05). Further study is needed to assess impact on fragmentation of care and financial implications.ConclusionsDirect critical results messaging from the radiologist to the surgical oncologist at a safety-net hospital significantly improves the time to complete a diagnostic workup and initiate definitive management with significantly more patients being seen by a relevant specialist.
A distributed approach to the interconnection of heterogeneous computer networks
Authors: Braden R. , Cole R. , Higginson P. , Lloyd P. 
Published: October 2012

This paper describes a distributed architecture for the flexible interconnection of heterogeneous networks with a number of mini- and micro computers, in a research environment. The interconnected networks include the DARPA Internet, which uses the DoD protocols, and the X25-based networks PSS and SERCNET.
The approach described here distributes the network access into a set of microcomputers acting as network frontends ("network access machines"), with a local area network (Cambridge Ring) as a common bus. Communication between the hosts and the network access machines uses an interprocessor communication mechanism with a standard transport-level virtualcall interface, which is described. This arrangement provides local hosts with flexible access to any of the networks, and supports a relay system which allows users on one network to access hosts and facilities on any of the other networks.
Genomic (In)stability of the Breast Tumor Microenvironment
Authors: Rummel Seth , Valente Allyson L. , Kane Jennifer L. , Shriver Craig D. , Ellsworth Rachel E. 
Published: October 2012

Abstract
The breast tumor microenvironment plays an active role in tumorigenesis. Molecular alterations have been identified in tumor-associated stroma; however, there is considerable debate as to whether the stroma is characterized by genomic instability or whether detection of chromosomal alterations reflects technological artifact rather than the true genomic content of the tumor microenvironment. Thus, breast stroma specimens from 112 women undergoing reductive mammoplasty (n = 7), prophylactic mastectomy (n = 6), or mastectomy for a breast disease (n = 99) were frozen in optimal cutting temperature medium. Allelic imbalance (AI) analysis was conducted using a panel of 52 microsatellite markers in 484 stromal specimens from 98 women, of which 92% had no detectable AI events. When compared with previously generated AI data from 77 formalin-fixed, paraffin-embedded (FFPE) stroma specimens, 42% of which harbored at least one detectable AI event, the frequency of AI in the FFPE specimens (4.62%) was significantly higher (P &lt; 0.001) than that found in frozen specimens (0.45%). This comparison of AI between FFPE and research-grade specimens suggests that past reports of AI in breast stroma reflect artifact in the archival specimens caused by formalin-fixation, paraffin-embedding and tissue storage. Furthermore, SNP data were generated from a subset of 86 stromal specimens using SNP arrays and copy number alterations were identified using Partek Genomics Suite. For 95% of the specimens, no detectable copy number alterations were found and the 11 changes that were detected were small and not shared between specimens. These data, therefore, support a model in which the tumor microenvironment is genetically stable. Mol Cancer Res; 10(12); 1526–31. ©2012 AACR.
Evaluation of Wave Forecasts Consistent with Tropical Cyclone Warning Center Wind Forecasts
Authors: Sampson Charles R. , Wittmann Paul A. , Serra Efren A. , Tolman Hendrik L. , Schauer Jessica , Marchok Timothy 
Published: October 2012

Abstract
An algorithm to generate wave fields consistent with forecasts from the official U.S. tropical cyclone forecast centers has been made available in near–real time to forecasters since summer 2007. The algorithm removes the tropical cyclone from numerical weather prediction model surface wind field forecasts, replaces the removed winds with interpolated values from surrounding grid points, and then adds a surface wind field generated from the official forecast into the background. The modified wind fields are then used as input into the WAVEWATCH III model to provide seas consistent with the official tropical cyclone forecasts. Although this product is appealing to forecasters because of its consistency and its superior tropical cyclone track forecast, there has been only anecdotal evaluation of resulting wave fields to date. This study evaluates this new algorithm for two years’ worth of Atlantic tropical cyclones and compares results with those of WAVEWATCH III run with U.S. Navy Operational Global Atmospheric Prediction System (NOGAPS) surface winds alone. Results show that the new algorithm has generally improved forecasts of maximum significant wave heights and 12-ft seas’ radii in proximity to tropical cyclones when compared with forecasts produced using only the NOGAPS surface winds.
Investigating the effect of nanoclay/carbon black on sulfur curing system of SBR/BR and NR/BR blends
Authors: Ghanbari Mohammad , Khorasani Saied Nouri , Talakesh Mohammad Mehdi , Farzadfar Alireza 
Published: October 2012

In this study, the effect of nanoclay and carbon black on the curing system of styrene-butadiene rubber (SBR)/butadiene rubber (BR) and natural rubber (NR)/BR blends were investigated. The dispersion of nanoclay and carbon black in blends was studied under the x-ray diffraction and scanning electron microscopy. Intercalated microstructure of SBR/BR blends is more stable than NR/BR blends. The presence of carbon black did not affect the dispersion state of nanoclay in NR/BR nanocomposites. By increasing the amount of nanoclay from 0 to 9 phr, the scorch time, optimum cure time, and difference between maximum and minimum torque were reduced in both the blends.
Clinical correlates and diagnostic utility of osmophobia in migraine
Authors: Wang Yen-Feng , Fuh Jong-Ling , Chen Shih-Pin , Wu Jaw-Ching , Wang Shuu-Jiun 
Published: October 2012

Background: Osmophobia is an under-investigated associated symptom in migraine. Objective: To evaluate the clinical correlates and diagnostic utility of osmophobia. Methods: Adult patients with migraine (with or without aura), probable migraine (PM), tension-type headache (TTH), and cluster headache (CH) were recruited retrospectively from our headache registration system. Migraine patients with and without osmophobia were compared. The newly proposed criteria for migraine requiring at least two of photo-, phono-, or osmophobia instead of both photo- and phonophobia were validated. Results: In total, 2883 patients were included: 1809 migraine, 792 PM, 138 TTH, and 144 CH. Osmophobia was more common in migraine (62.2%) than in PM (33.8%), TTH (14.5%), and CH (31.3%) (all p < 0.001). Migraine patients with osmophobia scored higher on the Hospital Anxiety and Depression Scale (HADS) than those without (15.6 ± 7.6 vs. 13.3 ± 7.8, p < 0.001). The concordance in headache diagnoses between ICHD-2 (International Classification of Headache Disorders, Second Edition) and the newly proposed criteria was “almost perfect” (κ = 0.886, p < 0.001). Additionally, 16.9% of ICHD-2 PM patients were reclassified as migraine using the newly proposed criteria. Conclusions: Osmophobia was prevalent in migraineurs, and was associated with higher HADS scores. The newly proposed criteria appear comparable to the ICHD-2 criteria, and may increase the diagnostic yield for Asian migraineurs, among whom photophobia was less common.
Specialists without Spirit, Sensualists without Heart: Psychotherapy as a Moral Endeavour
Authors: Dalal Farhad 
Published: October 2012

Over the last few years I have come to question the centrality and value attributed to the ideas of ‘analysis’ and ‘interpretation’ in the psychotherapies in general and the analytic traditions in particular—ideas which draw on the prestige of the natural sciences. The lecture develops the reasoning behind the shifts in my thinking and practice. With the help of the moral philosopher Raimond Gaita I will build on my prior thesis that the psyche is constituted by power-relations, to argue that it is also constituted by moral-relations. Gaita’s understanding of morality has affinities with Winnicott and Bowlby, and is also deeply congenial to the group analytic sensibility. I will show how these ways of thinking contribute towards the ethical constitution of our inner lives. I will then touch on some of the consequences of this way of thinking for the practice of psychotherapy (whatever the school or modality), in ways that do not entail a collapse into emotivism nor a rejection of the rational. I conclude that because psychotherapy is a moral endeavour, it requires the therapist to take up ‘an attitude towards a soul’ (Wittgenstein) rather than that of the detached clinician, and that therapy is better described as a very particular kind of embodied conversation rather than the scientistic conceptions of ‘analysis’ or ‘treatment’.
The diagnostic role of cardiac magnetic resonance imaging in detecting myocardial inflammation in systemic lupus erythematosus. Differentiation from viral myocarditis
Authors: Mavrogeni S , Bratis K , Markussis V , Spargias C , Papadopoulou E , Papamentzelopoulos S , Constadoulakis P , Matsoukas E , Kyrou L , Kolovou G 
Published: October 2012

Objective The objective of this paper is to evaluate the diagnostic role of cardiac magnetic resonance imaging (CMR) in detecting myocardial inflammation in systemic lupus erythematosus (SLE) and its differentiation from viral myocarditis. Patients and methods Fifty patients with suspected infective myocarditis (IM), with chest pain, dyspnoea or altered ECG, increase in troponin I and/or NT-pro BNP, with or without a history of flu-like syndrome or gastroenteritis and elevated C-reactive protein (CRP) within three to five (median four) weeks before admission, 25 active SLE patients, aged 38 ± 3 years, and 20 age-matched controls were prospectively evaluated by clinical assessment, ECG, echocardiogram and CMR. All patients underwent coronary angiography, and those with significant coronary artery disease (CAD) were excluded. CMR was performed using STIR T2-W (T2W), early T1-W (EGE) and late T1-W (LGE). Endomyocardial biopsies were performed when clinically indicated by current guidelines. Specimens were examined by immunohistological and polymerase chain reaction (PCR) analysis. Results Positive coronary angiography for CAD excluded 10/50 suspected IM and 5/25 active SLE. Positive clinical criteria for acute myocarditis were fulfilled by 28/40 suspected IM and only 5/20 active SLE. CMR was positive for myocarditis in 35/40 suspected IM and in 16/20 active SLE. Endomyocardial biopsy (EMB), performed in 25/35 suspected IM and 7/16 active SLE with positive CMR, showed positive immunohistology in 18/25 suspected IM and 3/7 active SLE. Infectious genomes were identified in 24/25 suspected IM and 1/7 active SLE. Conclusions CMR-positive IM patients were more symptomatic than active SLE. More than half of CMR-positive patients also had positive EMB. PCR was positive in almost all IM, but unusual in SLE. Due to the subclinical presentation of SLE myocarditis and the limitations of EMB, CMR presents the best alternative for the diagnosis of SLE myocarditis.
Four-Item Fatigue Screen
Authors: Davis Mellar P. , Khoshknabi Dilara , Walsh Declan , Lagman Ruth , Karafa Matthew T. , Aktas Aynur , Platt Alexandra 
Published: October 2012

Introduction: To develop a shorter and less burdensome cancer-related fatigue (CRF) questionnaire, the Four-Item Fatigue Scale (FIFS) was tested for validity against the Brief Fatigue Index (BFI). Methods: On day 1, patients with cancer completed the BFI and FIFS in a random order and the reverse on day 7. Sixty-five patients were needed for an 80% power and a Spearman correlation of .7 or greater. The FIFS was compared with the BFI in fatigue severity and changes in fatigue over time. Bonferroni corrections were made for multiple comparisons with International Classification of Diseases, Tenth Revision ( ICD-10) fatigue criteria. Results: Seventy-nine patients were enrolled, 65 patients completed both surveys. Spearman correlation between FIFS and BFI for day 1 was 0.69 (95% confidence interval [CI] 0.50-0.87) and 0.73 (95% CI 0.56-0.90) 1 week later. Fatigue severity did not predict survival with either questionnaire. Brief Fatigue Index severity correlated with ICD-10 items 1, 3, 7, and 10B. Regression analysis showed that on day 7 BFI correlated with ICD-10 items 1, 7, and 10. When the model was adjusted for day 1, only the ICD-10 item 5 correlated well in BFI over 1 week. The ICD-10 items 7 and 10 significantly correlated with day 1 FIFS fatigue changes over 7 days after adjustment for FIFS baseline score. Conclusions: Four-Item Fatigue Scale has concurrent validity for fatigue using the BFI. The FIFS and BFI correlated modestly over time. Certain ICD-10 items correlated with CRF severity depending on the questionnaire.