bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Expansion and Contraction ofcagACopy Number inHelicobacter pyloriImpact Development of Gastric Disease
Authors: Jang Sungil , Su Hanfu , Blum Faith C. , Bae Sarang , Choi Yun Hui , Kim Aeryun , Hong Youngmin A. , Kim Jinmoon , Kim Ji-Hye , Gunawardhana Niluka , Jeon Yeong-Eui , Yoo Yun-Jung , Merrell D. Scott , Ge Linhu , Cha Jeong-Heon 
Published: February 2017

ABSTRACTInfection withHelicobacter pyloriis a major risk factor for development of gastric disease, including gastric cancer. Patients infected withH. pyloristrains that express CagA are at even greater risk of gastric carcinoma. Given the importance of CagA, this report describes a new molecular mechanism by which thecagAcopy number dynamically expands and contracts inH. pylori. Analysis of strain PMSS1 revealed a heterogeneous population in terms of numbers ofcagAcopies; strains carried from zero to four copies ofcagAthat were arranged as direct repeats within the chromosome. Each of the multiple copies ofcagAwas expressed and encoded functional CagA; strains with morecagArepeats exhibited higher levels of CagA expression and increased levels of delivery and phosphorylation of CagA within host cells. This concomitantly resulted in more virulent phenotypes as measured by cell elongation and interleukin-8 (IL-8) induction. Sequence analysis of the repeat region revealed threecagAhomologous areas (CHAs) within thecagArepeats. Of these, CHA-ud flanked each of thecagAcopies and is likely important for the dynamic variation ofcagAcopy numbers. Analysis of a large panel of clinical isolates showed that 7.5% ofH. pyloristrains isolated in the United States harbored multiplecagArepeats, while none of the tested Korean isolates carried more than one copy ofcagA. Finally,H. pyloristrains carrying multiplecagAcopies were differentially associated with gastric disease. Thus, the dynamic expansion and contraction ofcagAcopy numbers may serve as a novel mechanism by whichH. pylorimodulates gastric disease development.IMPORTANCESeverity ofH. pylori-associated disease is directly associated with carriage of the CagA toxin. Though the sequences of the CagA protein can differ across strains, previous analyses showed that virtually allH. pyloristrains carry one or no copies ofcagA. This study showed thatH. pylorican carry multiple tandem copies ofcagAthat can change dynamically. Isolates harboring morecagAcopies produced more CagA, thus enhancing toxicity to host cells. Analysis of 314H. pyloriclinical strains isolated from patients in South Korea and the United States showed that 7.5% of clinical strains in the United States carried multiplecagAcopies whereas none of the South Korean strains did. This study demonstrated a novel molecular mechanism by whichH. pyloridynamically modulatescagAcopy number, which affects CagA expression and activity and may impact downstream development of gastric disease.
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
Authors: Olm Matthew R. , Butterfield Cristina N. , Copeland Alex , Boles T. Christian , Thomas Brian C. , Banfield Jillian F. 
Published: February 2017

ABSTRACT

In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of
Delftia acidovorans
SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples.
D. acidovorans
was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods.

IMPORTANCE
It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.
Mutation of the N-Terminal Region of Chikungunya Virus Capsid Protein: Implications for Vaccine Design
Authors: Taylor Adam , Liu Xiang , Zaid Ali , Goh Lucas Y. H. , Hobson-Peters Jody , Hall Roy A. , Merits Andres , Mahalingam Suresh 
Published: February 2017

ABSTRACT

Mosquito-transmitted chikungunya virus (CHIKV) is an arthritogenic alphavirus of the
Togaviridae
family responsible for frequent outbreaks of arthritic disease in humans. Capsid protein, a structural protein encoded by the CHIKV RNA genome, is able to translocate to the host cell nucleolus. In encephalitic alphaviruses, nuclear translocation induces host cell transcriptional shutoff; however, the role of capsid protein nucleolar localization in arthritogenic alphaviruses remains unclear. Using recombinant enhanced green fluorescent protein (EGFP)-tagged expression constructs and CHIKV infectious clones, we describe a nucleolar localization sequence (NoLS) in the N-terminal region of capsid protein, previously uncharacterized in CHIKV. Mutation of the NoLS by site-directed mutagenesis reduced efficiency of nuclear import of CHIKV capsid protein. In the virus, mutation of the capsid protein NoLS (CHIKV-NoLS) attenuated replication in mammalian and mosquito cells, producing a small-plaque phenotype. Attenuation of CHIKV-NoLS is likely due to disruption of the viral replication cycle downstream of viral RNA synthesis. In mice, CHIKV-NoLS infection caused no disease signs compared to wild-type CHIKV (CHIKV-WT)-infected mice; lack of disease signs correlated with significantly reduced viremia and decreased expression of proinflammatory factors. Mice immunized with CHIKV-NoLS, challenged with CHIKV-WT at 30 days postimmunization, develop no disease signs and no detectable viremia. Serum from CHIKV-NoLS-immunized mice is able to efficiently neutralize CHIKV infection
in vitro
. Additionally, CHIKV-NoLS-immunized mice challenged with the related alphavirus Ross River virus showed reduced early and peak viremia postchallenge, indicating a cross-protective effect. The high degree of CHIKV-NoLS attenuation may improve CHIKV antiviral and rational vaccine design.

IMPORTANCE
CHIKV is a mosquito-borne pathogen capable of causing explosive epidemics of incapacitating joint pain affecting millions of people. After a series of major outbreaks over the last 10 years, CHIKV and its mosquito vectors have been able to expand their range extensively, now making CHIKV a human pathogen of global importance. With no licensed vaccine or antiviral therapy for the treatment of CHIKV disease, there is a growing need to understand the molecular determinants of viral pathogenesis. These studies identify a previously uncharacterized nucleolar localization sequence (NoLS) in CHIKV capsid protein, begin a functional analysis of site-directed mutants of the capsid protein NoLS, and examine the effect of the NoLS mutation on CHIKV pathogenesis
in vivo
and its potential to influence CHIKV vaccine design. A better understanding of the pathobiology of CHIKV disease will aid the development of effective therapeutic strategies.
Periprocedural outcomes and early safety with the use of the Pipeline Flex Embolization Device with Shield Technology for unruptured intracranial aneurysms: preliminary results from a prospective clinical study
Authors: Martínez-Galdámez Mario , Lamin Saleh M , Lagios Konstantinos G , Liebig Thomas , Ciceri Elisa F , Chapot Rene , Stockx Luc , Chavda Swarupsinh , Kabbasch Christoph , Farago Giuseppe , Nordmeyer Hannes , Boulanger Thierry , Piano Mariangela , Boccardi Edoardo P 
Published: February 2017

Background and purposeThe Pipeline Embolization Device (PED) has become a routine first-line option for treatment of intracranial aneurysms (IAs). We assessed the early safety and technical success of a new version of PED, Pipeline Flex Embolization Device with Shield Technology (Pipeline Shield), which has the same design and configuration but has been modified to include a surface synthetic biocompatible polymer.Materials and methodsThe Pipeline Flex Embolization Device with Shield Technology (PFLEX) study is a prospective, single-arm, multicenter study for the treatment of unruptured IAs using Pipeline Shield. The primary study endpoints included the occurrence of major stroke in the territory supplied by the treated artery or neurologic death at 1 year post-procedure. Secondary endpoints included the rate of Pipeline Shield-related or procedure-related serious or non-serious adverse events. Analyses were conducted to evaluate early safety findings in the 30-day post-procedure period as well as technical procedural success outcomes.ResultsFifty patients with 50 unruptured target IAs were enrolled. Mean aneurysm diameter was 8.82±6.15 mm. Thirty-eight aneurysms (76%) were small (<10 mm). Device deployment was technically successful with 98% of devices. Complete wall apposition was achieved immediately post-procedure in 48 cases (96%). No major strokes or neurologic deaths were reported in the 30-day post-procedure period.ConclusionsThe results of this first experience with the new Pipeline Flex corroborate the early safety of the device. Mid-term and long-term follow-up examinations will provide data on safety outcomes at the 6-month and 1-year follow-up periods.Clinical trial registrationNCT02390037.
DOES ADOPTION OF MULTIPLE CLIMATE-SMART PRACTICES IMPROVE FARMERS’ CLIMATE RESILIENCE? EMPIRICAL EVIDENCE FROM THE NILE BASIN OF ETHIOPIA
Authors: TEKLEWOLD HAILEMARIAM , MEKONNEN ALEMU , KOHLIN GUNNAR , DI FALCO SALVATORE 
Published: February 2017

There is a paucity of information on conditioning factors that hinder or promote adoption of multiple climate-smart practices and on the synergies among such practices in increasing household resilience by improving agricultural income. This study analyzes how heat, rainfall, and rainfall variability affect farmers’ choices of a portfolio of potential climate smart practices — agricultural water management, improved crop seeds, and fertilizer — and the impact of these practices on farm income in the Nile Basin of Ethiopia. We apply a multinomial endogenous switching regression approach by modeling combinations of practices and net farm income for each combination as depending on household and farm characteristics and on a set of climatic variables based on geo-referenced historical precipitation and temperature data. A primary result of this study is that farmers are less likely to adopt fertilizer (either alone or in combination with improved varieties) in areas of greater rainfall variability. However, even when there is high variability in rainfall, farmers are more likely to adopt these two yield-increasing inputs when they choose to (and are able to) include the third part of the portfolio: agricultural water management. Net farm income responds positively to agricultural water management, improved crop variety or fertilizer when they are adopted in isolation as well as in combination. But this effect is greater when these practices are combined. Simulation results suggest that a warming temperature and decreased precipitation in future decades will make it less likely that farmers will adopt practices in isolation but more likely that they will adopt a combination of practices. Hence, a package approach rather than a piecemeal approach is needed to maximize the synergies implicit in various climate smart practices.
Modeling the diversity of spontaneous and agonist-induced electrical activity in anterior pituitary corticotrophs
Authors: Fletcher Patrick A. , Zemkova Hana , Stojilkovic Stanko S. , Sherman Arthur 
Published: February 2017

Pituitary corticotrophs fire action potentials spontaneously and in response to stimulation with corticotropin-releasing hormone (CRH) and arginine vasopressin (AVP), and such electrical activity is critical for calcium signaling and calcium-dependent adrenocorticotropic hormone secretion. These cells typically fire tall, sharp action potentials when spontaneously active, but a variety of other spontaneous patterns have also been reported, including various modes of bursting. There is variability in reports of the fraction of corticotrophs that are electrically active, as well as their patterns of activity, and the sources of this variation are not well understood. The ionic mechanisms responsible for CRH- and AVP-triggered electrical activity in corticotrophs are also poorly characterized. We use electrophysiological measurements and mathematical modeling to investigate possible sources of variability in patterns of spontaneous and agonist-induced corticotroph electrical activity. In the model, variation in as few as two parameters can give rise to many of the types of patterns observed in electrophysiological recordings of corticotrophs. We compare the known mechanisms for CRH, AVP, and glucocorticoid actions and find that different ionic mechanisms can contribute in different but complementary ways to generate the complex time courses of CRH and AVP responses. In summary, our modeling suggests that corticotrophs have several mechanisms at their disposal to achieve their primary function of pacemaking depolarization and increased electrical activity in response to CRH and AVP. NEW & NOTEWORTHY We and others recently demonstrated that the electrical activity and calcium dynamics of corticotrophs are strikingly diverse, both spontaneously and in response to the agonists CRH and AVP. Here we demonstrate this diversity with electrophysiological measurements and use mathematical modeling to investigate its possible sources. We compare the known mechanisms of agonist-induced activity in the model, showing how the context of ionic conductances dictates the effects of agonists even when their target is fixed.
Performance and Diagnostic Accuracy of a Urine-Based Human Papillomavirus Assay in a Referral Population
Authors: Cuzick Jack , Cadman Louise , Ahmad Amar S. , Ho Linda , Terry George , Kleeman Michelle , Lyons Deirdre , Austin Janet , Stoler Mark H. , Vibat Cecile Rose T. , Dockter Janel , Robbins David , Billings Paul R. , Erlander Mark G. 
Published: February 2017

Abstract
Background: Human papillomavirus (HPV) testing from clinician-collected cervical and self-collected cervico-vaginal samples is more sensitive for detecting CIN2+/CIN3+ than cytology-based screening, stimulating interest in HPV testing from urine. The objective was to determine the performance of the Trovagene HPV test for the detection of CIN2+ from urine and PreservCyt cervical samples.
Methods: Women referred for colposcopy at St Mary's Hospital (London, United Kingdom), following abnormal cytology, were recruited to this diagnostic accuracy study by convenience sampling (September 2011 to April 2013). A total of 501 paired urine and cervical samples were collected. Primary outcomes were sensitivity for CIN2+/CIN3+ and specificity for &lt;CIN2; secondary outcomes were comparisons with other HPV tests and agreement/kappa values between urine and cervical samples.
Results: Trovagene HPV test sensitivity and specificity from PreservCyt were similar to well-established tests [sensitivity for CIN3+ (n = 145) 96.3% (95% confidence interval (CI), 89.6–99.2); CIN2+ (n = 81) 94.5% (95% CI, 89.4–97.6); specificity for &lt;CIN2 25.3% (95% CI, 20.8–30.1)]. Sensitivity from urine was slightly, but not significantly, lower [CIN3+ 91.4% (95% CI, 83.0–96.5), P = 0.3; CIN2+ 88.3% (95% CI, 81.9–93.0), P = 0.06]. Specificity for &lt;CIN2 was similar: 24.7% (95% CI, 20.3–29.5), P = 0.9. A total of 403 Trovagene cervical and 396 urine HPV tests were positive. Overall agreement between paired samples was 82.6% (95% CI, 79.3–86.0).
Conclusions: Trovagene HPV test's performance on PreservCyt cervical samples was comparable with established HPV tests. Sensitivity in urine, although slightly lower, may nevertheless be adequate for self-sampling. This referral population's higher HPV positivity rate affects specificity, warranting further studies in a screening population.
Impact: This may prove useful for women not attending for cervical screening. Cancer Epidemiol Biomarkers Prev; 26(7); 1053–9. ©2017 AACR.
PD-L1 Studies Across Tumor Types, Its Differential Expression and Predictive Value in Patients Treated with Immune Checkpoint Inhibitors
Authors: Kluger Harriet M. , Zito Christopher R. , Turcu Gabriela , Baine Marina K. , Zhang Hongyi , Adeniran Adebowale , Sznol Mario , Rimm David L. , Kluger Yuval , Chen Lieping , Cohen Justine V. , Jilaveanu Lucia B. 
Published: February 2017

Abstract
Purpose: With recent approval of inhibitors of PD-1 in melanoma, non–small cell lung cancer (NSCLC) and renal cell carcinoma, extensive efforts are under way to develop biomarkers predictive of response. PD-L1 expression has been most widely studied, and is more predictive in NSCLC than renal cell carcinoma or melanoma. We therefore studied differences in expression patterns across tumor types.
Experimental Design: We used tissue microarrays with tumors from NSCLC, renal cell carcinoma, or melanoma and a panel of cell lines to study differences between tumor types. Predictive studies were conducted on samples from 65 melanoma patients treated with PD-1 inhibitors alone or with CTLA-4 inhibitors, characterized for outcome. PD-L1 expression was studied by quantitative immunofluorescence using two well-validated antibodies.
Results: PD-L1 expression was higher in NSCLC specimens than renal cell carcinoma, and lowest in melanoma (P = 0.001), and this finding was confirmed in a panel of cell lines. In melanoma tumors, PD-L1 was expressed either on tumor cells or immune-infiltrating cells. The association between PD-L1 expression in immune-infiltrating cells and progression-free or overall-survival in melanoma patients treated with ipilimumab and nivolumab was stronger than PD-L1 expression in tumor cells, and remained significant on multivariable analysis.
Conclusions: PD-L1 expression in melanoma tumor cells is lower than NSCLC or renal cell carcinoma cells. The higher response rate in melanoma patients treated with PD-1 inhibitors is likely related to PD-L1 in tumor-associated inflammatory cells. Further studies are warranted to validate the predictive role of inflammatory cell PD-L1 expression in melanoma and determine its biological significance. Clin Cancer Res; 23(15); 4270–9. ©2017 AACR.
Calcium-Dependent Enhancement by Extracellular Acidity of the Cytotoxicity of Mitochondrial Inhibitors against Melanoma
Authors: Noguchi Fumihito , Inui Shigeki , Fedele Clare , Shackleton Mark , Itami Satoshi 
Published: February 2017

Abstract
Extracellular acidity is a hallmark of cancers and is independent of hypoxia. Because acidity potentiates malignant phenotypes, therapeutic strategies that enhance the targeting of oncogenic mechanisms in an acidic microenvironment should be effective. We report here that drugs which abrogate mitochondrial respiration show enhanced cytotoxicity against melanoma cells in a normoxic but acidic extracellular pH, independent from P53 mutations, BRAF (V600E) mutations, and/or resistance against BRAF inhibitors. Conversely, the cytotoxicity against melanoma cells of mitochondrial inhibitors is impaired by a neutral or alkaline extracellular pH, and in vivo systemic alkalinization with NaHCO3 enhanced subcutaneous tumor growth and lung metastasis of B16F10 cells in mice treated with the mitochondrial inhibitor phenformin. Intracellular calcium (Ca2+) was significantly increased in melanoma cells treated with mitochondrial inhibitors at an acidic extracellular pH and an intracellular Ca2+ chelator, BAPTA/AM, inhibited cytoplasmic Ca2+ as well as melanoma cell death. Surprisingly, ROS scavengers synergized with increased apoptosis in cells treated with mitochondrial inhibitors, suggesting that ROS contributes to cell survival in this context. Notably, the cytotoxic enhancement of mitochondrial inhibitors by acidity was distinct from PGC1alpha-driven mitochondrial addiction, from therapy-induced senescence, and from slow, JARID1B-high–associated cell cycling, all of which have been shown to promote vulnerability to mitochondrial inhibition. These data indicate that extracellular pH profoundly modulates the cytotoxicity of mitochondrial inhibitors against cancer cells. Mol Cancer Ther; 16(5); 936–47. ©2017 AACR.
Role of STAT3 and FOXO1 in the Divergent Therapeutic Responses of Non-metastatic and Metastatic Bladder Cancer Cells to miR-145
Authors: Jiang Guosong , Huang Chao , Li Jingxia , Huang Haishan , Jin Honglei , Zhu Junlan , Wu Xue-Ru , Huang Chuanshu 
Published: February 2017

Abstract
Although miR-145 is the most frequently downregulated miRNA in bladder cancer, its exact stage association and downstream effector have not been defined. Here, we found that miR-145 was upregulated in human patients with bladder cancer with lymph node metastasis and in metastatic T24T cell line. Forced expression of miR-145 promoted anchorage-independent growth of T24T cells accompanied by the downregulation of forkhead box class O1 (FOXO1). In contrast, in non-metastatic T24 cells, miR-145 overexpression inhibited cell growth with upregulation of FOXO1, and the knockdown of FOXO1 abolished the miR-145–mediated inhibition of cell growth. Mechanistic studies revealed that miR-145 directly bound to and attenuated 3′-untranslated region (UTR) activity of foxo1 mRNA in both T24 and T24T cells. Interestingly, miR-145 suppressed STAT3 phosphorylation at Tyr705 and increased foxo1 promoter transcriptional activity in T24 cells, but not in T24T cells, suggesting a role of STAT3 in the divergent responses to miR-145. Supporting this was our finding that STAT3 knockdown mimicked miR-145–mediated upregulation of FOXO1 in T24T cells and inhibition of anchorage-independent growth. Consistently, ectopic expression of miR-145 promoted tumor formation of xenograft T24T cells, whereas such promoting effect became inhibitory due to specific knockdown of STAT3. Together, our findings demonstrate the stage-specific association and function of miR-145 in bladder cancers and provide novel insights into the therapeutic targeting of miR-145. Mol Cancer Ther; 16(5); 924–35. ©2017 AACR.