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1.  A new genus and species of Thyasiridae (Mollusca, Bivalvia) from deep-water, Beaufort Sea, northern Alaska 
ZooKeys  2014;11-26.
Bivalve mollusk shells were collected in 2350 m depth in the Beaufort Sea, Arctic Ocean off northern Alaska. Initial identification suggested the specimens were a member of the bivalve family Thyasiridae, but no known eastern Pacific or Arctic living or fossil thyasirid resembled these deep-water specimens. Comparisons were made with the type of the genera Maorithyas Fleming, 1950, Spinaxinus Oliver & Holmes, 2006, Axinus Sowerby, 1821, and Parathyasira Iredale, 1930. We determined the Beaufort Sea species represents a new genus, herein described as Wallerconcha. These specimens also represent a new species, herein named Wallerconcha sarae. These new taxa are compared with known modern and fossil genera and species of thyasirds.
doi:10.3897/zookeys.462.6790
PMCID: PMC4284429  PMID: 25589851
Thyasiridae; Beaufort Sea; Alaska; Mollusca; Bivalvia; Maorithyas; Wallerconcha; Spinaxinus; Axinus; Parathyasira; chemoautotrophic; endosymbiosis; taxonomy; Arctic Ocean
2.  Prevalence of HIV, Syphilis, and Other Sexually Transmitted Infections among MSM from Three Cities in Panama 
Respondent-driven sampling (RDS) was used to conduct a biobehavioral survey among men who have sex with men (MSM) in three cities in the Republic of Panama. We estimated the prevalence of HIV, syphilis, and other sexually transmitted infections (STIs), sociodemographic characteristics, and sexual risk behaviors. Among 603 MSM recruited, RDS-adjusted seroprevalences (95 % confidence intervals) were: HIV—David 6.6 % (2.2–11.4 %), Panama 29.4 % (19.7–39.7 %), and Colon 32.6 % (18.0–47.8 %); active syphilis—David 16.0 % (8.9–24.2 %), Panama 24.7 % (16.7–32.9 %), Colon 31.6 % (14.8–47.5 %); resolved HBV infection—David 10.0 % (4.8–16.8 %), Panama 29.4 % (20.0–38.3 %), and Colon 40.6 % (21.9–54.4 %); herpes simplex virus type 2—David 38.4 % (27.9–48.9 %), Panama 62.6 % (52.8–71.0 %), and Colon 72.9 % (57.4–85.8 %). At least a third of MSM in each city self-identified as heterosexual or bisexual. HIV prevalence is concentrated among MSM. Preventive interventions should focus on increasing HIV and syphilis testing, and increasing promotion of condom awareness and use.
doi:10.1007/s11524-014-9885-4
PMCID: PMC4134449  PMID: 24927712
HIV; Syphilis; Sexually transmitted diseases; Sexual behavior; Respondent-driven sampling; Sampling hidden populations; Panama
3.  Chlamydia trachomatis infection rates among a cohort of mobile soldiers stationed at Fort Bragg, North Carolina, 2005–2010 
BMC Public Health  2014;14:181.
Background
Fort Bragg, a large Army installation with reported high Chlamydia trachomatis (Ct) infection rates, is characterized by a highly mobile population and a surrounding Ct-endemic community. We assessed the rates of Ct incidence and recurrence among the installation’s active component Army personnel and determined the association of soldier transience, sociodemographic factors, and history of sexually transmitted infection (STI) with these rates.
Methods
A cohort of soldiers stationed at Fort Bragg during 2005 to mid-2010 was followed for incident and recurrent Ct infection using laboratory-confirmed reportable disease data. Linkage to demographic and administrative data permitted multivariate analysis to determine association of covariates with initial or recurrent infection.
Results
Among 67,425 soldiers, 2,198 (3.3%) contracted an incident Ct infection (crude incidence, 21.7 per 1,000 person-years). Among soldiers followed for incident infection, 223 (10.6%, crude incidence 110.8 per 1,000 person-years) contracted a recurrent Ct infection. Being female, of lower rank, under 26 years of age, of non-white race, single, or with a high school diploma or less was significantly associated with incident Ct infection. Having breaks in duty or having deployments during follow-up was associated with a lower infection rate. Among women, having prior deployments was associated with a lower rate of both incident and recurrent infection. Specifically associated with recurrent infection in women was age under 21 years or no education beyond high school.
Conclusions
This analysis reaffirms risk factors for Ct infection determined in other studies. In addition, infection risk was lower for more mobile soldiers and tied to the specific location of their regular duty assignment. The findings support the STI prevention efforts at Fort Bragg and the surrounding community, regardless of how often or for how long soldiers have deployed for military operations.
doi:10.1186/1471-2458-14-181
PMCID: PMC3943576  PMID: 24552420
Chlamydia; Army; Mobility
4.  Use of external defibrillator jacket to facilitate safe delivery of radiotherapy for lung cancer – A report of two cases 
Indian Heart Journal  2014;66(1):111-114.
The increasing rate of implantable cardioverter defibrillator (ICD) implantation coupled with shared risk factors between lung cancer and ischemic cardiac disease means that the need for radiotherapy in cardiac device patients is set to become commonplace. We describe two cases referred to our electrophysiology service over a 6-month period. Both had been diagnosed with lung cancer in tissue directly posterior to a previously implanted ICD device. The cases highlight the risks to device function caused by ionizing radiation, the practical difficulties and ethical dilemmas of delivering radiotherapy to cardiac device patients safely and a novel setting for the use of a wearable defibrillator system.
doi:10.1016/j.ihj.2013.12.004
PMCID: PMC4054845  PMID: 24581107
ICD; Radiotherapy; Wearable defibrillator jacket
5.  Where’s Waldo? A new commensal species, Waldo arthuri (Mollusca, Bivalvia, Galeommatidae), from the Northeastern Pacific Ocean 
ZooKeys  2013;67-80.
A galeommatid bivalve mollusk, representing a new species, is described from off the coasts of California and Vancouver Island, British Columbia. The new bivalve has a commensal relationship with the heart urchin, Brisaster latifrons. It has been observed crawling between the oral spines of this urchin, frequently near the peristome. The bivalve has been recorded from 80 (Vancouver Island) to 444 (southern California) meters depth, in muddy sediments.
In common with other galeommatoideans, the new species broods its young; however it differs from the large majority of commensal members in lacking planktotrophic larval development.
Waldo arthuri, new species, has multiple morphological, ecological and developmental similarities to other members of the genus Waldo Nicol, 1966, from the southern Atlantic and Antarctic Oceans. This is most pronounced for the Argentine species, Waldo paucitentaculatus Zelaya & Ituarte, 2013, Waldo arthuri’s sister speciesin nuclear and mitochondrial gene trees. Despite this close relationship, Waldo arthuri is phylogentically distinct and possesses several hinge, shell sculpture, foot, and mantle tentacle characteristics that merit its description as new.
doi:10.3897/zookeys.316.4256
PMCID: PMC3713335  PMID: 23878515
Commensal relationships; Bivalvia; Galeommatidae; Waldo; Echinodea; urchin; taxonomy
6.  HIV, hepatitis B, and hepatitis C prevalence and associated risk behaviors among female sex workers in three Afghan cities 
AIDS (London, England)  2010;24(0 2):S69-S75.
Objective
To assess prevalence of HIV, syphilis, and hepatitis B (HBV) and C virus and associated risk behaviors among female sex workers (FSWs) in three Afghan cities. Design: Cross-sectional prevalence assessment.
Methods
Consented FSWs from Jalalabad, Kabul, and Mazar-i-Sharif completed an interviewer-administered questionnaire, pre and post-test counseling, and rapid and confirmatory testing for HIV, HCV, HBV and syphilis. Logistic regression was used to detect correlates associated with HBV infection.
Results
Of 520 participants, median age and age of initiating sex work were 29 and 23 years, respectively, and median number of monthly clients was 12. Few FSWs reported ever having used illicit drugs (6.9%) or alcohol (4.7%). Demographic and risk behaviors varied significantly by enrollment site, with Kabul FSWs more likely to report sexually-transmitted infection (STI) symptoms, longer sex work duration, and sex work in other cities. Prevalence of HIV was 0.19%, HCV was 1.92%, and HBV was 6.54%, with no cases of syphilis detected. HBV was independently associated with ≥12 clients monthly (AOR=3.15, 95% CI: 1.38 – 7.17), ever using alcohol (AOR=2.61, 95% CI: 1.45 – 4.69), anal sex (AOR=2.42, 95% CI: 1.15 – 5.08), and having children (AOR=2.12, 95% CI: 1.72 – 2.63) in site-controlled multivariate analysis.
Conclusions
While prevalence of HIV, HCV, and syphilis is currently low in these three Afghan cities, risky sexual practices were common and associated with HBV. Programming inclusive of voluntary testing for HIV, viral hepatitis, and STIs, hepatitis vaccination, substance abuse prevention, and condom promotion for both FSWs and clients should be pursued in Afghanistan.
doi:10.1097/01.aids.0000386736.25296.8d
PMCID: PMC3650731  PMID: 20610952
HIV; hepatitis B; female sex worker; Afghanistan
7.  Effects of Chronic Transfusions on Abdominal Sonographic Abnormalities in Children with Sickle Cell Anemia 
The Journal of Pediatrics  2011;160(2):281-285.e1.
Objective
To assess the effects of chronic erythrocyte transfusions on prevalence of sonographic incidence of organ damage in children with sickle cell anemia (SCA).
Study design
Children (n=148; mean age, 13.0 years) with SCA, receiving chronic transfusions (average, 7 years) underwent abdominal sonography at 25 institutions. After central imaging review, spleen, liver and kidney measurements were compared with published normal values. Potential relations between ultrasound, clinical and laboratory data were explored via Analysis of Variance, Student t-test and Cochran Mantel Haenzel tests of non-zero correlation.
Results
Average spleen length was similar to normal children, but over one-third had spleen volumes > 300mL, 15 had previous splenectomy for splenomegaly and 24 had abnormal splenic echotexture. Two-thirds had hepatobiliary disease; 37 had prior cholecystectomy, 46 had gallstones, 16 had gallbladder sludge. Gallbladder disease correlated with older age (p = 0.002), longer liver length (p < 0.001), longer duration of transfusions (p = 0.034) and higher total bilirubin (p < 0.001). Liver (p < 0.001) and renal lengths (p ≤ 0.005) were larger than published norms.
Conclusions
In children with SCA, long-term transfusion therapy may not prevent development or progression of abdominal organ dysfunction.
doi:10.1016/j.jpeds.2011.07.050
PMCID: PMC3237893  PMID: 21907352
sickle cell anemia; iron overload; splenomegaly; gallstones; hepatomegaly; nephromegaly
8.  Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata 
PLoS ONE  2012;7(12):e51687.
Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® ‘Second Generation DNA Sequencing (2GS)’ and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique protein-coding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) protein-coding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites.
doi:10.1371/journal.pone.0051687
PMCID: PMC3522722  PMID: 23272141
9.  The British Sign Language Versions of the Patient Health Questionnaire, the Generalized Anxiety Disorder 7-Item Scale, and the Work and Social Adjustment Scale 
The present study is aimed to translate 3 widely used clinical assessment measures into British Sign Language (BSL), to pilot the BSL versions, and to establish their validity and reliability. These were the Patient Health Questionnaire (PHQ-9), the Generalized Anxiety Disorder 7-item (GAD-7) scale, and the Work and Social Adjustment Scale (WSAS). The 3 assessment measures were translated into BSL and piloted with the Deaf signing population in the United Kingdom (n = 113). Participants completed the PHQ-9, GAD-7, WSAS, and Clinical Outcomes in Routine Evaluation–Outcome Measure (CORE-OM) online. The reliability and validity of the BSL versions of PHQ-9, GAD-7, and WSAS have been examined and were found to be good. The construct validity for the PHQ-9 BSL version did not find the single-factor solution as found in the hearing population. The BSL versions of PHQ-9, GAD-7, and WSAS have been produced in BSL and can be used with the signing Deaf population in the United Kingdom. This means that now there are accessible mental health assessments available for Deaf people who are BSL users, which could assist in the early identification of mental health difficulties.
doi:10.1093/deafed/ens040
PMCID: PMC3521778  PMID: 23197315
10.  Cloned Defective Interfering Influenza Virus Protects Ferrets from Pandemic 2009 Influenza A Virus and Allows Protective Immunity to Be Established 
PLoS ONE  2012;7(12):e49394.
Influenza A viruses are a major cause of morbidity and mortality in the human population, causing epidemics in the winter, and occasional worldwide pandemics. In addition there are periodic outbreaks in domestic poultry, horses, pigs, dogs, and cats. Infections of domestic birds can be fatal for the birds and their human contacts. Control in man operates through vaccines and antivirals, but both have their limitations. In the search for an alternative treatment we have focussed on defective interfering (DI) influenza A virus. Such a DI virus is superficially indistinguishable from a normal virus but has a large deletion in one of the eight RNAs that make up the viral genome. Antiviral activity resides in the deleted RNA. We have cloned one such highly active DI RNA derived from segment 1 (244 DI virus) and shown earlier that intranasal administration protects mice from lethal disease caused by a number of different influenza A viruses. A more cogent model of human influenza is the ferret. Here we found that intranasal treatment with a single dose of 2 or 0.2 µg 244 RNA delivered as A/PR/8/34 virus particles protected ferrets from disease caused by pandemic virus A/California/04/09 (A/Cal; H1N1). Specifically, 244 DI virus significantly reduced fever, weight loss, respiratory symptoms, and infectious load. 244 DI RNA, the active principle, was amplified in nasal washes following infection with A/Cal, consistent with its amelioration of clinical disease. Animals that were treated with 244 DI RNA cleared infectious and DI viruses without delay. Despite the attenuation of infection and disease by DI virus, ferrets formed high levels of A/Cal-specific serum haemagglutination-inhibiting antibodies and were solidly immune to rechallenge with A/Cal. Together with earlier data from mouse studies, we conclude that 244 DI virus is a highly effective antiviral with activity potentially against all influenza A subtypes.
doi:10.1371/journal.pone.0049394
PMCID: PMC3521014  PMID: 23251341
11.  Comparison of the protection of ferrets against pandemic 2009 influenza A virus (H1N1) by 244 DI influenza virus and oseltamivir 
Antiviral Research  2012;96(3):376-385.
Highlights
► We compared the ability of DI RNA and Tamiflu to protect ferrets from influenza. ► We treated ferrets with one 2 μg intranasal dose of DI RNA delivered as DI virus. ► Or we treated ferrets with 10 oral doses of Tamiflu totalling 25 mg over 5 days. ► Pandemic A/California/04/09 amplified the DI RNA by >25,000-fold. ► DI virus was more effective than Tamiflu in combatting pandemic A/California/04/09.
The main antivirals employed to combat seasonal and pandemic influenza are oseltamivir and zanamivir which act by inhibiting the virus-encoded neuraminidase. These have to be deployed close to the time of infection and antiviral resistance to the more widely used oseltamivir has arisen relatively rapidly. Defective interfering (DI) influenza virus is a natural antiviral that works in a different way to oseltamivir and zanamivir, and a cloned version (segment 1 244 DI RNA in a cloned A/PR/8/34 virus; 244/PR8) has proved effective in preclinical studies in mice. The active principle is the DI RNA, and this is thought to interact with all influenza A viruses by inhibiting RNA virus synthesis and packaging of the cognate virion RNA into nascent DI virus particles. We have compared the ability of DI virus and oseltamivir to protect ferrets from intranasal 2009 pandemic influenza virus A/California/04/09 (A/Cal, H1N1). Ferrets were treated with a single 2 μg intranasal dose of 244 DI RNA delivered as 244/PR8 virus, or a total of 25 mg/kg body weight of oseltamivir given as 10 oral doses over 5 days. Both DI virus and oseltamivir reduced day 2 infectivity and the influx of cells into nasal fluids, and permitted the development of adaptive immunity. However DI virus, but not oseltamivir, significantly reduced weight loss, facilitated better weight gain, reduced respiratory disease, and reduced infectivity on days 4 and 6. 244 DI RNA was amplified by A/Cal by >25,000-fold, consistent with the amelioration of clinical disease. Treatment with DI virus did not delay clearance or cause persistence of infectious virus or DI RNA. Thus in this system DI virus was overall more effective than oseltamivir in combatting pandemic A/California/04/09.
doi:10.1016/j.antiviral.2012.09.017
PMCID: PMC3526778  PMID: 23041142
Influenza virus; Defective interfering virus; Ferret; Protection; Oseltamivir
12.  Short Communication: Investigation of Incident HIV Infections Among U.S. Army Soldiers Deployed to Afghanistan and Iraq, 2001–2007 
AIDS Research and Human Retroviruses  2012;28(10):1308-1312.
Abstract
The U.S. Army initiated an investigation in response to observations of a possible increase in HIV incidence among soldiers deployed to combat. Human immunodeficiency virus (HIV)-infected U.S. Army soldiers are not eligible to deploy. Combat presents a health hazard to HIV-infected soldiers and they pose a threat to the safety of the battlefield blood supply and their contacts. All soldiers are routinely screened for HIV every 2 years and those who deploy are also screened both prior to and after deployment. Seroconversion rates were estimated for all soldiers who deployed to Afghanistan or Iraq in the period 2001–2007 and all active duty soldiers who did not. Seroconverters with an estimated date of infection, based on calculation of the midpoint between the last seronegative and first seropositive test date, that was either before or during deployment were eligible for inclusion. Confidential interviews and medical record reviews were conducted to determine the most likely time, geographic location, and mode of infection. Reposed predeployment samples were tested for HIV ribonucleic acid. The HIV seroconversion rate among all soldiers who deployed was less than the rate among those who did not deploy: 1.04 and 1.42 per 10,000 person-years, respectively. Among 48 cases, most were determined to have been infected in the United States or Germany and prior to deployment (n=20, 42%) or during rest and relaxation leave (n=13, 27%). Seven seronegative acute infections were identified in the predeployment period. Subtype was determined for 40 individuals; all were subtype B infections. All were acquired through sexual contact. These findings can inform development of preventive interventions and refinement of existing screening policy to further reduce HIV-infected deployed soldier person time.
doi:10.1089/aid.2011.0363
PMCID: PMC3448093  PMID: 22280248
13.  Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae 
Journal of Bacteriology  2012;194(6):1494-1504.
Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.
doi:10.1128/JB.06403-11
PMCID: PMC3294861  PMID: 22247511
14.  Cross-sectional assessment of prevalence and correlates of blood-borne and sexually-transmitted infections among Afghan National Army recruits 
BMC Infectious Diseases  2012;12:196.
Background
Few data are available in Afghanistan to shape national military force health practices, particularly with regard to sexually-transmitted infections (STIs). We measured prevalence and correlates of HIV, syphilis, herpes simplex 2 virus (HSV-2), and hepatitis C virus (HCV) among Afghan National Army (ANA) recruits.
Methods
A cross-sectional sample of male ANA recruits aged 18–35 years were randomly selected at the Kabul Military Training Center between February 2010 and January 2011. Participants completed an interviewer-administered questionnaire and serum-based rapid testing for syphilis and hepatitis C virus antibody on-site; HIV and HSV-2 screening, and confirmatory testing were performed off-site. Prevalence of each infection was calculated and logistic regression analysis performed to identify correlates.
Results
Of 5313 recruits approached, 4750 consented to participation. Participants had a mean age of 21.8 years (SD±3.8), 65.5% had lived outside Afghanistan, and 44.3% had no formal education. Few reported prior marijuana (16.3%), alcohol (5.3%), or opiate (3.4%) use. Of sexually active recruits (58.7%, N = 2786), 21.3% reported paying women for sex and 21.3% reported sex with males. Prevalence of HIV (0.063%, 95% CI: 0.013- 0.19), syphilis (0.65%, 95% CI: 0.44 – 0.93), and HCV (0.82%, 95% CI: 0.58 – 1.12) were quite low. Prevalence of HSV-2 was 3.03% (95% CI: 2.56 - 3.57), which was independently associated with age (Adjusted Odds Ratio (AOR) = 1.04, 95% CI: 1.00 - 1.09) and having a television (socioeconomic marker) (AOR = 1.46, 95% CI: 1.03 – 2.05).
Conclusion
Though prevalence of HIV, HCV, syphilis, and HSV-2 was low, sexual risk behaviors and intoxicant use were present among a substantial minority, indicating need for prevention programming. Formative work is needed to determine a culturally appropriate approach for prevention programming to reduce STI risk among Afghan National Army troops.
doi:10.1186/1471-2334-12-196
PMCID: PMC3482585  PMID: 22909128
Afghanistan; Military populations; HIV; Sexual risk behavior; Drug use
15.  Dominant and diet-responsive groups of bacteria within the human colonic microbiota 
The ISME journal  2010;5(2):220-230.
The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that ‘blooms' in specific bacterial groups occurred rapidly after a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of RS remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual's gut microbiota.
doi:10.1038/ismej.2010.118
PMCID: PMC3105703  PMID: 20686513
human colon; resistant starch; 16S rRNA; phylotypes; Ruminococcus; temporal change
16.  Contraceptive Utilization and Pregnancy Termination Among Female Sex Workers in Afghanistan 
Journal of Women's Health  2010;19(11):2057-2062.
Abstract
Background
To determine the prevalence and correlates of prior pregnancy termination and unmet need for contraception among female sex workers (FSWs) in Afghanistan.
Methods
FSWs in Jalalabad, Kabul, and Mazar-i-Sharif were recruited between June 2006 and December 2007 through outreach programs. Participants completed an interviewer-administered survey describing demographics, behaviors associated with risk of sexually transmitted infections (STIs) and unplanned pregnancy, and medical history. Correlates of prior pregnancy termination and current unmet need for contraception were assessed with logistic regression analysis, controlling for site.
Results
Of 520 FSWs, most (82.3%) had been pregnant at least once (mean 4.9 ± 2.7, range 1–17), among whom unplanned pregnancy (36.9%) and termination (33.2%) were common. Jalalabad participants were more likely to report both prior unplanned pregnancy (60.6% vs. 48.3% in Kabul or 20.7% in Mazar, p < 0.001) and prior termination (54.9% vs. 31.8% in Kabul or 26.8% in Mazar, p < 0.001). Most FSWs (90.0%) stated pregnancy was not currently desirable, and 85.2% were using contraception. Unmet need for contraception (14.7% of participants) was positively associated with having sold sex outside their city of residence (adjusted odds ratio [AOR] 1.88, 95% confidence interval [CI] 1.28-2.77) and inversely associated with illicit drug use (AOR 0.41, 95% CI 0.31-0.53).
Conclusions
Although FSWs in Afghanistan report high rates of contraceptive use, unplanned pregnancy is common. Reproductive health services should be included in programming for FSWs to reduce unplanned pregnancies and to reduce HIV/STI risks.
doi:10.1089/jwh.2010.1947
PMCID: PMC2971650  PMID: 20879869
17.  Defective interfering influenza virus confers only short-lived protection against influenza virus disease: Evidence for a role for adaptive immunity in DI virus-mediated protection in vivo 
Vaccine  2011;29(38-6):6584-6591.
We have shown earlier that a single dose of cloned defective interfering (DI) influenza A virus strongly protects mice from disease following a lethal challenge with different subtypes of influenza A virus. These animals suffered no clinical disease but experienced a subclinical infection which rendered them immune to reinfection with the same challenge virus. However, little is known about how DI virus achieves such protection. Here we investigated the role of adaptive immunity in DI virus-mediated protection using severe-combined immunodeficient (SCID) mice, which lack competence in both B- and T-cell compartments but retain NK cell activity. SCID mice which were treated with DI virus and infected with influenza virus initially remained completely well, while infected litter mates that received UV-inactivated DI virus became seriously ill and died. However, after 10 days of good health, the DI virus-protected SCID mice developed a clinical disease that was similar, but not completely identical, to the acute influenza disease. Disease was delayed longer by a higher dose of DI virus. We excluded the possibilities that the DI virus load in the lungs had declined, that the DI RNA sequence had changed so that it no longer interfered with the infectious genome, or that infectious virus had become resistant to the DI virus. These data show that while DI virus provides full protection from the acute disease in the absence of adaptive immunity, that same immunity is essential for clearing the infection. This indicates that the conventional view that DI virus-induced protection is mediated solely by competition for replication with the challenge virus is incorrect for influenza virus.
doi:10.1016/j.vaccine.2011.06.114
PMCID: PMC3163266  PMID: 21762748
Influenza; Defective interfering; Immunity; Protection; SCID
18.  Dominant and diet-responsive groups of bacteria within the human colonic microbiota 
The ISME journal  2010;5(2):220-230.
The populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. Here we examined the influence of precisely controlled diets in 14 overweight males. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSP), and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequences in stool samples of six volunteers detected 320 phylotypes (defined at >98% identity) of which 26, including 19 cultured species, each accounted for >1% of sequences. Although samples clustered more strongly by individual than by diet, time courses obtained by targeted qPCR revealed that “blooms” in specific bacterial groups occurred rapidly following a dietary change. These were rapidly reversed by the subsequent diet. Relatives of Ruminococcus bromii (“R-ruminococci”) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, while the uncultured Oscillibacter group increased on the RS and WL diets. Relatives of Eubacterium rectale increased on RS (to mean 10.1%) but decreased, along with Collinsella aerofaciens, on WL. Inter-individual variation was marked, however, with >60% of resistant starch remaining unfermented in two volunteers on the RS diet, compared to <4% in the other 12 volunteers; these two individuals also showed low numbers of R-ruminococci (<1%). Dietary non-digestible carbohydrate can produce marked changes in the gut microbiota, but these depend on the initial composition of an individual’s gut microbiota.
doi:10.1038/ismej.2010.118
PMCID: PMC3105703  PMID: 20686513
19.  Defective interfering virus protects elderly mice from influenza 
Virology Journal  2011;8:212.
Background
We have identified and characterised a defective-interfering (DI) influenza A virus particles containing a highly deleted segment 1 RNA that has broad-spectrum antiviral activity. In young adult mice it exerts protection against several different subtypes of influenza A virus (defined here as homologous or genetically compatible protection) and against a paramyxovirus and an influenza B virus (heterologous or genetically unrelated protection). Homologous protection is mediated by replication competition between the deleted and full-length genomes, and heterologous protection occurs through stimulation of innate immunity, especially interferon type I.
Methods
A single dose of the protective DI virus was administered intranasally to elderly mice at -7, -1 and +1 days relative to intranasal challenge with influenza A virus.
Results
A single dose of the DI virus given 1 or 7 days protected elderly mice, reducing a severe, sometimes fatal disease to a subclinical or mild infection. In contrast, all members of control groups treated with inactivated DI virus before challenge became extremely ill and most died. Despite the subclinical/mild nature of their infection, protected mice developed solid immunity to a second infectious challenge.
Conclusions
The defective interfering virus is effective in preventing severe influenza A in elderly mice and may offer a new approach to protection of the human population.
doi:10.1186/1743-422X-8-212
PMCID: PMC3117841  PMID: 21549019
elderly; defective-interfering virus; geriatric; influenza; mice; treatment
20.  Distinct Circulating Recombinant HIV-1 Strains Among Injecting Drug Users and Sex Workers in Afghanistan 
Abstract
Little information is available regarding a circulating HIV genotype among high-risk groups in Afghanistan; we describe HIV genotypes among injecting drug users (IDUs) and sex workers (SWs) in four Afghan cities. Participants completed behavioral questionnaires and HIV testing. Western blot–confirmed specimens had peripheral mononuclear blood cells isolated for genotyping. Analysis of recombinants was done by bootscanning and manual sequence alignment. The single SW sample harbored a CRF01_AE strain. Of 10 IDUs available for analysis, all were CRF35_AD and from Hirat. Analyzed subregions (gag p17 and env C1-C5) revealed close homology between the Hirat specimens. Three distinct subclusters comprising two or three strains were identified, whereas two other strains were generally equidistant from previously identified Kabul strains. Results suggest that the nascent HIV epidemic among IDUs in Hirat is largely, if not entirely, subtype CRF35_AD, and the close homology suggests recent infection; harm reduction should be supported to avert further transmission.
doi:10.1089/aid.2009.0226
PMCID: PMC2933162  PMID: 20438383
21.  Perinatal Exposure to Low Doses of Dioxin Can Permanently Impair Human Semen Quality 
Environmental Health Perspectives  2011;119(5):713-718.
Background
In recent decades, young men in some industrialized areas have reportedly experienced a decrease in semen quality.
Objective
We examined effects of perinatal dioxin exposure on sperm quality and reproductive hormones.
Methods
We investigated sperm quality and hormone concentrations in 39 sons (mean age, 22.5 years) born between 1977 and 1984 to mothers exposed to dioxin after the accident in Seveso, Italy (1976), and 58 comparisons (mean age, 24.6 years) born to mothers exposed only to background dioxin. Maternal dioxin levels at conception were extrapolated from the concentrations measured in 1976 serum samples.
Results
The 21 breast-fed sons whose exposed mothers had a median serum dioxin concentration as low as 19 ppt at conception had lower sperm concentration (36.3 vs. 86.3 million/mL; p = 0.002), total count (116.9 vs. 231.1; p = 0.02), progressive motility (35.8 vs. 44.2%; p = 0.03), and total motile count (38.7 vs. 98 million; p = 0.01) than did the 36 breast-fed comparisons. The 18 formula-fed exposed and the 22 formula-fed and 36 breast-fed comparisons (maternal dioxin background 10 ppt at conception) had no sperm-related differences. Follicle-stimulating hormone was higher in the breast-fed exposed group than in the breast-fed comparisons (4.1 vs. 2.63 IU/L; p = 0.03) or the formula-fed exposed (4.1 vs. 2.6 IU/L; p = 0.04), and inhibin B was lower (breast-fed exposed group, 70.2; breast-fed comparisons, 101.8 pg/mL, p = 0.01; formula-fed exposed, 99.9 pg/mL, p = 0.02).
Conclusions
In utero and lactational exposure of children to relatively low dioxin doses can permanently reduce sperm quality.
doi:10.1289/ehp.1002134
PMCID: PMC3094426  PMID: 21262597
breast-feeding; dioxin; environmental endocrine disrupters; human sperm impairment; human sperm quality; perinatal exposure; reproductive hormones; TCDD
22.  Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities 
The ISME Journal  2010;5(5):780-791.
Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed.
doi:10.1038/ismej.2010.175
PMCID: PMC3105771  PMID: 21151003
commonness and rarity; oral microbiota; polymicrobial infections; pulmonary disease; species abundance distributions
23.  Antibiotic Treatment of Clostridium difficile Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts ▿ †  
Infection and Immunity  2009;77(9):3661-3669.
Clostridium difficile persists in hospitals by exploiting an infection cycle that is dependent on humans shedding highly resistant and infectious spores. Here we show that human virulent C. difficile can asymptomatically colonize the intestines of immunocompetent mice, establishing a carrier state that persists for many months. C. difficile carrier mice consistently shed low levels of spores but, surprisingly, do not transmit infection to cohabiting mice. However, antibiotic treatment of carriers triggers a highly contagious supershedder state, characterized by a dramatic reduction in the intestinal microbiota species diversity, C. difficile overgrowth, and excretion of high levels of spores. Stopping antibiotic treatment normally leads to recovery of the intestinal microbiota species diversity and suppresses C. difficile levels, although some mice persist in the supershedding state for extended periods. Spore-mediated transmission to immunocompetent mice treated with antibiotics results in self-limiting mucosal inflammation of the large intestine. In contrast, transmission to mice whose innate immune responses are compromised (Myd88−/−) leads to a severe intestinal disease that is often fatal. Thus, mice can be used to investigate distinct stages of the C. difficile infection cycle and can serve as a valuable surrogate for studying the spore-mediated transmission and interactions between C. difficile and the host and its microbiota, and the results obtained should guide infection control measures.
doi:10.1128/IAI.00558-09
PMCID: PMC2737984  PMID: 19564382
24.  The Level and Duration of RSV-Specific Maternal IgG in Infants in Kilifi Kenya 
PLoS ONE  2009;4(12):e8088.
Background
Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infection in infants. The rate of decay of RSV-specific maternal antibodies (RSV-matAb), the factors affecting cord blood levels, and the relationship between these levels and protection from infection are poorly defined.
Methods
A birth cohort (n = 635) in rural Kenya, was studied intensively to monitor infections and describe age-related serological characteristics. RSV specific IgG antibody (Ab) in serum was measured by the enzyme linked immunosorbent assay (ELISA) in cord blood, consecutive samples taken 3 monthly, and in paired acute and convalescent samples. A linear regression model was used to calculate the rate of RSV-matAb decline. The effect of risk factors on cord blood titres was investigated.
Results
The half-life of matAb in the Kenyan cohort was calculated to be 79 days (95% confidence limits (CL): 76–81 days). Ninety seven percent of infants were born with RSV-matAb. Infants who subsequently experienced an infection in early life had significantly lower cord titres of anti-RSV Ab in comparison to infants who did not have any incident infection in the first 6 months (P = 0.011). RSV infections were shown to have no effect on the rate of decay of RSV-matAb.
Conclusion
Maternal-specific RSV Ab decline rapidly following birth. However, we provide evidence of protection against severe disease by RSV-matAb during the first 6–7 months. This suggests that boosting maternal-specific Ab by RSV vaccination may be a useful strategy to consider.
doi:10.1371/journal.pone.0008088
PMCID: PMC2779853  PMID: 19956576

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