bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transrectal ultrasound based prostate volume determination: Is the frustum algorithm more accurate than planimetry?
Authors: Liu Derek , Usmani Nawaid , Sloboda Ron S. 
Published: February 2013

Purpose:To compare reconstructed volumes calculated via planimetry and frustum algorithms in the context of stepped transrectal ultrasound (US) imaging, and to estimate the reconstruction error for prostate volumes.Methods:Prostate contours for 40 permanent implant patients were delineated on magnetic resonance (MR) and transrectal US images by a radiation oncologist. Simulated images of ellipsoid and truncated cone geometrical objects were constructed to determine volume calculation accuracy. Simulation results were used to deduce the algorithm‐associated error made when calculating transrectal US prostate volumes.Results:For imaging without deliberate slice positioning, planimetry reconstruction was mostly accurate while the frustum algorithm underestimated the volume. The discrepancy was mostly due to the end slice reconstruction. For slice positioning that reflected US image acquisition, planimetry overestimated by half the superior slice volume on average while frustum underestimated by half the inferior slice volume. The estimated algorithm errors for prostate contours were 4% and −3%, respectively.Conclusions:The planimetry and frustum algorithms offer different interpretations for reconstruction and yield systematic differences in calculated volumes. Both algorithms introduce bias into transrectal US prostate volume determinations that may have clinical implications, planimetry overestimating and frustum underestimating the volume.
Activating Mutations in HER2: Neu Opportunities and Neu Challenges
Authors: Weigelt Britta , Reis-Filho Jorge S. 
Published: February 2013

Abstract
Summary: Twenty-five years after the publication of seminal studies showing that HER2 gene amplification and protein overexpression are oncogenic in breast cancer, Bose and colleagues report on the identification of activating HER2 somatic mutations that, albeit rare, may determine the response of breast cancer cells to anti-HER2 agents. These results herald a new era for the potential use of existing HER2-targeted agents for the treatment of patients with HER2-mutant breast cancer. Cancer Discov; 3(2); 145–7. ©2012 AACR.
See related article by Bose et al., p. 224
Mitotic Control of Cancer Stem Cells
Authors: Venere Monica , Miller Tyler E. , Rich Jeremy N. 
Published: February 2013

Abstract
Summary: Cancer stem cells are self-renewing, tumorigenic cells at the apex of tumor hierarchies, and postulated to be quiescent in many tumor types. This issue of Cancer Discovery highlights a study that links the presentation of kinetochores within mitosis to an essential requirement for BUB1B/BubR1, broadening our understanding of the cell-cycle machinery in cancer stem cells. Cancer Discov; 3(2); 141–4. ©2013 AACR.
See related article by Ding et al., p. 198
Elevated Blood Pressure in Pregnancy and Subsequent Chronic Disease Risk
Authors: Männistö Tuija , Mendola Pauline , Vääräsmäki Marja , Järvelin Marjo-Riitta , Hartikainen Anna-Liisa , Pouta Anneli , Suvanto Eila 
Published: February 2013

Background—
Preeclampsia, a new-onset hypertensive disorder of pregnancy, is associated with lifetime cardiovascular disease risk, but less is known about risk after other pregnancy-related hypertension.

Methods and Results—

The Northern Finland Birth Cohort 1966 included all expected births from 1 year (
N
=12 055 women). Blood pressure measurements and other prospective data were determined from prenatal care records and questionnaires for 10 314 women. Subsequent diagnoses were ascertained from Finnish registries (average follow-up, 39.4 years). Adjusted hazard ratios (HRs) with 95% confidence intervals (CIs) estimate risks in hypertensive women compared with normotensive women. Hypertension during pregnancy was associated with increased risk of subsequent cardiovascular disease and arterial hypertension. Women with chronic hypertension and superimposed preeclampsia/eclampsia had high risk for future diseases. Gestational hypertension was associated with increased risk of ischemic heart disease (HR, 1.44 [95% CI, 1.24–1.68]), myocardial infarcts (HR, 1.75 [95% CI, 1.40–2.19]), myocardial infarct death (HR, 3.00 [95% CI, 1.98–4.55]), heart failure (HR, 1.78 [95% CI, 1.43–2.21]), ischemic stroke (HR, 1.59 [95% CI, 1.24–2.04]), kidney disease (HR, 1.91 [95% CI, 1.18–3.09]), and diabetes mellitus (HR, 1.52 [95% CI, 1.21–1.89]). Isolated systolic hypertension was associated with increased risk of myocardial infarct death (HR, 2.15 [95% CI, 1.35–3.41]), heart failure (HR, 1.43 [95% CI, 1.13–1.82]), and diabetes mellitus (HR, 1.42 [95% CI, 1.13–1.78]), whereas isolated diastolic hypertension was associated with increased risk of ischemic heart disease (HR, 1.26 [95% CI, 1.05–1.50]). Results were similar in nonsmoking women aged <35 years with normal weight and no diabetes mellitus during pregnancy.

Conclusions—
Elevated blood pressure during pregnancy, regardless of type and even without known risk factors, signals high risk of later cardiovascular disease, chronic kidney disease, and diabetes mellitus. Clinical monitoring, risk factor evaluation, and early intervention could benefit women with hypertension in pregnancy.
A Glider Network Design Study for a Synoptic View of the Oceanic Mesoscale Variability
Authors: L'Hévéder Blandine , Mortier Laurent , Testor Pierre , Lekien François 
Published: February 2013

Abstract
This study presents an Observing System Simulation Experiment (OSSE) with a network of gliders in a realistic mesoscale field of eddies and filaments. The main objective is to demonstrate that the analysis skill evaluation, performed with different statistics, determines the optimal number of gliders needed to survey a “glider observatory” with a given simple topology of the glider array, in the shape of a “double comb.” Metrics, based on a spatial interpolation of the sampled data with a multiscale objective analysis method, are elaborated to evaluate the reconstruction of the three-dimensional temperature field with several glider networks, at a weekly time scale. The mesoscale structures obtained by the optimal network (front, eddies, eddies detachment) are also compared with the structures of the original simulation. This comparison demonstrates the efficiency of a glider fleet to sample a well-defined area at a given spatiotemporal scale. In this particular situation (midlatitude region, domain of 400 km × 600 km, reconstruction of weekly snapshots), the optimum network is composed of 10 gliders. A relationship is highlighted between the spatial scales of the sampled area, the physical characteristics of the studied region, the reconstruction time scale, and the optimum number of gliders. The results presented here can be applied to design an actual in situ experiment.
A Harmonic Approach for Calculating Daily Temperature Normals Constrained by Homogenized Monthly Temperature Normals
Authors: Arguez Anthony , Applequist Scott 
Published: February 2013

Abstract
NOAA released the new 1981–2010 climate normals in July 2011. These included monthly and daily normals of minimum and maximum temperature. Monthly normals were computed from monthly temperature values that were corrected for biases (i.e., homogenized) due to changes in observing practices over the course of the normals period (station moves, changes in observation time, and changes in instrumentation). Daily temperature observations, however, are not homogenized, which could lead to inconsistencies between the daily and monthly normals. This study offers a constrained harmonic technique that forces the daily temperature normals to be consistent with the monthly temperature normals. This approach replaces the cubic spline interpolation of monthly temperature normals that was used to compute earlier versions of NOAA's daily temperature normals. It effectively passes the homogenization applied at the monthly scale down to the daily scale, resulting in a smooth annual cycle devoid of day-to-day sampling variability and intermonth discontinuities.
The time course of morphological processing in a second language
Authors: Clahsen Harald , Balkhair Loay , Schutter John-Sebastian , Cunnings Ian 
Published: February 2013

We report findings from psycholinguistic experiments investigating the detailed timing of processing morphologically complex words by proficient adult second (L2) language learners of English in comparison to adult native (L1) speakers of English. The first study employed the masked priming technique to investigate - ed forms with a group of advanced Arabic-speaking learners of English. The results replicate previously found L1/L2 differences in morphological priming, even though in the present experiment an extra temporal delay was offered after the presentation of the prime words. The second study examined the timing of constraints against inflected forms inside derived words in English using the eye-movement monitoring technique and an additional acceptability judgment task with highly advanced Dutch L2 learners of English in comparison to adult L1 English controls. Whilst offline the L2 learners performed native-like, the eye-movement data showed that their online processing was not affected by the morphological constraint against regular plurals inside derived words in the same way as in native speakers. Taken together, these findings indicate that L2 learners are not just slower than native speakers in processing morphologically complex words, but that the L2 comprehension system employs real-time grammatical analysis (in this case, morphological information) less than the L1 system.
CP7_E2alf oral vaccination confers partial protection against early classical swine fever virus challenge and interferes with pathogeny-related cytokine responses
Authors: Renson Patricia , Le Dimna Mireille , Keranflech André , Cariolet Roland , Koenen Frank , Le Potier Marie-Frédérique 
Published: February 2013

AbstractThe conventional C-strain vaccine induces early protection against classical swine fever (CSF), but infected animals cannot be distinguished from vaccinated animals. The CP7_E2alf marker vaccine, a pestivirus chimera, could be a suitable substitute for C-strain vaccine to control CSF outbreaks. In this study, single oral applications of CP7_E2alf and C-strain vaccines were compared for their efficacy to induce protection against a CSF virus (CSFV) challenge with the moderately virulent Bas-Rhin isolate, in pigs as early as two days post-immunization. This work emphasizes the powerful potential of CP7_E2alf vaccine administered orally by a rapid onset of partial protection similar to that induced by the C-strain vaccine. Furthermore, our results revealed that both vaccinations attenuated the effects induced by CSFV on production of the pig major acute phase protein (PigMAP), IFN-α, IL-12, IL-10, and TGF-β1 cytokines. By this interference, several cytokines that may play a role in the pathogeny induced by moderately virulent CSFV strains were revealed. New hypotheses concerning the role of each of these cytokines in CSFV pathogeny are discussed. Our results also show that oral vaccination with either vaccine (CP7_E2alf or C-strain) enhanced CSFV–specific IgG2 production, compared to infection alone. Interestingly, despite the similar antibody profiles displayed by both vaccines post-challenge, the production of CSFV-specific IgG1 and neutralizing antibodies without challenge was lower with CP7_E2alf vaccination than with C-strain vaccination, suggesting a slight difference in the balance of adaptive immune responses between these vaccines.
Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome
Authors: Ambrosio Alinne Batista , do Nascimento Leandro Costa , Oliveira Bruno V , L Teixeira Paulo José P , Tiburcio Ricardo A , Toledo Thomazella Daniela P , Leme Adriana F P , Carazzolle Marcelo F , Vidal Ramon O , Mieczkowski Piotr , Meinhardt Lyndel W , Pereira Gonçalo A G , Cabrera Odalys G 
Published: February 2013

Abstract

Background
The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated “omics” approaches.

Results
The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization.

Conclusions
The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.
Combined ChIP-Seq and transcriptome analysis identifies AP-1/JunD as a primary regulator of oxidative stress and IL-1β synthesis in macrophages
Authors: Hull Richard P , Srivastava Prashant K , D’Souza Zelpha , Atanur Santosh S , Mechta-Grigoriou Fatima , Game Laurence , Petretto Enrico , Cook H Terence , Aitman Timothy J , Behmoaras Jacques 
Published: February 2013

Abstract

Background
The oxidative burst is one of the major antimicrobial mechanisms adopted by macrophages. The WKY rat strain is uniquely susceptible to experimentally induced macrophage-dependent crescentic glomerulonephritis (Crgn). We previously identified the AP-1 transcription factor JunD as a determinant of macrophage activation in WKY bone marrow-derived macrophages (BMDMs). JunD is over-expressed in WKY BMDMs and its silencing reduces Fc receptor-mediated oxidative burst in these cells.

Results
Here we combined Jund RNA interference with microarray analyses alongside ChIP-sequencing (ChIP-Seq) analyses in WKY BMDMs to investigate JunD-mediated control of macrophage activation in basal and lipopolysaccharide (LPS) stimulated cells. Microarray analysis following Jund silencing showed that Jund activates and represses gene expression with marked differential expression (>3 fold) for genes linked with oxidative stress and IL-1β expression. These results were complemented by comparing whole genome expression in WKY BMDMs with Jund congenic strain (WKY.LCrgn2) BMDMs which express lower levels of JunD. ChIP-Seq analyses demonstrated that the increased expression of JunD resulted in an increased number of binding events in WKY BMDMs compared to WKY.LCrgn2 BMDMs. Combined ChIP-Seq and microarray analysis revealed a set of primary JunD-targets through which JunD exerts its effect on oxidative stress and IL-1β synthesis in basal and LPS-stimulated macrophages.

Conclusions
These findings demonstrate how genetically determined levels of a transcription factor affect its binding sites in primary cells and identify JunD as a key regulator of oxidative stress and IL-1β synthesis in primary macrophages, which may play a role in susceptibility to Crgn.
2D ultrasonography and contrast enhanced ultrasound for the evaluation of cavitating mesenteric lymph node syndrome in a patient with refractory celiac disease and enteropathy T cell lymphoma
Authors: Pojoga Cristina , Ciobanu Lidia , Badea Alexandru Florin , Boţan Emil , Caraiani Cosmin , Hagiu Claudia , Băciuţ Grigore , Badea Radu 
Published: February 2013

Abstract

Background
The cavitating mesenteric lymph node syndrome (CMLNS) is a rare manifestation of celiac disease, with an estimated mortality rate of 50%. Specific infections and malignant lymphoma may complicate its clinical course and contribute to its poor prognosis. Diagnosing the underlying cause of CMLNS can be challenging. This is the first report on contrast enhanced ultrasound (CEUS) findings in enteropathy associated T-cell lymphoma (EATL) complicating CMLNS in a gluten-free compliant patient with persistent symptoms and poor outcome.

Case presentation
We present the case of a 51-year old Caucasian male patient, diagnosed with celiac disease and CMLNS. Despite his compliance to the gluten-free diet the symptoms persisted and we eventually considered the possible development of malignancy. No mucosal changes suggestive of lymphoma were identified with capsule endoscopy. Low attenuation mesenteric lymphadenopathy, without enlarged small bowel segments were seen on computed tomography. CEUS revealed arterial rim enhancement around the necrotic mesenteric lymph nodes, without venous wash-out. No malignant cells were identified on laparoscopic mesenteric lymph nodes biopsies. The patient died due to fulminant liver failure 14 months later; the histopathological examination revealed CD3/CD30-positive atypical T-cell lymphocytes in the liver, mesenteric tissue, spleen, gastric wall, kidney, lung and bone marrow samples; no malignant cells were present in the small bowel samples.

Conclusions
CEUS findings in EATL complicating CMLNS include arterial rim enhancement of the mesenteric tissue around the cavitating lymph nodes, without venous wash-out. This vascular pattern is not suggestive for neoangiogenesis, as arteriovenous shunts from malignant tissues are responsible for rapid venous wash-out of the contrast agent. CEUS failed to provide a diagnosis in this case.
Prevalence of hyperglycemia among adults with newly diagnosed HIV/AIDS in China
Authors: Shen Yinzhong , Wang Zhenyan , Liu Li , Zhang Renfang , Zheng Yufang , Lu Hongzhou 
Published: February 2013

AbstractBackgroundThe prevalence of hyperglycemia among HIV-infected persons who are not receiving antiretroviral therapy is unknown. We conducted a cross-sectional survey to estimate the prevalence of hyperglycemia among Chinese adults with newly diagnosed HIV/AIDS.MethodsTwo thousand and six newly diagnosed HIV/AIDS patients from 10 provinces and municipalities in China were selected during 2009 to 2010. After an overnight fast, serum samples were collected to measure glucose concentrations. Demographics and medical histories were recorded. Factors associated with the presence of diabetes were analysed by logistic regression.ResultsAmong the 2006 patients, 75.67% were male. Median age was 40 years (range: 18–86 years). 19.99% had hyperglycemia, 9.47% had impaired fasting glucose (IFG) and 10.52% had diabetes. The prevalences of hyperglycemia, of IFG and of diabetes were 21.54%, 10.28% and 11.27% among men and 15.16%, 6.97% and 8.20% among women, respectively. The prevalence of diabetes increased with increasing age (7.00%, 13.36% and 21.21% among patients who were 18–40, 40–60, and ≥60 years of age respectively) and with decreasing CD4 count (6.74%, 8.45%, 9.69%, and 12.66% among patients with CD4 count of ≥350, 200–350, 50–200, and < 50/mm3respectively). The prevalence of diabetes was higher among ethnic minority patients than among the Han patients (14.37% versus 9.24%). The logistic analysis showed that older age, lower CD4 count and minority ethnicity were significantly associated with an increased risk of diabetes.ConclusionsHyperglycemia is highly prevalent among Chinese adults with newly diagnosed HIV/AIDS. Older age, lower CD4 count and minority ethnicity are associated with increased risk of diabetes. All newly diagnosed HIV/AIDS individuals should be routinely evaluated for hyperglycemia.
Antioxidant supplementation for the prevention of post-endoscopic retrograde cholangiopancreatography pancreatitis: a meta-analysis of randomized controlled trials
Authors: Gu Wan-Jie , Wei Chun-Yin , Yin Rui-Xing 
Published: February 2013

Abstract

Background
Acute pancreatitis remains the most common major complication of endoscopic retrograde cholangiopancreatography (ERCP). The pathogenesis of post-ERCP acute pancreatitis may be mediated by oxygen-derived free radicals, which could be ameliorated by antioxidants. Antioxidant supplementation may potentially prevent post-ERCP pancreatitis. We performed a meta-analysis of randomized controlled trials to evaluate the effect of prophylactic antioxidant supplementation compared with control on the prevention of post-ERCP pancreatitis.

Methods
PubMed and Embase databases were searched to identify relevant trials. A standardized Excel file was used to extract data by two independent authors. Results were expressed as risk ratio (RR) with accompanying 95% confidence interval (CI). The meta-analysis was performed with the fixed-effects model or random-effects model according to heterogeneity.

Results
Eleven studies involving 3,010 patients met our inclusion criteria. Antioxidant supplementation did not significantly decrease the incidence of post-ERCP pancreatitis (RR, 0.92; 95% CI, 0.65-1.32; P = 0.665). There was also no statistical difference in the severity grades between the antioxidant group and control group.

Conclusions
Based on current evidence, antioxidant supplementation shows no beneficial effect on the incidence and the severity of post-ERCP pancreatitis; thus, there is currently a lack of evidence to support using antioxidants for the prevention of post-ERCP pancreatitis.
I3S: Intelligent spectrum sensing scheme for cognitive radio networks
Authors: Ejaz Waleed , ul Hasan Najam , Lee Seok , Kim Hyung Seok 
Published: February 2013

Abstract
Reliable spectrum sensing is one of the most crucial aspects for the successful deployment of cognitive radio (CR) technology. For CR, it is not possible to transmit on a licensed band and sense it simultaneously, therefore sensing must be interleaved with transmission. Spectrum sensing in CR is challenged by a number of uncertainties, which degrade the sensing performance and in turn require much more time to achieve the targeted sensing efficiency. Hence, the authors propose a spectrum sensing scheme which obtains reliable results with less mean detection time. First, the scheme determines a better matched filter, or a combination of energy and cyclostationary detectors based on the power and band of interest. In the combined energy and cyclostationary detector, an energy detector with a bi-threshold is used, and the cyclostationary detector is applied only if the energy of the signal lies between two thresholds. Second, sensing is performed by the selection choice resulting from the first step. To evaluate the scheme’s performance, the results are compared with those where only an energy detector, matched filter, or cyclostationary detector are performed. The performance metrics are the probability of detection, probability of false alarm, and mean detection time.