Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum Samples From Middle-aged Adults Vaccinated Annually with Seasonal Influenza Vaccines Cross-neutralize Some Potential Pandemic Influenza Viruses

Abstract We examined serum samples from adults ages 48–64 who received multiple seasonal influenza vaccines from 2004 to 2009 for cross-neutralizing antibodies to potential pandemic strains. Using pseudoviruses bearing various hemagglutinins (HA-pseudoviruses), we found serum neutralization titers (≥160) in 100% against A/Japan/305/1957 (H2N2), 53% against A/Hong Kong/1073/99 (H9N2), 56% against the H3N2 variant A/Indiana/08/11 (H3N2v), 11% against A/Hong Kong/G9/97 (H9N2), and 36% A/chicken/Hong Kong/SF4/01 (H6N1). None had titers >160 to A/Shanghai/2/13 (H7N9) or A/Netherlands/219/03 (H7N7). Thirty-six percent to 0% had neutralization titers to various H5N1 strains. Titers to H9, H6, and H5 HA-pseudoviruses correlated with each other, but not with H3N2v, suggesting group-specific cross-neutralization.
Role of Sequencing the Measles Virus Hemagglutinin Gene and Hypervariable Region in the Measles Outbreak Investigations in Sweden During 2013-2014.

INTRODUCTION It is increasingly difficult to differentiate measles viruses (MeVs) relating to certain outbreaks on the basis of the nucleoprotein (N) gene sequence only, as the diversity of circulating MeV strains has decreased. We studied genomic regions that could provide better molecular discrimination between epidemiologically linked and unlinked MeV variants identified in Sweden during 2013-2014. METHODS The hemagglutinin (H) gene and hypervariable region between the fusion and matrix genes (MF-HVR) from 53 MeV-positive samples were amplified and sequenced. Data on phylogenetic clustering of MeVs on the basis of N, H, and MF-HVR sequences were compared to epidemiological data. RESULTS MeVs were genotyped: 27 were B3, and 26 were D8. One genotype B3 cluster based on the N gene sequence contained epidemiologically unrelated viruses from 4 outbreaks, whereas analysis of H and MF-HVR sequences separated them into phylogenetic clusters consistent with the epidemiological data. Similarly, the single cluster of viruses with a genotype D8 N gene could be divided into the 5 outbreak groups on the basis of the phylogeny of MF-HVR sequences. CONCLUSIONS A detailed picture of MeV circulation with more-defined links between outbreaks was obtained by sequencing the H gene and MF-HVR. Further identification and better genetic characterization of MeVs internationally is essential in identifying sources and routes of MeV spread within and beyond Europe in the elimination end game.
The cyclic GMP‐AMP synthetase–STING signaling pathway is required for both the innate immune response against HBV and the suppression of HBV assembly

During viral replication, the innate immune response is induced through the recognition of viral replication intermediates by host factor(s). One of these host factors, cyclic GMP‐AMP synthetase (cGAS), was recently reported to be involved in the recognition of viral DNA derived from DNA viruses. However, it is uncertain whether cGAS is involved in the recognition of hepatitis B virus (HBV), which is a hepatotropic DNA virus. In the present study, we demonstrated that HBV genome‐derived double‐stranded DNA induced the innate immune response through cGAS and its adaptor protein, stimulator of interferon genes (STING), in human hepatoma Li23 cells expressing high levels of cGAS. In addition, we demonstrated that HBV infection induced ISG56 through the cGAS–STING signaling pathway. This signaling pathway also showed an antiviral response towards HBV through the suppression of viral assembly. From these results, we conclude that the cGAS–STING signaling pathway is required for not only the innate immune response against HBV but also the suppression of HBV assembly. The cGAS–STING signaling pathway may thus be a novel target for anti‐HBV strategies.
Age-Specific Race and Ethnicity Disparities in HIV Infection and Awareness Among Men Who Have Sex With Men--20 US Cities, 2008-2014.

BACKGROUND Over half of human immunodeficiency virus (HIV) infections in the United States occur among men who have sex with men (MSM). Among MSM, 16% of estimated new infections in 2010 occurred among black MSM <25 years old. METHODOLOGY We analyzed National HIV Behavioral Surveillance data on MSM from 20 cities. Poisson models were used to test racial disparities, by age, in HIV prevalence, HIV awareness, and sex behaviors among MSM in 2014. Data from 2008, 2011, and 2014 were used to examine how racial/ethnic disparities changed across time. RESULTS While black MSM did not report greater sexual risk than other MSM, they were most likely to be infected with HIV and least likely to know it. Among black MSM aged 18-24 years tested in 2014, 26% were HIV positive. Among white MSM aged 18-24 years tested in 2014, 3% were HIV positive. The disparity in HIV prevalence between black and white MSM increased from 2008 to 2014, especially among young MSM. CONCLUSIONS Disparities in HIV prevalence between black and white MSM continue to increase. Black MSM may be infected with HIV at younger ages than other MSM and may benefit from prevention efforts that address the needs of younger men.
Cancer and work in Canada with particular reference to occupational risk factors in breast cancer patients in one community and related selected research methods used to investigate those factors.

Cancer represents a major cause of human morbidity and mortality. There is no scientific consensus regarding cancer causality or prevention. Occupational exposure potentially remains a major contributor to the incidence of this group of diseases, but the data to assess its impact continues to elude researchers and public health advocates. Among women in industrialised countries, breast cancer is the most prevalent cancer. The known or suspected risk factors, including family history and lifetime oestrogen load, can account for less than 50 percent of the cases. New hypotheses about the role of xenoestrogens and endocrine disrupting compounds are challenging the previous scientific precepts regarding cancer causality. Within this context, the extent to which a community-based occupational history data collection initiative can contribute to advancing our scientific understanding of associations between cancer and work is explored. The possibility that occupational histories data can find associations missed in conventional breast cancer research that ignore occupation is also explored. More specifically, the extent to which data derived from an occupational history questionnaire can provide insight into the potential association between breast cancer risk and farming is examined. Occupational histories of cancer patients contain data that could help to elucidate and inform our understanding of cancer aetiology and prevention. In the community of Windsor, Ontario, Canada a local cancer treatment centre responded to community concerns by cooperating in a collaborative research project to collect the occupational histories of cancer patients. Computerised Record of' Occupation Made Easy (CROME) was an innovative method that allowed individual
Adipose tissue inflammation, liver fat and insulin resistance in humans

9 INTRODUCTION 11 REVIEW OF THE LITERATURE 12 1. Lipid and glucose metabolism under normal physiological conditions 12 1.1. Adipose tissue 12 1.1.1. Triacylglycerol storage and release 12 1.1.2. Glucose metabolism 13 1.1.3. Adipocytokines 14 1.2. The liver 16 1.2.1. Glucose metabolism 16 1.2.2. Lipid metabolism 16 1.3. Skeletal muscle 17 1.3.1. Glucose metabolism 17 1.3. 2. Lipid metabolism 18 2. Insulin resistance in adipose tissue 19 2.1. Defects in in vivo insulin action in adipose tissue 19 2.2. Inflammation 20 2.3. Adipocytokines and insulin resistance 23 2.4. 11β-hydroxysteroid dehydrogenase 31 2.5. Peroxisome proliferator-activated receptor γ 32 2.6. PPARγ coactivator 1α 33 2.7. Lipid mediators of insulin resistance 33 2.7. 1. Free fatty acids 33 2.7. 2. Diacylglycerols 35 2.7. 3. Ceramides 36 3. Insulin resistance in the liver 38 3.1. Non-alcoholic fatty liver disease and insulin resistance 38 3.1.1. Definition 38 3.1.2. Prevalence and significance 38 3.1.3. The metabolic syndrome and hepatic insulin resistance 39 3.1. 4. Causes of liver fat and hepatic insulin resistance 40 AIMS OF THE STUDY 42 SUBJECTS AND STUDY DESIGNS 43 1. Subjects 43 2. Study designs 45 METHODS 47 1. Whole body insulin sensitivity 47
Hepatitis B Virus (HBV) Core-Related Antigen During Nucleos(t)ide Analog Therapy Is Related to Intra-hepatic HBV Replication and Development of Hepatocellular Carcinoma.

BACKGROUND Although nucleos(t)ide analog (NA) therapy effectively reduces the hepatitis B virus (HBV) DNA load in the serum of patients with chronic hepatitis B, it does not completely reduce the incidence of hepatocellular carcinoma (HCC). METHODS AND RESULTS A total of 109 patients who had chronic hepatitis B and were receiving NA therapy were analyzed. Multivariate Cox regression analysis showed that age (>60 years had a hazard ratio [HR] of 2.66), FIB-4 index (an index of >2.1 had a HR of 2.57), and the presence of HBV core-related antigen (HBcrAg; HR, 3.53) during treatment were significantly associated with the development of HCC. The amount of HBV DNA and pregenomic RNA in liver were significantly higher in 16 HBcrAg-positive patients, compared with 12 HBcrAg-negative patients, suggesting active HBV replication in HBcrAg-positive livers. Hepatic gene expression profiling showed that HBV-promoting transcriptional factors, including HNF4α, PPARα, and LRH1, were upregulated in HBcrAg-positive livers. HepAD38 cells overexpressing LRH1 increased HBV replication, characterized by higher HBV DNA and pregenomic RNA levels, during long-term exposure to entecavir. Conversely, overexpression of precore/core in HepG2 cells increased levels of these transcriptional factors. Metformin efficiently repressed HBV replication in primary human hepatocytes. CONCLUSIONS Modulating HBV transcriptional factors by metformin in combination with NA therapy would potentiate anti-HBV activity and reduce the incidence of HCC in HBcrAg-positive patients.
Influenza Vaccine Effectiveness Against 2009 Pandemic Influenza A(H1N1) Virus Differed by Vaccine Type During 2013-2014 in the United States.

BACKGROUND The predominant strain during the 2013-2014 influenza season was 2009 pandemic influenza A(H1N1) virus (A[H1N1]pdm09). This vaccine-component has remained unchanged from 2009. METHODS The US Flu Vaccine Effectiveness Network enrolled subjects aged ≥6 months with medically attended acute respiratory illness (MAARI), including cough, with illness onset ≤7 days before enrollment. Influenza was confirmed by reverse-transcription polymerase chain reaction (RT-PCR). We determined the effectiveness of trivalent or quadrivalent inactivated influenza vaccine (IIV) among subjects ages ≥6 months and the effectiveness of quadrivalent live attenuated influenza vaccine (LAIV4) among children aged 2-17 years, using a test-negative design. The effect of prior receipt of any A(H1N1)pdm09-containing vaccine since 2009 on the effectiveness of current-season vaccine was assessed. RESULTS We enrolled 5999 subjects; 5637 (94%) were analyzed; 18% had RT-PCR-confirmed A(H1N1)pdm09-related MAARI. Overall, the effectiveness of vaccine against A(H1N1)pdm09-related MAARI was 54% (95% confidence interval [CI], 46%-61%). Among fully vaccinated children aged 2-17 years, the effectiveness of LAIV4 was 17% (95% CI, -39% to 51%) and the effectiveness of IIV was 60% (95% CI, 36%-74%). Subjects aged ≥9 years showed significant residual protection of any prior A(H1N1)pdm09-containing vaccine dose(s) received since 2009, as did children <9 years old considered fully vaccinated by prior season. CONCLUSIONS During 2013-2014, IIV was significantly effective against A(H1N1)pdm09. Lack of LAIV4 effectiveness in children highlights the importance of continued annual monitoring of effectiveness of influenza vaccines in the United States.
Limited Effector Memory B-Cell Response to Envelope Glycoprotein B During Primary Human Cytomegalovirus Infection.

BACKGROUND Following primary human cytomegalovirus (HCMV) infection, the production of antibodies against envelope glycoprotein B (gB) is delayed, compared with production of antibodies against tegument proteins, and this likely reduces the control of HCMV dissemination. METHODS The frequency and the phenotype of gB-specific and tegument protein-specific B cells were studied in a cohort of pregnant women with primary HCMV infection. Healthy adults who had chronic HCMV infection or were recently immunized with tetanus toxoid (TT) were included as controls. RESULTS Primary HCMV infection was associated with high and similar frequencies of gB-specific and tegument protein-specific B cells following primary HCMV infection. During primary infection, tegument protein-specific B cells expressed an activated (CD21(low)) memory B-cell (MBC) phenotype. Activated MBCs were also induced by TT booster immunization, indicating that the expansion of this subset is part of the physiological B-cell response to protein antigens. In contrast, gB-specific B cells had a predominant classical (CD21(+)) MBC phenotype during both primary and chronic infections. CONCLUSIONS The delayed production of gB-specific immunoglobulin G (IgG) during primary HCMV infection is associated with a limited induction of MBCs with effector potential. This novel mechanism by which HCMV may interfere with the production of neutralizing antibodies could represent a target for therapeutic immunization.
The Effect of Round Window vs Cochleostomy Surgical Approaches on Cochlear Implant Electrode Position: A Flat-Panel Computed Tomography Study.

IMPORTANCE The round window insertion (RWI) and cochleostomy approaches are the 2 most common surgical techniques used in cochlear implantation (CI). However, there is no consensus on which approach is ideal for electrode array insertion, in part because visualization of intracochlear electrode position is challenging, so postoperative assessment of intracochlear electrode contact is lacking. OBJECTIVE To measure and compare electrode array position between RWI and cochleostomy approaches for CI insertion. DESIGN, SETTING, AND PARTICIPANTS Retrospective case-comparison study of 17 CI users with Med-El standard-length electrode arrays who underwent flat-panel computed tomography scans after CI surgery at a tertiary referral center. The data was analyzed in October 2015. EXPOSURES Flat-panel computed tomography scans were collected between January 1 and August 31, 2013, for 22 electrode arrays. The surgical technique was identified by a combination of operative notes and imaging. Eight cochleae underwent RWI and 14 cochleae underwent cochleostomy approaches anterior and inferior to the round window. MAIN OUTCOMES AND MEASURES Interscalar electrode position and electrode centroid distance to the osseous spiral lamina, lateral bony wall, and central axis of the modiolus. RESULTS Nine participants were men, and 8, women; the mean age was 54.4 (range, 21-64) years. Electrode position was significantly closer to cochlear neural elements with RWI than cochleostomy approaches. Between the 2 surgical approaches, the RWI technique produced shorter distances between the electrode and the modiolus (mean difference, -0.33 [95% CI, -0.29 to -0.39] mm in the apical electrode; -1.42 [95% CI, -1.24 to -1.57] mm in the basal electrode). This difference, which was most prominent in the first third and latter third of the basal turn, decreased after the basal turn. CONCLUSIONS AND RELEVANCE The RWI approach was associated with an increased likelihood of perimodiolar placement. Opting to use RWI over cochleostomy approaches in CI candidates may position electrodes closer to cochlear neural substrates and minimize current spread. These findings need to be interpreted in light of the increased potential for osseous spiral lamina trauma with reduced distances between the electrode array and modiolus.
Ascaris lumbricoides, Ascaris suum, or "Ascaris lumbrisuum"?

Financial support. This work was supported by the Fundacao de Amparo a Pesquisa do Estado do Rio de Janeiro, Universidade Federal Fluminense and Laboratorio de Doencas Parasitarias, Instituto Oswaldo Cruz-Fiocruz. The authors thank Andre Barbosa for their technical support and UFF-Platform sequencing.
RubisCO selection using the vigorously aerobic and metabolically versatile bacterium Ralstonia eutropha

Recapturing atmospheric CO2 is key to reducing global warming and increasing biological carbon availability. Ralstonia eutropha is a biotechnologically useful aerobic bacterium that uses the Calvin–Benson–Bassham (CBB) cycle and the enzyme ribulose 1,5‐bisphosphate carboxylase/oxygenase (RubisCO) for CO2 utilization, suggesting that it may be a useful host to bioselect RubisCO molecules with improved CO2‐capture capabilities. A host strain of R. eutropha was constructed for this purpose after deleting endogenous genes encoding two related RubisCOs. This strain could be complemented for CO2‐dependent growth by introducing native or heterologous RubisCO genes. Mutagenesis and suppressor selection identified amino acid substitutions in a hydrophobic region that specifically influences RubisCO's interaction with its substrates, particularly O2, which competes with CO2 at the active site. Unlike most RubisCOs, the R. eutropha enzyme has evolved to retain optimal CO2‐fixation rates in a fast‐growing host, despite the presence of high levels of competing O2. Yet its structure‐function properties resemble those of several commonly found RubisCOs, including the higher plant enzymes, allowing strategies to engineer analogous enzymes. Because R. eutropha can be cultured rapidly under harsh environmental conditions (e.g., with toxic industrial flue gas), in the presence of near saturation levels of oxygen, artificial selection and directed evolution studies in this organism could potentially impact efforts toward improving RubisCO‐dependent biological CO2 utilization in aerobic environments.
PREVALENCIA DE STAPHYLOCOCCUS AUREUS RESISTENTE A METICILINA EN INFECCIONES DE PIEL Y PARTES BLANDAS EN PACIENTES AMBULATORIOS

UNLABELLED An increased prevalence of community-acquired methicillin resistant Staphylococcus aureus (MRSA) in skin and soft tissue infections (SSTI) has been recently reported. Epidemiological data in Argentina is limited. Our objectives were to evaluate etiological agents, clinical presentation, risk factors and evolution of SSTI in ambulatory patients, in a descriptive and prospective study that was performed at the Infectious Diseases Department, Hospital Fernandez, City of Buenos Aires, Argentina, from 10/01/2009 to 01/31/2011. A total of 130 samples were analyzed from 130 patients. Median age: 36 years old (IQR 25.9-43.5); 61.5% were men. HIV infection: 46.9%. Positive cultures were obtained from 100 samples (76.9%): S. aureus 83, Streptococcus spp. 8, and other microorganisms 9. Sixty two (74.7%) of S. aureus isolates were oxacilin resistant, 12 (14.4%) clindamycin resistant, 14 (16.7%) erythromycin resistant and 5 (6%) ciprofloxacin resistant. Some samples presented more than one resistance. All were susceptible to rifampicin and minocycline and 98.8% (82) to trimethoprim-sulfamethoxazole. Of the MRSA patients, 83.8% (52) had at least one risk factor. No significant differences were found in relation to patients with bacterial infections different from MRSA. The most frequent clinical presentation of MRSA-SSTI was furuncle; 56.5% (35/62) vs. 28.9% (11/38) in other SSTI isolations (p = 0.013). Oxacilin resistance was similar among HIV positive and negative patients (79.1 vs. 70%, p = 0.179) (34/43 vs. 28/40). IN CONCLUSION a high prevalence of MRSA was found in this population, irrespective of HIV serology or the presence of risk factors. Empirical treatment options for this microorganism are minocycline and trimethoprim-sulfamethoxazole.
Infant Feeding Options, Practices and Determinants of Feeding Practices among HIV Seropositive Mothers in Abuja, Nigeria.

Objective: To evaluate infant feeding feeding practices and its determinants among HIV positive mothers in Abuja, the Federal Capital Territory of Nigeria. Materials and Methods: This was a cross-sectional descriptive study conducted among sero-positive women diagnosed during pregnancy and had counseling on infant feeding options. The study was conducted in general hospital Asokoro and Gwagwalada specialist Hospital, both of which offer PMTCT services including free breast milk substitutes (infant formula). Results: A total of fifty HIV-positive pregnant mothers participated in the study. Most of the respondents (63%) were in age range of 21–30years, while that of the spouses were 31– 40years respectively. Forty six percent of respondents had secondary education, while 88% were gainfully employed. Majority of respondents (84%) notified their partners of their sero-status, while 93% of them were counseled along with their spouse/partners (Table 1). All the respondents were counseled on different infant feeding options. Forty percent and 46% of respondents respectively chose exclusive breast milk substitute (EB) and exclusive breastfeeding (EBF) for those who opted for replacement feeding. The main reasons given for the choices were: stigma of HIV status, partner support, availability of supply. Infant feeding choices were significantly related to the level of education and awareness of respondents (x2 = 32.8, df = 16, p = 0.05, x2 = 7.4, df = 2, p = 0.05) Conclusion: Replaccement feeding under the present PMTCT programme seems feasible in urban areas of Nigeria. However, public awareness campaigns are needed for its increased acceptability coupled with adequate support that must be provided for mothers who opted for it. Additional training for counseling in HIV and infant feeding options is recommeded for health care providers. Keywords : HIV sero-positive mothers, infant feeding choices, determinants, Nigeria. Note: there is an erratum at the end of this article
Monitoring for Human Papillomavirus Vaccine Impact Among Gay, Bisexual, and Other Men Who Have Sex With Men-United States, 2012-2014.

BACKGROUND Gay, bisexual, and other men who have sex with men (MSM) are at high risk for human papillomavirus (HPV) infection; vaccination is recommended for US males, including MSM through age 26 years. We assessed evidence of HPV among vaccine-eligible MSM and transgender women to monitor vaccine impact. METHODS During 2012-2014, MSM aged 18-26 years at select clinics completed a computer-assisted self-interview regarding sexual behavior, human immunodeficiency virus (HIV) status, and vaccinations. Self-collected anal swab and oral rinse specimens were tested for HPV DNA (37 types) by L1 consensus polymerase chain reaction; serum was tested for HPV antibodies (4 types) by a multiplexed virus-like particle-based immunoglobulin G direct enzyme-linked immunosorbent assay. RESULTS Among 922 vaccine-eligible participants, the mean age was 23 years, and the mean number of lifetime sex partners was 37. Among 834 without HIV infection, any anal HPV was detected in 69.4% and any oral HPV in 8.4%, yet only 8.5% had evidence of exposure to all quadrivalent vaccine types. In multivariate analysis, HPV prevalence varied significantly (P < .05) by HIV status, sexual orientation, and lifetime number of sex partners, but not by race/ethnicity. DISCUSSIONS Most young MSM lacked evidence of current or past infection with all vaccine-type HPV types, suggesting that they could benefit from vaccination. The impact of vaccination among MSM may be assessed by monitoring HPV prevalence, including in self-collected specimens.