bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of LexA on Chromosomal Integration of CTXϕ in Vibrio cholerae
Authors: Pant Archana , Anbumani D , Bag Satyabrata , Mehta Ojasvi , Kumar Pawan , Saxena Shruti , Nair G. Balakrish , Das Bhabatosh 
Published: October 2015

ABSTRACT

The genesis of toxigenic
Vibrio cholerae
involves acquisition of CTXϕ, a single-stranded DNA (ssDNA) filamentous phage that encodes cholera toxin (CT). The phage exploits host-encoded tyrosine recombinases (XerC and XerD) for chromosomal integration and lysogenic conversion. The replicative genome of CTXϕ produces ssDNA by rolling-circle replication, which may be used either for virion production or for integration into host chromosome. Fine-tuning of different ssDNA binding protein (Ssb) levels in the host cell is crucial for cellular functioning and important for CTXϕ integration. In this study, we mutated the master regulator gene of SOS induction,
lexA
, of
V. cholerae
because of its known role in controlling levels of Ssb proteins in other bacteria. CTXϕ integration decreased in cells with a Δ
lexA
mutation and increased in cells with an SOS-noninducing mutation,
lexA
(Ind
−
). We also observed that overexpression of host-encoded Ssb (VC0397) decreased integration of CTXϕ. We propose that LexA helps CTXϕ integration, possibly by fine-tuning levels of host- and phage-encoded Ssbs.

IMPORTANCE
Cholera toxin is the principal virulence factor responsible for the acute diarrheal disease cholera. CT is encoded in the genome of a lysogenic filamentous phage, CTXϕ.
Vibrio cholerae
has a bipartite genome and harbors single or multiple copies of CTXϕ prophage in one or both chromosomes. Two host-encoded tyrosine recombinases (XerC and XerD) recognize the folded ssDNA genome of CTXϕ and catalyze its integration at the dimer resolution site of either one or both chromosomes. Fine-tuning of ssDNA binding proteins in host cells is crucial for CTXϕ integration. We engineered the
V. cholerae
genome and created several reporter strains carrying Δ
lexA
or
lexA
(Ind
−
) alleles. Using the reporter strains, the importance of LexA control of Ssb expression in the integration efficiency of CTXϕ was demonstrated.
How GPs value guidelines applied to patients with multimorbidity: a qualitative study
Authors: Luijks Hilde , Lucassen Peter , van Weel Chris , Loeffen Maartje , Lagro-Janssen Antoine , Schermer Tjard 
Published: October 2015

ObjectivesTo explore and describe the value general practitioner (GPs) attribute to medical guidelines when they are applied to patients with multimorbidity, and to describe which benefits GPs experience from guideline adherence in these patients. Also, we aimed to identify limitations from guideline adherence in patients with multimorbidity, as perceived by GPs, and to describe their empirical solutions to manage these obstacles.DesignFocus group study with purposive sampling of participants. Focus groups were guided by an experienced moderator who used an interview guide. Interviews were transcribed verbatim. Data analysis was performed by two researchers using the constant comparison analysis technique and field notes were used in the analysis. Data collection proceeded until saturation was reached.SettingPrimary care, eastern part of The Netherlands.ParticipantsDutch GPs, heterogeneous in age, sex and academic involvement.Results25 GPs participated in five focus groups. GPs valued the guidance that guidelines provide, but experienced shortcomings when they were applied to patients with multimorbidity. Taking these patients’ personal circumstances into account was regarded as important, but it was impeded by a consistent focus on guideline adherence. Preventative measures were considered less appropriate in (elderly) patients with multimorbidity. Moreover, the applicability of guidelines in patients with multimorbidity was questioned. GPs’ extensive practical experience with managing multimorbidity resulted in several empirical solutions, for example, using their ‘common sense’ to respond to the perceived shortcomings.ConclusionsGPs applying guidelines for patients with multimorbidity integrate patient-specific factors in their medical decisions, aiming for patient-centred solutions. Such integration of clinical experience and best evidence is required to practise evidence-based medicine. More flexibility in pay-for-performance systems is needed to facilitate this integration. Several improvements in guideline reporting are necessary to enhance the applicability of guidelines in patients with multimorbidity.
The Malaysian Breast Cancer Survivorship Cohort (MyBCC): a study protocol
Authors: Islam Tania , Bhoo-Pathy Nirmala , Su Tin Tin , Majid Hazreen Abdul , Nahar Azmi Mohd , Ng Chong Guan , Dahlui Maznah , Hussain Samsinah , Cantwell Marie , Murray Liam , Taib Nur Aishah ,   MyBCC study group
Published: October 2015

IntroductionOver recent decades, the burden of breast cancer has been increasing at an alarming rate in Asia. Prognostic research findings from Western countries may not readily be adapted to Asia, as the outcome of breast cancer depends on a multitude of factors ranging from genetic, clinical and histological predictors, to lifestyle and social predictors. The primary aim of this study is to determine the impact of lifestyle (eg, nutrition, physical activity), mental and sociocultural condition, on the overall survival and quality of life (QoL) among multiethnic Malaysian women following diagnosis of breast cancer. This study aims to advance the evidence on prognostic factors of breast cancer within the Asian setting. The findings may guide management of patients with breast cancer not only during active treatment but also during the survivorship period.MethodsThis hospital-based prospective cohort study will comprise patients with breast cancer (18 years and above), managed in the University Malaya Medical Centre (UMMC). We aim to recruit 1000 cancer survivors over a 6-year period. Data collection will occur at baseline (within 3 months of diagnosis), 6 months, and 1, 3 and 5 years following diagnosis. The primary outcomes are disease-free survival and overall survival, and secondary outcome is QoL. Factors measured are demographic and socioeconomic factors, lifestyle factors (eg, dietary intake, physical activity), anthropometry measurements (eg, height, weight, waist, hip circumference, body fat analysis), psychosocial aspects, and complementary and alternative medicine (CAM) usage.Ethics and disseminationThis protocol was approved by the UMMC Ethical Committee in January 2012. All participants are required to provide written informed consent. The findings from our cohort study will be disseminated via scientific publication as well as presentation to stakeholders including the patients, clinicians, the public and policymakers, via appropriate avenues.
Comparative safety and effectiveness of long-acting inhaled agents for treating chronic obstructive pulmonary disease: a systematic review and network meta-analysis
Authors: Tricco Andrea C , Strifler Lisa , Veroniki Areti-Angeliki , Yazdi Fatemeh , Khan Paul A , Scott Alistair , Ng Carmen , Antony Jesmin , Mrklas Kelly , D'Souza Jennifer , Cardoso Roberta , Straus Sharon E 
Published: October 2015

ObjectiveTo compare the safety and effectiveness of long-acting β-antagonists (LABA), long-acting antimuscarinic agents (LAMA) and inhaled corticosteroids (ICS) for managing chronic obstructive pulmonary disease (COPD).SettingSystematic review and network meta-analysis (NMA).Participants208 randomised clinical trials (RCTs) including 134 692 adults with COPD.InterventionsLABA, LAMA and/or ICS, alone or in combination, versus each other or placebo.Primary and secondary outcomesThe proportion of patients with moderate-to-severe exacerbations. The number of patients experiencing mortality, pneumonia, serious arrhythmia and cardiovascular-related mortality (CVM) were secondary outcomes.ResultsNMA was conducted including 20 RCTs for moderate-to-severe exacerbations for 26 141 patients with an exacerbation in the past year. 32 treatments were effective versus placebo including: tiotropium, budesonide/formoterol, salmeterol, indacaterol, fluticasone/salmeterol, indacaterol/glycopyrronium, tiotropium/fluticasone/salmeterol and tiotropium/budesonide/formoterol. Tiotropium/budesonide/formoterol was most effective (99.2% probability of being the most effective according to the Surface Under the Cumulative RAnking (SUCRA) curve). NMA was conducted on mortality (88 RCTs, 97 526 patients); fluticasone/salmeterol was more effective in reducing mortality than placebo, formoterol and fluticasone alone, and was the most effective (SUCRA=71%). NMA was conducted on CVM (37 RCTs, 55 156 patients) and the following were safest: salmeterol versus each OF placebo, tiotropium and tiotropium (Soft Mist Inhaler (SMR)); fluticasone versus tiotropium (SMR); and salmeterol/fluticasone versus tiotropium and tiotropium (SMR). Triamcinolone acetonide was the most harmful (SUCRA=81%). NMA was conducted on pneumonia occurrence (54 RCTs, 61 551 patients). 24 treatments were more harmful, including 2 that increased risk of pneumonia versus placebo; fluticasone and fluticasone/salmeterol. The most harmful agent was fluticasone/salmeterol (SUCRA=89%). NMA was conducted for arrhythmia; no statistically significant differences between agents were identified.ConclusionsMany inhaled agents are available for COPD, some are safer and more effective than others. Our results can be used by patients and physicians to tailor administration of these agents.Protocol registration numberPROSPERO # CRD42013006725.
Resilience as a correlate of acute stress disorder symptoms in patients with acute myocardial infarction
Authors: Meister Rebecca E , Weber Tania , Princip Mary , Schnyder Ulrich , Barth Jürgen , Znoj Hansjörg , Schmid Jean-Paul , von Känel Roland 
Published: October 2015

ObjectivesMyocardial infarction (MI) may be experienced as a traumatic event causing acute stress disorder (ASD). This mental disorder has an impact on the daily life of patients and is associated with the development of post-traumatic stress disorder. Trait resilience has been shown to be a protective factor for post-traumatic stress disorder, but its association with ASD in patients with MI is elusive and was examined in this study.MethodsWe investigated 71 consecutive patients with acute MI within 48 h of having stable haemodynamic conditions established and for 3 months thereafter. All patients completed the Acute Stress Disorder Scale and the Resilience Scale to self-rate the severity of ASD symptoms and trait resilience, respectively.ResultsHierarchical regression analysis showed that greater resilience was associated with lower symptoms of ASD independent of covariates (b=−0.22, p<0.05). Post hoc analysis revealed resilience level to be inversely associated with the ASD symptom clusters of re-experiencing (b=−0.05, p<0.05) and arousal (b=−0.09, p<0.05), but not with dissociation and avoidance.ConclusionsThe findings suggest that patients with acute MI with higher trait resilience experience relatively fewer symptoms of ASD during MI. Resilience was particularly associated with re-experiencing and arousal symptoms. Our findings contribute to a better understanding of resilience as a potentially important correlate of ASD in the context of traumatic situations such as acute MI. These results emphasise the importance of identifying patients with low resilience in medical settings and to offer them adequate support.
Acute neurological visual loss in young adults: causes, diagnosis and management
Authors: Sawaya R , El Ayoubi N , Hamam R 
Published: October 2015

ABSTRACTVisual loss in the young adult can be caused by demyelinating diseases, inflammatory and autoimmune processes, infections, ischaemic events, and compressive lesions of the optic nerve. Diagnosis of the aetiologies of visual loss is reached by combining data from radiological studies, electrophysiological tests, and blood and cerebrospinal fluid analysis. Treatment is primarily aimed at decreasing the insult on the optic nerve and eventually controlling the primary disorder. The literature discusses separately the different aetiologies of visual loss. We present a review of the clinical characteristics of visual loss in the young adult, the different diagnostic measures, and the latest therapeutic strategies. The aim of this work is to summarise this entity in a practical way to guide clinicians in the diagnosis and management of this disorder.
Orbifold Tutte embeddings
Authors: Aigerman Noam , Lipman Yaron 
Published: October 2015

Injective parameterizations of surface meshes are vital for many applications in Computer Graphics, Geometry Processing and related fields. Tutte's embedding, and its generalization to convex combination maps, are among the most popular approaches for computing parameterizations of surface meshes into the plane, as they guarantee injectivity, and their computation only requires solving a sparse linear system. However, they are only applicable to disk-type and toric surface meshes.
In this paper we suggest a generalization of Tutte's embedding to other surface topologies, and in particular the common, yet untreated case, of sphere-type surfaces. The basic idea is to enforce certain boundary conditions on the parameterization so as to achieve a Euclidean orbifold structure. The orbifold-Tutte embedding is a seamless, globally bijective parameterization that, similarly to the classic Tutte embedding, only requires solving a sparse linear system for its computation.
In case the cotangent weights are used, the orbifold-Tutte embedding globally minimizes the Dirichlet energy and is shown to approximate conformal and four-point quasiconformal mappings. As far as we are aware, this is the first fully-linear method that produces bijective approximations to conformal mappings.
Aside from parameterizations, the orbifold-Tutte embedding can be used to generate bijective inter-surface mappings with three or four landmarks and symmetric patterns on sphere-type surfaces.
Anaplastic Lymphoma Kinase as a Cancer Target in Pediatric Malignancies
Authors: Mossé Yael P. 
Published: October 2015

AbstractIn this era of more rational therapies, substantial efforts are being made to identify optimal targets. The discovery of translocations involving the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase in a subset of non–small cell lung cancers has become a paradigm for precision medicine. Notably, ALK was initially discovered as the fusion gene in anaplastic large cell non-Hodgkin lymphoma, a disease predominantly of childhood. The discovery of activating kinase domain mutations of the full-length ALK receptor as the major cause of hereditary neuroblastoma, and that somatically acquired mutations and amplification events often drive the malignant process in a subset of sporadic tumors, has established ALK as a tractable molecular target across histologically diverse tumors in which ALK is a critical mediator of oncogenesis. We are now uncovering the reexpression of this developmentally regulated protein in a broader subset of pediatric cancers, providing therapeutic targeting opportunities for diseases with shared molecular etiology. This review focuses on the role of ALK in pediatric malignancies, alongside the prospects and challenges associated with the development of effective ALK-inhibition strategies. Clin Cancer Res; 22(3); 546–52. ©2015 AACR.
Urban Effects on Regional Climate: A Case Study in the Phoenix and Tucson “Sun Corridor”
Authors: Yang Zhao , Dominguez Francina , Gupta Hoshin , Zeng Xubin , Norman Laura 
Published: October 2015

Abstract
Land-use and land-cover change (LULCC) due to urban expansion alter the surface albedo, heat capacity, and thermal conductivity of the surface. Consequently, the energy balance in urban regions is different from that of natural surfaces. To evaluate the changes in regional climate that could arise because of projected urbanization in the Phoenix–Tucson corridor, Arizona, this study applied the coupled WRF Model–Noah–Urban Canopy Model (UCM; which includes a detailed urban radiation scheme) to this region. Land-cover changes were represented using land-cover data for 2005 and projections to 2050, and historical North American Regional Reanalysis (NARR) data were used to specify the lateral boundary conditions. Results suggest that temperature changes will be well defined, reflecting the urban heat island (UHI) effect within areas experiencing LULCC. Changes in precipitation are less robust but seem to indicate reductions in precipitation over the mountainous regions northeast of Phoenix and decreased evening precipitation over the newly urbanized area.
Convective Self-Aggregation and Tropical Cyclogenesis under the Hypohydrostatic Rescaling
Authors: Boos William R. , Fedorov Alexey , Muir Les 
Published: October 2015

Abstract
The behavior of rotating and nonrotating aggregated convection is examined at various horizontal resolutions using the hypohydrostatic, or reduced acceleration in the vertical (RAVE), rescaling. This modification of the equations of motion reduces the scale separation between convective- and larger-scale motions, enabling the simultaneous and explicit representation of both types of flow in a single model without convective parameterization. Without the RAVE rescaling, a dry bias develops when simulations of nonrotating radiative–convective equilibrium are integrated at coarse resolution in domains large enough to permit convective self-aggregation. The rescaling reduces this dry bias, and here it is suggested that the rescaling moistens the troposphere by weakening the amplitude and slowing the group velocity of gravity waves, thus reducing the subsidence drying around aggregated convection. Separate simulations of rotating radiative–convective equilibrium exhibit tropical cyclogenesis; as horizontal resolution is coarsened without the rescaling, the resulting storms intensify more slowly and achieve lower peak intensities. At a given horizontal resolution, using RAVE increases peak storm intensity and reduces the time needed for tropical cyclogenesis—effects here suggested to be caused at least in part by the environmental moistening produced by RAVE. Consequently, the RAVE rescaling has the potential to improve simulations of tropical cyclones and other aggregated convection in models with horizontal resolutions of order 10–100 km.
Extreme Water Deficit in Brazil Detected from Space
Authors: Getirana Augusto 
Published: October 2015

Abstract
Extreme droughts have caused significant socioeconomic and environmental damage worldwide. In Brazil, ineffective energy development and water management policies have magnified the impacts of recent severe droughts, which include massive agricultural losses, water supply restrictions, and energy rationing. Spaceborne remote sensing data advance our understanding of the spatiotemporal variability of large-scale droughts and enhance the detection and monitoring of extreme water-related events. In this study, data derived from the Gravity Recovery and Climate Experiment (GRACE) mission are used to detect and quantify an extended major drought over eastern Brazil and provide estimates of impacted areas and region-specific water deficits. Two structural breakpoint detection methods were applied to time series of GRACE-based terrestrial water storage anomalies (TWSA), determining when two abrupt changes occurred. One, in particular, defines the beginning of the current drought. Using TWSA, a water loss rate of −6.1 cm yr−1 over southeastern Brazil was detected from 2012 to 2015. Based on analysis of Global Land Data Assimilation System (GLDAS) outputs, the extreme drought is mostly related to lower-than-usual precipitation rates, resulting in high soil moisture depletion and lower-than-usual rates of evapotranspiration. A reduction of 20%–23% of precipitation over an extended period of 3 years is enough to raise serious water scarcity conditions in the country. Correlations between monthly time series of both grid-based TWSA and ground-based water storage measurements at 16 reservoirs located within southeastern Brazil varied from 0.42 to 0.82. Differences are mainly explained by reservoir sizes and proximity to the drought nucleus.
Statistical Evaluation of Time Multiplexing to Mitigate Differential Reflectivity Bias Due to Cross-Polar Coupling
Authors: Ivić Igor R. 
Published: October 2015

AbstractOne of the main challenges to the use of phased array radar for weather observations is the implementation of dual polarization with acceptable levels of cross-polar fields induced by the antenna. For example, to achieve acceptable differential reflectivity (ZDR) bias (e.g., less than 0.1 dB) using simultaneous transmission and reception of H and V polarized waves, the isolation between coaxial cross-polar and copolar beams needs to be in excess of 50 dB. Because such isolation cannot be achieved at an affordable price by antenna hardware, additional methods are required to attain supplementary isolation of orthogonal channels. One such option is time multiplexing. Herein, this approach is evaluated from the statistical aspect, whereby the depolarization caused by the radar hardware is accounted for in this study. An evaluation is conducted using theoretical analysis as well as simulated and time series data from a weather radar. The main criteria for evaluation are the bias and standard deviation of differential reflectivity estimates. The results indicate that the implementation of the time-multiplexing method has the capability to significantly improve upon the radar intrinsic cross-polar isolation. However, it is demonstrated herein that the reflectivity gradients in range adversely affect the efficacy of the method and that the standard deviation of estimates can significantly increase as a result of the time-multiplexing application.
Atmospheric Kármán Vortex Shedding from Jeju Island, East China Sea: A Numerical Study*
Authors: Ito Junshi , Niino Hiroshi 
Published: October 2015

Abstract
A mesoscale atmospheric numerical model is used to simulate two cases of Kármán vortex shedding in the lee of Jeju Island, South Korea, in the winter of 2013. Observed cloud patterns associated with the Kármán vortex shedding are successfully reproduced. When the winter monsoon flows out from the Eurasian continent, a convective mixed layer develops through the supply of heat and moisture from the relatively warm Yellow Sea and encounters Jeju Island and dynamical conditions favorable for the formation of lee vortices are realized. Vortices that form behind the island induce updrafts to trigger cloud formation at the top of the convective boundary layer. A sensitivity experiment in which surface drag on the island is eliminated demonstrates that the formation mechanism of the atmospheric Kármán vortex shedding is different from that behind a bluff body in classical fluid mechanics.