bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward improved target conformity for two spot scanning proton therapy delivery systems using dynamic collimation
Authors: Moignier Alexandra , Gelover Edgar , Smith Blake R. , Wang Dongxu , Flynn Ryan T. , Kirk Maura L. , Lin Liyong , Solberg Timothy D. , Lin Alexander , Hyer Daniel E. 
Published: February 2016

Purpose:To quantify improvement in target conformity in brain and head and neck tumor treatments resulting from the use of a dynamic collimation system (DCS) with two spot scanning proton therapy delivery systems (universal nozzle, UN, and dedicated nozzle, DN) with median spot sizes of 5.2 and 3.2 mm over a range of energies from 100 to 230 MeV.Methods:Uncollimated and collimated plans were calculated with both UN and DN beam models implemented within our in‐house treatment planning system for five brain and ten head and neck datasets in patients previously treated with spot scanning proton therapy. The prescription dose and beam angles from the clinical plans were used for both the UN and DN plans. The average reduction of the mean dose to the 10‐mm ring surrounding the target between the uncollimated and collimated plans was calculated for the UN and the DN. Target conformity was analyzed using the mean dose to 1‐mm thickness rings surrounding the target at increasing distances ranging from 1 to 10 mm.Results:The average reductions of the 10‐mm ring mean dose for the UN and DN plans were 13.7% (95% CI: 11.6%–15.7%; p < 0.0001) and 11.5% (95% CI: 9.5%–13.5%; p < 0.0001) across all brain cases and 7.1% (95% CI: 4.4%–9.8%; p < 0.001) and 6.3% (95% CI: 3.7%–9.0%; p < 0.001), respectively, across all head and neck cases. The collimated UN plans were either more conformal (all brain cases and 60% of the head and neck cases) than or equivalent (40% of the head and neck cases) to the uncollimated DN plans. The collimated DN plans offered the highest conformity.Conclusions:The DCS added either to the UN or DN improved the target conformity. The DCS may be of particular interest for sites with UN systems looking for a more economical solution than upgrading the nozzle to improve the target conformity of their spot scanning proton therapy system.
Human Papillomavirus Laboratory Testing: the Changing Paradigm
Authors: Burd Eileen M. 
Published: February 2016

SUMMARY
High-risk human papillomaviruses (HPVs) cause essentially all cervical cancers, most anal and oropharyngeal cancers, and some vaginal, vulvar, and penile cancers. Improved understanding of the pathogenesis of infection and the availability of newer tests are changing the approach to screening and diagnosis. Molecular tests to detect DNA from the most common high-risk HPVs are FDA approved for use in conjunction with cytology in cervical cancer screening programs. More-specific tests that detect RNA from high-risk HPV types are now also available. The use of molecular tests as the primary screening tests is being adopted in some areas. Genotyping to identify HPV16 and -18 has a recommended role in triaging patients for colposcopy who are high-risk HPV positive but have normal cytology. There are currently no recommended screening methods for anal, vulvar, vaginal, penile, or oropharyngeal HPV infections. HPV testing has limited utility in patients at high risk for anal cancer, but p16 immunohistochemistry is recommended to clarify lesions in tissue biopsy specimens that show moderate dysplasia or precancer mimics. HPV testing is recommended for oropharyngeal squamous cell tumors as a prognostic indicator. Ongoing research will help to improve the content of future guidelines for screening and diagnostic testing.
HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay
Authors: Sunshine Sara , Kirchner Rory , Amr Sami S. , Mansur Leandra , Shakhbatyan Rimma , Kim Michelle , Bosque Alberto , Siliciano Robert F. , Planelles Vicente , Hofmann Oliver , Ho Sui Shannan , Li Jonathan Z. 
Published: February 2016

ABSTRACTAntiretroviral therapy (ART) is successful in the suppression of HIV but cannot target and eradicate the latent proviral reservoir. The location of retroviral integration into the human genome is thought to play a role in the clonal expansion of infected cells and HIV persistence. We developed a high-throughput targeted sequence capture assay that uses a pool of HIV-specific probes to enrich Illumina libraries prior to deep sequencing. Using an expanded clonal population of ACH-2 cells, we demonstrate that this sequence capture assay has an extremely low false-positive rate. This assay assessed four cellular models commonly used to study HIV latency and latency-reversing agents: ACH-2 cells, J-Lat cells, the Bcl-2-transduced primary CD4+model, and the cultured TCM(central memory) CD4+model. HIV integration site characteristics and genes were compared between these cellular models and to previously reported patient data sets. Across these cellular models, there were significant differences in integration site characteristics, including orientation relative to that of the host gene, the proportion of clonally expanded sites, and the proportion located within genic regions and exons. Despite a greater diversity of minority integration sites than expected in ACH-2 cells, their integration site characteristics consistently differed from those of the other models and from the patient samples. Gene ontology analysis of highly represented genes from the patient samples found little overlap with HIV-containing genes from the cell lines. These findings show that integration site differences exist among the commonly used cellular models of HIV latency and in comparison to integration sites found in patient samples.IMPORTANCEDespite the success of ART, currently there is no successful therapy to eradicate integrated proviruses. Cellular models of HIV latency are used to test the efficacy of latency-reversing agents, but it is unclear how well these models reflect HIV integration into the human genomein vivo. We have developed a novel probe-based sequence enrichment assay to sequence and analyze integrated HIV. We compared HIV integration site characteristics between four cellular models and to previously described patient data sets. Significant differences were detected in the distribution of HIV integration sites between cellular models of HIV latency and compared to data sets from patient samples. The results from this study have implications for how well these cellular models of HIV infection truly reflect HIV integrationin vivoand their applicability in drug discovery for novel latency-reversing agents.
Mucosa-Associated Invariant T Cells Are Systemically Depleted in Simian Immunodeficiency Virus-Infected Rhesus Macaques
Authors: Vinton Carol , Wu Fan , Rossjohn Jamie , Matsuda Kenta , McCluskey James , Hirsch Vanessa , Price David A. , Brenchley Jason M. 
Published: February 2016

ABSTRACT
Mucosa-associated invariant T (MAIT) cells contribute to host immune protection against a wide range of potential pathogens via the recognition of bacterial metabolites presented by the major histocompatibility complex class I-related molecule MR1. Although bacterial products translocate systemically in human immunodeficiency virus (HIV)-infected individuals and simian immunodeficiency virus (SIV)-infected Asian macaques, several studies have shown that MAIT cell frequencies actually decrease in peripheral blood during the course of HIV/SIV disease. However, the mechanisms underlying this proportional decline remain unclear. In this study, we characterized the phenotype, activation status, functionality, distribution, and clonotypic structure of MAIT cell populations in the peripheral blood, liver, mesenteric lymph nodes (MLNs), jejunum, and bronchoalveolar lavage (BAL) fluid of healthy and SIV-infected rhesus macaques (RMs). Low frequencies of MAIT cells were observed in the peripheral blood, MLNs, and BAL fluid of SIV-infected RMs. These numerical changes were coupled with increased proliferation and a highly public T cell receptor alpha (TCRα) repertoire in the MAIT cell compartment without redistribution to other anatomical sites. Collectively, our data show systemically decreased frequencies of MAIT cells likely attributable to enhanced turnover in SIV-infected RMs. This process may impair protective immunity against certain opportunistic infections with progression to AIDS.

IMPORTANCE
The data presented in this study reveal for the first time that MAIT cells are systemically depleted in an AIDS virus infection. These findings provide a new mechanistic link with our current understanding of HIV/SIV pathogenesis and implicate MAIT cell depletion in the disease process.
Use of the Microparticle Nanoscale Silicon Dioxide as an Adjuvant To Boost Vaccine Immune Responses against Influenza Virus in Neonatal Mice
Authors: Russell Ryan F. , McDonald Jacqueline U. , Lambert Laura , Tregoning John S. 
Published: February 2016

ABSTRACTNeonates are at a high risk of infection, but vaccines are less effective in this age group; tailored adjuvants could potentially improve vaccine efficacy. Increased understanding about danger sensing by the innate immune system has led to the rational design of novel adjuvants. But differences in the neonatal innate immune response, for example, to Toll-like receptor (TLR) agonists, can reduce the efficacy of these adjuvants in early life. We therefore targeted alternative danger-sensing pathways, focusing on a range of compounds described as inflammasome agonists, including nanoscale silicon dioxide (NanoSiO2), calcium pyrophosphate dihydrate (CPPD) crystals, and muramyl tripeptide (M-Tri-DAP), for their ability to act as adjuvants.In vitro, these compounds induced an interleukin 1-beta (IL-1β) response in the macrophage-like cell line THP1.In vivo, adult CB6F1 female mice were immunized intramuscularly with H1N1 influenza vaccine antigens in combination with NanoSiO2, CPPD, or M-Tri-DAP and subsequently challenged with H1N1 influenza virus (A/England/195/2009). The adjuvants boosted anti-hemagglutinin IgG and IgA antibody levels. Both adult and neonatal animals that received NanoSiO2-adjuvanted vaccines lost significantly less weight and recovered earlier after infection than control animals treated with antigen alone. Administration of the adjuvants led to an influx of activated inflammatory cells into the muscle but to little systemic inflammation measured by serum cytokine levels. Blocking IL-1β or caspase 1in vivohad little effect on NanoSiO2 adjuvant function, suggesting that it may work through pathways other than the inflammasome. Here we demonstrate that NanoSiO2 can act as an adjuvant and is effective in early life.IMPORTANCEVaccines can fail to protect the most at-risk populations, including the very young, the elderly, and the immunocompromised. There is a gap in neonatal immunity between the waning of maternal protection and routine infant immunization schedules, exacerbated by the failure of vaccines to work in the first months of life. One approach is to design age-specific formulations, with more-effective adjuvants, based on our understanding of the nature of the neonatal immune response. We chose to target the inflammasome, a molecular complex capable of detecting infection and cell damage and of triggering IL-1β-driven inflammation. We screened a range of compoundsin vitroandin vivoand identified three lead candidates: NanoSiO2, CPPD, and M-Tri-DAP. Of these, NanoSiO2 was the most effective and boosted the anti-influenza virus response in both adult and neonatal mice. This finding is important for the development of age-specific vaccines, designed using our knowledge of the neonatal immune response.
Predicting the outcome of hip fracture patients by using N-terminal fragment of pro-B-type natriuretic peptide
Authors: Nordling Pauliina , Kiviniemi Tuomas , Strandberg Marjatta , Strandberg Niko , Airaksinen Juhani 
Published: February 2016

ObjectiveTo examine the prognostic value of perioperative N-terminal fragment of pro-brain natriuretic peptide (NT-proBNP) in hip fracture patients.DesignBlinded prospective cohort study.SettingSingle centre trial at Turku University Hospital in Finland.ParticipantsInclusion criterion was admittance to the study hospital due to hip fracture during the trial period of October 2009—May 2010. Exclusion criteria were the patient's refusal and inadequate laboratory tests. The final study population consisted of 182 patients.Primary and secondary outcome measuresNT-proBNP was assessed once during the perioperative period and later if clinically indicated, and troponin T (TnT) and ECG recordings were evaluated repeatedly. The short-term (30-day) and long-term (1000 days) mortalities were studied.ResultsMedian (IQR) follow-up time was 3.1 (0.3) years. The median (IQR) NT-proBNP level was 1260 (2298) ng/L in preoperative and 1600 (3971) ng/L in postoperative samples (p=0.001). TnT was elevated in 66 (36%) patients, and was significantly more common in patients with higher NT-proBNP. Patients with high (>2370 ng/L) and intermediate (806–2370 ng/L) NT-proBNP level had significantly higher short-term mortality compared with patients having a low (<806 ng/L) NT-proBNP level (15 vs 11 vs 2%, p=0.04), and the long-term mortality remained higher in these patients (69% vs 49% vs 27%, p<0.001). Intermediate or high NT-proBNP level (HR 7.8, 95% CI 1.03 to 59.14, p<0.05) was the only independent predictor of short-term mortality, while intermediate or high NT-proBNP level (HR 2.27, 95% CI 1.30 to 3.96, p=0.004), the presence of dementia (HR 1.74, 95% CI 1.13 to 2.66, p=0.01) and higher preoperative American Society of Anesthesiologists’ (ASA) classification (HR 1.59, 95% CI 1.06 to 2.38, p=0.02) were independent predictors of long-term mortality.ConclusionAn elevated perioperative NT-proBNP level is common in hip fracture patients, and it is an independent predictor of short-term and long-term mortality superior to the commonly used clinical risk scores.Trial registration numberNCT01015105; Results.
Gut microbiota, obesity and diabetes
Authors: Patterson Elaine , Ryan Paul M , Cryan John F , Dinan Timothy G , Ross R Paul , Fitzgerald Gerald F , Stanton Catherine 
Published: February 2016

AbstractThe central role of the intestinal microbiota in the progression and, equally, prevention of metabolic dysfunction is becoming abundantly apparent. The symbiotic relationship between intestinal microbiota and host ensures appropriate development of the metabolic system in humans. However, disturbances in composition and, in turn, functionality of the intestinal microbiota can disrupt gut barrier function, a trip switch for metabolic endotoxemia. This low-grade chronic inflammation, brought about by the influx of inflammatory bacterial fragments into circulation through a malfunctioning gut barrier, has considerable knock-on effects for host adiposity and insulin resistance. Conversely, recent evidence suggests that there are certain bacterial species that may interact with host metabolism through metabolite-mediated stimulation of enteric hormones and other systems outside of the gastrointestinal tract, such as the endocannabinoid system. When the abundance of these keystone species begins to decline, we see a collapse of the symbiosis, reflected in a deterioration of host metabolic health. This review will investigate the intricate axis between the microbiota and host metabolism, while also addressing the promising and novel field of probiotics as metabolic therapies.
Hand hygiene of medical students and resident physicians: predictors of attitudes and behaviour
Authors: Barroso Violeta , Caceres Wendy , Loftus Pooja , Evans Kambria H , Shieh Lisa 
Published: February 2016

AbstractObjectivesWe measured medical students' and resident trainees' hand hygiene behaviour, knowledge and attitudes in order to identify important predictors of hand hygiene behaviour in this population.MethodsAn anonymous, web-based questionnaire was distributed to medical students and residents at Stanford University School of Medicine in August of 2012. The questionnaire included questions regarding participants' behaviour, knowledge, attitude and experiences about hand hygiene. Behaviour, knowledge and attitude indices were scaled from 0 to 1, with 1 representing superior responses. Using multivariate regression, we identified positive and negative predictors of superior hand hygiene behaviour. We investigated effectiveness of interventions, barriers and comfort reminding others.Results280 participants (111 students and 169 residents) completed the questionnaire (response rate 27.8%). Residents and medical students reported hand hygiene behaviour compliance of 0.45 and 0.55, respectively (p=0.02). Resident and medical student knowledge was 0.80 and 0.73, respectively (p=0.001). The attitude index for residents was 0.56 and 0.55 for medical students. Regression analysis identified experiences as predictors of hand hygiene behaviour (both positive and negative influence). Knowledge was not a significant predictor of behaviour, but a working gel dispenser and observing attending physicians with good hand hygiene practices were reported by both groups as the most effective strategy in influencing trainees.ConclusionsMedical students and residents have similar attitudes about hand hygiene, but differ in their level of knowledge and compliance. Concerns about hierarchy may have a significant negative impact on hand hygiene advocacy.
Gauging quantum groups: Yang–Baxter joining Yang–Mills
Authors: Wu Yong-Shi 
Published: February 2016

This review is an expansion of my talk at the conference on Sixty Years of Yang–Mills Theory. I review and explain the line of thoughts that lead to a recent joint work with Hu and Geer [Hu et al., arXiv:1502.03433] on the construction, exact solutions and ubiquitous properties of a class of quantum group gauge models on a honey-comb lattice. Conceptually the construction achieves a synthesis of the ideas of Yang–Baxter equations with those of Yang–Mills theory. Physically the models describe topological anyonic states in 2D systems.
Cemitérios verticais, espaço urbano e meio ambiente: O novo discurso científico universitário de incentivo a verticalização do cemitério e cremação.
Authors: Thompson Barbara 
Published: February 2016

􀀈􀂕􀂖􀂇􀀃􀂇􀂕􀂖􀂗􀂆􀂑􀀃􀂘􀂋􀂕􀂃􀀃􀂝􀀃􀂃􀂐􀂞􀂎􀂋􀂕􀂇􀀃􀂆􀂑􀀃􀂆􀂋􀂕􀂅􀂗􀂔􀂕􀂑􀀃􀂅􀂋􀂇􀂐􀂖Este estudo visa à análise do discurso científico que, nos últimos tempos, vem difundindo e incentivando a implantação de cemintérios verticais e de crematórios no Brasil. Entre 2000 e 2014, diversos artigos acadêmicos abordaram a contaminação das águas subterrâneas devido ao necrochorume produzido pela decomposição dos corpos. Assim, esta análise se apresenta como uma ponderação favorável à reestruturação dos cemitérios, enquanto parte da solução do problema de degradação ambiental. De antemão, faz-se necessário esclarecer a inviabilidade de conclusões categóricas, dada a atualidade do estudo – ainda em andamento. Visa-se, então, a fim de corroborar para a literatura específica de um estudo tão recente, a comparação entre o discurso higienista dos séculos XVIII e XIX, e o discurso científico hodierno da sustentabilidade ambiental. A relevância dessa comparação reside na configuração do espaço urbano, que leva em conta a forma como a sociedade concebe a morte. O discurso mais antigo, por exemplo, foi responsável pelo afastamento dos cemitérios da Igreja Católica em relação à cidade. No atual contexto, por outro lado, a verticalização dos cemitérios é cientificamenete favorecida pelo fator meio ambiente. Tais investigações convergem para um desenredo que, embora aponte para valorização da sustentabilidade, apresenta-se ainda dicotômico: a defesa do meio ambiente é tão válida quanto necessária, todavia consiste num discurso científico que oculta a negação da morte, presente em nossa sociedade. O cemitério vertical extingue símbolos que promovem a memória dos mortos e dos grupos. Com a decadência do objeto material da memória, isto é, do túmulo monumental, os grupos que se relacionam com essa memória poderão ser enfraquecidos.
Steinernema beitlechemi n. sp., a new entomopathogenic nematode (Nematoda: Steinernematidae) from South Africa
Authors: Çimen Harun , Půža Vladimír , Nermuť Jiří , Hatting Justin , Ramakuwela Tshima , Faktorová Lucie , Hazir Selcuk 
Published: February 2016

Steinernema beitlechemin. sp. is a new species of entomopathogenic nematode isolated from soil samples collected in Bethlehem, Free State province, South Africa. The infective juveniles ofS. beitlechemin. sp. are characterised by a body length of 696 (606-768) μm, position of nerve ring of 96 (86-105) μm from the head and lateral fields with six ridges (i.e., seven lines) in mid-body. First-generation males ofS. beitlechemin. sp. can be distinguished by a spicule length of 93 (88-100) μm and 12 pairs of genital papillae. First-generation females have a moderately protruding vulva and a rounded tail tip bearing one spine-like projection. The new species is further characterised by sequences of the ITS and partial 28S regions of the ribosomal DNA. Phylogenetic analyses showS. beitlechemin. sp. as a member of a strongly supported monophyletic clade with three other African species:S. sacchari,S. cameroonenseandS. nyetense.
On the Zonal Near-Constancy of Fractional Solar Absorption in the Atmosphere
Authors: Hakuba Maria Z. , Folini Doris , Wild Martin 
Published: February 2016

Abstract
Over Europe, a recent study found the fractional all-sky atmospheric solar absorption to be largely unaffected by variations in latitude, remaining nearly constant at its regional mean of 23% ± 1%, relative to the respective top-of-atmosphere insolation. The satellite-based CERES EBAF dataset (2000–10) confirms the weak latitude dependence within 23% ± 2%, representative of the near-global scale between 60°S and 60°N. Under clear-sky conditions, the fractional absorption follows the spatial imprint of the water vapor path, peaking in the tropics and decreasing toward the poles, accompanied by a slight hemispheric asymmetry. In the northern extratropics, the clear-sky absorption attains zonal near-constancy due to combined water vapor, surface albedo, and aerosol effects that are largely amiss in the Southern Hemisphere. In line with earlier studies, the CERES EBAF suggests an increase in atmospheric solar absorption due to clouds by on average 1.5% (5 W m−2) from 21.5% (78 W m−2) under clear-sky conditions to 23% (83 W m−2) under all-sky conditions (60°S–60°N). The low-level clouds in the extratropics act to enhance the absorption, whereas the high clouds in the tropics exhibit a near-zero effect. Consequently, clouds reduce the latitude dependence of fractional atmospheric solar absorption and yield a near-constant zonal mean pattern under all-sky conditions. In the GEWEX-SRB satellite product and the historical simulations from phase 5 of CMIP (CMIP5; 1996–2005, multimodel mean) the amount of insolation absorbed by the atmosphere is reduced by around −1.3% (5 W m−2) with respect to the CERES EBAF mean. The zonal variability and magnitude of the atmospheric cloud effect are, however, largely in line.