bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection
Authors: Sunshine Justine E. , Larsen Brendan B. , Maust Brandon , Casey Ellie , Deng Wenje , Chen Lennie , Westfall Dylan H. , Kim Moon , Zhao Hong , Ghorai Suvankar , Lanxon-Cookson Erinn , Rolland Morgane , Collier Ann C. , Maenza Janine , Mullins James I. , Frahm Nicole 
Published: July 2015

ABSTRACT

To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24
gag
were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (
r
= 0.43;
P
= 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack.

IMPORTANCE
Rapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens.
Discriminating Majorana neutrino phases in the light of lepton flavor violation and leptogenesis in type I+II seesaw models
Authors: Kalita Rupam , Borah Debasish 
Published: July 2015

We study the effects of Majorana neutrino phases in lepton flavor violation and the origin of matter–antimatter asymmetry through the mechanism of leptogenesis within the framework of a model where both type I and type II seesaw mechanisms can contribute to tiny neutrino masses. We parametrize the type I seesaw mass matrix by assuming it to give rise to a tri-bimaximal (TBM) type neutrino mixing which predicts [Formula: see text]. The type II seesaw mass matrix is then constructed in such a way that the necessary deviation from TBM mixing and the best fit values of neutrino parameters can be obtained when both type I and type II seesaw contributions are taken into account. Considering both subleading as well as equally dominating type II seesaw term, we first constrain the Majorana CP phases from the requirement of producing correct baryon asymmetry through leptogenesis and then incorporating the experimental bounds on lepton flavor violating decays [Formula: see text] and [Formula: see text].
Computing history & ethics
Authors: Huggins James K. 
Published: July 2015

We discuss the use of real-world scenarios in a computing history and ethics course to promote social change.
CS-300, "The Computing Professional", is a course offered by Kettering University's Department of Computer Science. The course has an equal focus on computing history and computing ethics. Besides completing assigned readings and participating in classroom discussions, students are required to research an important figure or artifact from the history of computing, as well as a contemporary issue in computing ethics. Historical research is informed by considerations of the significance of the idea's value proposition. Ethics research is informed by a required analysis using the technique of paramedic ethics. Both research projects culminate in an oral presentation and a written research paper.
Teaching computing history and ethics in a single course has been an effective combination. Anecdotally, students appreciate the variety of topics covered each week, as "too much" history or ethics in one sitting can drain interest. Together, students find themselves looking both backwards and forwards in time, seeing how decisions in the past led to the computing world we know today.
Historical discussions are informed by consideration of the "value equation" (essentially, an "elevator pitch") that a new computational artifact provides. Often, advocates for a new technology focus on the attributes of the technology itself, rather than the need of the customer that the new technology might fulfill. An effective value equation focuses instead on the customer's need. Similarly, advocates for social change ought to focus on how the change they want to see addresses the needs of those making the change (for example, recent research showing how diverse research teams produce more valuable patents).
Ethical discussions often begin with classic imaginary case studies (e.g. the trolley problem). In our experience, students tend to react to imaginary case studies as if the case studies were games, seeking to change the parameters of each game, in order to avoid dealing with the ethical dilemma being presented, or to create an obvious "winning" condition for the game. In contrast, students react much more appropriately to real-world ethical scenarios. Students are much less likely to seek to change the conditions of the case study, since the events already occurred. Real scenarios contain a wealth of details that must be evaluated, with irrelevant details discarded. And students have an easier time visualizing themselves in the scenario (especially if the conclusion of the story is omitted).
No Association Between Vitamin D Intake,VDRPolymorphisms, and Colorectal Cancer in a Population-Based Case–Control Study
Authors: Ashmore Joseph H. , Gallagher Carla J. , Lesko Samuel M. , Muscat Joshua E. , Hartman Terryl J. , Lazarus Philip 
Published: July 2015

AbstractBackground: Epidemiologic evidence indicates that greater intakes of vitamin D may decrease the risk of colorectal cancer. Variants in the vitamin D receptor (VDR) gene have the potential to modify associations between vitamin D intake and colorectal cancer.Methods: Associations between intakes of vitamin D and colorectal cancer were studied in a large case–control study conducted in central and northeastern Pennsylvania including 1,012 cases with histologically confirmed colorectal cancer and 1,080 population-based controls. Associations between 35 tagSNPs encompassing the VDR gene and risk for colorectal cancer as well as gene–diet associations were also assessed among a subset of the population (770 controls, 710 cases).Results: No significant trends were observed between vitamin D intake and colorectal cancer risk. After adjustment for multiple comparisons, none of the SNPs or haplotypes within the VDR gene were associated with colorectal cancer. There were also no interactions between dietary factors and variants in the entire VDR gene.Conclusions: Overall, results from this study suggest that vitamin D intake and variants in the VDR gene have little effect on risk for colorectal cancer.Impact: Increasing vitamin D intake from the diet may not result in decreasing the incidence of colorectal cancer. Cancer Epidemiol Biomarkers Prev; 24(10); 1635–7. ©2015 AACR.
Non-valvular atrial fibrillation patients with none or one additional risk factor of the CHA2DS2-VASc score
Authors: Skjøth Flemming , Nielsen Peter , Larsen Torben Bjerregaard , Lip Gregory 
Published: July 2015

SummaryOral anticoagulation (OAC) to prevent stroke has to be balanced against the potential harm of serious bleeding, especially intracranial haemorrhage (ICH). We determined the net clinical benefit (NCB) balancing effectiveness and safety of no antithrombotic therapy, aspirin and warfarin in AF patients with none or one stroke risk factor. Using Danish registries, we determined NCB using various definitions intrinsic to our cohort (Danish weights at 1 and 5 year follow-up), with risk weights which were derived from the hazard ratio (HR) of death following an event, relative to HR of death after ischaemic stroke. When aspirin was compared to no treatment, NCB was neutral or negative for both risk strata. For warfarin vs no treatment, NCB using Danish weights was neutral where no risk factors were present and using five years follow-up. For one stroke risk factor, NCB was positive for warfarin vs no treatment, for one year and five year follow-up. For warfarin vs aspirin use in patients with no risk factors, NCB was positive with one year follow-up, but neutral with five year follow-up. With one risk factor, NCB was generally positive for warfarin vs aspirin. In conclusion, we show a positive overall advantage (i.e. positive NCB) of effective stroke prevention with OAC, compared to no therapy or aspirin with one additional stroke risk factor, using Danish weights. ‘Low risk’ AF patients with no additional stroke risk factors (i.e. CHA2DS2-VASc 0 in males, 1 in females) do not derive any advantage (neutral or negative NCB) with aspirin, nor with warfarin therapy in the long run.Note: The review process for this manuscript was fully handled by Christian Weber, Editor in Chief.
Dietary Sodium Consumption Predicts Future Blood Pressure and Incident Hypertension in the Japanese Normotensive General Population
Authors: Takase Hiroyuki , Sugiura Tomonori , Kimura Genjiro , Ohte Nobuyuki , Dohi Yasuaki 
Published: July 2015

Background
Although there is a close relationship between dietary sodium and hypertension, the concept that persons with relatively high dietary sodium are at increased risk of developing hypertension compared with those with relatively low dietary sodium has not been studied intensively in a cohort.

Methods and Results
We conducted an observational study to investigate whether dietary sodium intake predicts future blood pressure and the onset of hypertension in the general population. Individual sodium intake was estimated by calculating 24‐hour urinary sodium excretion from spot urine in 4523 normotensive participants who visited our hospital for a health checkup. After a baseline examination, they were followed for a median of 1143 days, with the end point being development of hypertension. During the follow‐up period, hypertension developed in 1027 participants (22.7%). The risk of developing hypertension was higher in those with higher rather than lower sodium intake (hazard ratio 1.25, 95% CI 1.04 to 1.50). In multivariate Cox proportional hazards regression analysis, baseline sodium intake and the yearly change in sodium intake during the follow‐up period (as continuous variables) correlated with the incidence of hypertension. Furthermore, both the yearly increase in sodium intake and baseline sodium intake showed significant correlations with the yearly increase in systolic blood pressure in multivariate regression analysis after adjustment for possible risk factors.

Conclusions
Both relatively high levels of dietary sodium intake and gradual increases in dietary sodium are associated with future increases in blood pressure and the incidence of hypertension in the Japanese general population.
Premotor Cortex Activation Elicited during Word Comprehension Relies on Access of Specific Action Concepts
Authors: Lin Nan , Wang Xiaoying , Zhao Ying , Liu Yanping , Li Xingshan , Bi Yanchao 
Published: July 2015

AbstractThe relationship between the lexical-semantic and sensory-motor systems is an important topic in cognitive neuroscience. An important finding indicating that these two systems interact is that reading action verbs activates the motor system of the human brain. Two constraints have been proposed to modulate this activation: the effector information associated with the action concepts and statistical regularities between sublexical features and grammatical classes. Using fMRI, we examined whether these two types of information can activate the motor system in the absence of specific motor-semantic content by manipulating the existence of a sublexical cue, called the hand radical, which strongly indicates the semantic feature “hand-related” and grammatical class “verb.” Although hand radical characters referring to specific manual actions evoked stronger activation in the premotor cortex than the control characters, hand radical pseudocharacters did not evoke specific activation within the motor system. These results indicated that activation of the premotor cortex during word reading relies on the access of specific action concepts.
Visual Awareness Is Limited by the Representational Architecture of the Visual System
Authors: Cohen Michael A. , Nakayama Ken , Konkle Talia , Stantić Mirta , Alvarez George A. 
Published: July 2015

Abstract
Visual perception and awareness have strict limitations. We suggest that one source of these limitations is the representational architecture of the visual system. Under this view, the extent to which items activate the same neural channels constrains the amount of information that can be processed by the visual system and ultimately reach awareness. Here, we measured how well stimuli from different categories (e.g., faces and cars) blocked one another from reaching awareness using two distinct paradigms that render stimuli invisible: visual masking and continuous flash suppression. Next, we used fMRI to measure the similarity of the neural responses elicited by these categories across the entire visual hierarchy. Overall, we found strong brain–behavior correlations within the ventral pathway, weaker correlations in the dorsal pathway, and no correlations in early visual cortex (V1–V3). These results suggest that the organization of higher level visual cortex constrains visual awareness and the overall processing capacity of visual cognition.
Augmentations to the Noah Model Physics for Application to the Yellow River Source Area. Part II: Turbulent Heat Fluxes and Soil Heat Transport
Authors: Zheng Donghai , van der Velde Rogier , Su Zhongbo , Wang Xin , Wen Jun , Booij Martijn J. , Hoekstra Arjen Y. , Chen Yingying 
Published: July 2015

Abstract
This is the second part of a study on the assessment of the Noah land surface model (LSM) in simulating surface water and energy budgets in the high-elevation source region of the Yellow River. Here, there is a focus on turbulent heat fluxes and heat transport through the soil column during the monsoon season, whereas the first part of this study deals with the soil water flow. Four augmentations are studied for mitigating the overestimation of turbulent heat flux and underestimation of soil temperature measurements: 1) the muting effect of vegetation on the thermal heat conductivity is removed from the transport of heat from the first to the second soil layer, 2) the exponential decay factor imposed on is calculated using the ratio of the leaf area index (LAI) over the green vegetation fraction (GVF), 3) Zilitinkevich’s empirical coefficient for turbulent heat transport is computed as a function of the momentum roughness length , and 4) the impact of organic matter is considered in the parameterization of the thermal heat properties. Although usage of organic matter for calculating improves the correspondence between the estimates and laboratory measurements of heat conductivities, it is shown to have a relatively small impact on the Noah LSM performance even for large organic matter contents. In contrast, the removal of the muting effect of vegetation on and the parameterization of greatly enhances the soil temperature profile simulations, whereas turbulent heat flux and surface temperature computations mostly benefit from the modified formulation. Further, the nighttime surface temperature overestimation is resolved from a coupled land–atmosphere perspective.
Calcium Metabolism Profile in Rat Inner Ear Indicated by MRI After Tympanic Medial Wall Administration of Manganese Chloride
Authors: Zou Jing , Pyykkö Ilmari 
Published: July 2015

Objectives: To evaluate the efficacy of the novel method for the targeted delivery of Mn++ to the inner ear and monitor calcium metabolism activity in the inner ear. Materials and Methods: Dynamic signal changes of Mn++ in the rat inner ear were followed using T1-weighted magnetic resonance imaging (MRI) after administration of 2.5 µl MnCl2 (500 mM) to the medial wall of the middle ear cavity. Results: Mn++ passed through both the oval and round windows and distributed in the perilymphatic compartments, where it formed bright sharp lines along the fluid-cellular borders 12 minutes post administration and entered the endolymph sufficiently after 45 minutes. After 6 hours, the distribution of Mn++ shifted from a fluid-dominant pattern to a cell-dominant pattern. Mn++ concentrated in the area of the basilar membrane, periphery process, and soma of the spiral ganglion on day 2; became more distinguishable on day 4; declined on day 8; and remained detectable for 16 days post administration. Conclusions: The novel targeted delivery method efficiently introduced Mn++ into the inner ear. The dynamic distribution pattern of Mn++ in the inner ear shown by MRI indicates that this method can be used to monitor calcium metabolism activity in the inner ear.
Wind velocity effects on the quality and efficiency of ventilation in the modelling of outdoor spaces. Case studies
Authors: Padilla-Marcos Miguel Ángel , Feijó-Muñoz Jesús , Meiss Alberto 
Published: July 2015

Outdoor spaces are air volumes between buildings that are open to atmospheric air. Surrounding buildings hinder and alter airflow, which affect the exchange process and its quality. Given that this outdoor air is captured to ventilate a building’s interior, the geometric characteristics and wind exposure of these outdoor spaces are vital to optimising these processes. One of the parameters under study is the variable wind speed. The goal of this article is to ascertain whether different wind velocities affect airflow patterns in these spaces. To this end, eight archetypal shape/volumetric cases of urban buildings are examined from an air exchange efficiency perspective. Practical application: The result is described by a mathematical expression that links the exchange efficiency with a range of wind velocities (0.75–6.00 m/s), which confirmed that this wind velocity range implies variations of only ±1.0% in interior courtyards, ±1.6% in adjacent exterior spaces between buildings, and ±2.4% in the considered control volume.
Assessment of anti-Müllerian hormone levels in premenopausal patients with systemic lupus erythematosus
Authors: Gasparin A A , Souza L , Siebert M , Xavier R M , Chakr R M S , Palominos P E , Brenol J C T , Monticielo O A 
Published: July 2015

Objective The ovarian reserve of patients with systemic lupus erythematosus (SLE) may be affected by disease activity and medication use. Studies have found that patients with SLE have similar fertility rates as healthy women of the same age. The goal of the present study was to investigate the ovarian reserve of patients with SLE by measuring anti-Müllerian hormone (AMH) levels, and compare it to that of healthy controls. Method This was a case-control study performed on 80 premenopausal women, of whom 40 fulfilled the 1997 American College of Rheumatology (ACR) criteria for SLE and 40 healthy controls paired by oral contraceptive use. Serum concentrations of AMH in peripheral venous blood were measured using a human AMH ELISA kit (CUSABIO, Wuhan, China). Results AMH serum levels did not differ between patients with SLE and controls (22.79 ± 17.32 ng/ml versus 21.41 ± 16.22 ng/ml, respectively, p = 0.7), even after adjusting for age (21.03 ± 2.074 ng/ml versus 23.97 ± 2.71 ng/ml; p = 0.5 ). AHM levels were not significantly correlated with disease duration ( r = 0.2; p = 0.3), body mass index ( r = 0.2; p = 0.2) and disease activity (SLEDAI ( r = 0.1; p = 0.7)) and damage indices (SLICC ( r = 0.1; p = 0.7)). No associations were found between AMH and ethnicity, current smoking, as well as current or prior use of cyclophosphamide and other immunosuppressants. Conclusion In this cross-sectional study, women with SLE demonstrated similar AMH levels as healthy controls, suggesting preserved ovarian reserve in this population.
Police Mental Health Partnership project: Police Ambulance Crisis Emergency Response (PACER) model development
Authors: Huppert David , Griffiths Matthew 
Published: July 2015

Objectives: To review internationally recognized models of police interactions with people experiencing mental health crises that are sometimes complex and associated with adverse experience for the person in crisis, their family and emergency service personnel. To develop, implement and review a partnership model trial between mental health and emergency services that offers alternative response pathways with improved outcomes in care. Methods: Three unique models of police and mental health partnership in the USA were reviewed and used to develop the PACER (Police Ambulance Crisis Emergency Response) model. A three month trial of the model was implemented and evaluated. Results: Significant improvements in response times, the interactions with and the outcomes for people in crisis were some of the benefits shown when compared with usual services. Conclusions: The pilot showed that a partnership involving mental health and police services in Melbourne, Australia could be replicated based on international models. Initial data supported improvements compared with usual care. Further data collection regarding usual care and this new model is required to confirm observed benefits.