Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3-6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses--using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2-7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.

Early-life soy exposure and age at menarche.

This study examines the timing of menarche in relation to infant-feeding methods, specifically addressing the potential effects of soy isoflavone exposure through soy-based infant feeding. Subjects were participants in the Avon Longitudinal Study of Parents and Children (ALSPAC). Mothers were enrolled during pregnancy and their children have been followed prospectively. Early-life feeding regimes, categorised as primarily breast, early formula, early soy and late soy, were defined using infant-feeding questionnaires administered during infancy. For this analysis, age at menarche was assessed using questionnaires administered approximately annually between ages 8 and 14.5. Eligible subjects were limited to term, singleton, White females. We used Kaplan-Meier survival curves and Cox proportional hazards models to assess age at menarche and risk of menarche over the study period. The present analysis included 2920 girls. Approximately 2% of mothers reported that soy products were introduced into the infant diet at or before 4 months of age (early soy). The median age at menarche [interquartile range (IQR)] in the study sample was 153 months [144-163], approximately 12.8 years. The median age at menarche among early soy-fed girls was 149 months (12.4 years) [IQR, 140-159]. Compared with girls fed non-soy-based infant formula or milk (early formula), early soy-fed girls were at 25% higher risk of menarche throughout the course of follow-up (hazard ratio 1.25 [95% confidence interval 0.92, 1.71]). Our results also suggest that girls fed soy products in early infancy may have an increased risk of menarche specifically in early adolescence. These findings may be the observable manifestation of mild endocrine-disrupting effects of soy isoflavone exposure. However, our study is limited by few soy-exposed subjects and is not designed to assess biological mechanisms. Because soy formula use is common in some populations, this subtle association with menarche warrants more in-depth evaluation in future studies.

Association between attention-deficit/hyperactivity disorder symptoms and obesity and hypertension in early adulthood: a population-based study.

OBJECTIVE: To examine the associations between attention-deficit/hyperactivity disorder (ADHD) symptoms, obesity and hypertension in young adults in a large population-based cohort. DESIGN, SETTING AND PARTICIPANTS: The study population consisted of 15,197 respondents from the National Longitudinal Study of Adolescent Health, a nationally representative sample of adolescents followed from 1995 to 2009 in the United States. Multinomial logistic and logistic models examined the odds of overweight, obesity and hypertension in adulthood in relation to retrospectively reported ADHD symptoms. Latent curve modeling was used to assess the association between symptoms and naturally occurring changes in body mass index (BMI) from adolescence to adulthood. RESULTS: Linear association was identified between the number of inattentive (IN) and hyperactive/impulsive (HI) symptoms and waist circumference, BMI, diastolic blood pressure and systolic blood pressure (all P-values for trend <0.05). Controlling for demographic variables, physical activity, alcohol use, smoking and depressive symptoms, those with three or more HI or IN symptoms had the highest odds of obesity (HI 3+, odds ratio (OR)=1.50, 95% confidence interval (CI) = 1.22-2.83; IN 3+, OR = 1.21, 95% CI = 1.02-1.44) compared with those with no HI or IN symptoms. HI symptoms at the 3+ level were significantly associated with a higher OR of hypertension (HI 3+, OR = 1.24, 95% CI = 1.01-1.51; HI continuous, OR = 1.04, 95% CI = 1.00-1.09), but associations were nonsignificant when models were adjusted for BMI. Latent growth modeling results indicated that compared with those reporting no HI or IN symptoms, those reporting 3 or more symptoms had higher initial levels of BMI during adolescence. Only HI symptoms were associated with change in BMI. CONCLUSION: Self-reported ADHD symptoms were associated with adult BMI and change in BMI from adolescence to adulthood, providing further evidence of a link between ADHD symptoms and obesity.

Early versus delayed fixed dose combination abacavir/lamivudine/zidovudine in patients with HIV and tuberculosis in Tanzania.

Fixed dose combination abacavir/lamivudine/zidovudine (ABC/3TC/ZDV) among HIV-1 and tuberculosis (TB)-coinfected patients was evaluated and outcomes between early vs. delayed initiation were compared. In a randomized, pilot study conducted in the Kilimanjaro Region of Tanzania, HIV-infected inpatients with smear-positive TB and total lymphocyte count <1200/mm(3) were randomized to initiate ABC/3TC/ZDV either 2 (early) or 8 (delayed) weeks after commencing antituberculosis therapy and were followed for 104 weeks. Of 94 patients screened, 70 enrolled (41% female, median CD4 count 103 cells/mm(3)), and 33 in each group completed 104 weeks. Two deaths and 12 serious adverse events (SAEs) were observed in the early arm vs. one death, one clinical failure, and seven SAEs in the delayed arm (p = 0.6012 for time to first grade 3/4 event, SAE, or death). CD4 cell increases were +331 and +328 cells/mm(3), respectively. TB-immune reconstitution inflammatory syndromes (TB-IRIS) were not observed in any subject. Using intent-to-treat (ITT), missing = failure analyses, 74% (26/35) vs. 89% (31/35) randomized to early vs. delayed therapy had HIV RNA levels <400 copies/ml at 104 weeks (p = 0.2182) and 66% (23/35) vs. 74% (26/35), respectively, had HIV RNA levels <50 copies/ml (p = 0.6026). In an analysis in which switches from ABC/3TC/ZDV = failure, those receiving early therapy were less likely to be suppressed to <400 copies/ml [60% (21/35) vs. 86% (30/35), p = 0.030]. TB-IRIS was not observed among the 70 coinfected subjects beginning antiretroviral treatment. ABC/3TC/ZDV was well tolerated and resulted in steady immunologic improvement. Rates of virologic suppression were similar between early and delayed treatment strategies with triple nucleoside regimens when substitutions were allowed.

Three Voices in the Wilderness: Foote, Bloch, and Korngold in the Early Twentieth-Century America

Barbara Hanning points out in her book Concise History of Western Music, that "Twentieth-century American music was in large measure an extension of European music" (Hanning 1998, 515). My dissertation/perforrnance project features cello works written by three contemporary composers who lived in America but were connected to the European heritage in different ways; each contributed significantly to the development of American classical concert life, music education, and even popular culture. Programs of my performances are intended to illustrate their unique compositional styles. The first recital consists of five cello compositions of Massachusetts-born Arthur Foote (1853 - 1937): Drei Stucke fur Pianoforte und Violoncello, Op. 1; Scherzo, Op.22; Romanza, Op.33; Aubade, Op.77; and Sonata for Violoncello and Piano, Op.78. Foote was influenced by the German-trained John Knowles Paine at Harvard University; he composed music famous for its extensive chromaticism in both harmony and melodic line, and for clearly-defined formal structure. The second recital explores the music of Swiss-American composer Ernest Bloch (1880-1959): a short Meditation Hebraique, a Suite No. I for Violoncello Solo and the famous rhapsody Schelomo. Born in Geneva, Switzerland, and settling in the United States in 1916, Bloch is a composer deeply influenced by the European late-Romantic tradition and is also well-known for employing "Hebraic" elements into his works. The final performance comprises two other of Bloch's cello works and one cello concerto by the Austrian-American composer, Erich Wolfgang Korngold (1897- 1957). Bloch's Voice in the Wilderness is a symphonic poem for orchestra and cello (accompanied by piano in this performance), consisting of six movements performed without pause. His Suite No.3 for Cello Solo is shorter and has a simpler style than the first Suite. Korngold was recognized as a child prodigy in his native Austria. After a Nazi-induced exile, he immigrated to America and became a film music composer in Hollywood. The Cello Concerto was used in the movie "Deception" (1 946), for which Korngold provided the film score. The impassioned harmonic language and lavish melodic lines inherited from the high-romanticism make this work one of comparative discordant beauty among other compositions of his time.

Selected Works from Character Pieces in the 19th - Early 20th Centuries

During the Romantic Era, the character piece flourished and became one of the most important genres. Even though character pieces existed as early as the eighteenth century, it was not until the nineteenth century that Romantic Era literary figures discovered that music was as powerful as any other artistic medium in expressing unspeakable emotions. The character piece allowed composers to express a definite mood, a programmatic idea, or a pictorial association. Character pieces often have titles that suggest briehess or casualness, such as a Beethoven Bagatelle, a Schubert Impromptu or Moment musicaux. Others have expressive programmatic titles, such as Schumann's Kreisleriana and Liszt's Apres une lecture de Dante. Ths dissertation was based on selected works from the nineteenth century and early-twentieth century in order to demonstrate the great variety of musical thought and stylistic development. I have examined composers from different countries and of different nationalities to establish what and how they contributed to the remarkable diversity in this genre. The selected works allowed for very personal programs. These concerts, in addition to being good combinations of pieces, are representative of the genre. The first program consisted of Chopin's Preludes, Op. 28; three pieces from Debussy7s Images Books I and 11; and Liszt7s Apres une lecture de Dante. The second program included seven of Beethoven's Bagatelles, Op. 33; Schumann's Kinderscenen, Op. 15; Poulenc's Mouvements perpetuels and Intermezzo in A-jlat Major; Faure7s Nocturne in B Major, Op. 33, No. 2 and Impromptu No. 2 in F Minor; three of Mompou's Canciones y Danzas; four of Villa-Lobos Prole do bebe Suite No. 1; and Albkniz's Navarra. The third and final program comprised four selections from Rachrnaninoff s Moment musicaux, Op. 16; five pieces from Grieg's Lyric Pieces; and Arensky7s Suite No. 1 for Two Pianos and Suite No. 2 for Two Pianos. I wanted to bring out nuances specific to the individual composers and show how their character pieces helped in shaping the Romantic Era. Even in the twenty-first century, an era of highly specialized musical tastes, the popularity and accessibility of character pieces stand out.

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures.

Features of programmed cell death in intact Xenopus oocytes and early embryos revealed by near-infrared fluorescence and real-time monitoring.

Factors influencing apoptosis of vertebrate eggs and early embryos have been studied in cell-free systems and in intact embryos by analyzing individual apoptotic regulators or caspase activation in static samples. A novel method for monitoring caspase activity in living Xenopus oocytes and early embryos is described here. The approach, using microinjection of a near-infrared caspase substrate that emits fluorescence only after its proteolytic cleavage by active effector caspases, has enabled the elucidation of otherwise cryptic aspects of apoptotic regulation. In particular, we show that brief caspase activity (10 min) is sufficient to cause apoptotic death in this system. We illustrate a cytochrome c dose threshold in the oocyte, which is lowered by Smac, a protein that binds thereby neutralizing the inhibitor of apoptosis proteins. We show that meiotic oocytes develop resistance to cytochrome c, and that the eventual death of oocytes arrested in meiosis is caspase-independent. Finally, data acquired through imaging caspase activity in the Xenopus embryo suggest that apoptosis in very early development is not cell-autonomous. These studies both validate this assay as a useful tool for apoptosis research and reveal subtleties in the cell death program during early development. Moreover, this method offers a potentially valuable screening modality for identifying novel apoptotic regulators.

Early social exposure in wild chimpanzees: mothers with sons are more gregarious than mothers with daughters.

In many mammals, early social experience is critical to developing species-appropriate adult behaviors. Although mother-infant interactions play an undeniably significant role in social development, other individuals in the social milieu may also influence infant outcomes. Additionally, the social skills necessary for adult success may differ between the sexes. In chimpanzees (Pan troglodytes), adult males are more gregarious than females and rely on a suite of competitive and cooperative relationships to obtain access to females. In fission-fusion species, including humans and chimpanzees, subgroup composition is labile and individuals can vary the number of individuals with whom they associate. Thus, mothers in these species have a variety of social options. In this study, we investigated whether wild chimpanzee maternal subgrouping patterns differed based on infant sex. Our results show that mothers of sons were more gregarious than mothers of daughters; differences were especially pronounced during the first 6 mo of life, when infant behavior is unlikely to influence maternal subgrouping. Furthermore, mothers with sons spent significantly more time in parties containing males during the first 6 mo. These early differences foreshadow the well-documented sex differences in adult social behavior, and maternal gregariousness may provide sons with important observational learning experiences and social exposure early in life. The presence of these patterns in chimpanzees raises questions concerning the evolutionary history of differential social exposure and its role in shaping sex-typical behavior in humans.

Pharmacogenomics in early-phase clinical development.

Pharmacogenomics (PGx) offers the promise of utilizing genetic fingerprints to predict individual responses to drugs in terms of safety, efficacy and pharmacokinetics. Early-phase clinical trial PGx applications can identify human genome variations that are meaningful to study design, selection of participants, allocation of resources and clinical research ethics. Results can inform later-phase study design and pipeline developmental decisions. Nevertheless, our review of the clinicaltrials.gov database demonstrates that PGx is rarely used by drug developers. Of the total 323 trials that included PGx as an outcome, 80% have been conducted by academic institutions after initial regulatory approval. Barriers for the application of PGx are discussed. We propose a framework for the role of PGx in early-phase drug development and recommend PGx be universally considered in study design, result interpretation and hypothesis generation for later-phase studies, but PGx results from underpowered studies should not be used by themselves to terminate drug-development programs.

Neutralizing BAFF/APRIL with atacicept prevents early DSA formation and AMR development in T cell depletion induced nonhuman primate AMR model.

Depletional strategies directed toward achieving tolerance induction in organ transplantation have been associated with an increased incidence and risk of antibody-mediated rejection (AMR) and graft injury. Our clinical data suggest correlation of increased serum B cell activating factor/survival factor (BAFF) with increased risk of antibody-mediated rejection in alemtuzumab treated patients. In the present study, we tested the ability of BAFF blockade (TACI-Ig) in a nonhuman primate AMR model to prevent alloantibody production and prolong allograft survival. Three animals received the AMR inducing regimen (CD3-IT/alefacept/tacrolimus) with TACI-Ig (atacicept), compared to five control animals treated with the AMR inducing regimen only. TACI-Ig treatment lead to decreased levels of DSA in treated animals at 2 and 4 weeks posttransplantation (p < 0.05). In addition, peripheral B cell numbers were significantly lower at 6 weeks posttransplantation. However, it provided only a marginal increase in graft survival (59 ± 22 vs. 102 ± 47 days; p = 0.11). Histological analysis revealed a substantial reduction in findings typically associated with humoral rejection with atacicept treatment. More T cell rejection findings were observed with increased graft T cell infiltration in atacicept treatment, likely secondary to the graft prolongation. We show that BAFF/APRIL blockade using concomitant TACI-Ig treatment reduced the humoral portion of rejection in our depletion-induced preclinical AMR model.

The distribution of early childhood memories.

The quantitative distribution of autobiographical memories for the first decade of life is described. The distribution, based on over 11,000 autobiographical memories from age 10 and younger from published studies, is nearly identical for males and females, for participants of different ages, and for different methods of collecting data, including using words to cue memories from anywhere in the lifespan or from just the childhood years, exhaustive listing of all early memories, and interviews.

Things learned in early adulthood are remembered best.

Evidence is reviewed that for older adults the period from 10 to 30 years of age produces recall of the most autobiographical memories, the most vivid memories, and the most important memories. It is the period from which peoples' favorite films, music, and books come and the period from which they judge the most important world events to have originated. Factual, semantic, general-knowledge, multiple-choice questions about the Academy Awards, the World Series, and current events from this period were answered more accurately by two different groups of 30 older adults tested 10 years apart. A cognitive theory based on the importance of transitions and several noncognitive theories are considered as explanations of this pervasive phenomenon.

VINTAGE MODERNISM: EARLY EXPERIMENTALIST MUSIC FOR VIOLIN IN THE UNITED STATES

The historical narrative of concert music in the early twentieth century has focused a great deal on the influence of European composers as well as the American composers who went to Europe to study. Often overlooked, however, is the influence of an entire generation of composers working in the United States during that time period. These artists experimented with polyrhythm, polytonality, dissonant counterpoint, and a whole host of other musical techniques in order to express their perceptions of a changing world. Over the years, the new techniques became associated with various movements including futurism, experimentalism and ultramodernism. Regardless of label, these composers were some of the first to introduce the new musical styles to the listening public.The recitals that make up this dissertation explore the sound world of experimentalist composers working in the United States during the early twentieth century. Serving as the foundation of these recitals are all four of the violin sonatas by Charles Ives, the “grandfather” of modernist music whose financial support helped to foster a whole generation of American composers. Also prominently featured is the music of Henry Cowell. His Suite for Violin and Piano, Mosaic Quartet (String Quartet No. 3), and Quartet Euphometric demonstrate the composer's use of cluster tones, dissonant counterpoint, polymeter, and indeterminate form. Additional works by George Antheil, Leo Ornstein, Wallingford Riegger, Dane Rudhyar, Carl Ruggles, and Ruth Crawford (Seeger) highlight other approaches taken by members of the ultra-modernist movement. Rounding out the repertoire for these recitals are works by Johanna Beyer and Conlon Nancarrow, both of whom either worked with or were influenced by Cowell in some way. All of the pieces selected date roughly from 1900 to the mid 1930's. Thus, the purpose of these recitals is not to provide a comprehensive overview of each composer's development, but rather to examine the influence and interconnections of a specific cross-section of the musical landscape.