bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Networks of Amino Acid Covariances Are Common among Viruses
Authors: Donlin Maureen J. , Szeto Brandon , Gohara David W. , Aurora Rajeev , Tavis John E. 
Published: January 2012

ABSTRACT

Coordinated variation among positions in amino acid sequence alignments can reveal genetic dependencies at noncontiguous positions, but methods to assess these interactions are incompletely developed. Previously, we found genome-wide networks of covarying residue positions in the hepatitis C virus genome (R. Aurora, M. J. Donlin, N. A. Cannon, and J. E. Tavis, J. Clin. Invest.
119:
225–236, 2009). Here, we asked whether such networks are present in a diverse set of viruses and, if so, what they may imply about viral biology. Viral sequences were obtained for 16 viruses in 13 species from 9 families. The entire viral coding potential for each virus was aligned, all possible amino acid covariances were identified using the observed-minus-expected-squared algorithm at a false-discovery rate of ≤1%, and networks of covariances were assessed using standard methods. Covariances that spanned the viral coding potential were common in all viruses. In all cases, the covariances formed a single network that contained essentially all of the covariances. The hepatitis C virus networks had hub-and-spoke topologies, but all other networks had random topologies with an unusually large number of highly connected nodes. These results indicate that genome-wide networks of genetic associations and the coordinated evolution they imply are very common in viral genomes, that the networks rarely have the hub-and-spoke topology that dominates other biological networks, and that network topologies can vary substantially even within a given viral group. Five examples with hepatitis B virus and poliovirus are presented to illustrate how covariance network analysis can lead to inferences about viral biology.
Acupuncture in practice: mapping the providers, the patients and the settings in a national cross-sectional survey
Authors: Hopton A K , Curnoe S , Kanaan M , MacPherson H 
Published: January 2012

BackgroundThere is relatively limited knowledge about the practitioners who provide acupuncture treatment within the UK, what conditions patients consult for and the treatment provided.ObjectivesTo characterise the conditions treated and by whom, to examine characteristics of the treatment and to explore trends over time.MethodA cross-sectional survey of the UK acupuncture practitioners was conducted; 800 practitioners were selected by computer-generated randomisation sequences from the four major UK-based professional associations. Data collected on the practitioners included demographic details, association membership, statutorily regulated status, practice setting, style of acupuncture, diagnostic methods and needle response sought. Practitioners recorded details of their 10 most recent patients, including demographic details, primary reason for consulting and lifestyle advice provided.Results330 practitioners responded comprising doctors (29%) physiotherapists (29%), nurses (15%) and independent acupuncturists (27%): 62% were women with median age of 48 years. The majority (68%) practiced in independent settings and 42% practiced within the National Health Service. Patients most commonly consulted for low back, neck, shoulder and knee pain, as well as headaches and migraine. Treatment for infertility by independent acupuncturists was found to have increased fivefold in 10 years.ConclusionAcupuncture provides a substantial contribution to the healthcare of the UK, with an estimated 4 million sessions provided annually. The primary complaints for which patients consult reflect the growing evidence base on acupuncture for these conditions. These data provide a basis for decision-making regarding policy and practice.
Risk and protective factors associated with gang affiliation among high-risk youth: a public health approach
Authors: McDaniel Dawn Delfin 
Published: January 2012

BackgroundGang violence accounted for 20% of homicides in large cities from 2002 to 2006. Preventing gang affiliation (ie, youth who either desire or have gang membership) might reduce subsequent gang activity. Previous research has focused on identifying risk factors for gang affiliation; however, little information is available on protective factors.AimTo identify risk and protective factors to provide more direction for gang violence prevention strategies.MethodsThe author analysed cross-sectional survey data from 4131 youths in grades 7, 9, 11 and 12. Data were collected in 2004 from students in a high-risk, urban public school district. Regression analyses were conducted to assess the association between gang affiliation and alcohol and drug use, delinquency, depressed mood, suicidal ideation, peer victimisation, parental monitoring and positive reinforcement, adult, family and peer support, coping skills, and school connectedness. Analyses were controlled for sex, race/ethnicity and age.ResultsAn estimated 7% of youths were gang affiliated. Adjusting for all factors, gang affiliation was positively associated with engaging in any delinquent behaviours (prevalence OR: 2.07; 95% CI 1.18 to 3.64), frequent alcohol use (OR: 2.62; 95% CI 1.85 to 3.72) and frequent drug use (OR: 1.95; 95% CI 1.15 to 3.29). Gang affiliation was negatively associated with moderate levels of parental monitoring (OR: 0.67; 95% CI 0.54 to 0.85) and coping skills (OR: 0.54; 95% CI 0.42 to 0.71).ConclusionsThe findings suggest the potential benefit of increasing parental monitoring and coping skills and reducing delinquency, alcohol use and drug use to prevent gang affiliation.
212Pb-Radioimmunotherapy Induces G2 Cell-Cycle Arrest and Delays DNA Damage Repair in Tumor Xenografts in a Model for Disseminated Intraperitoneal Disease
Authors: Yong Kwon Joong , Milenic Diane E. , Baidoo Kwamena E. , Brechbiel Martin W. 
Published: January 2012

Abstract
In preclinical studies, targeted radioimmunotherapy using 212Pb-TCMC-trastuzumab as an in vivo generator of the high-energy α-particle emitting radionuclide 212Bi is proving an efficacious modality for the treatment of disseminated peritoneal cancers. To elucidate mechanisms associated with this therapy, mice bearing human colon cancer LS-174T intraperitoneal xenografts were treated with 212Pb-TCMC-trastuzumab and compared with the nonspecific control 212Pb-TCMC-HuIgG, unlabeled trastuzumab, and HuIgG, as well as untreated controls. 212Pb-TCMC-trastuzumab treatment induced significantly more apoptosis and DNA double-strand breaks (DSB) at 24 hours. Rad51 protein expression was downregulated, indicating delayed DNA double-strand damage repair compared with 212Pb-TCMC-HuIgG, the nonspecific control. 212Pb-TCMC-trastuzumab treatment also caused G2-M arrest, depression of the S phase fraction, and depressed DNA synthesis that persisted beyond 120 hours. In contrast, the effects produced by 212Pb-TCMC-HuIgG seemed to rebound by 120 hours. In addition, 212Pb-TCMC-trastuzumab treatment delayed open chromatin structure and expression of p21 until 72 hours, suggesting a correlation between induction of p21 protein and modification in chromatin structure of p21 in response to 212Pb-TCMC-trastuzumab treatment. Taken together, increased DNA DSBs, impaired DNA damage repair, persistent G2-M arrest, and chromatin remodeling were associated with 212Pb-TCMC-trastuzumab treatment and may explain its increased cell killing efficacy in the LS-174T intraperitoneal xenograft model for disseminated intraperitoneal disease. Mol Cancer Ther; 11(3); 639–48. ©2012 AACR.
Exemestane for Breast Cancer Prevention: A Critical Shift?
Authors: DeCensi Andrea , Dunn Barbara K. , Puntoni Matteo , Gennari Alessandra , Ford Leslie G. 
Published: January 2012

Abstract
The Mammary Prevention 3 (MAP.3) placebo-controlled randomized trial in 4,560 high-risk postmenopausal women showed a 65% reduction in invasive breast cancer with the use of exemestane at 35 months median follow-up. Few differences in adverse events were observed between the arms, suggesting a promising risk:benefit balance with exemestane for use in chemoprevention. Yet, the MAP.3 design and implementation raise concerns regarding limited data maturity and not prospectively including key bone-related and other toxicities as study end points. Exemestane for prevention is juxtaposed against selective estrogen receptor modulators and the other aromatase inhibitors. Additional issues for prevention, including the influence of obesity, alternative dosing, and biomarker use in phase III trials, are addressed.
Significance: The recently completed MAP.3 trial of exemestane for breast cancer prevention offers a potential new standard for pharmaceutical risk reduction in high-risk postmenopausal women. In addition to describing key findings from the publication of MAP.3 and related trials, our review undertakes a detailed analysis of the strengths and weaknesses of MAP.3 as well as the implications for future prevention research. Cancer Discovery; 2(1); 25–40. ©2012 AACR.
Correction of Excessive Precipitation over Steep and High Mountains in a GCM
Authors: Chao Winston C. 
Published: January 2012

Abstract
Excessive precipitation over steep and high mountains (EPSM) is a well-known problem in GCMs and mesoscale models. This problem impairs simulation and data assimilation products. Among the possible causes investigated in this study, it was found that the most important one, by far, is a missing upward transport of heat out of the boundary layer due to the vertical circulations forced by the daytime upslope winds, which are forced by heated boundary layer on the subgrid-scale slopes. These upslope winds are associated with large subgrid-scale topographic variation, which is found over steep and high mountains. Without such subgrid-scale heat ventilation, the resolvable-scale upslope flow in the boundary layer generated by surface sensible heat flux along the mountain slopes is excessive. Such an excessive resolvable-scale upslope flow combined with the high moisture content in the boundary layer results in excessive moisture transport toward mountaintops, which in turn gives rise to EPSM. Other possible causes investigated include 1) a poorly designed horizontal moisture flux in the terrain-following coordinates, 2) the conditions for cumulus convection being too easily satisfied at mountaintops, 3) conditional instability of the computational kind, and 4) the absence of blocked flow drag. They are all minor or inconsequential.
The ventilation effects of the subgrid-scale heated-slope-induced vertical circulation (SHVC) have been parameterized by removing heat from the boundary layer and depositing it in the layers higher up when topographic variance exceeds a critical value. Test results using the NASA Goddard Earth Observing System GCM version 5 (GEOS-5) have shown that the EPSM problem is largely solved.
The Structure of Low-Altitude Clouds over the Southern Ocean as Seen by CloudSat
Authors: Huang Yi , Siems Steven T. , Manton Michael J. , Hande Luke B. , Haynes John M. 
Published: January 2012

Abstract
A climatology of the structure of the low-altitude cloud field (tops below 4 km) over the Southern Ocean (40°–65°S) in the vicinity of Australia (100°–160°E) has been constructed with CloudSat products for liquid water and ice water clouds. Averaging over longitude and time, CloudSat produces a roughly uniform cloud field between heights of approximately 750 and 2250 m across the extent of the domain for both winter and summer. This cloud field makes a transition from consisting primarily of liquid water at the lower latitudes to ice water at the higher latitudes. This transition is primarily driven by the gradient in the temperature, which is commonly between 0° and −20°C, rather than by direct physical observation.
The uniform lower boundary is a consequence of the CloudSat cloud detection algorithm being unable to reliably separate radar returns because of the bright surface versus returns due to clouds, in the lowest four range bins above the surface. This is potentially very problematic over the Southern Ocean where the depth of the boundary layer has been observed to be as shallow as 500 m. Cloud fields inferred from upper-air soundings at Macquarie Island (54.62°S, 158.85°E) similarly suggest that the peak frequency lies between 260 and 500 m for both summer and winter. No immediate explanation is available for the uniformity of the cloud-top boundary. This lack of a strong seasonal cycle is, perhaps, remarkable given the large seasonal cycles in both the shortwave (SW) radiative forcing experienced and the cloud condensation nuclei (CCN) concentration over the Southern Ocean.
Forecast Skill of the South American Monsoon System
Authors: Jones Charles , Carvalho Leila M. V. , Liebmann Brant 
Published: January 2012

Abstract
The South American monsoon system (SAMS) is the most important climatic feature in South America and is characterized by pronounced seasonality in precipitation. This study uses the National Centers for Environmental Prediction Climate Forecast System, reforecasts version 2 (CFSRv2), to investigate the skill of probabilistic forecasts of onset and demise dates, duration, and amplitude of SAMS during 1982–2009. A simple index based on the empirical orthogonal function of precipitation anomalies is employed to characterize onsets, demises, durations, and amplitudes of SAMS. The CFSv2 model has useful skill to forecast seasonal changes in SAMS. Probabilistic forecasts of onset and demise dates have 16.5% and 43.3% improvements, respectively, over climatological forecasts. Verification of hindcasts of durations and amplitudes of SAMS shows relatively small biases and root-mean-square errors.
Evaluation of Global Satellite Rainfall Products over Continental Europe
Authors: Stampoulis Dimitrios , Anagnostou Emmanouil N. 
Published: January 2012

Abstract
An extensive evaluation of two global-scale high-resolution satellite rainfall products is performed using 8 yr (2003–10) of reference rainfall data derived from a network of rain gauges over Europe. The comparisons are performed at a daily temporal scale and 0.25° spatial grid resolution. The satellite rainfall techniques investigated in this study are the Tropical Rainfall Measuring Mission (TRMM) 3B42 V6 (gauge-calibrated version) and the Climate Prediction Center morphing technique (CMORPH). The intercomparison and validation of these satellite products is performed both qualitatively and quantitatively. In the qualitative part of the analysis, error maps of various validation statistics are shown, whereas the quantitative analysis provides information about the performance of the satellite products relative to the rainfall magnitude or ground elevation. Moreover, a time series analysis of certain error statistics is used to depict the temporal variations of the accuracy of the two satellite techniques. The topographical and seasonal influences on the performance of the two satellite products over the European domain are also investigated. The error statistics presented herein indicate that both orography and seasonal variability affect the efficiency of the satellite rainfall retrieval techniques. Specifically, both satellite techniques underestimate rainfall over higher elevations, especially during the cold season, and their performance is subject to seasonal changes. A significant difference between the two satellite products is that TRMM 3B42 V6 generally overestimates rainfall, while CMORPH underestimates it. CMORPH’s mean error is shown to be of higher magnitude than that of 3B42 V6, while in terms of random error variance, CMORPH exhibits lower (higher) values than those of 3B42 V6 in the winter (summer) months.
The Effect of Apparent Latency on Simulator Sickness While Using a See-Through Helmet-Mounted Display
Authors: Buker Timothy J. , Vincenzi Dennis A. , Deaton John E. 
Published: January 2012

Objective: The aim of this study was to determine the effect of head movement frequency and predictive compensation on (a) latency produced in a monocular see-through helmet-mounted display (HMD) test bed and (b) simulator sickness experienced by users wearing the HMD. Background: There is conflicting research regarding latency as a significant factor in the onset of simulator sickness. Predictive compensation has been shown to mitigate the magnitude of latency, but little is known about the extent of its effect on simulator sickness. Method: A video camera recorded HMD and simulator imagery to accurately measure apparent latency produced at three head movement frequencies. Predictive compensation strategies were manipulated to measure the difference in apparent latency produced by the test bed in various conditions. Similar methodology was employed with human participants to measure simulator sickness experienced by users of this test bed. Results: In Experiment 1, apparent latency increased significantly as head movement frequency increased. Predictive compensation strategies significantly reduced apparent latency present in the test bed. In Experiment 2, predictive compensation significantly reduced the magnitude of simulator sickness. Conclusion: Predictive compensation can be effectively implemented to reduce apparent latency, resulting in a lower magnitude of simulator sickness. Application: Potential applications include HMD use in which head position is tracked and visual imagery is linked to head or body movement, such as in virtual and augmented reality systems, and is thus critical to functionality and performance.
An Adaptive Driver Support System
Authors: Dijksterhuis Chris , Stuiver Arjan , Mulder Ben , Brookhuis Karel A. , de Waard Dick 
Published: January 2012

Objective: The aim of this study was to test the implementation of an adaptive driver support system. Background: Providing support might not always be desirable from a safety perspective, as support may lead to problems related to a human operator being out of the loop. In contrast, adaptive support systems are designed to keep the operator in the loop as much as possible by providing support only when necessary. Method: A total of 31 experienced drivers were exposed to three modes of lane-keeping support: nonadaptive, adaptive, and no support. Support involved continuously updated lateral position feedback shown on a head-up display. When adaptive, support was triggered by performance-based indications of effort investment. Narrowing lane width and increasing density of oncoming traffic served to increase steering demand, and speed was fixed in all conditions to prevent any compensatory speed reactions. Results: Participants preferred the adaptive support mode mainly as a warning signal and tended to ignore nonadaptive feedback. Furthermore, driving behavior was improved by adaptive support in that participants drove more centrally, displayed less lateral variation and drove less outside the lane’s delineation when support was in the adaptive mode compared with both the no-support mode and the nonadaptive support mode. Conclusion: A human operator is likely to use machine-triggered adaptations as an indication that thresholds have been passed, regardless of the support that is initiated. Therefore supporting only the sensory processing stage of the human information processing system with adaptive automation may not feasible. Application: These conclusions are relevant for designing adaptive driver support systems.
Generating design reference years from the UKCP09 projections and their application to future air-conditioning loads
Authors: Du H , Underwood CP , Edge JS 
Published: January 2012

A method is developed to generate future design reference year (DRY) data from the United Kingdom Climate Impact Programme's 2009 (UKCP09) climate change projections for a variety of future time horizons and carbon emission assumptions. The method selects three near-extreme summer months and three near-extreme winter months and weaves them into an existing test reference year (TRY). Risk levels associated with the 85th percentile (broadly equivalent to existing Chartered Institution of Building Services Engineers [CIBSE] design summer years) of the cumulative distribution function of dry-bulb temperature and, for comparison, the 99th percentile are used. A comparison is made with DRYs generated using alternative methods from other research groups. The data are applied to future air-conditioning (cooling) loads analysis for a wide range of non-domestic case study building types. Simulations using a control DRY set applied to these buildings are used to develop a simplified regression-based calculation method for predicting future air-conditioning loads. The simplified model is shown to be applicable to future weather data without loss of accuracy, which makes it possible to carry out large numbers of future cooling loads predictions without the need to perform extensive and complex energy simulations. Practical applications: It is becoming increasingly necessary to design energy and comfort services for buildings with a whole-life perspective. To assist with this, the CIBSE future weather years can be used for building simulations through to the 2080s. In June 2009, the UK’s Department of the Environment, Food and Rural Affairs (Defra) with the support of the United Kingdom Climate Impacts Programme (UKCIP) published updated climate change projections using a probabilistic method. In future, the responsibility will rest with designers to select design data from a large number of probabilistic outcomes. This work develops a technique to select design weather data called a DRY at two alternative risk levels for use in building simulations through to the 2080s. A simplified method is also proposed to allow practitioners to generate large numbers of probabilistic design cooling loads without the need to perform extensive simulations.