bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiologically guided approach to characterizing respiratory motion
Authors: White Benjamin M. , Zhao Tianyu , Lamb James M. , Bradley Jeffrey D. , Low Daniel A. 
Published: November 2013

Purpose:To characterize radiation therapy patient breathing patterns based on measured external surrogate information.Methods:Breathing surrogate data were collected during 4DCT from a cohort of 50 patients including 28 patients with lung cancer and 22 patients without lung cancer. A spirometer and an abdominal pneumatic bellows were used as the surrogates. The relationship between these measurements was assumed to be linear within a small phase difference. The signals were correlated and drift corrected using a previously published method to convert the signal into tidal volume. The airflow was calculated with a first order time derivative of the tidal volume using a window centered on the point of interest and with a window length equal to the CT gantry rotation period. The airflow was compared against the tidal volume to create ellipsoidal patterns that were binned into 25 ml × 25 ml/s bins to determine the relative amount of time spent in each bin. To calculate the variability of the maximum inhalation tidal volume within a free‐breathing scan timeframe, a metric based on percentile volume ratios was defined. The free breathing variability metric (κ) was defined as the ratio between extreme inhalation tidal volumes (defined as >93 tidal volume percentile of the measured tidal volume) and normal inhalation tidal volume (defined as >80 tidal volume percentile of the measured tidal volume).Results:There were three observed types of volume‐flow curves, labeled Types 1, 2, and 3. Type 1 patients spent a greater duration of time during exhalation withκ = 1.37 ± 0.11. Type 2 patients had equal time duration spent during inhalation and exhalation with κ = 1.28 ± 0.09. The differences between the mean peak exhalation to peak inhalation tidal volume, breathing period, and the 85th tidal volume percentile for Type 1 and Type 2 patients were statistically significant at the 2% significance level. The difference between κ and the 98th tidal volume percentile for Type 1 and Type 2 patients was found to be statistically significant at the 1% significance level. Three patients did not display a breathing stability curve that could be classified as Type 1 or Type 2 due to chaotic breathing patterns. These patients were classified as Type 3 patients.Conclusions:Based on an observed volume‐flow curve pattern, the cohort of 50 patients was divided into three categories called Type 1, Type 2, and Type 3. There were statistically significant differences in breathing characteristics between Type 1 and Type 2 patients. The use of volume‐flow curves to classify patients has been demonstrated as a physiological characterization metric that has the potential to optimize gating windows in radiation therapy.
Subtractive Phage Display Selection from Canine Visceral Leishmaniasis Identifies Novel Epitopes That Mimic Leishmania infantum Antigens with Potential Serodiagnosis Applications
Authors: Costa Lourena E. , Lima Mayara I. S. , Chávez-Fumagalli Miguel A. , Menezes-Souza Daniel , Martins Vivian T. , Duarte Mariana C. , Lage Paula S. , Lopes Eliane G. P. , Lage Daniela P. , Ribeiro Tatiana G. , Andrade Pedro H. R. , de Magalhães-Soares Danielle F. , Soto Manuel , Tavares Carlos A. P. , Goulart Luiz R. , Coelho Eduardo A. F. 
Published: November 2013

ABSTRACTVisceral leishmaniasis (VL) is a zoonotic disease that is endemic to Brazil, where dogs are the main domestic parasite reservoirs, and the percentages of infected dogs living in regions where canine VL (CVL) is endemic have ranged from 10% to 62%. Despite technological advances, some problems have been reported with CVL serodiagnosis. The present study describes a sequential subtractive selection through phage display technology from polyclonal antibodies of negative and positive sera that resulted in the identification of potential bacteriophage-fused peptides that were highly sensitive and specific to antibodies of CVL. A negative selection was performed in which phage clones were adhered to purified IgGs from healthy andTrypanosoma cruzi-infected dogs to eliminate cross-reactive phages. The remaining supernatant nonadhered phages were submitted to positive selection against IgG from the blood serum of dogs that were infected withLeishmania infantum. Phage clones that adhered to purified IgGs from the CVL-infected serum samples were selected. Eighteen clones were identified and their reactivities tested by a phage enzyme-linked immunosorbent assay (phage-ELISA) against the serum samples from infected dogs (n= 31) compared to those from vaccinated dogs (n= 21), experimentally infected dogs with cross-reactive parasites (n= 23), and healthy controls (n= 17). Eight clones presented sensitivity, specificity, and positive and negative predictive values of 100%, and they showed no cross-reactivity withT. cruzi- orEhrlichia canis-infected dogs or with dogs vaccinated with two different commercial CVL vaccines in Brazil. Our study identified eight mimotopes ofL. infantumantigens with 100% accuracy for CVL serodiagnosis. The use of these mimotopes by phage-ELISA proved to be an excellent assay that was reproducible, simple, fast, and inexpensive, and it can be applied in CVL-monitoring programs.
Illustration of the Difficulty of Identifying Streptococcus equi Strains at the Subspecies Level through a Case of Endocarditis in an Immunocompetent Man
Authors: Daubié Anne Sophie , Defrance Carine , Renvoisé Aurélie , Barreda Eleodoro , D'Alessandro Cosimo , Brossier Florence , Jarlier Vincent , Aubry Alexandra 
Published: November 2013

ABSTRACT

We report a case of endocarditis caused by
Streptococcus equi
in an immunocompetent patient who was subsequently cured after appropriate antibiotherapy and cardiac surgery. However, it was challenging to identify the strain to the subspecies level, which highlights the necessity of developing reliable molecular tools to discriminate between the subspecies.
Direct, Interferon-Independent Activation of the CXCL10 Promoter by NF-κB and Interferon Regulatory Factor 3 during Hepatitis C Virus Infection
Authors: Brownell Jessica , Bruckner Jacob , Wagoner Jessica , Thomas Emmanuel , Loo Yueh-Ming , Gale Michael , Liang T. Jake , Polyak Stephen J. 
Published: November 2013

ABSTRACT

Hepatitis C virus (HCV) infection of hepatocytes leads to transcriptional induction of the chemokine CXCL10, which is considered an interferon (IFN)-stimulated gene. However, we have recently shown that IFNs are not required for CXCL10 induction in hepatocytes during acute HCV infection. Since the CXCL10 promoter contains binding sites for several proinflammatory transcription factors, we investigated the contribution of these factors to CXCL10 transcriptional induction during HCV infection
in vitro
. Wild-type and mutant CXCL10 promoter-luciferase reporter constructs were used to identify critical sites of transcriptional regulation. The proximal IFN-stimulated response element (ISRE) and NF-κB binding sites positively regulated CXCL10 transcription during HCV infection as well as following exposure to poly(I·C) (a Toll-like receptor 3 [TLR3] stimulus) and 5′ poly(U) HCV RNA (a retinoic acid-inducible gene I [RIG-I] stimulus) from two viral genotypes. Conversely, binding sites for AP-1 and CCAAT/enhancer-binding protein β (C/EBP-β) negatively regulated CXCL10 induction in response to TLR3 and RIG-I stimuli, while only C/EBP-β negatively regulated CXCL10 during HCV infection. We also demonstrated that interferon-regulatory factor 3 (IRF3) is transiently recruited to the proximal ISRE during HCV infection and localizes to the nucleus in HCV-infected primary human hepatocytes. Furthermore, IRF3 activated the CXCL10 promoter independently of type I or type III IFN signaling. The data indicate that sensing of HCV infection by RIG-I and TLR3 leads to direct recruitment of NF-κB and IRF3 to the CXCL10 promoter. Our study expands upon current knowledge regarding the mechanisms of CXCL10 induction in hepatocytes and lays the foundation for additional mechanistic studies that further elucidate the combinatorial and synergistic aspects of immune signaling pathways.
Liposome-Antigen-Nucleic Acid Complexes Protect Mice from Lethal Challenge with Western and Eastern Equine Encephalitis Viruses
Authors: Phillips Aaron T. , Schountz Tony , Toth Ann M. , Rico Amber B. , Jarvis Donald L. , Powers Ann M. , Olson Ken E. 
Published: November 2013

ABSTRACTAlphaviruses are mosquito-borne viruses that cause significant disease in animals and humans. Western equine encephalitis virus (WEEV) and eastern equine encephalitis virus (EEEV), two New World alphaviruses, can cause fatal encephalitis, and EEEV is a select agent of concern in biodefense. However, we have no antiviral therapies against alphaviral disease, and current vaccine strategies target only a single alphavirus species. In an effort to develop new tools for a broader response to outbreaks, we designed and tested a novel alphavirus vaccine comprised of cationic lipid nucleic acid complexes (CLNCs) and the ectodomain of WEEV E1 protein (E1ecto). Interestingly, we found that the CLNC component, alone, had therapeutic efficacy, as it increased survival of CD-1 mice following lethal WEEV infection. Immunization with the CLNC-WEEV E1ecto mixture (lipid-antigen-nucleic acid complexes [LANACs]) using a prime-boost regimen provided 100% protection in mice challenged with WEEV subcutaneously, intranasally, or via mosquito. Mice immunized with LANACs mounted a strong humoral immune response but did not produce neutralizing antibodies. Passive transfer of serum from LANAC E1ecto-immunized mice to nonimmune CD-1 mice conferred protection against WEEV challenge, indicating that antibody is sufficient for protection. In addition, the LANAC E1ecto immunization protocol significantly increased survival of mice following intranasal or subcutaneous challenge with EEEV. In summary, our LANAC formulation has therapeutic potential and is an effective vaccine strategy that offers protection against two distinct species of alphavirus irrespective of the route of infection. We discuss plausible mechanisms as well the potential utility of our LANAC formulation as a pan-alphavirus vaccine.
ISG15 Is Counteracted by Vaccinia Virus E3 Protein and Controls the Proinflammatory Response against Viral Infection
Authors: Eduardo-Correia Benedito , Martínez-Romero Carles , García-Sastre Adolfo , Guerra Susana 
Published: November 2013

ABSTRACT

Conjugation of ISG15 inhibits replication of several viruses. Here, using an expression system for assaying human and mouse ISG15 conjugations (ISGylations), we have demonstrated that vaccinia virus E3 protein binds and antagonizes human and mouse ISG15 modification. To study ISGylation importance in poxvirus infection, we used a mouse model that expresses deconjugating proteases. Our results indicate that ISGylation restricts
in vitro
replication of the vaccinia virus VVΔE3L mutant but unconjugated ISG15 is crucial to counteract the inflammatory response produced after VVΔE3L infection.
Accuracy in self-reported health literacy screening: a difference between men and women in Taiwan
Authors: Lee Shoou-Yih Daniel , Tsai Tzu-I , Tsai Yi-Wen 
Published: November 2013

ObjectiveSelf-reported screening questions are considered as an effective way to identify patients with limited health literacy. Yet research has shown that individuals tend to over-report their reading level. Moreover, the likelihood of over-reporting may differ between gender groups. This study examined if systematic differences exist between men and women in their response to self-reported screening questions.DesignA national survey in Taiwan with participants selected using a multistage stratified, probability-proportional-to-size sampling strategy.ParticipantsA total of 5682 Taiwanese adults aged 18 and older were sampled and recruited. Of those adults, 3491 participated in the survey, resulting in a 62.1% response rate. Both gender groups were equally represented in the final study sample.Main measuresSelf-reported health literacy was assessed using two sets of questions that asked how difficult it was for the respondent to understand written health materials and how often the participant needed assistance from others to understand written health materials. The objective level of health literacy was measured using the Mandarin Health Literacy Scale (MHLS).ResultsA significant gender difference was observed among participants who had inadequate health literacy: while women's self-report was in line with the MHLS test result, men had a significant tendency to over-report their comprehension of health information.ConclusionsIn Taiwan, screening questions are prone to socially desirable response and may underidentify male patients with inadequate health literacy. Development of a brief and easy-to-use health literacy test may be a more effective approach to health literacy screening in clinical settings. Alternatively, clinicians can verify patient comprehension of health information via the ‘teach back’ or ‘show me’ technique in order to improve communication and patient care. Research is needed to examine if gender differences in self-report of health literacy exist in other countries.
A Naturally Derived Small Molecule Disrupts Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Human Prostate Cancer Cells
Authors: Amin Karishma S. , Jagadeesh Shankar , Baishya Gakul , Rao Paruchuri G. , Barua Nabin C. , Bhattacharya Samir , Banerjee Partha P. 
Published: November 2013

AbstractContinued reliance on androgen receptor (AR) signaling is a hallmark of prostate cancer, including the development of castration-resistant prostate cancer (CRPC), making it an attractive therapeutic target for prostate cancer treatment. Mahanine is a novel carbazole alkaloid derived from the leaves of Murraya koenigii, commonly known as the curry leaf plant, which grows widely across East-Asia. We show here that mahanine possesses the ability to inhibit ligand-dependent and -independent AR transactivation, leading to a prominent decline in AR target gene expression. Mahanine treatment causes a time- and dose-dependent decline in AR protein levels, including truncated AR splice variants, in a panel of androgen-responsive and -independent prostate cancer cells. The decrease in AR levels induced by mahanine occurs posttranslationally by proteasomal degradation, without any change in the AR gene expression. Mahanine treatment induces an outward movement of the AR from the nucleus to the cytoplasm, leading to an initial increase in cytoplasmic AR levels, followed by a gradual decline in the AR levels in both cellular compartments. Ligand-induced AR phosphorylation at Ser-81, a phospho-site associated with prostate cancer cell growth and AR transactivity, is greatly diminished in the presence of mahanine. The decline in AR phosphorylation at Ser-81 by mahanine occurs via the inactivation of mitotic kinase CDK1. Collectively, our data demonstrate that mahanine strongly disrupts AR signaling and inhibits the growth of androgen-dependent and -independent prostate cancer cells, thereby implicating a therapeutic role of mahanine in prostate cancer treatment. Mol Cancer Ther; 13(2); 341–52. ©2013 AACR.
Synoptic Typing and Precursors of Heavy Warm-Season Precipitation Events at Montreal, Québec
Authors: Milrad Shawn M. , Atallah Eyad H. , Gyakum John R. , Dookhie Giselle 
Published: November 2013

Abstract
A precipitation climatology is compiled for warm-season events at Montreal, Québec, Canada, using 6-h precipitation data. A total of 1663 events are recorded and partitioned into three intensity categories (heavy, moderate, and light), based on percentile ranges. Heavy (top 10%) precipitation events (n = 166) are partitioned into four types, using a unique manual synoptic typing based on the divergence of Q-vector components. Type A is related to cyclones and strong synoptic-scale quasigeostrophic (QG) forcing for ascent, with high-θe air being advected into the Montreal region from the south. Types B and C are dominated by frontogenesis (mesoscale QG forcing for ascent). Specifically, type B events are warm frontal and feature a near-surface temperature inversion, while type C events are cold frontal and associated with the largest-amplitude synoptic-scale precursors of any type. Finally, type D events are associated with little synoptic or mesoscale QG forcing for ascent and, thus, are deemed to be convective events triggered by weak shortwave vorticity maxima moving through a long-wave ridge environment, in the presence of an anomalously warm, humid, and unstable air mass that is conducive to convection. In general, types A and B feature the strongest dynamical forcing for ascent, while types C and D feature the lowest atmospheric stability. Systematic higher precipitation amounts are not preferential to any event type, although a handful of the largest warm-season precipitation events appear to be slow-moving type C (stationary front) cases.
In vitro synergistic activity of colistin with tigecycline or β-lactam antibiotic/β-lactamase inhibitor combinations against carbapenem-resistant Acinetobacter baumannii
Authors: Karaoglan Ilkay , Zer Yasemin , Bosnak Vuslat Kecik , Mete Ayse Ozlem , Namıduru Mustafa 
Published: November 2013

Objective Nosocomial infection caused by carbapenem-resistant Acinetobacter baumannii is a worldwide problem and treatment options remain controversial. This study investigated the in vitro effect of various antibiotic combinations against carbapenem-resistant A. baumannii strains. Methods Antibiotic susceptibility of A. baumannii strains was analysed. In vitro synergistic efficacy of colistin combined with tigecycline, cefoperazone/sulbactam or piperacillin/tazobactam was tested against carbapenem-resistant A. baumannii strains. Synergy studies were performed using an eplisometer test-strip method. Results Of the 50 carbapenem-resistant A. baumannii strains tested, 96% were susceptible to colistin and 64% were susceptible to tigecycline. Colistin–tigecycline, colistin–cefoperazone/sulbactam and colistin–piperacillin/tazobactam combinations were found to have synergistic effects against six (12%), two (4%), and one (2%), respectively, of the strains tested. Conclusions Colistin combined with tigecycline, cefoperazone/sulbactam or piperacillin/tazobactam revealed synergistic effects in some carbapenem-resistant A. baumannii strains. These results, together with the shortage of treatment options and the risk of developing resistance to colistin, suggest that clinicians should use colistin combined with other antibiotics or β-lactamase inhibitors when treating carbapenem-resistant A. baumannii infection.
A novel and essential role for FcγRIIa in cancer cell–induced platelet activation
Authors: Mitrugno Annachiara , Williams David , Kerrigan Steven W. , Moran Niamh 
Published: November 2013

Key PointsThe immune receptor FcγRIIa is a key mediator of tumor cell activation of platelets in the circulation. Secretion of adenosine 5′-diphosphate from dense granules is the primary response of platelets to activation by tumor cells.
Genome wide gene-expression analysis of facultative reproductive diapause in the two-spotted spider mite Tetranychus urticae
Authors: Bryon Astrid , Wybouw Nicky , Dermauw Wannes , Tirry Luc , Van Leeuwen Thomas 
Published: November 2013

Abstract

Background
Diapause or developmental arrest, is one of the major adaptations that allows mites and insects to survive unfavorable conditions. Diapause evokes a number of physiological, morphological and molecular modifications. In general, diapause is characterized by a suppression of the metabolism, change in behavior, increased stress tolerance and often by the synthesis of cryoprotectants. At the molecular level, diapause is less studied but characterized by a complex and regulated change in gene-expression. The spider mite Tetranychus urticae is a serious polyphagous pest that exhibits a reproductive facultative diapause, which allows it to survive winter conditions. Diapausing mites turn deeply orange in color, stop feeding and do not lay eggs.

Results
We investigated essential physiological processes in diapausing mites by studying genome-wide expression changes, using a custom built microarray. Analysis of this dataset showed that a remarkable number, 11% of the total number of predicted T. urticae genes, were differentially expressed. Gene Ontology analysis revealed that many metabolic pathways were affected in diapausing females. Genes related to digestion and detoxification, cryoprotection, carotenoid synthesis and the organization of the cytoskeleton were profoundly influenced by the state of diapause. Furthermore, we identified and analyzed an unique class of putative antifreeze proteins that were highly upregulated in diapausing females. We also further confirmed the involvement of horizontally transferred carotenoid synthesis genes in diapause and different color morphs of T. urticae.

Conclusions
This study offers the first in-depth analysis of genome-wide gene-expression patterns related to diapause in a member of the Chelicerata, and further adds to our understanding of the overall strategies of diapause in arthropods.
Prioritizing genes responsible for host resistance to influenza using network approaches
Authors: Bao Suying , Zhou Xueya , Zhang Liangcai , Zhou Jie , To Kelvin Kai-Wang , Wang Binbin , Wang Liqiu , Zhang Xuegong , Song You-Qiang 
Published: November 2013

AbstractBackgroundThe genetic make-up of humans and other mammals (such as mice) affects their resistance to influenza virus infection. Considering the complexity and moral issues associated with experiments on human subjects, we have only acquired partial knowledge regarding the underlying molecular mechanisms. Although influenza resistance in inbred mice has been mapped to several quantitative trait loci (QTLs), which have greatly narrowed down the search for host resistance genes, only few underlying genes have been identified.ResultsTo prioritize a list of promising candidates for future functional investigation, we applied network-based approaches to leverage the information of known resistance genes and the expression profiles contrasting susceptible and resistant mouse strains. The significance of top-ranked genes was supported by different lines of evidence from independent genetic associations, QTL studies, RNA interference (RNAi) screenings, and gene expression analysis. Further data mining on the prioritized genes revealed the functions of two pathways mediated by tumor necrosis factor (TNF): apoptosis and TNF receptor-2 signaling pathways. We suggested that the delicate balance between TNF’s pro-survival and apoptotic effects may affect hosts’ conditions after influenza virus infection.ConclusionsThis study considerably cuts down the list of candidate genes responsible for host resistance to influenza and proposed novel pathways and mechanisms. Our study also demonstrated the efficacy of network-based methods in prioritizing genes for complex traits.