bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Aspergillus and Mucorales PCR Testing of Different Bronchoalveolar Lavage Fluid Fractions from Patients with Suspected Invasive Pulmonary Fungal Disease
Authors: Springer Jan , White P. Lewis , Kessel Johanna , Wieters Imke , Teschner Daniel , Korczynski Daniel , Liebregts Tobias , Cornely Oliver A. , Schwartz Stefan , Elgeti Thomas , Meintker Lisa , Krause Stefan W. , Posso Raquel B. , Heinz Werner J. , Fuhrmann Sandra , Vehreschild Jörg Janne , Einsele Hermann , Rickerts Volker , Loeffler Juergen 
Published: November 2017

ABSTRACT

In patients with hematological malignancies, bronchoalveolar lavage fluid (BALF) specimens are commonly used for the diagnosis of mold infections. However, it is not clear whether the cell pellet (P) or the supernatant fraction (S) of the BALF specimen is optimal for molecular diagnostic testing. Thus, 99 BALF specimens were collected from 96 hematology patients with or without allogeneic hematopoietic stem cell transplant. The cell pellets and supernatants were processed alone and in combination (S/P) for testing by two fungus-specific real-time PCR assays compliant with international recommendations. The results achieved with S/P were revealed to be superior in comparison to those achieved with S and P alone, with the use of each single fraction showing a reduced sensitivity for the detection of
Aspergillus
DNA (82% and 43% for S and P, respectively). In 57% of the samples, testing of the combination of S and P generated a lower quantification cycle value than testing of S or P alone. Molds would have been missed in 5 and 16 out of 28 samples if only S or P, respectively, was analyzed. No sample was positive by testing of S or P only. Similar results were obtained for the detection of Mucorales DNA in BALF specimens (reduced sensitivity of 67% and 50% for S and P, respectively). Study patients were categorized according to the current European Organization for the Research and Treatment of Cancer/Mycoses Study Group classification for invasive fungal disease (IFD), revealing that 35 patients had proven/probable IFD (36%), 47 patients had possible IFD (49%), and 14 patients had undetermined IFD (15%).
General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins
Authors: Wagner Jonathan M. , Christensen Devin E. , Bhattacharya Akash , Dawidziak Daria M. , Roganowicz Marcin D. , Wan Yueping , Pumroy Ruth A. , Demeler Borries , Ivanov Dmitri N. , Ganser-Pornillos Barbie K. , Sundquist Wesley I. , Pornillos Owen 
Published: November 2017

ABSTRACT

Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity (

K
D

of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity (

K
D

of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition.

IMPORTANCE
Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.
Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes
Authors: Du Yushen , Zhang Tian-Hao , Dai Lei , Zheng Xiaojuan , Gorin Aleksandr M. , Oishi John , Wu Ting-Ting , Yoshizawa Janice M. , Li Xinmin , Yang Otto O. , Martinez-Maza Otoniel , Detels Roger , Sun Ren 
Published: November 2017

ABSTRACT

Certain “protective” major histocompatibility complex class I (MHC-I) alleles, such as B*57 and B*27, are associated with long-term control of HIV-1
in vivo
mediated by the CD8
+
cytotoxic-T-lymphocyte (CTL) response. However, the mechanism of such superior protection is not fully understood. Here we combined high-throughput fitness profiling of mutations in HIV-1 Gag,
in silico
prediction of MHC-peptide binding affinity, and analysis of intraperson virus evolution to systematically compare differences with respect to CTL escape mutations between epitopes targeted by protective MHC-I alleles and those targeted by nonprotective MHC-I alleles. We observed that the effects of mutations on both viral replication and MHC-I binding affinity are among the determinants of CTL escape. Mutations in Gag epitopes presented by protective MHC-I alleles are associated with significantly higher fitness cost and lower reductions in binding affinity with respect to MHC-I. A linear regression model accounting for the effect of mutations on both viral replicative capacity and MHC-I binding can explain the protective efficacy of MHC-I alleles. Finally, we found a consistent pattern in the evolution of Gag epitopes in long-term nonprogressors versus progressors. Overall, our results suggest that certain protective MHC-I alleles allow superior control of HIV-1 by targeting epitopes where mutations typically incur high fitness costs and small reductions in MHC-I binding affinity.

IMPORTANCE
Understanding the mechanism of viral control achieved in long-term nonprogressors with protective HLA alleles provides insights for developing functional cure of HIV infection. Through the characterization of CTL escape mutations in infected persons, previous researchers hypothesized that protective alleles target epitopes where escape mutations significantly reduce viral replicative capacity. However, these studies were usually limited to a few mutations observed
in vivo
. Here we utilized our recently developed high-throughput fitness profiling method to quantitatively measure the fitness of mutations across the entirety of HIV-1 Gag. The data enabled us to integrate the results with
in silico
prediction of MHC-peptide binding affinity and analysis of intraperson virus evolution to systematically determine the differences in CTL escape mutations between epitopes targeted by protective HLA alleles and those targeted by nonprotective HLA alleles. We observed that the effects of Gag epitope mutations on HIV replicative fitness and MHC-I binding affinity are among the major determinants of CTL escape.
Wide-field en face swept-source optical coherence tomography angiography using extended field imaging in diabetic retinopathy
Authors: Hirano Takao , Kakihara Shinji , Toriyama Yuichi , Nittala Muneeswar Gupta , Murata Toshinori , Sadda Srinivas 
Published: November 2017

AimsTo examine the feasibility of wide-field en face swept-source optical coherence tomography angiography (SS-OCTA) with extended field imaging (EFI) for evaluation of the retinal vasculature in diabetic retinopathy (DR).MethodsThis study included 37 eyes of 27 patients (age, 65±10 years; male patients, 18; female patients, 9) with DR. All patients underwent comprehensive ophthalmological examination, including OCTA and fluorescein angiography (FA). The imaging methods were compared for visible field of view, presence and extent of non-perfused areas (NPAs), presence and number of new blood vessels (NVs), vessel density (VD) and patient comfort level measured by Visual Analogue Scale.ResultsSS-OCTA with EFI allowed capture of larger areas (by 1.80±0.18 times on average) of the fundus than SS-OCTA without EFI. Compared with FA, the sensitivities of SS-OCTA with EFI for detection of NPAs and NVs were 96% and 79%, respectively, with specificities of 100% and 96%, respectively. There was no significant difference in extent of NPAs (61.2±45.8 vs 61.5±55.0 disc areas, P=0.99) or number of NVs (1.5±3.3 vs 0.9±1.8, P=0.68) between FA and SS-OCTA with EFI. VD showed significantly lower values in EFI SS-OCTA than in those acquired without EFI (31.6%±4.3%  vs 34.2%±4.3%, P<0.001). Wide-field OCTA with EFI was significantly more comfortable for patients than FA (P<0.001).ConclusionsSS-OCTA with EFI allows acquisition of wide-field en face images of the retinal vasculature in patients with DR, with greater patient comfort than FA.
Intra-arterial oxidative stress correlates negatively with cognitive function and positively with postoperative ischemic lesions in carotid artery stenosis stenting
Authors: Shimamura Norihito , Naraoka Masato , Matsuda Naoya , Katayama Kosuke , Kakuta Kiyohide , Katagai Takeshi , Fujiwara Nozomi , Fumoto Toshio , Ohkuma Hiroki 
Published: November 2017

Background and purposeCarotid plaque contains biologically active substances released into the blood during carotid artery stenting (CAS). The main purpose of this prospective study was to analyse sequential changes in oxidative stress during CAS and their relationship to clinical factors.MethodsTwenty-two consecutive CAS procedures were performed between May 2014 and April 2016. Arterial blood was collected four times: (1) after the sheath insertion without edaravone; (2) pre-angioplasty with edaravone from the carotid artery; (3) after post-stenting angioplasty from an occluded carotid artery; and (4) before sheath removal. Derivatives of reactive oxygen metabolites (d-ROMs) and biological antioxidant potential (BAP) were measured photometrically. The relationship between d-ROMs or BAP and preoperatively investigated biochemical parameters, cognitive function, and number of diffusion-weighted image (DWI) high spot lesions was analysed using one-way ANOVA and the Tukey–Kramer HSD test.ResultsThe d-ROM values for CAS were 355±58.8 Carratelli Units at sheath insertion, 315±57.2 after edaravone infusion, 328±56.8 after post-stenting angioplasty, and 315±53.0 just before sheath removal. The d-ROM values were reduced significantly after edaravone infusion (P<0.05). The BAP at sheath insertion was reduced significantly according to age (P<0.05). The d-ROMs at sheath insertion correlated negatively with the dementia scale and positively with the post-CAS DWI high spots (1.00±1.07; P<0.05). Other biochemical parameters did not correlate with the d-ROM values or BAP.ConclusionOxidative stress is correlated negatively with cognitive function and positively with postoperative ischemic lesions. Antioxidant potential decreases with ageing.
Disparities in Prostate, Lung, Breast, and Colorectal Cancer Survival and Comorbidity Status among Urban American Indians and Alaskan Natives
Authors: Emerson Marc A. , Banegas Matthew P. , Chawla Neetu , Achacoso Ninah , Alexeeff Stacey E. , Adams Alyce S. , Habel Laurel A. 
Published: November 2017

Abstract
Cancer is the second leading cause of death among American Indians and Alaskan Natives (AIAN), although cancer survival information in this population is limited, particularly among urban AIAN. In this retrospective cohort study, we compared all-cause and prostate, breast, lung, and colorectal cancer–specific mortality among AIAN (n = 582) and non-Hispanic white (NHW; n = 82,696) enrollees of Kaiser Permanente Northern California (KPNC) diagnosed with primary invasive breast, prostate, lung, or colorectal cancer from 1997 to 2015. Tumor registry and other electronic health records provided information on sociodemographic, comorbidity, tumor, clinical, and treatment characteristics. Cox regression models were used to estimate adjusted survival curves and hazard ratios (HR) with 95% confidence intervals (CI). AIAN had a significantly higher comorbidity burden compared with NHW (P &lt; 0.05). When adjusting for patient, disease characteristics, and Charlson comorbidity scores, all-cause mortality and cancer-specific mortality were significantly higher for AIAN than NHW patients with breast cancer (HR, 1.47; 95% CI, 1.13–1.92) or with prostate cancer (HR, 1.87; 95% CI, 1.14–3.06) but not for AIAN patients with lung and colorectal cancer. Despite approximately equal access to preventive services and cancer care in this setting, we found higher mortality for AIAN than NHW with some cancers, and a greater proportion of AIAN cancer patients with multiple comorbid conditions. This study provides severely needed information on the cancer experience of the 71% of AIANs who live in urban areas and access cancer care outside of the Indian Health Services, from which the vast majority of AIAN cancer information comes. Cancer Res; 77(23); 6770–6. ©2017 AACR.
National Identity after a Conflict: National Identity Choice among Northern Irish Youth
Authors: Bingham Natasha , Duffy Christopher 
Published: November 2017

AbstractThis work uses multinomial logistic regression to explore how Northern Irish youth view their national identity and the factors that shape their self-identification post-1998 Good Friday Agreement. We use the 2005-2015 Northern Ireland Young Life and Times Surveys of 16-year-olds to investigate these questions. The results indicate that intergroup contact is less influential than environmental factors on national identity. Residential and school composition has more of an effect on solidifying Irish identity than British identity (relative to that of a Northern Irish identity). Our work adds to the literature on national identity development and choice among young adults in post-conflict and post-peace-agreement environments.
Truth-telling, decision-making, and ethics among cancer patients in nursing practice in China
Authors: Ling Dong-Lan , Yu Hong-Jing , Guo Hui-Ling 
Published: November 2017

Background: Truth-telling toward terminally ill patients is a challenging ethical issue in healthcare practice. However, there are no existing ethical guidelines or frameworks provided for Chinese nurses in relation to decision-making on truth-telling of terminal illness and the role of nurses thus is not explicit when encountering this issue. Objectives: The intention of this paper is to provide ethical guidelines or strategies with regards to decision-making on truth-telling of terminal illness for Chinese nurses. Methods: This paper initially present a case scenario and then critically discuss the ethical issue in association with ethical principles and philosophical theories. Instead of focusing on attitudes toward truth disclosure, it aims to provide strategies regarding this issue for nurses. It highlights and discusses some of the relevant ethical assumptions around the perceived role of nurses in healthcare settings by focusing on nursing ethical virtues, nursing codes of ethics, and philosophical perspectives. And Confucian culture is discussed to explicate that deontology does not consider family-oriented care in China. Conclusion: Treating each family individually to explore the family’s beliefs and values on this issue is essential in healthcare practice and nurses should tailor their own approach to individual needs regarding truth-telling in different situations. Moreover, the Chinese Code of Ethics should be modified to be more specific and applicable. Finally, a narrative ethics approach should be applied and teamwork between nurses, physicians and families should be established to support cancer patients and to ensure their autonomy and hope. Ethical considerations: This paper was approved by the Ethics Committee of The Second Affiliated Hospital of Guangzhou Medical University. The authors have obtained consent to use the case study and it has been anonymised to preserve the patient's confidentiality.
Advances in the diagnosis and treatment of Von Willebrand disease
Authors: Sharma Ruchika , Flood Veronica H. 
Published: November 2017

AbstractVon Willebrand disease (VWD) is the most common inherited bleeding disorder, yet diagnosis and management remain challenging. Development and use of bleeding assessment tools allows for improved stratification of which patients may require further assessment and which patients are most likely to require treatment of their VWD. New options for laboratory assessment of von Willebrand factor (VWF) activity include a new platelet-binding assay, the VWF:GPIbM, which is subject to less variability than the ristocetin cofactor activity assay, and collagen-binding assays that provide insight into a different function of VWF. Genetic testing may be helpful in some cases where a type 2 VWD variant is suspected but is usually not helpful in type 1 VWD. Finally, treatment options for VWD are reviewed, including the use of recombinant VWF. Despite these advances, still more work is required to improve diagnosis, treatment, and quality of life for affected patients.
Hospitalist Perspective of Interactions with Medicine Subspecialty Consult Services
Authors: Adams Traci N. , Bonsall Joanna , Hunt Daniel , Puig Alberto , Richards Jeremy B. , Yu Liyang , McSparron Jakob I. , Shah Nainesh , Weissler Jonathan , Miloslavsky Eli M. 
Published: November 2017

BACKGROUNDMedicine subspecialty consultation is becoming increasingly important in inpatient medicine.OBJECTIVEWe conducted a survey study in which we examined hospitalist practices and attitudes regarding medicine subspecialty consultation.DESIGN AND SETTINGThe survey instrument was developed by the authors based on prior literature and administered online anonymously to hospitalists at 4 academic medical centers in the United States.MEASUREMENTSThe survey evaluated 4 domains: (1) current consultation practices, (2) preferences regarding consultation, (3) barriers to and facilitating factors of effective consultation, and (4) a comparison between hospitalist–fellow and hospitalist–subspecialty attending interactions.RESULTSOne hundred twenty‐two of 261 hospitalists (46.7%) responded. The majority of hospitalists interacted with fellows during consultation. Of those, 90.9% reported that in‐person communication occurred during less than half of consultations, and 64.4% perceived pushback at least “sometimes” in their consult interactions. Participants viewed consultation as an important learning experience, preferred direct communication with the consulting service, and were interested in more teaching during consultation. The survey identified a number of barriers to and facilitating factors of an effective hospitalist–consultant interaction, which impacted both hospitalist learning and patient care. Hospitalists reported more positive experiences when interacting with subspecialty attendings compared to fellows with regard to multiple aspects of the consultation.CONCLUSIONThe hospitalist–consultant interaction is viewed as important for both hospitalist learning and patient care. Multiple barriers and facilitating factors impact the interaction, many of which are amenable to intervention.
Maresin 1 Promotes Inflammatory Resolution, Neuroprotection, and Functional Neurological Recovery After Spinal Cord Injury
Authors: Francos-Quijorna Isaac , Santos-Nogueira Eva , Gronert Karsten , Sullivan Aaron B. , Kopp Marcel A. , Brommer Benedikt , David Samuel , Schwab Jan M. , López-Vales Ruben 
Published: November 2017

Resolution of inflammation is defective after spinal cord injury (SCI), which impairs tissue integrity and remodeling and leads to functional deficits. Effective pharmacological treatments for SCI are not currently available. Maresin 1 (MaR1) is a highly conserved specialized proresolving mediator (SPM) hosting potent anti-inflammatory and proresolving properties with potent tissue regenerative actions. Here, we provide evidence that the inappropriate biosynthesis of SPM in the lesioned spinal cord hampers the resolution of inflammation and leads to deleterious consequences on neurological outcome in adult female mice. We report that, after spinal cord contusion injury in adult female mice, the biosynthesis of SPM is not induced in the lesion site up to 2 weeks after injury. Exogenous administration of MaR1, a highly conserved SPM, propagated inflammatory resolution after SCI, as revealed by accelerated clearance of neutrophils and a reduction in macrophage accumulation at the lesion site. In the search of mechanisms underlying the proresolving actions of MaR1 in SCI, we found that this SPM facilitated several hallmarks of resolution of inflammation, including reduction of proinflammatory cytokines (CXCL1, CXCL2, CCL3, CCL4, IL6, and CSF3), silencing of major inflammatory intracellular signaling cascades (STAT1, STAT3, STAT5, p38, and ERK1/2), redirection of macrophage activation toward a prorepair phenotype, and increase of the phagocytic engulfment of neutrophils by macrophages. Interestingly, MaR1 administration improved locomotor recovery significantly and mitigated secondary injury progression in a clinical relevant model of SCI. These findings suggest that proresolution, immunoresolvent therapies constitute a novel approach to improving neurological recovery after acute SCI.SIGNIFICANCE STATEMENTInflammation is a protective response to injury or infection. To result in tissue homeostasis, inflammation has to resolve over time. Incomplete or delayed resolution leads to detrimental effects, including propagated tissue damage and impaired wound healing, as occurs after spinal cord injury (SCI). We report that inflammation after SCI is dysregulated in part due to inappropriate synthesis of proresolving lipid mediators. We demonstrate that the administration of the resolution agonist referred to as maresin 1 (MaR1) after SCI actively propagates resolution processes at the lesion site and improves neurological outcome. MaR1 is identified as an interventional candidate to attenuate dysregulated lesional inflammation and to restore functional recovery after SCI.