bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subtype‐independent near full‐length HIV‐1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management
Authors: Grossmann Sebastian , Nowak Piotr , Neogi Ujjwal 
Published: June 2015

IntroductionHIV‐1 near full‐length genome (HIV‐NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large‐scale population‐based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high‐risk population groups. Thus, the main objective of this study was to develop a simplified subtype‐independent, cost‐ and labour‐efficient HIV‐NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies.MethodsPlasma samples (n=30) were obtained from HIV‐1B (n=10), HIV‐1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV‐NFLG. GRT was validated against ViroSeq™ HIV‐1 Genotyping System.ResultsAfter excluding four plasma samples with low‐quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV‐NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples.ConclusionsOur high efficiency subtype‐independent HIV‐NFLG is a simple and promising approach to be used in large‐scale molecular epidemiological studies. It will facilitate the understanding of the HIV‐1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.
Pheochromocytoma Diagnosis After an Abnormal Stress Test: Case Report and Review of the Literature
Authors: Treyger German , Silver Shawn A. , Sakharova Alla A. 
Published: June 2015

Abstract
Pheochromocytoma is a rare adrenal gland tumor that is often difficult for physicians to diagnose because of its general, nonspecific complaints. Diagnosis is particularly difficult in patients with neurofibromatosis 1, because pheochromocytoma in these patients will mimic other cardiovascular abnormalities. The authors report the case of a 60-year-old woman with an extensive history of hyperlipidemia, malignant hypertension, coronary artery disease, and neurofibromatosis 1 who was referred for an elective cardiac catheterization as a result of an abnormal stress test. The patient returned to the hospital 3 days after the procedure complaining of increased angina and palpitations. While hospitalized, she developed severe episodic hypertension. A computed tomographic scan revealed bilateral adrenal masses. Findings of biochemical and imaging evaluation confirmed the diagnosis of bilateral pheochromocytoma. Early screening of pheochromocytomas in high-risk populations is essential for prompt diagnosis and successful management.
Low‐Energy Ultrasound Treatment Improves Regional Tumor Vessel Infarction by Retargeted Tissue Factor
Authors: Brand Caroline , Dencks Stefanie , Schmitz Georg , Mühlmeister Mareike , Stypmann Jörg , Ross Rebecca , Hintelmann Heike , Schliemann Christoph , Müller-Tidow Carsten , Mesters Rolf M. , Berdel Wolfgang E. , Schwöppe Christian 
Published: June 2015

ObjectivesTo enhance the regional antitumor activity of the vascular‐targeting agent truncated tissue factor (tTF)‐NGR by combining the therapy with low‐energy ultrasound (US) treatment.MethodsFor the in vitro US exposure of human umbilical vein endothelial cells (HUVECs), cells were put in the focus of a US transducer. For analysis of the US‐induced phosphatidylserine (PS) surface concentration on HUVECs, flow cytometry was used. To demonstrate the differences in the procoagulatory efficacy of TF‐derivative tTF‐NGR on binding to HUVECs with a low versus high surface concentration of PS, we performed factor X activation assays. For low‐energy US pretreatment, HT1080 fibrosarcoma xenotransplant‐bearing nude mice were treated by tumor‐regional US‐mediated stimulation (ie, destruction) of microbubbles. The therapy cohorts received the tumor vessel‐infarcting tTF‐NGR protein with or without US pretreatment (5 minutes after US stimulation via intraperitoneal injection on 3 consecutive days).ResultsCombination therapy experiments with xenotransplant‐bearing nude mice significantly increased the antitumor activity of tTF‐NGR by regional low‐energy US destruction of vascular microbubbles in tumor vessels shortly before application of tTF‐NGR (P < .05). Mechanistic studies proved the upregulation of anionic PS on the outer leaflet of the lipid bilayer of endothelial cell membranes by low‐energy US and a consecutive higher potential of these preapoptotic endothelial cells to activate coagulation via tTF‐NGR and coagulation factor X as being a basis for this synergistic activity.ConclusionsCombining retargeted tTF to tumor vessels with proapoptotic stimuli for the tumor vascular endothelium increases the antitumor effects of tumor vascular infarction. Ultrasound treatment may thus be useful in this respect for regional tumor therapy.
Left Ventricular Ejection Time Derived From the Common Carotid Artery Doppler Waveform
Authors: Polak Joseph F. , Alessi-Chinetti Jean M. , Estes James M. , Patel Ayan R. 
Published: June 2015

ObjectivesLeft ventricular ejection time (LVET) is measured from blood pressure tracings as the interval from end diastole to the dicrotic notch and shows associations with left ventricular ejection fraction (LVEF) and heart failure. LVET can be measured on common carotid artery Doppler waveforms. We therefore studied the possible associations of common carotid artery LVET with LVEF measured by echocardiography and heart failure.MethodsWe performed a retrospective study of 110 patients who had transthoracic echocardiography and carotid Doppler evaluations within 1 day of each other. LVEF was determined by the biplane modified Simpson method. LVET was measured from left common carotid artery Doppler tracings. Linear regression was used to evaluate associations between LVET and LVEF. We also used logistic regression with LVEF of less than 40% as a cut point for heart failure to generate a receiver operating characteristic curve, estimate the area under the curve, and calculate sensitivity and specificity.ResultsLVET was associated with LVEF (P < .0001). The area under the curve of LVET for heart failure was 0.81 (95% confidence interval [CI], 0.72–0.87), and the sensitivity and specificity were 76.9% (95% CI, 65.4%–88.4%) and 65.5% (95% CI, 53.4%–77.8%), respectively, for LVET of 321 milliseconds.ConclusionsLVET measured on common carotid artery Doppler tracings decreases with LVEF and is strongly associated with prevalent heart failure. Based on what is known of blood pressure–measured LVET, common carotid artery Doppler waveform–derived LVET could be used to serially monitor cardiac function.
Integrating Sonography Training Into Undergraduate Medical Education
Authors: Day James , Davis Joshua , Riesenberg Lee Ann , Heil Daniel , Berg Katherine , Davis Robyn , Berg Dale 
Published: June 2015

ObjectivesSonography is a crucial and versatile tool within the field of medicine. Recent advancements in technology have led to increased use of point‐of‐care sonography. We designed a survey to assess prior point‐of‐care sonography training among incoming interns at an academic teaching hospital.MethodsIn 2012 and 2013, we surveyed incoming interns (n = 154 and 145, respectively) regarding point‐of‐care sonography training received during medical school. The survey questions included formal didactic sessions, bedside instruction, and the use of simulation technology.ResultsOne‐fourth (26.3% in 2012 and 23.4% in 2013) of responding interns reported having never done an ultrasound scan at the bedside. In 2012 and 2013, 55.0% and 55.6% of respondents reported never having done an ultrasound scan in a simulation center, respectively. Interns agreed that sonography education should be provided during medical school. On average, interns disagreed with the statement that sonography should be taught in residency only. There was no significant difference in the sex or general previous experience with sonography across both intern classes.ConclusionsPoint‐of‐care sonography is inconsistently taught in medical school. The interns in our study also thought that sonography education should begin in medical school, and sonography should be taught by using simulation and at the bedside.
Evaluating the Optimal Definition of Abnormal First‐Trimester Uterine Artery Doppler Parameters to Predict Adverse Pregnancy Outcomes
Authors: Carter Ebony B. , Goetzinger Katherine , Tuuli Methodius G. , Odibo Linda , Cahill Alison G. , Macones George A. , Odibo Anthony O. 
Published: June 2015

ObjectivesTo investigate the optimal definition of abnormal first‐trimester uterine artery Doppler parameters associated with adverse pregnancy outcomes.MethodsA prospective cohort of women with singleton gestations between 11 and 14 weeks consented to uterine artery Doppler measurements. Doppler parameters were measured bilaterally, and mean pulsatility index (PI) and resistive index (RI) values were calculated. The presence of notching was also determined. Each parameter was evaluated for prediction of preeclampsia, early preeclampsia (<34 weeks), preterm birth (<37 weeks), early preterm birth (<34 weeks), and small for gestational age (SGA; birth weight <10th percentile). Descriptive statistics evaluated the association between abnormal Doppler indices and outcomes. A receiver operating characteristic (ROC) analysis was used to define the best cutoff points for mean PI and RI. The sensitivity, specificity, positive predictive value, and negative predictive value (NPV) were calculated for bilateral notching and mean PI and RI percentiles.ResultsOf 1192 patients with complete outcome data, preeclampsia was seen in 8.4%, early preeclampsia in 1.8%, preterm birth in 12.9%, early preterm birth in 5.6%, and SGA in 8.5%. A mean PI above the 75th percentile (>1.91) was the best index for predicting early preeclampsia (sensitivity, 45.0%; specificity, 75.5%; NPV, 98.7%; ROC area, 0.65). A mean PI above the 75th percentile was also the best index for predictive early preterm birth (sensitivity, 40.0%; specificity, 76.0%; NPV, 95.5%; ROC area, 0.65). None of the parameters were significant for predicting SGA.ConclusionsA mean uterine PI above the 75th percentile is the most discriminative abnormal uterine artery Doppler parameter for predicting both early preeclampsia and early preterm birth.
Sonography of the Optic Nerve Sheath Diameter for Detection of Raised Intracranial Pressure Compared to Computed Tomography
Authors: Ohle Robert , McIsaac Sarah M. , Woo Michael Y. , Perry Jeffrey J. 
Published: June 2015

ObjectivesThe diagnosis of raised intracranial pressure (ICP) is important in many critically ill patients. The optic nerve sheath is contiguous with the subarachnoid space; thus, an increase in ICP results in a corresponding increase in the optic nerve sheath diameter. The objective of this study was to assess the diagnostic accuracy of sonography of the optic nerve sheath diameter compared to computed tomography (CT) for predicting raised ICP.MethodsWe searched PubMed, EMBASE, and the Cochrane database from 1986 to August 2013 and performed hand searches. Two independent reviewers extracted data. Study quality was assessed by using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool. We calculated κ agreement for study selection and evaluated clinical and quality homogeneity before the meta‐analysis.ResultsFrom 1214 studies, we selected 45 for full review. Twelve studies with 478 participants were included (κ = 0.89). Ocular sonography yielded sensitivity of 95.6% (95% confidence interval [CI], 87.7%–98.5%), specificity of 92.3% (95% CI, 77.9%–98.4%), a positive likelihood ratio of 12.5 (95% CI, 4.16–37.5), and a negative likelihood ratio of 0.05 (95% CI, 0.02–0.14). Average quality according to the QUADAS tool was 7.4 of 11. There was moderate to high heterogeneity based on the prediction ellipse area and variance logit of sensitivity (2.1754) and specificity (2.6720).ConclusionsOcular sonography shows good diagnostic test accuracy for detecting raised ICP compared to CT: specifically, high sensitivity for ruling out raised ICP in a low‐risk group and high specificity for ruling in raised ICP in a high‐risk group. This noninvasive point‐of‐care method could lead to rapid interventions for raised ICP, assist centers without CT, and monitor patients during transport or as part of a protocol to reduce CT use.
Imaging three‐dimensional crustal conductivity structures reflecting continental flood basalt effects hidden beneath thick intracratonic sedimentary basin
Authors: Padilha Antonio L. , Vitorello Ícaro , Antunes Cassio E. , Pádua Marcelo B. 
Published: June 2015

AbstractA large‐scale array of long‐period magnetic data and a deep‐probing magnetotelluric profile were recorded in the intracratonic Paraná sedimentary basin in central eastern South America, which presents a thick and extensive sedimentary‐magmatic sequence that allows its basement to be investigated only by indirect methods. Integration of the results from both methods showed that the crust beneath the basin presents several quasi‐linear highly conductive channeled zones with limited lateral extent, in coincidence with some of the main tectonic structures recognized at the surface, and a moderate but pervasive lithosphere conductivity enhancement beneath its central part. Upward movement of CO2‐bearing volatiles and magmas precipitating highly conducting mineral phases along discrete subvertical fault zones that served as feeder conduits for Early Cretaceous voluminous continental flood basalts was a likely process responsible for the localized conductivity enhancements. Correlation between some of the linear conductive zones and elongated magnetic anomalies and between the maximum depth occurrence of most of these conductive anomalies and the Curie depth at which crustal rocks lose their magnetism gives strong support to interconnected iron oxides (especially magnetite) and iron sulfides (such as pyrrhotite) as the main conductive sources. The moderate bulk conductivity increase in the crust and upper mantle beneath the central part of the basin is unexpected for a postulated cratonic basement and is tentatively associated with impregnation of the lithosphere by conducting minerals related either to widespread tectonic events in the Ordovician or Late Precambrian or to dispersed magmatic residues of an Early Cretaceous magma differentiation contaminating the entire lithosphere.
A chemistry‐climate model study of past changes in the Brewer‐Dobson circulation
Authors: Oberländer‐Hayn Sophie , Meul Stefanie , Langematz Ulrike , Abalichin Janna , Haenel Florian 
Published: June 2015

AbstractModel simulations indicate an acceleration of the Brewer‐Dobson circulation (BDC) in the past with a direct impact on the exchange of air masses between the troposphere and the stratosphere. However, most observational data sets do not confirm the model results. Bönisch et al. (2011) and Ray et al. (2010) indicate a strengthening of the BDC in its shallow branch and a weakening in its deep branch. In contrast, balloon‐borne measurements and Michelson Interferometer for Passive Atmospheric Sounding satellite observations show no significant acceleration of the BDC at Northern Hemisphere (NH) midlatitudes. In our study, the change of the BDC in the recent past is analyzed from simulations with the chemistry‐climate model ECHAM/MESSy Atmospheric Chemistry. As the sign of change considerably depends on the underlying forcings, namely, changes in concentrations of greenhouse gases (GHGs) and ozone‐depleting substances (ODSs), as well as their interactions, we separate their contributions by using sensitivity simulations. The changes in tropical upward mass flux indicate a strengthening of the BDC between 1960 and 2000 in NH winter season in the lower and a weakening in the upper stratosphere with a change in sign at 10 hPa. While the lower stratospheric increase of about 2%/decade is caused by equal contributions from rising GHGs and ODSs, rising ODS concentrations counteract the GHG effect in the middle and upper stratosphere with a total decrease of about 0.5%/decade. Changes in mean age of air show a decrease of about 0.13 yr/decade in the lower and middle stratosphere and a slight increase in the Arctic upper stratosphere and lower mesosphere, which is induced by interactions between the forcings.
Fault Zone Guided Wave generation on the locked, late interseismic Alpine Fault, New Zealand
Authors: Eccles J. D. , Gulley A. K. , Malin P. E. , Boese C. M. , Townend J. , Sutherland R. 
Published: June 2015

AbstractFault Zone Guided Waves (FZGWs) have been observed for the first time within New Zealand's transpressional continental plate boundary, the Alpine Fault, which is late in its typical seismic cycle. Ongoing study of these phases provides the opportunity to monitor interseismic conditions in the fault zone. Distinctive dispersive seismic codas (~7–35 Hz) have been recorded on shallow borehole seismometers installed within 20 m of the principal slip zone. Near the central Alpine Fault, known for low background seismicity, FZGW‐generating microseismic events are located beyond the catchment‐scale partitioning of the fault indicating lateral connectivity of the low‐velocity zone immediately below the near‐surface segmentation. Initial modeling of the low‐velocity zone indicates a waveguide width of 60–200 m with a 10–40% reduction in S wave velocity, similar to that inferred for the fault core of other mature plate boundary faults such as the San Andreas and North Anatolian Faults.
Comparison of wave propagation through ice covers in calm and storm conditions
Authors: Li Jingkai , Kohout Alison L. , Shen Hayley H. 
Published: June 2015

AbstractMotivated by a dramatic reduction in Arctic sea ice cover, interest in the field of wave‐ice interaction has accelerated over the past few years. Recent observations have identified that large waves (>3 m) have a linear attenuation rate, rather than the previously assumed exponential rate that is found for small waves. This suggests that waves penetrate further into the ice cover than previously expected. To explore this further we tested two exponentially decaying wave models. Contributions from nonlinear and wind generation source terms enabled both models to reproduce the observed regime shift. Essentially, the accumulation of nonlinear and wind energy contributions to long (and thus higher amplitude) waves can offset the ice damping, thus reducing the apparent attenuation. This study highlights the relevance of considering frequency dependence when analyzing wave attenuation in sea ice field data.
High‐latitude intermittent ionospheric scintillations: Exploring the Castaing distribution
Authors: Mezaoui H. , Hamza A. M. , Jayachandran P. T. 
Published: June 2015

AbstractWe present a multiscale analysis of the received amplitude fluctuations of the L1 GPS signal. The analysis consists of constructing a differential amplitude signal by taking the difference between the signal at time t and the signal at time t + τ, where τ represents a time lag. The probability density functions of the measured differential amplitude fluctuations are computed and fitted with Castaing distributions. The fourth normalized moment of the distributions is used to investigate the intermittent nature of the signal. The results reveal direct evidence that the intermittent aspect of the investigated scintillation events is more pronounced at small differential time lags than at long ones.
Impact of the perturbation zonal velocity variation on the spatio/temporal occurrence pattern of L band scintillation—A case study
Authors: Bagiya Mala S. , Sridharan R. , Sunda Surendra , Jose Lijo , Pant Tarun K , Choudhary Rajkumar 
Published: June 2015

AbstractThe earlier evolved method for the forecast of the spatiotemporal variation of L band scintillation based on the expected variation of the perturbations, under favorable ionospheric/thermospheric conditions, has been refined by duly accounting for the local time variation of the zonal velocity of the perturbations. The unique combination of the two geostationary satellites (GSAT‐8 and GSAT‐10) over the Indian zone has been used to estimate the typical local time dependence of the perturbation velocities by closely following identifiable features in the scintillation pattern. The measured velocities, that registered a steady decrease with the progression of night, had been shown to significantly alter the forecast pattern of the scintillations with respect to longitude and local time. The significant improvement in the forecast pattern has been demonstrated through a case study putting the forecast method on a firmer footing.
Solar activity dependency of multiday oscillations in the nighttime thermospheric winds observed by Fabry‐Perot interferometer
Authors: Liu Xiao , Xu Jiyao , Zhang Shun‐Rong , Zhou Qihou , Yuan Wei 
Published: June 2015

AbstractAn 11 year (1989–1995 and 2010–2013) nighttime thermospheric wind (at ~250 km) data set from Fabry‐Perot interferometer at Millstone Hill (42.6°N, 71.5°W) is used to investigate multiday oscillations (6–30 days) in the thermospheric nighttime winds. Dependencies of multiday oscillations on solar radiation (F10.7), solar wind speed (SW), and geomagnetic activity (Kp) are determined. We found that (1) there exist prominent quasi 27 day oscillations in the thermospheric zonal (meridional) wind, which appears to be more correlated to the same periodic oscillations in Kp and SW than in F10.7 during the solar maximum (solar declining phase and minimum); (2) quasi 13.5 day oscillations in the zonal wind occur during the solar maximum and increasing phases and are also more correlated to the same periodic oscillations in Kp and SW; and (3) in general, the correlations of the multiday oscillations in the thermospheric winds are more correlated with Kp and SW than F10.7. Our analyses also show that the zonal wind is more sensitive to SW than the meridional wind. We further find that (4) for high F10.7, the premidnight zonal wind is more westward toward increasing SW; for low F10.7, the postmidnight zonal wind is also more westward toward increasing SW; and (5) meridional winds tend to be more southward with increasing SW for medium and high F10.7.
Charged nanoparticles produced by splashing of raindrops
Authors: Kamra A. K. , Gautam A. S. , Siingh Devendraa 
Published: June 2015

AbstractThe mobility distribution of ions generated by splashing of raindrops is investigated. Our observations show four maxima in the mobility distribution in the small, intermediate, light large, and heavy large ion size ranges. Ion concentration of all categories increases as the rain intensity increases to ~ 50–60 mm h−1 and then tends to level off for higher rain intensities. Negative ion concentration is always more than that of positive ions. However, positive small ions of mobility ≥ 2–3 cm2 V−1 s−1 which are also generated during splashing are more numerous than negative ions. Our observations show that the mechanism responsible for the generation of intermediate ions is more efficient than that for the generation of heavy large ions during periods of high rain intensity. Relative roles of Lenard and Blanchard effects are suggested in generating excess of negative intermediate ions in the initial stages and excess of positive cluster ions, in the later stages of a rain shower, respectively.