bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring magnetosomal pH of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using pH-sensitive fluorescent proteins
Authors: Eguchi Yukako , Fukumori Yoshihiro , Taoka Azuma 
Published: March 2018

Abstract
Magnetotactic bacteria synthesize uniform-sized and regularly shaped magnetic nanoparticles in their organelles termed magnetosomes. Homeostasis of the magnetosome lumen must be maintained for its role accomplishment. Here, we developed a method to estimate the pH of a single living cell of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using a pH-sensitive fluorescent protein E2GFP. Using the pH measurement, we estimated that the cytoplasmic pH was approximately 7.6 and periplasmic pH was approximately 7.2. Moreover, we estimated pH in the magnetosome lumen and cytoplasmic surface using fusion proteins of E2GFP and magnetosome-associated proteins. The pH in the magnetosome lumen increased during the exponential growth phase when magnetotactic bacteria actively synthesize magnetite crystals, whereas pH at the magnetosome surface was not affected by the growth stage. This live-cell pH measurement method will help for understanding magnetosome pH homeostasis to reveal molecular mechanisms of magnetite biomineralization in the bacterial organelle.
Political Freedom as an Islamic Value
Authors: Decosimo David 
Published: March 2018

AbstractThe esteemed scholar Michael Cook has recently argued that political freedom is “not an Islamic value” but is in tension with Islam. This paper contends that Cook is mistaken. It moves in four steps. First, I consider the very idea of an “Islamic value,” sketching a nonessentialist way of conceiving such a thing. Next, I show that the particular “liberal” notion of political freedom that Cook rightly claims is absent is but one of three distinct conceptions of political freedom: he neglects to consider the possible presence of an alternate “republican” conception. Then, taking some of the very evidence Cook cites along with the case of al-Ghazālī, I show that this republican conception figures in Islamic thought and practice. I conclude by considering some broader interpretive issues that bear on this matter and have wider significance. Political freedom, it turns out, is an Islamic value after all.
Discovery of a radio nebula around PSR J0855−4644
Authors: Maitra C , Roy S , Acero F , Gupta Y 
Published: March 2018

Abstract
We report the discovery of a diffuse radio emission around PSR J0855−4644 using an upgraded GMRT (uGMRT) observation at 1.35 GHz. The radio emission is spatially coincident with the diffuse X-ray pulsar wind nebula (PWN) seen with XMM–Newton but is much larger in extent compared to the compact axisymmetric PWN seen with Chandra. The morphology of the emission, with a bright partial ring-like structure and two faint tail-like features strongly resembles a bow shock nebula, and indicates a velocity of 100 km s−1 through the ambient medium. We conclude that the emission is most likely to be associated with the radio PWN of PSR J0855−4644. From the integrated flux density, we estimate the energetics of the PWN.
AzBio Speech Understanding Performance in Quiet and Noise in High Performing Cochlear Implant Users
Authors: Brant Jason A. , Eliades Steven J. , Kaufman Hannah , Chen Jinbo , Ruckenstein Michael J. 
Published: March 2018

Objective:
To evaluate high-performing cochlear implant patients’ performance on AzBio sentence testing.

Methods:
Retrospective review of prospectively collected database at a tertiary care hospital. Unilateral cochlear implant patients with AzBio testing were included. The primary outcome of interest was AzBio performance scores in quiet and at +10 and +5 decibels signal to noise (dB S/N).

Results:
One hundred eighty five subjects met inclusion criteria with scores for AzBio in quiet, 114 at +10 dB S/N, and 66 at +5 dB S/N. Linear mixed effects models showed performance significantly correlated with time since activation in all conditions (8.4%/yr; p < 0.0001). Strong correlations between mean performance in quiet and at +10 dB S/N (r = 0.77, p < 0.0001), and between +10 and +5 dB S/N (r = 0.73, p < 0.0001) were found. The correlation between quiet and +5 dB S/N (r = 0.45, p = 0.01) was less robust. Shapiro-Wilks test of normality found only +10 dB S/N to correspond to a normal distribution. Skew analysis demonstrated values of –0.64, –0.11, and 0.8 for quiet, +10 dB S/N, and +5 dB S/N, respectively.

Conclusions:
AzBio scores at +10 dB S/N show a strong correlation with, but avoid the ceiling effects that limit the usefulness of testing in quiet for high performing cochlear implant users, making it the preferred test in this population. Significant complexities exist in the study of outcomes in cochlear implant recipients, and there is no single test that is ideal for the entirety of this population.
Risky Sexual Behavior Among Individuals Receiving Buprenorphine/Naloxone Opiate Dependency Treatment: HIV Prevention Trials Network (HPTN) 058
Authors: Shava Emily , Lipira Lauren E. , Beauchamp Geetha G. , Donnell Deborah J. , Lockman Shahin , Ruan Yuhua , Shao Yiming 
Published: March 2018

Introduction:
Understanding the role of opiate dependency treatment in risky sexual behavior could help optimize interventions for people who inject drugs (PWID).

Objectives:
We evaluated whether long-term medication-assisted treatment (LT-MAT) of opiate dependency with buprenorphine/naloxone influenced risky sexual behavior among HIV-uninfected PWID and identified predictors of risky sexual behavior.

Methods:
We used data from HPTN 058, a randomized controlled trial of LT-MAT vs. short-term medication-assisted treatment among PWID in China and Thailand. We evaluated associations between randomized opiate dependency treatment group and self-reported risky sexual behaviors within the past month: condomless sex with primary partner, condomless sex with nonprimary partner, multiple partners, and more than 3 sexual acts. We used generalized estimating equations to conduct intention-to-treat, as-treated, and exploratory analyses of these associations.

Results:
Of 1250 participants included in the analysis, 92% were male, with median age of 34 years (interquartile range 28–39). At baseline, referring to the past month, 36% of participants reported condomless sex with primary partner, 4% reported condomless sex with nonprimary partner, 6% reported multiple sex partners, and 30% reported more than 3 sexual acts. Risky sexual behaviors did not differ significantly between treatment groups at any point. Significant predictors (P < 0.05) of condomless sex with nonprimary partner were history of incarceration and noninjection drug use. Number of needle-sharing partners, noninjection drug use, and higher income were predictors for multiple sexual partners.

Conclusions:
LT-MAT did not significantly modify risky sexual behavior among HIV-uninfected PWID. Interventions that reduce sexual risk should target PWID with history of incarceration, alcohol use, and needle sharing.
FDG-Avid Focal Liver Reaction From Proton Therapy in a Patient With Primary Esophageal Adenocarcinoma
Authors: Ahmed Hena S. , Pantel Austin R. , Metz James M. , Plastaras John P. , Farwell Michael D. 
Published: March 2018

Abstract
A 25-year-old man with IgA deficiency was treated with 2 months of chemotherapy and proton therapy for gastroesophageal junction adenocarcinoma. Restaging PET/CT 18 days posttherapy demonstrated 2 new foci of increased FDG uptake in the left hepatic lobe, which were favored to represent radiation injury as opposed to new metastases. Follow-up MRI with contrast 2 weeks later demonstrated hypoenhancement and T1/T2 hypointensity in the liver, without restricted diffusion, which correlated with the dominant FDG-avid focus. The hepatic lesions resolved on subsequent FDG PET/CT and MRI studies, confirming the diagnosis of acute radiation injury.
Three Primary Carcinomas on 18F-FDG PET/CT
Authors: Wu Dayong , Hu Yujing , Wei Qiang , Tian Congna , Bian Yanzhu 
Published: March 2018

Abstract
A CT scan was performed on a 67-year-old man newly diagnosed with acute pancreatitis. The scan revealed a low-density lesion in the liver, a left renal nodule, and a right renal cystic mass. Intense 18F-FDG uptake was observed in the liver lesion and left renal nodule. No abnormal uptake was observed in the right renal mass. In addition, another focal intense uptake was observed in segment VII of the liver. Biopsies revealed intrahepatic cholangiocarcinomas in the 2 liver lesions, papillary renal cell carcinoma in the left renal lesion and clear cell renal cell carcinoma in the right renal lesion.
Unusually Elevated Gastric Radioactivity on 18F-FDG PET/CT in Diffuse Large B-Cell Lymphoma
Authors: Yin Hongyan , Liu Guobing , Xiu Yan , Luo Rongkui , Shi Hongcheng 
Published: March 2018

Abstract
A 41-year-old woman presented with abdominal distention, inappetence, and rapid emaciation for 1 month. Diffuse bulky gastric wall thickening with lymph nodes enlargement and peritoneal nodules were revealed using abdominal CT. Staging 18F-FDG PET/CT performed after admission demonstrated intensely diffuse FDG uptake in stomach, FDG-avid lymph nodes, and peritoneal nodular lesions. Postoperatively, these lesions were diagnosed as diffuse large B-cell lymphoma.
Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria
Authors: Zoledowska Sabina , Presta Luana , Fondi Marco , Decorosi Francesca , Giovannetti Luciana , Mengoni Alessio , Lojkowska Ewa 
Published: March 2018

ABSTRACTUnderstanding the plant-microbe interactions are crucial for improving plant productivity and plant protection. The latter aspect is particularly relevant for sustainable agriculture and development of new preventive strategies against the spread of plant diseases. Constraint-based metabolic modeling is providing one of the possible ways to investigate the adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. In this study, we present a curated metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193. Using flux balance analysis (FBA), we predict the metabolic adaptation to two different ecological niches, relevant for the persistence and the plant colonization by this bacterium: soil and rhizosphere. We performed in silico gene deletions to predict the set of core essential genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen and a scaffold to interpret future –omics datasets for this bacterium.
Explaining international footballer selection through Poisson modelling
Authors: Butler David , Butler Robert , Doran Justin , O’Connor Sean 
Published: March 2018

Purpose
Growing evidence suggests regional economic factors impact on individual outcomes, such as life expectancy and well-being. The purpose of this paper is to investigate the impact that player-specific and regional differences have on the number of senior international appearances football players accumulate over the course of their careers, for six UEFA member countries, from 1993 to 2014.

Design/methodology/approach
The research employs a Poisson regression model to analyse the impact of individual and regional factors on the number of senior international caps a footballer receives over the course of their career.

Findings
The results indicate that both individual and regional variables can explain the number of caps a player receives over the course of their career. The authors find that an individual’s career length positively influences the number of international caps accrued. Players born in wealthier and more populous regions accumulate a greater number of international appearances. Distance from the capital has no effect, however, the number of youth academies in the player’s region of birth has a significant positive effect.

Research limitations/implications
The analysis is limited to regional variations within economically developed states. It would be interesting to test whether the correlation between relative regional development and international success exists in less developed countries. The authors only address mens international football in this study and cannot comment on the generality of the findings across genders or sports.

Practical implications
The results can provide insights for local football authorities and policy makers concerned with regional characteristics and those interested in the development of elite talent.

Originality/value
This is the first study to analyse a pan-European data set, using an increasingly adopted econometric method to understanding regional economic development – Poisson modelling.
Deep-Sequencing Analysis of the Dynamics of HIV-1 Quasiespecies in Naive Patients during a Short Exposure to Maraviroc
Authors: Cascajero Almudena , Rastrojo Alberto , Díez-Fuertes Francisco , Hernández-Novoa Beatriz , Aguado Begoña , Moreno Santiago , Alcami José , Pérez-Olmeda Mayte 
Published: March 2018

ABSTRACT

In this study, we have characterized quasispecies dynamics and the evolution of viral tropism in naive HIV-1-infected patients treated with a short course of maraviroc monotherapy (ClinicalTrials.gov registration no. NCT01060618) independently of the tropism of the infecting virus. We randomly selected 20 patients infected with viruses displaying different basal tropisms—10 carrying R5 and 10 carrying dual/mixed X4 (DM/X4) viruses—at recruitment as determined by phenotypic assay (Trofile). Evolution of viral quasiespecies at the end of treatment was determined by ultradeep sequencing of the V3 region using a 454 Life Sciences Platform and geno2pheno (g2p) algorithm for viral tropism prediction. The false-positive rate (FPR) that defines the probability of classifying an R5 virus falsely as X4 was set at 10%. X4-specific HIV-1 viral load (VL) was calculated from sequences with an FPR of <3.75%. Virological response as defined as >1-log
10
copies/ml reduction in VL was detected in 70% of patients independently of the basal tropism of the infecting virus. Viral tropism remained stable, and nonsignificant differences in FPR values before and after treatment were found for the majority of patients in both tropism groups. Only three patients (one with R5 and two with DM/X4 viruses) showed an increased (>1 log) X4 VL, and one patient harboring a DM/X4-tropic virus displayed a significant reduction in FPR values at the end of treatment. Fast changes in the composition of viral populations were observed in all patients after 10 days of maraviroc (MVC) monotherapy treatment, and a complete replacement of viral quasiespecies was found in 3/10 patients carrying R5-using viruses and 4/10 patients carrying DM/X4-using viruses.

IMPORTANCE
Initiation of treatment with maraviroc requires previous determination of viral tropism by genotypic or phenotypic methods because of the risk of treatment failure and selection of DM/X4-tropic variants. In this study, we confirm previous work showing that the virologic response to maraviroc is independent of basal tropism. By deep-sequencing analysis, we determined that fast changes in viral populations were due to the emergence of minority variants in some patients whereas in others generation of new strains was detected. The risk of DM/X4 selection was very low as FPR values remained stable, and only one patient showed a detrimental switch to DM/X4 variants. Our data show that some DM/X4 viruses are sensitive to maraviroc treatment probably because only a low proportion of DM/X4 viruses use preferentially the X4 receptor and contain authentically maraviroc-resistant viruses that are not accurately detected by current assays.
Characterization of H5N1 Influenza Virus Quasispecies with Adaptive Hemagglutinin Mutations from Single-Virus Infections of Human Airway Cells
Authors: Watanabe Yohei , Arai Yasuha , Kawashita Norihito , Ibrahim Madiha S. , Elgendy Emad M. , Daidoji Tomo , Kajikawa Junichi , Hiramatsu Hiroaki , Sriwilaijaroen Nongluk , Ono Takao , Takagi Tatsuya , Takahashi Kazuo , Shioda Tatsuo , Matsumoto Kazuhiko , Suzuki Yasuo , Nakaya Takaaki 
Published: March 2018

ABSTRACT
Transmission of avian influenza (AI) viruses to mammals involves phylogenetic bottlenecks that select small numbers of variants for transmission to new host species. However, little is known about the AI virus quasispecies diversity that produces variants for virus adaptation to humans. Here, we analyzed the hemagglutinin (HA) genetic diversity produced during AI H5N1 single-virus infection of primary human airway cells and characterized the phenotypes of these variants. During single-virus infection, HA variants emerged with increased fitness to infect human cells. These variants generally had decreased HA thermostability, an indicator of decreased transmissibility, that appeared to compensate for their increase in α2,6-linked sialic acid (α2,6 Sia) binding specificity and/or in the membrane fusion pH threshold, each of which is an advantageous mutational change for viral infection of human airway epithelia. An HA variant with increased HA thermostability also emerged but could not outcompete variants with less HA thermostability. These results provided data on HA quasispecies diversity in human airway cells.

IMPORTANCE
The diversity of the influenza virus quasispecies that emerges from a single infection is the starting point for viral adaptation to new hosts. A few studies have investigated AI virus quasispecies diversity during human adaptation using clinical samples. However, those studies could be appreciably affected by individual variability and multifactorial respiratory factors, which complicate identification of quasispecies diversity produced by selective pressure for increased adaptation to infect human airway cells. Here, we found that detectable HA genetic diversity was produced by H5N1 single-virus infection of human airway cells. Most of the HA variants had increased fitness to infect human airway cells but incurred a fitness cost of less HA stability. To our knowledge, this is the first report to characterize the adaptive changes of AI virus quasispecies produced by infection of human airway cells. These results provide a better perspective on AI virus adaptation to infect humans.
ERAP1-Dependent Antigen Cross-Presentation Determines Efficacy of Adoptive T-cell Therapy in Mice
Authors: Schmidt Karin , Keller Christin , Kühl Anja A. , Textor Ana , Seifert Ulrike , Blankenstein Thomas , Willimsky Gerald , Kloetzel Peter-Michael 
Published: March 2018

Abstract
Cytotoxic T lymphocytes can reject established tumors if their target peptide is efficiently presented by MHC class I molecules (pMHC-I) on the surface of cancerous cells. Therapeutic success upon adoptive T-cell transfer (ATT), however, requires additional cross-presentation of the same pMHC-I on noncancerous cells. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an enzyme that customizes the N-terminus of proteasome-generated peptides so they can be loaded onto MHC-I molecules in the endoplasmic reticulum (ER). We show here that ERAP1 is critically involved in the process of tumor rejection and assumes a dual role by independently operating on both sides. Direct presentation of two MHC-I–restricted epitopes of a cancer-driving transplantation rejection antigen through ERAP1 moderately affected tumor rejection by adoptively transferred T-cell receptor gene–modified T cells in each case. ERAP1 expression by antigen cross-presenting cells of the ATT recipients was critical for expansion of therapeutic monospecific T cells and correlated with tumor rejection. Specifically, lack of ERAP1 expression in the ATT recipient's noncancerous cells enabled progression of pMHC-I–positive, IFNγ-responsive tumors, despite the presence of antigen-specific functional cytotoxic T lymphocytes. These data reveal a decisive role for ERAP1 in T-cell–mediated tumor rejection and will enhance the choice of MHC-I–restricted epitopes targeted by adoptive T-cell transfer.
Significance: This study demonstrates a role of ERAP1 in the efficacy of adoptive T-cell transfer and has potential to improve personalized T-cell therapy for solid tumors. Cancer Res; 78(12); 3243–54. ©2018 AACR.
Adjuvant Treatment for POLE Proofreading Domain–Mutant Cancers: Sensitivity to Radiotherapy, Chemotherapy, and Nucleoside Analogues
Authors: Van Gool Inge C. , Rayner Emily , Osse Elisabeth M. , Nout Remi A. , Creutzberg Carien L. , Tomlinson Ian P.M. , Church David N. , Smit Vincent T.H.B.M. , de Wind Niels , Bosse Tjalling , Drost Mark 
Published: March 2018

Abstract
Purpose: Pathogenic POLE proofreading domain mutations are found in many malignancies where they are associated with ultramutation and favorable prognosis. The extent to which this prognosis depends on their sensitivity to adjuvant treatment is unknown, as is the optimal therapy for advanced-staged or recurrent POLE-mutant cancers.
Experimental Design: We examined the recurrence-free survival of women with POLE-mutant and POLE–wild-type endometrial cancers (EC) in the observation arm of the randomized PORTEC-1 endometrial cancer trial (N = 245 patients with stage I endometrial cancer for analysis). Sensitivity to radiotherapy and selected chemotherapeutics was compared between Pole-mutant mouse-derived embryonic stem (mES) cells, generated using CRISPR-Cas9 (Pole mutations D275A/E275A, and cancer-associated P286R, S297F, V411L) and isogenic wild-type cell lines.
Results: In the observation arm of the PORTEC-1 trial (N = 245), women with POLE-mutant endometrial cancers (N = 16) had an improved recurrence-free survival (10-year recurrence-free survival 100% vs. 80.1% for POLE–wild-type; HR, 0.143; 95% confidence interval, 0.001–0.996; P = 0.049). Pole mutations did not increase sensitivity to radiotherapy nor to chemotherapeutics in mES cells. In contrast, Pole-mutant cells displayed significantly increased sensitivity to cytarabine and fludarabine (IC50 Pole P286R–mutant vs. wild-type: 0.05 vs. 0.17 μmol/L for cytarabine, 4.62 vs. 11.1 μmol/L for fludarabine; P &lt; 0.001 for both comparisons).
Conclusions: The favorable prognosis of POLE-mutant cancers cannot be explained by increased sensitivity to currently used adjuvant treatments. These results support studies exploring minimization of adjuvant therapy for early-stage POLE-mutant cancers, including endometrial and colorectal cancers. Conversely, POLE mutations result in hypersensitivity to nucleoside analogues, suggesting the use of these compounds as a potentially effective targeted treatment for advanced-stage POLE-mutant cancers. Clin Cancer Res; 24(13); 3197–203. ©2018 AACR.
„Ich bewirke Rettung …“ (Ps 12,6)
Authors: Weber Beat 
Published: March 2018

AbstractTo date there have only been a few examinations of the psalms in terms of communication analysis. This article will illustrate the fruitfulness of such an approach by analysing Ps 12 according to it. First it will be demonstrated that the psalm consists of a series of speeches that occur in a liturgical sequence. It opens and closes with intercessory prayer, which forms a frame around a divine oracle in the centre. This oracle is itself further embedded in two instances of human address speech. The speaker functions as a “mediator” on behalf of a persecuted group. He presents their concerns to God in prayer, communicates God’s response back to them, and also communicates messages to them. The closest parallel to such a sequence can be found in the prophets (Habakkuk); as such Ps 12 is reminiscent of “cult prophecy.”
The Unplaced Fragments of P.Bodmer ii (P66)
Authors: Nongbri Brent , Sharp Daniel B. 
Published: March 2018

Abstract
Based on autopsy inspection of the fragmentary leaves of P.Bodmer ii (P66), this article assesses previous efforts to properly position the fragments of P.Bodmer ii that were left unplaced in the initial publication of the codex and offers new suggestions for placements.