bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality associated with Blastomyces dermatitidis infection: A systematic review of the literature and meta-analysis
Authors: Carignan Alex , Denis Mélina , Abou Chakra Claire Nour 
Published: April 2019

Abstract
Published case fatality in blastomycosis patients ranges between 4% and 78%. This study aimed to assess mortality associated with blastomycosis and identify its associated risk factors. We conducted a systematic review of publications related to Blastomyces dermatitidis available in PubMed and Scopus databases. Studies that reported data on blastomycosis mortality and that were published from inception through February 2018 were assessed and included in the analysis. Using the R meta package, a random-effect model meta-analysis was used to calculate pooled and stratified estimates of case-fatality proportions and risk ratios. Of 1553 publications, we included 20 studies reporting on a total of 2820 cases of blastomycosis between 1970 and 2014 and three case series reports with 10, 21, and 36 patients. The mean or median ages ranged from 28 to 59 years. Mortality was defined as attributable mortality caused by blastomycosis in 13 studies. Among 14 studies with a standard error ≤0.05, the overall pooled mortality was 6.6% (95% confidence interval [CI], 4.9–8.2) with 57% heterogeneity. The mortality rate was 37% (95% CI, 23–51) in immunocompromised patients and 75% (95% CI, 53–96) in patients who developed an acute respiratory distress syndrome (ARDS) (n = 3 studies each). ARDS was the only identified risk factor in general patients (risk ratio = 10.2). The overall mortality was significantly higher in studies involving immunocompromised patients and ARDS patients. Our analysis showed considerable heterogeneity among studies. Inconsistent mortality definitions may have contributed to the observed heterogeneity. Further research is needed to assess potential risk factors for mortality.
On the geometry of the X-ray emission from pulsars: the changing aspect of the Be/X-ray pulsar SXP348
Authors: Cappallo R , Laycock S G T , Christodoulou D M , Coe M J , Zezas A 
Published: April 2019

ABSTRACT
The X-ray source SXP348 is a high-mass X-ray binary system in the Small Magellanic Cloud. Since its 1998 discovery by BeppoSAX, this pulsar has exhibited a spin period of ∼340−350 s. In an effort to determine the orientation and magnetic geometry of this source, we used our geometric model Polestar to fit 71 separate pulse profiles extracted from archival Chandra and XMM-Newton observations over the past two decades. During 2002, pulsations ceased being detectable for nine months despite the source remaining in a bright state. When pulsations resumed, our model fits changed, displaying a change in accretion geometry. Furthermore, in 2006, detectable pulsations again ceased, with 2011 marking the last positive detection of SXP348 as a point source. These profile fits will be released for public use as part of the database of Magellanic Cloud pulsars.
Influence of galactic arm scale dynamics on the molecular composition of the cold and dense ISM – II. Molecular oxygen abundance
Authors: Wakelam V , Ruaud M , Gratier P , Bonnell I A 
Published: April 2019

ABSTRACT
Molecular oxygen has been the subject of many observational searches as chemical models predicted it to be a reservoir of oxygen. Although it has been detected in two regions of the interstellar medium, its rarity is a challenge for astrochemical models. In this paper, we have combined the physical conditions computed with smoothed particle hydrodynamics simulations with our full gas–grain chemical model Nautilus, to study the predicted O2 abundance in interstellar material forming cold cores. We thus follow the chemical evolution of gas and ices in parcels of material from the diffuse interstellar conditions to the cold dense cores. Most of our predicted O2 abundances are below 10−8 (with respect to the total proton density) and the predicted column densities in simulated cold cores are at maximum a few 10−14 cm−2, in agreement with the non-detection limits. This low O2 abundance can be explained by the fact that, in a large fraction of the interstellar material, the atomic oxygen is depleted on to the grain surface (and hydrogenated to form H2O) before O2 can be formed in the gas-phase and protected from ultraviolet photodissociations. We could achieve this result only because we took into account the full history of the evolution of the physical conditions from the diffuse medium to the cold cores.
Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities
Authors: Gupta Ankita , Lad Shailesh B , Ghodke Pratibha P , Pradeepkumar P I , Kondabagil Kiran 
Published: April 2019

AbstractAcanthamoeba polyphaga mimivirus is an amoeba-infecting giant virus with over 1000 genes including several involved in DNA replication and repair. Here, we report the biochemical characterization of gene product 577 (gp577), a hypothetical protein (product of L537 gene) encoded by mimivirus. Sequence analysis and phylogeny suggested gp577 to be a primase-polymerase (PrimPol)—the first PrimPol to be identified in a nucleocytoplasmic large DNA virus (NCLDV). Recombinant gp577 protein purified as a homodimer and exhibited de novo RNA as well as DNA synthesis on circular and linear single-stranded DNA templates. Further, gp577 extends a DNA/RNA primer annealed to a DNA or RNA template using deoxyribonucleoties (dNTPs) or ribonucleotides (NTPs) demonstrating its DNA/RNA polymerase and reverse transcriptase activity. We also show that gp577 possesses terminal transferase activity and is capable of extending ssDNA and dsDNA with NTPs and dNTPs. Mutation of the conserved primase motif residues of gp577 resulted in the loss of primase, polymerase, reverse transcriptase and terminal transferase activities. Additionally, we show that gp577 possesses translesion synthesis (TLS) activity. Mimiviral gp577 represents the first protein from an NCLDV endowed with primase, polymerase, reverse transcriptase, terminal transferase and TLS activities.
The PSIPRED Protein Analysis Workbench: 20 years on
Authors: Buchan Daniel W A , Jones David T 
Published: April 2019

Abstract
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.
Nephrology and Public Policy Committee propositions to stimulate research collaboration in adults and children in Europe
Authors: Massy Ziad A , Caskey Fergus J , Finne Patrik , Harambat Jerome , Jager Kitty J , Nagler Evi , Stengel Benedicte , Sever Mehmet Sukru , Vanholder Raymond , Blankestijn Peter J , Bruchfeld Annette , Capasso Giovambattista , Fliser Danilo , Fouque Denis , Goumenos Dimitrios , Soler Maria Jose , Rychlík Ivan , Spasovski Goce , Stevens Kathryn , Wanner Christoph , Zoccali Carmine 
Published: April 2019

AbstractThe strengths and the limitations of research activities currently present in Europe are explored in order to outline how to proceed in the near future. Epidemiological and clinical research and public policy in Europe are generally considered to be comprehensive and successful, and the European Renal Association – European Dialysis and Transplant Association (ERA-EDTA) is playing a key role in the field of nephrology research. The Nephrology and Public Policy Committee (NPPC) aims to improve the current situation and translation into public policy by planning eight research topics to be supported in the coming 5 years by ERA-EDTA.
Epidemiology of neonatal stroke: A population-based study
Authors: Clive Breanna , Vincer Michael , Ahmad Tahani , Khan Naeem , Afifi Jehier , El-Naggar Walid 
Published: April 2019

Abstract

Objective
The goal of this study was to obtain population-based data on the incidence, clinical presentation, management, imaging features, and long-term outcomes of patients with all types of neonatal stroke (NS).

Methods
Full-term neonates with NS born between January 2007 and December 2013 were identified through the Nova Scotia Provincial Perinatal Follow-up Program Database. Perinatal data and neonatal course were reviewed. Neurodevelopmental outcomes were assessed at 18 and 36 months of age using standardized testing.

Results
Twenty-nine neonates with NS were identified during the study period, giving an incidence of 47 per 100,000 live births in Nova Scotia. Arterial ischemic stroke was the most common stroke type (76%), followed by neonatal hemorrhagic stroke (17%), then cerebral sinovenous thrombosis (7%). The majority of neonates presented with seizures (86%) on the first day of life (76%). At 36 months of age, 23 (79%) of the children had a normal outcome, while 3 (10%) were diagnosed with cerebral palsy (2 with neonatal arterial stroke and one with neonatal hemorrhagic stroke) and 3 (10%) had recurrent seizures (1 patient from each stroke subtype group).

Conclusion
The incidence of NS in Nova Scotia is higher than what has been reported internationally in the literature. However, the neurodevelopmental outcomes at 3 years of age are better. Further studies are required to better understand the reasons for these findings.
CHANGES OF ABSORBED DOSE RATE IN AIR BY CAR-BORNE SURVEY IN NAMIE TOWN, FUKUSHIMA PREFECTURE AFTER THE FUKUSHIMA DAIICHI NUCLEAR POWER PLANT ACCIDENT
Authors: Shiroma Y , Hosoda M , Iwaoka K , Hegedűs M , Kudo H , Tsujiguchi T , Yamaguchi M , Akata N , Kashiwakura I , Tokonami S 
Published: April 2019

Abstract
The latest car-borne survey was carried out by Hirosaki University in order to grasp the local distribution of the absorbed dose rate in air after the evacuation order was lifted on Namie Town in 2017. The car-borne survey of absorbed dose rate in air was carried out on most of the roads which were accessible by car in Namie Town using a 3-in × 3-in NaI(Tl) scintillation spectrometer. The range of the absorbed dose rate in air was calculated to be 0.041–11 μGy h−1. The distribution maps of the absorbed dose rate in air were drawn based on the data obtained during the surveys in 2011, 2015 and 2017. The comparison of these absorbed dose rates in air suggests that the elevated absorbed dose rate in air in Namie Town caused by the FDNPP accident may be decreasing faster than natural decline which includes weathering effect and physical decay due to the artificial decontamination.
A-107 A general description of the HTLV-1 Cohort at the Institute of Tropical Medicine Alexander von Humboldt (1989–2015)
Authors: Gotuzzo Eduardo , González Elsa , Mejía Fernando , Ramos Yessica , Alvarez Carolina , Verdonck Kristien 
Published: April 2019

In Peru, the Institute of Tropical Medicine Alexander von Humboldt, in partnership with Hospital Cayetano Heredia, promotes specialized care for persons with HTLV-1 infection since 1989. Briefly, we offer pre and post-test counseling, diagnostic services, and medical attention. People are eligible for diagnostic services if they have: a prior seropositive result in Blood Banks; a first-degree relative or sexual partner with HTLV-1 infection; a potential diagnosis of HTLV-1-associated diseases (mainly: HTLV-1-associated myelopathy (HAM/TSP), Strongyloides stercoralis (SS) infection, T-cell leukemia/lymphoma, uveitis, infective dermatitis). Given the limited capacity to continuously afford confirmatory testing, HTLV infection is also diagnosed with repeatedly reactive ELISA tests. Cases receive post-test counseling, and specialized medical services. This setting has promoted our HTLV-1 Cohort; for those consenting, enrollment is at time of HTLV-1 testing.
Until June 2015, 8845 persons were enrolled in the cohort; the median age was 38.8 years (interquartile range: 26.5–52.3), 5042 (57.5%) were women and 4337 (49.0%) did not report being related to someone with HTLV-1 infection and were thus defined as index cases. The leading reasons for HTLV testing were family studies (3987, 45.1%), followed by potential diagnosis of HTLV-1 associated diseases (3365, 38.0%), and seropositive results in Blood Banks (718, 8.5%).
HTLV infection was diagnosed in 3359 persons (48.0%), including 1202 (13.6%) with available confirmatory testing. Most (58.3%) were women; the median age was 43 years (IQR: 31.0–55.6), but 285 were children. The proportion of HTLV diagnosis varied by reason for testing: 79.0% for those with potential HAM/TPS, 69.8% for potential ATL, 31.0% in cases with SS; 79.0% in donors and 34.0% when testing was done as part of family studies. At entry, the cases with HTLV infection included potential HAM/TSP (621, 18.5%); other complications mostly of infectious nature (338, 10.1%); SS infection (238, 7.0%), and ATL (5.6%).
Most cases (1426, 43.0%) were lost to follow-up in the first year after diagnosis; in those remaining, with 8227 person-years of follow-up up to December 31, 2016, there were 88 incident cases of HAM/TSP, 47 of SS, and 8 of ATL. In those not lost-to-follow-up, 113 out of 1933 (5.6%) died.
Our cohort offers a valuable platform to increase the quality of evidence regarding clinical consequences of HTLV-1 infection; at the same time, the number of pediatric cases remark the imperative need to implement sound actions for prevention of transmission of HTLV-1 from mother-to-child.
H-103 Clinical landscape of adult T-cell leukemia: Its impacts on hematology, virology, and immunology
Authors: Matsuoka Masao 
Published: April 2019

Prof. Takatsuki and his colleagues reported adult T-cell leukemia (ATL) as the distinct clinical entity based on the clinical features including the presence of leukemic cells with characteristic nuclear shape (flower cells), skin lesion, hypercalcemia and frequent opportunistic infections, and mature T-cell immunophenotyped (Uchiyama T, et al, Blood, 1977). Importantly, they already predicted that ATL is caused by the pathogen since the birth places of ATL patients accumulated in the southwestern Japan (Kyushu and Okinawa). In 1980, Prof. Gallo and his colleagues reported the first human retrovirus, human T-cell leukemia virus (HTLV), from a patient with cutaneous T-cell lymphoma who was later diagnosed as ATL. Thereafter, it was established that HTLV causes ATL. Since Prof. Gallo found another human retrovirus, the first human retrovirus was named human T-cell leukemia virus type 1 (HTLV-1).
Detection of anti-HTV-1 antibody enables us to identify HTLV infected individuals, which discloses unique distribution of HTLV-1carriers in Japan and the world. In addition, serological studies disclosed clinical landscape of ATL. Based on clinical features, ATL is classified to 4 clinical subtypes: acute, chronic, lymphoma-type and smoldering types (Yamguchi K, et al, Blood, 1983). In addition, the familial clustering of ATL cases was prominent, suggesting that genetic or virological factors are involved in development of ATL. Serological analyses found that HTLV-1 mainly transmits from male to female in horizontal transmission. Another clinical feature of ATL is the frequent spontaneous remission, which suggests immunological mechanism.
Early studies of HTLV-1 focused on Tax, which not only transactivates viral genes transcription from the plus strand, but also influences cellular genes. However, Prof. Takatsuki's group thought that clinical ATL samples contain clue of leukemogenic mechanisms by HTLV-1. We found that Tax was not expressed in half of ATL cases, and 3 mechanisms of inactivation of Tax expression: deletion of 5′ long terminal repeat (LTR), DNA methylation of 5′LTR, and genetic changes of the tax gene (nonsense mutation, deletion and insertion), indicating that Tax is not necessary for maintenance of ATL (Tamiya S, et al, Blood, 1996). However, pX region and 3′LTR remain intact in all ATL cases, indicating that this region is critical for ATL. Thereafter, we showed that HTLV-1 bZIP factor (HBZ), which is encoded by the minus strand, plays critical roles for pathogenesis by HTLV-1.
ATL is the first human disease caused by retrovirus. Tremendous efforts on HTLV-1 research by many researchers contribute to studies of next human retrovirus, human immunodeficiency virus (HIV). Thus, discovery of ATL in association with identification of causative human retrovirus leads to great contribution to medical science.
PC-6 Cardiac morbidity in HIV is associated with checkpoint inhibitor LAG-3
Authors: Pahwa Rajendra , Pallikkuth Suresh , Kausalya Bagavathi , Saravanan Shanmugam , Kumarasamy Nagalingesawaran , Pahwa Savita 
Published: April 2019

Background:
Cardiovascular disease (CVD) is a major contributor to mortality and morbidity in HIV infection. The impact of viral suppression with combination antiretroviral therapy and underlying pathophysiologic mechanisms are under investigation. Elevated expression of certain checkpoint inhibitor (CPI) molecules (eg, PD-1, TIGIT, LAG3, TIM3) on T cells is associated with dampened immunity. Recent evidence for expression of receptors for CPI at the tissue level with selective enrichment of LAG3 receptors in the heart point to a control mechanism for organ immune homeostasis (Rev Immunity 44, 2016). This study was aimed at defining the relationship of CPI molecules on immune cells and CVD in HIV infection in a low resource setting.

Methods:
Study participants were recruited in YRG CARE, a tertiary care HIV service provider in Chennai, India. ART naive viremic (Gp1, n = 102) and ART experienced aviremic (Gp2, n = 172) were compared to healthy volunteers (Gp3, n = 64) in a cross-sectional analysis of cardiac function and immunologic markers including CPI molecules on CD4 and CD8 T cells.

Results:
In Gp1 findings of CVD were significant (Mann-Whitney’ U test) for lower cardiac ejection time, stroke volume, stroke volume index, cardiac output and small arterial elasticity with higher systemic vascular resistance compared to Gp2 and Gp3 respectively. Large arterial elasticity was lower in comparison to Gp2. Immune activation and inflammatory cytokines were maximally altered in Gp1. Frequencies of CPI molecules showed differences among the groups, with higher frequencies of CD4+ T cells expressing LAG3 and PD1 in Gp1 compared to GPs 2 and 3, while TIGIT and TIM3 did not differ significantly among the groups (LAG3 Gp1: 4.9 ± 3.4; Gp2: 2.5 ± 1.5; Gp3: 2.4 ± 1.3; PD1 Gp1: 6.2 ± 7.3; Gp2: 1.5 ± 2.5; Gp3: 0.9 ± 1.6; TIGIT Gp1: 34.2 ± 14.9; Gp2: 33.5 ± 11.8; Gp3: 30.1 ± 7.8 and Tim3 Gp1: 1.7 ± 2.7; Gp2: 1.3 ± 1; Gp3: 1.3 ± 0.9). Frequencies of CD4+ T cells positive for LAG3, PD1, and for dual expression of LAG3 plus PD1 were inversely correlated with cardiac ejection time, cardiac output, cardiac index, stroke volume, stroke volume index and systemic vascular resistance in Gp1 and with large artery elasticity, and except for PD1, also with small artery elasticity in Gp2.

Conclusions:
In ART naive HIV subjects continuous antigenic stimulation of the immune system results in upregulation of multiple CPI molecules in association with immune activation. Our finding of the association of LAG3 and PD1 expressing CD4 cells in cardiac morbidity points to a dominant role of these pathways in regulating cardiac health, given that LAG3 receptors are enriched at the tissue level in the heart. Investigations to understand the immune mechanisms involved could provide insight into potential role of LAG3 immunotherapy (which is in early clinical trials in cancer) in prevention or treatment of cardiac dysfunction in HIV.
Application of the New Centers for Disease Control and Prevention Surveillance Criteria for Ventilator-Associated Events to a Cohort of PICU Patients Identifies Different Patients Compared With the Previous Definition and Physician Diagnosis*
Authors: Ziegler Katherine M. , Haywood Jonathan D. , Sontag Marci K. , Mourani Peter M. 
Published: April 2019

Objectives:
We sought to compare the performance of the 2008 Centers for Disease Control and Prevention Pediatric criteria for ventilator-associated pneumonia, the 2013 Adult Ventilator-Associated Condition criteria, the new Draft Pediatric Ventilator-Associated Condition criteria, and physician-diagnosed ventilator-associated pneumonia in a cohort of PICU patients.

Design:
Secondary analysis of a previously conducted prospective observational study.

Setting:
PICU within a tertiary care children’s hospital between April 1, 2010, and April 1, 2011.

Patients:
Patients between 31 days and 18 years old, mechanically ventilated via endotracheal tube for more than 72 hours and no limitations of care.

Interventions:
None.

Measurements and Main Results:
Ventilator-associated pneumonia criteria applied in real time and ventilator-associated condition criteria applied retrospectively. Outcomes assessed between cases and noncases within criteria. Of the 133 eligible participants, 24 (18%) had ventilator-associated pneumonia by 2008 Pediatric criteria and 27 (20%) by physician diagnosis. Sixteen (12%) and 10 (8%) had ventilator-associated condition by 2013 Adult and Draft Pediatric criteria, respectively. We found significant overlap between cases identified with 2008 Pediatric criteria and physician diagnosis (p = 0.549), but comparisons between the other definitions revealed that the newer criteria identify different patients than previous Centers for Disease Control and Prevention ventilator-associated pneumonia criteria and physician diagnosis (p < 0.01). Although 20 participants were diagnosed with ventilator-associated pneumonia by 2008 Pediatric criteria and physician diagnosis, only three participants were identified by all four criteria. Three subjects uniquely identified by the Draft Pediatric criteria were noninfectious in etiology. Cases identified by all criteria except Draft Pediatric had higher ratios of actual ICU length of stay to Pediatric Risk of Mortality III-adjusted expected length of stay compared with noncases.

Conclusions:
The Draft Pediatric criteria identify fewer and different patients than previous ventilator-associated pneumonia criteria or physician diagnosis, potentially missing patients with preventable harms, but also identified patients with potentially preventable noninfectious respiratory deteriorations. Further investigations are required to maximize the identification of patients with preventable harms from mechanical ventilation.