bluuebunny/crossref_metadata_2025_split huggingface dataset:
FRET in a Synthetic Flavin‐ and Bilin‐binding Protein
Authors: Simon Julian , Losi Aba , Zhao Kai‐Hong , Gärtner Wolfgang 
Published: January 2017

AbstractThe last decade has seen development and application of a large number of novel fluorescence‐based techniques that have revolutionized fluorescence microscopy in life sciences. Preferred tags for such applications are genetically encoded fluorescent proteins (FP), mostly derivatives of the green fluorescent protein (GFP). Combinations of FPs with wavelength‐separated absorption/fluorescence properties serve as excellent tools for molecular interaction studies, for example, protein–protein complexes or enzyme–substrate interactions, based on the FRET phenomenon (Förster resonance energy transfer). However, alternatives are requested for experimental conditions where FP proteins or FP couples are not or less efficiently applicable. We here report as a “proof of principle” a specially designed, non‐naturally occurring protein (LG1) carrying a combination of a flavin‐binding LOV‐ and a photochromic bilin‐binding GAF domain and demonstrate a FRET process between both chromophores.
Spermine and Spermidine Alter Gene Expression and Antigenic Profile of Borrelia burgdorferi
Authors: Lin Ying-Han , Romo Jesus A. , Smith Trever C. , Reyes Ann N. , Karna S. L. Rajasekhar , Miller Christine L. , Van Laar Tricia A. , Yendapally Raghunandan , Chambers James P. , Seshu J. 
Published: January 2017

ABSTRACT

Borrelia burgdorferi
, the agent of Lyme disease, responds to numerous host-derived signals to alter adaptive capabilities during its enzootic cycle in an arthropod vector and mammalian host. Molecular mechanisms that enable
B. burgdorferi
to detect, channel, and respond to these signals have become an intense area of study for developing strategies to limit transmission/infection. Bioinformatic analysis of the borrelial genome revealed the presence of polyamine transport components (PotA, PotB, PotC, and PotD), while homologs for polyamine biosynthesis were conspicuously absent. Although
potABCD
is cotranscribed, the level of PotA was elevated under
in vitro
growth conditions mimicking unfed ticks compared to the level in fed ticks, while the levels of PotD were similar under the aforementioned conditions in
B. burgdorferi
. Among several polyamines and polyamine precursors, supplementation of spermine or spermidine in the borrelial growth medium induced synthesis of major regulators of gene expression in
B. burgdorferi
, such as RpoS and BosR, with a concomitant increase in proteins that contribute to colonization and survival of
B. burgdorferi
in the mammalian host. Short transcripts of
rpoS
were elevated in response to spermidine, which was correlated with increased protein levels of RpoS. Transcriptional analysis of
rpoZ
and
B. burgdorferi
rel
(

rel
Bbu

;
bb0198
) in the presence of spermidine revealed the interplay of multiple regulatory factors in
B. burgdorferi
gene expression. The effect of spermidine on the levels of select borrelial proteins was also influenced by serum factors. These studies suggest that multiple host-derived signals/nutrients and their transport systems contribute to
B. burgdorferi
adaptation during the vector and vertebrate host phases of infection.
Enhanced Antibody Detection and Diagnosis of Coccidioidomycosis with the MiraVista IgG and IgM Detection Enzyme Immunoassay
Authors: Malo Joshua , Holbrook Eric , Zangeneh Tirdad , Strawter Chris , Oren Eyal , Robey Ian , Erickson Heidi , Chahal Racquel , Durkin Michelle , Thompson Cindy , Hoover Susan E. , Ampel Neil M. , Wheat L. Joseph , Knox Kenneth S. 
Published: January 2017

ABSTRACT

Coccidioidomycosis is a common cause of community-acquired pneumonia in areas of the southwestern United States in which the disease is endemic. Clinical presentations range from self-limited disease to severe disseminated disease. Therefore, early and accurate diagnosis is essential to ensure appropriate treatment and monitoring. Currently available diagnostic tests have variable accuracy, particularly in certain patient populations, and new tests may offer improved accuracy for the diagnosis of coccidioidomycosis. Serum samples from 103 cases of coccidioidomycosis and 373 controls were tested for IgG and IgM antibodies using the MVista anti-
Coccidioides
antibody enzyme immunoassay. Serum specimens from 170 controls from areas in which the disease is endemic and 44 cases were tested by immunodiffusion at MiraVista Diagnostics. The sensitivity of the MVista antibody assay was 88.3%, and the specificity was 90%. The sensitivity was maintained in the presence of immunocompromising conditions or immunosuppressive therapies. The sensitivity of immunodiffusion was 60.2%, and the specificity was 98.8%. The sensitivity of complement fixation (62 cases) was 66.1%, but the specificity could not be determined. The MVista anti-
Coccidioides
antibody enzyme immunoassay offers improved sensitivity, compared with immunodiffusion and complement fixation, is not impaired in immunocompromised patients, and permits highly reproducible semiquantification.
Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment
Authors: Li Tengguo , Unger Elizabeth R. , Batra Dhwani , Sheth Mili , Steinau Martin , Jasinski Jean , Jones Jennifer , Rajeevan Mangalathu S. 
Published: January 2017

ABSTRACTWe designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.
Calibration of BK Virus Nucleic Acid Amplification Testing to the 1st WHO International Standard for BK Virus
Authors: Tan Susanna K. , Milligan Stephen , Sahoo Malaya K. , Taylor Nathaniel , Pinsky Benjamin A. 
Published: January 2017

ABSTRACT

Significant interassay variability in the quantification of BK virus (BKV) DNA precludes establishing broadly applicable thresholds for the management of BKV infection in transplantation. The 1st WHO International Standard for BKV (primary standard) was introduced in 2016 as a common calibrator for improving the harmonization of BKV nucleic acid amplification testing (NAAT) and enabling comparisons of biological measurements worldwide. Here, we evaluated the Altona RealStar BKV assay (Altona) and calibrated the results to the international unit (IU) using the Exact Diagnostics BKV verification panel, a secondary standard traceable to the primary standard. The primary and secondary standards on Altona had nearly identical linear regression equations (primary standard, Y = 1.05X − 0.28,
R
2
= 0.99; secondary standard, Y = 1.04X − 0.26,
R
2
= 0.99) and conversion factors (primary standard, 1.11 IU/copy; secondary standard, 1.09 IU/copy). A comparison of Altona with a laboratory-developed BKV NAAT assay in IU/ml versus copies/ml using Passing-Bablok regression revealed similar regression lines, no proportional bias, and improvement in the systematic bias (95% confidence interval of intercepts: copies/ml, −0.52 to −1.01; IU/ml, 0.07 to −0.36). Additionally, Bland-Altman analyses revealed a clinically significant reduction of bias when results were reported in IU/ml (IU/ml, −0.10 log
10
; copies/ml, −0.70 log
10
). These results indicate that the use of a common calibrator improved the agreement between the two assays. As clinical laboratories worldwide use calibrators traceable to the primary standard to harmonize BKV NAAT results, we anticipate improved interassay comparisons with a potential for establishing broadly applicable quantitative BKV DNA load cutoffs for clinical practice.
GRP78 Is an Important Host Factor for Japanese Encephalitis Virus Entry and Replication in Mammalian Cells
Authors: Nain Minu , Mukherjee Sriparna , Karmakar Sonali Porey , Paton Adrienne W. , Paton James C. , Abdin M. Z. , Basu Anirban , Kalia Manjula , Vrati Sudhanshu 
Published: January 2017

ABSTRACT
Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is the leading cause of viral encephalitis in Southeast Asia with potential to become a global pathogen. Here, we identify glucose-regulated protein 78 (GRP78) as an important host protein for virus entry and replication. Using the plasma membrane fractions from mouse neuronal (Neuro2a) cells, mass spectroscopy analysis identified GRP78 as a protein interacting with recombinant JEV envelope protein domain III. GRP78 was found to be expressed on the plasma membranes of Neuro2a cells, mouse primary neurons, and human epithelial Huh-7 cells. Antibodies against GRP78 significantly inhibited JEV entry in all three cell types, suggesting an important role of the protein in virus entry. Depletion of GRP78 by small interfering RNA (siRNA) significantly blocked JEV entry into Neuro2a cells, further supporting its role in virus uptake. Immunofluorescence studies showed extensive colocalization of GRP78 with JEV envelope protein in virus-infected cells. This interaction was also confirmed by immunoprecipitation studies. Additionally, GRP78 was shown to have an important role in JEV replication, as treatment of cells post-virus entry with subtilase cytotoxin that specifically cleaved GRP78 led to a substantial reduction in viral RNA replication and protein synthesis, resulting in significantly reduced extracellular virus titers. Our results indicate that GRP78, an endoplasmic reticulum chaperon of the HSP70 family, is a novel host factor involved at multiple steps of the JEV life cycle and could be a potential therapeutic target.

IMPORTANCE
Recent years have seen a rapid spread of mosquito-borne diseases caused by flaviviruses. The flavivirus family includes West Nile, dengue, Japanese encephalitis, and Zika viruses, which are major threats to public health with potential to become global pathogens. JEV is the major cause of viral encephalitis in several parts of Southeast Asia, affecting a predominantly pediatric population with a high mortality rate. This study is focused on identification of crucial host factors that could be targeted to cripple virus infection and ultimately lead to development of effective antivirals. We have identified a cellular protein, GRP78, that plays a dual role in virus entry and virus replication, two crucial steps of the virus life cycle, and thus is a novel host factor that could be a potential therapeutic target.
Ethnic differences in coeliac disease autoimmunity in childhood: the Generation R Study
Authors: Jansen Michelle A E , Beth Sytske A , van den Heuvel Diana , Kiefte-de Jong Jessica C , Raat Hein , Jaddoe Vincent W V , van Zelm Menno C , Moll Henriette A 
Published: January 2017

ObjectiveThe aim was to identify whether ethnic differences in coeliac disease autoimmunity (CDA) in children at 6 years of age exist, and when present, to evaluate how these differences may be explained by sociodemographic and environmental factors.DesignThis study was embedded within a multi-ethnic population-based prospective cohort study.Setting and patients4442 six-year-old children born between 2002 and 2006 were included. Information on ethnicity, environmental and lifestyle characteristics was assessed by questionnaires. Ethnicity was categorised into Western (Dutch, European, Indonesian, American, Oceanian) and non-Western (Turkish, Moroccan, Cape Verdean, Antillean, Surinamese). Serum transglutaminase type 2 antibody (TG2A) levels were measured with fluorescence enzyme immunoassay. Serum IgG levels against cytomegalovirus (CMV) were measured by ELISA.Main outcome measuresTG2A positivity was defined as TG2A ≥7 U/mL, strong TG2A positivity as TG2A ≥10 upper limit normal (70 U/mL).ResultsOf 4442 children, 60 (1.4%) children were TG2A positive, of whom 31 were strong positive. 66% of children were Western, 33% non-Western. Western ethnicity, high socioeconomic position and daycare attendance were positively associated with strong TG2A positivity (odds ratio (OR) 6.85 (1.62 to 28.8) p<0.01, OR 3.70 (1.40 to 9.82) p<0.01, OR 3.90 (1.38 to 11.0) p=0.01 resp.), whereas CMV seropositivity was inversely related to strong TG2A positivity (OR 0.32 (0.12 to 0.84) p=0.02). Together, these factors explained up to 47% (−67 to −17; p=0.02) of the ethnic differences in TG2A positivity between Western and non-Western children.ConclusionsEthnic differences in children with CDA are present in childhood. Socioeconomic position, daycare attendance and CMV seropositivity partly explained these differences, which may serve as targets for prevention strategies for CDA.
Cancer incidence and mortality risks in a large US Barrett's oesophagus cohort
Authors: Cook Michael B , Coburn Sally B , Lam Jameson R , Taylor Philip R , Schneider Jennifer L , Corley Douglas A 
Published: January 2017

ObjectiveBarrett's oesophagus (BE) increases the risk of oesophageal adenocarcinoma by 10–55 times that of the general population, but no community-based cancer-specific incidence and cause-specific mortality risk estimates exist for large cohorts in the USA.DesignWithin Kaiser Permanente Northern California (KPNC), we identified patients with BE diagnosed during 1995–2012. KPNC cancer registry and mortality files were used to estimate standardised incidence ratios (SIR), standardised mortality ratios (SMR) and excess absolute risks.ResultsThere were 8929 patients with BE providing 50 147 person-years of follow-up. Compared with the greater KPNC population, patients with BE had increased risks of any cancer (SIR=1.40, 95% CI 1.31 to 1.49), which slightly decreased after excluding oesophageal cancer. Oesophageal adenocarcinoma risk was increased 24 times, which translated into an excess absolute risk of 24 cases per 10 000 person-years. Although oesophageal adenocarcinoma risk decreased with time since BE diagnosis, oesophageal cancer mortality did not, indicating that the true risk is stable and persistent with time. Relative risks of cardia and stomach cancers were increased, but excess absolute risks were modest. Risks of colorectal, lung and prostate cancers were unaltered. All-cause mortality was slightly increased after excluding oesophageal cancer (SMR=1.24, 95% CI 1.18 to 1.31), but time-stratified analyses indicated that this was likely attributable to diagnostic bias. Cause-specific SMRs were elevated for ischaemic heart disease (SMR=1.39, 95% CI 1.18 to 1.63), respiratory system diseases (SMR=1.51, 95% CI 1.29 to 1.75) and digestive system diseases (SMR=2.20 95% CI 1.75 to 2.75).ConclusionsPatients with BE had a persistent excess risk of oesophageal adenocarcinoma over time, although their absolute excess risks for this cancer, any cancer and overall mortality were modest.
Descending antinociception induced by secondary somatosensory cortex stimulation in experimental neuropathy: role of the medullospinal serotonergic pathway
Authors: Sagalajev Boriss , Viisanen Hanna , Wei Hong , Pertovaara Antti 
Published: January 2017

Stimulation of the secondary somatosensory cortex (S2) has attenuated pain in humans and inflammatory nociception in animals. Here we studied S2 stimulation-induced antinociception and its underlying mechanisms in an experimental animal model of neuropathy induced by spinal nerve ligation (SNL). Effect of S2 stimulation on heat-evoked limb withdrawal latency was assessed in lightly anesthetized rats that were divided into three groups based on prior surgery and monofilament testing before induction of anesthesia: 1) sham-operated group and 2) hypersensitive and 3) nonhypersensitive (mechanically) SNL groups. In a group of hypersensitive SNL animals, a 5-HT1Areceptor agonist was microinjected into the rostroventromedial medulla (RVM) to assess whether autoinhibition of serotonergic cell bodies blocks antinociception. Additionally, effect of S2 stimulation on pronociceptive ON-cells and antinociceptive OFF-cells in the RVM or nociceptive spinal wide dynamic range (WDR) neurons were assessed in anesthetized hypersensitive SNL animals. S2 stimulation induced antinociception in hypersensitive but not in nonhypersensitive SNL or sham-operated animals. Antinociception was prevented by a 5-HT1Areceptor agonist in the RVM. Antinociception was associated with decreased duration of heat-evoked response in RVM ON-cells. In spinal WDR neurons, heat-evoked discharge was delayed by S2 stimulation, and this antinociceptive effect was prevented by blocking spinal 5-HT1Areceptors. The results indicate that S2 stimulation suppresses nociception in SNL animals if SNL is associated with tactile allodynia-like hypersensitivity. In hypersensitive SNL animals, S2 stimulation induces antinociception mediated by medullospinal serotonergic pathways acting on the spinal 5-HT1Areceptor, and partly through reduction of the RVM ON-cell discharge.NEW & NOTEWORTHY Stimulation of S2 cortex, but not that of an adjacent cortical area, induced descending heat antinociception in rats with the spinal nerve ligation-induced model of neuropathy. Antinociception was bilateral, and it involved suppression of pronociceptive medullary cells and activation of serotonergic pathways that act on the spinal 5-HT1Areceptor. S2 stimulation failed to induce descending antinociceptive effect in sham-operated controls or in nerve-ligated animals that had not developed mechanical hypersensitivity.
Endometrial Cancer Risk Factors, Hormone Receptors, and Mortality Prediction
Authors: Busch Evan L. , Crous-Bou Marta , Prescott Jennifer , Chen Maxine M. , Downing Michael J. , Rosner Bernard A. , Mutter George L. , De Vivo Immaculata 
Published: January 2017

AbstractBackground: Endometrial tumors arise from a hormonally responsive tissue. Defining subtypes by hormone receptor expression might better inform etiology and prediction of patient outcomes. We evaluated the potential role of tumor estrogen receptor (ER) and progesterone receptor (PR) expression to define endometrial cancer subtypes.Methods: We measured semi-continuous ER and PR protein expression in tissue specimens from 360 endometrial primary tumors from the Nurses' Health Study. To explore the impact of different definitions of marker positivity, we dichotomized ER and PR expression at different cut points in increments of 5% positive cells. Logistic regression was used to estimate associations between endometrial cancer risk factors, such as body mass index, with dichotomous ER or PR status. Reclassification statistics were used to assess whether adding dichotomous ER or PR status to standard prognostic factors of stage, grade, and histologic type would improve endometrial cancer-specific mortality prediction.Results: Compared with not being obese, obesity increased the odds of having an ER-positive tumor at cut points of 0% to 20% [maximum OR, 2.92; 95% confidence interval (CI), 1.34–6.33] as well as the odds of having a PR-positive tumor at cut points of 70% to 90% (maximum OR, 2.53; 95% CI, 1.36–4.68). Adding dichotomous tumor ER or PR status to the panel of standard predictors did not improve both model discrimination and calibration.Conclusions: Obesity may be associated with greater endometrial tumor expression of ER and PR. Adding either marker does not appear to improve mortality prediction beyond the standard predictors.Impact: Body mass index might explain some of the biological variation among endometrial tumors. Cancer Epidemiol Biomarkers Prev; 26(5); 727–35. ©2017 AACR.
Fixed-Dose Combinations of Pioglitazone and Metformin for Lung Cancer Prevention
Authors: Seabloom Donna E. , Galbraith Arthur R. , Haynes Anna M. , Antonides Jennifer D. , Wuertz Beverly R. , Miller Wendy A. , Miller Kimberly A. , Steele Vernon E. , Miller Mark Steven , Clapper Margie L. , O'Sullivan M. Gerard , Ondrey Frank G. 
Published: January 2017

Abstract
Combination treatment with pioglitazone and metformin is utilized clinically in the treatment of type II diabetes. Treatment with this drug combination reduced the development of aerodigestive cancers in this patient population. Our goal is to expand this treatment into clinical lung cancer chemoprevention. We hypothesized that dietary delivery of metformin/pioglitazone would prevent lung adenoma formation in A/J mice in a benzo[a]pyrene (B[a]P)-induced carcinogenesis model while modulating chemoprevention and anti-inflammatory biomarkers in residual adenomas. We found that metformin (500 and 850 mg/kg/d) and pioglitazone (15 mg/kg/d) produced statistically significant decreases in lung adenoma formation both as single-agent treatments and in combination, compared with untreated controls, after 15 weeks. Treatment with metformin alone and in combination with pioglitazone resulted in statistically significant decreases in lung adenoma formation at both early- and late-stage interventions. Pioglitazone alone resulted in significant decreases in adenoma formation only at early treatment intervention. We conclude that oral metformin is a viable chemopreventive treatment at doses ranging from 500 to 1,000 mg/kg/d. Pioglitazone at 15 mg/kg/d is a viable chemopreventive agent at early-stage interventions. Combination metformin and pioglitazone performed equal to metformin alone and better than pioglitazone at 15 mg/kg/d. Because the drugs are already FDA-approved, rapid movement to human clinical studies is possible. Cancer Prev Res; 10(2); 116–23. ©2017 AACR.
Árabe, fale hebraico: a língua como último reduto da batalha identitária do árabe israelense
Authors: Schlesinger Juliana Portenoy 
Published: January 2017

A língua é um componente importante quando abordamos a questão da identidade. No caso das crônicas do escritor árabe israelense Sayed Kashua, a temática da língua de escrita aparece quase que de maneira obsessiva. A maneira como Kashua trata o tema da língua não é convencional e nem poderia ser. Sayed Kashua é um árabe israelense que escreve toda a sua obra ficcional e jornalística em hebraico. Baseando-se na análise de diversas crônicas do autor publicadas no jornal israelense Haaretz, este artigo analisa como Kashua lida com a língua como uma ferramenta de identidade. Por meio do humor e da autoironia, este árabe israelense transita entre culturas, fidelidades e infidelidades e coloca a língua, tanto o hebraico quanto o árabe, no centro da batalha identitária e último reduto do árabe em contato com o ethos judaico israelense.