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The study reports on a set of questions added to the 1997-98 Annual Survey of Deaf and Hard of Hearing Children and Youth designed to take into consideration the functioning of children in their classrooms in nine functional areas. Basing information on 30,198 students, the study describes prevalence rates of reported limitations in these functional areas for deaf and hard of hearing students, compares these to rates resulting from the reporting of categorically defined additional disabilities, and examines interrelationships among the items. Results of school estimates of students' functional hearing abilities are presented. The study's findings suggest a broader range and higher prevalence of functional limitations than would be assumed by analyzing categories of additional disabilities alone. The study's findings support the viability of functional assessment through large surveys. The discussion emphasizes the importance of functional assessment for the provision of appropriate educational services to deaf and hard of hearing children. [ABSTRACT FROM AUTHOR]

Prodrugs are chemistry-enabled drug delivery modifications of active molecules designed to enhance their pharmacokinetic, pharmacodynamic and/or biopharmaceutical properties. Ideally, prodrugs are efficiently converted in vivo, through chemical or enzymatic transformations, to the active parent molecule. The goal of this work is to enhance the colonic absorption of a drug molecule with a short half-life via a prodrug approach to deliver sustained plasma exposure and enable once daily (QD) dosing. The compound has poor absorption in the colon and by the addition of a promoiety to block the ionization of the molecule as well as increase lipophilicity, the relative colonic absorption increased from 9% to 40% in the retrograde dog colonic model. A combination of acceptable solubility and stability in the gastrointestinal tract (GI) as well as permeability was used to select suitable prodrugs to optimize colonic absorption.

Babesiosis is usually acquired from a tick bite or through a blood transfusion. We report a case of babesiosis in an infant for whom vertical transmission was suggested by evidence of Babesia spp. antibodies in the heel-stick blood sample and confirmed by detection of Babesia spp. DNA in placenta tissue.

The development of a weakly basic compound is often challenging due to changes in pH that the drug experiences throughout the gastrointestinal tract. As the drug transitions from the low pH of the stomach to the higher pH of the small intestine, drug solubility decreases. A stomach with a higher pH, caused by food or achlorhydric conditions brought about by certain medications, decreases even the initial solubility. This decreased drug solubility is reflected in lower in vivo exposures. In many cases, a solubility-enabling approach is needed to counteract the effect of gastrointestinal pH changes. Solid dispersions of amorphous drug in a polymer matrix have been demonstrated to be an effective tool to enhance bioavailability, with the potential to mitigate the food and achlorhydric effects frequently observed with conventional formulations. Because solid dispersions are in a metastable state, they are particularly sensitive to processing routes that may control particle attributes, stability, drug release profile, and bioperformance. A better understanding of the impacts of processing routes on the solid dispersion properties will not only enhance our ability to control the product properties, but also lower development risks. In this study, a weakly basic compound with greatly reduced solubility in higher pHs was incorporated into a solid dispersion via both spray drying and hot melt extrusion. The properties of the solid dispersion via these two processing routes were compared, and the impact on dissolution behavior and in vivo performance of the dispersions was investigated.

For the four-dimensional nonhomogeneous wave equation boundary value problems that are multidimensional analogues of Darboux problems in the plane are studied. It is known that for smooth right-hand side functions the unique generalized solution may have a strong power-type singularity at only one point. This singularity is isolated at the vertex O of the boundary light characteristic cone and does not propagate along the bicharacteristics. The present paper describes asymptotic expansions of the generalized solutions in negative powers of the distance to O. Some necessary and sufficient conditions for existence of bounded solutions are proven and additionally a priori estimates for the singular solutions are obtained.

Deaf children of hearing parents (DOH) are at risk for early language delays (ELD) due to environmental and etiological factors, compounding the previously reported higher incidence of ELD in deaf children of deaf parents (DOD) compared to the general population. Archival data from the online database of the Visual Communication and Sign Language Checklist yielded 147 ratings of DOH 3- to 5-year-old children whose parents reported American sign language (ASL) being used in the home at least equally to spoken language. Research goals included (1) examining the incidence of ELD in this cohort, (2) investigating differences in outcomes based on the scaling method used, (3) exploring patterns among the ratings of DOH children identified with ELD, (4) comparing the DOH outcomes to published DOD data, and (5) investigating differences between ratings and individual children. The DOH outcomes suggested an incidence of ELD twice that of the previous DOD sample, with a higher percentage of more severe delays. Even DOH children not identified with ELD demonstrated less well-developed ASL skills than their DOD peers. This emphasizes the need for ongoing monitoring of early ASL skills to allow for early identification of needs and adjustment of interventions to address ASL development., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Introduction: Hypoxia is a common pathological driver contributing to various forms of pulmonary vascular diseases leading to pulmonary hypertension (PH). Pulmonary interstitial macrophages (IMs) play pivotal roles in immune and vascular dysfunction, leading to inflammation, abnormal remodeling, and fibrosis in PH. However, IMs' response to hypoxia and their role in PH progression remain largely unknown. We utilized a murine model of hypoxia-induced PH to investigate the repertoire and functional profiles of IMs in response to acute and prolonged hypoxia, aiming to elucidate their contributions to PH development., Methods: We conducted single-cell transcriptomic analyses to characterize the repertoire and functional profiles of murine pulmonary IMs following exposure to hypobaric hypoxia for varying durations (0, 1, 3, 7, and 21 days). Hallmark pathways from the mouse Molecular Signatures Database were utilized to characterize the molecular function of the IM subpopulation in response to hypoxia., Results: Our analysis revealed an early acute inflammatory phase during acute hypoxia exposure (Days 1-3), which was resolved by Day 7, followed by a pro-remodeling phase during prolonged hypoxia (Days 7-21). These phases were marked by distinct subpopulations of IMs: MHCII hi CCR2 + EAR2 + cells characterized the acute inflammatory phase, while TLF + VCAM1 hi cells dominated the pro-remodeling phase. The acute inflammatory phase exhibited enrichment in interferon-gamma, IL-2, and IL-6 pathways, while the pro-remodeling phase showed dysregulated chemokine production, hemoglobin clearance, and tissue repair profiles, along with activation of distinct complement pathways., Discussion: Our findings demonstrate the existence of distinct populations of pulmonary interstitial macrophages corresponding to acute and prolonged hypoxia exposure, pivotal in regulating the inflammatory and remodeling phases of PH pathogenesis. This understanding offers potential avenues for targeted interventions, tailored to specific populations and distinct phases of the disease. Moreover, further identification of triggers for pro-remodeling IMs holds promise in unveiling novel therapeutic strategies for pulmonary hypertension., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Kumar, Mickael, Kumar, Prasad, Campbell, Zhang, Li, McKeon, Allen, Graham, Yu and Stenmark.)

Research has demonstrated that deaf children of deaf signing parents (DOD) are afforded developmental advantages. This can be misconstrued as indicating that no DOD children exhibit early language delays (ELDs) because of their early access to a visual language. Little research has studied this presumption. In this study, we examine 174 ratings of DOD 3- to 5-year-old children, for whom signing in the home was indicated, using archival data from the online database of the Visual Communication and Sign Language Checklist. Our goals were to (1) examine the incidence of ELDs in a cohort of DOD children; (2) compare alternative scaling strategies for identifying ELD children; (3) explore patterns among behavioral ratings with a view toward developing a greater understanding of the types of language behaviors that may lie at the root of language delays; and (4) suggest recommendations for parents and professionals working with language-delayed DOD children. The results indicated that a significant number of ratings suggested ELDs, with a subset significantly delayed. These children likely require further evaluation. Among the less delayed group, ASL skills, rather than communication or cognition, were seen as the major concern, suggesting that even DOD children may require support developing linguistically accurate ASL. Overall, these findings support the need for early and ongoing evaluation of visual language skills in young DOD children., (© The Author(s) 2023. Published by Oxford University Press.)

Design features of American Sign Language (ASL)-English bilingual storybook apps on the tablet computers, based on learning research, are intended to facilitate independent and interactive learning of English print literacy and of ASL skill among young learners. In 2013, the Science of Learning Center on Visual Language and Visual Learning introduced the first in a series of storybook apps for the iPad based on literacy and reading research. The current study, employing a sample of signing deaf children examined children's self-motivated engagement with the various design features presented in the earliest of the apps, The Baobab, and analyzed the relationships of engagement with ASL skill and age of first exposure to ASL, ASL narrative ability, and grade-appropriate English reading ability. Results indicated a robust level of engagement with the app, and a relationship between app pages specifically targeting reading and early exposure and skill levels in ASL. No evidence of relationships between narrative and vocabulary skills and app reading engagement was found. Topics for future research, and strategies for app improvement are discussed., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Language development is an important facet of early life. Deaf children may have exposure to various languages and communication modalities, including spoken and visual. Previous research has documented the rate of growth of English skills among young deaf children, but no studies have investigated the rate of ASL acquisition. The current paper examines young deaf children's acquisition of ASL skills, the rate of growth over time, and factors impacting levels and growth rates. Seventy-three children ages birth to 5 were rated three times using the Visual Communication and Sign Language Checklist and given a scaled score at each rating. An average monthly gain score was calculated for each participant. The presence of a deaf parent, use of ASL at home, use of cochlear implant(s), whether the child was born deaf, and age of initial diagnosis were analyzed for their impact on the level of ASL skill and rate of growth. Results indicated that the use of ASL in the home has a significant positive effect on deaf children's ASL skill level. Additionally, children with lower initial ratings showed higher rates of growth than those with higher initial ratings, especially among school-aged children. The paper discusses implications and directions for future studies., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Since its publication in 2013, the Visual Communication and Sign Language (VCSL) Checklist has been widely utilized to assess the development of early American Sign Language skills of deaf children from birth to age 5. However, little research has been published using the results of VCSL assessments. Notably, no psychometric analyses have been conducted to verify the validity of the VCSL in a population whose characteristics are different from those of the small sample of native signing children from whom the published norms were created. The current paper, using data from the online version of the VCSL (VCSL:O), addresses this shortcoming. Ratings of the 114 VCSL items from 562 evaluations were analyzed using a partial-credit Rasch model. Results indicate that the underlying skill across the age range comprises an adequate single dimension. Within the items' age groupings, however, the dimensionality is not so clear. Item ordering, as well as item fit, is explored in detail. In addition, the paper reports the benefits of using the resulting Rasch scale scores, which, unlike the published scoring strategy that focuses on basal and ceiling performance, makes use of the ratings of partial credit, or emerging, skills. Strategies for revising the VCSL are recommended., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The COVID-19 induced abrupt transition to online learning that occurred in the Spring of 2020 presented particular challenges to the adaptation of hands-on laboratory courses in biomedical engineering. This paper describes the transition of such a course in one undergraduate program, assessment of this transition, and how this assessment has led to the design of the Fall 2020 online delivery format. In the spring, instruction was delivered online via asynchronous lectures and recorded video demonstrations, while raw data was provided to students to simulate specific laboratory techniques. Additionally, synchronous and asynchronous forms of student support were offered, including office hours and discussions. Student feedback was assessed via an end-of-semester survey designed specifically to analyze the students' perceptions of the Spring 2020 transition to remote learning, as well as a comparison of Spring 2020 and Spring 2019 (when the course was taught in-person) student performance deliverables. Student performance was comparable to (or even better than) that in 2019. Students responded very positively to the transition, with most students agreeing or strongly agreeing that they had the resources needed to succeed (4.43 on a Likert scale), although on average, the students also found that the shift made learning more challenging, with increased effort required to engage with the material. Students especially found the recorded demonstration of laboratory techniques, asynchronous lectures, the learning management system chat feature, and virtual office hours useful. Many students felt that even with these resources, they still lost some of the experience that comes with in-person hands-on application, and some students found working in teams to be more challenging. While the overall approach implemented in the abrupt transition was effective in terms of student learning outcomes, engagement and immersion in a more realistic experience is a concern moving forward in Fall 2020. Based on our outcomes and on data from the literature, we will add gamified virtual lab simulations, shown to enhance student experience and create a more engaging and effective learning environment in lieu of in-person instruction., (© Biomedical Engineering Society 2020.)

Cells are exposed to frequent mechanical and/or chemical stressors that can compromise the integrity of the plasma membrane and underlying cortical cytoskeleton. The molecular mechanisms driving the immediate repair response launched to restore the cell cortex and circumvent cell death are largely unknown. Using microarrays and drug-inhibition studies to assess gene expression, we find that initiation of cell wound repair in the Drosophila model is dependent on translation, whereas transcription is required for subsequent steps. We identified 253 genes whose expression is up-regulated (80) or down-regulated (173) in response to laser wounding. A subset of these genes were validated using RNAi knockdowns and exhibit aberrant actomyosin ring assembly and/or actin remodeling defects. Strikingly, we find that the canonical insulin signaling pathway controls actin dynamics through the actin regulators Girdin and Chickadee (profilin), and its disruption leads to abnormal wound repair. Our results provide new insight for understanding how cell wound repair proceeds in healthy individuals and those with diseases involving wound healing deficiencies., Competing Interests: The authors have declared that no competing interests exist.

Disruption of mitochondrial function selectively targets tumour cells that are dependent on oxidative phosphorylation. However, due to their high energy demands, cardiac cells are disproportionately targeted by mitochondrial toxins resulting in a loss of cardiac function. An analysis of the effects of mubritinib on cardiac cells showed that this drug did not inhibit HER2 as reported, but directly inhibits mitochondrial respiratory complex I, reducing cardiac-cell beat rate, with prolonged exposure resulting in cell death. We used a library of chemical variants of mubritinib and showed that modifying the 1 H -1,2,3-triazole altered complex I inhibition, identifying the heterocyclic 1,3-nitrogen motif as the toxicophore. The same toxicophore is present in a second anti-cancer therapeutic carboxyamidotriazole (CAI) and we demonstrate that CAI also functions through complex I inhibition, mediated by the toxicophore. Complex I inhibition is directly linked to anti-cancer cell activity, with toxicophore modification ablating the desired effects of these compounds on cancer cell proliferation and apoptosis., Competing Interests: ZS, RH, KP, SM, RH, RS, IC, TA, MS, MM, PF, JH, BK, AW No competing interests declared, (© 2020, Stephenson et al.)

Previous research has established a correlation between literacy skills and sign language skills among deaf children raised in signing families, but little research has examined the impact of early signing skills on the rate of growth of emergent literacy in early childhood. A subset of data was extracted from a larger dataset containing national longitudinal data from a three-year investigation of early literacy development of deaf children who were between the ages of three and six at the outset of the study. Selection criteria for inclusion in this limited sample included: 1) being rated as having little or no access to spoken language and 2) being raised in homes in which signs were regularly used as a means of communication (N = 56). Our purpose was twofold: 1) to examine and describe the trajectories of growth in letter and word identification skill for this sample in relation to the participants' initial ages; and 2) to assess the degree to which the presence or deaf parents in the home (DoD) and the receptive American Sign Language (ASL) skills of the participants impacted both the level of emerging print literacy and its rate of growth over the three year period. We hypothesized that both the presence of a deaf parent in the home and the acquisition of ASL skills, a strong native language, would contribute to both the overall letter and word identification skills and to the rates of growth of this skill over time. Results indicated that having a deaf parent did, indeed, impact emergent literacy attainment, but its effect was rendered nonsignificant when ASL skill was taken into consideration. Possession of stronger ASL skills, whether or not the children had deaf parents, contributed significantly to both the levels and rate of growth. The findings contribute to the body of work that emphasizes the importance early language skills (spoken or signed) to later academic success and dispels the myth that deaf children with deaf parents have exclusive access to the acquisition of these skills., Competing Interests: The authors have declared that no competing interests exist.

South Africa's rise in noncommunicable diseases (NCDs) and health care provider shortages has generated the need for community health workers (CHWs) in rural areas. However, roles and interactions with clinic staff are not well understood. Interviews with health care workers at community clinics in Limpopo Province revealed common themes, including resource scarcity, clinic-patient partnerships, management of NCDs, and collaboration between professionals. The data did not support CHW-physician interactions, necessitating further research to describe these practices and to evaluate CHWs' impact on patient outcomes. The CHW involvement in rural clinics is essential to patient-clinic partnerships and may help close treatment gaps in resource-poor areas.

The adverse outcome pathway (AOP) framework provides an alternative to traditional in vivo experiments for the risk assessment of chemicals. AOPs consist of a number of key events (KEs) linked by key event relationships across a range of biological organization backed by scientific evidence. The first KE in the pathway is the molecular initiating event (MIE)-the initial chemical trigger that starts an AOP. Over the past 3 years the AOP conceptual framework has gained a large amount of momentum in toxicology as an alternative to animal methods, and so the MIE has come into the spotlight. What is an MIE? How can MIEs be measured or predicted? What research is currently contributing to our understanding of MIEs? In this Perspective we outline answers to these key questions.

Molecular initiating events (MIEs) can be boiled down to chemical interactions. Chemicals that interact must have intrinsic properties that allow them to exhibit this behavior, be these properties stereochemical, electronic, or otherwise. In an attempt to discover some of these chemical characteristics, we have constructed structural alert-style structure-activity relationships (SARs) to computationally predict MIEs. This work utilizes chemical informatics approaches, searching the ChEMBL database for molecules that bind to a number of pharmacologically important human toxicology targets, including G-protein coupled receptors, enzymes, ion channels, nuclear receptors, and transporters. By screening these compounds to find common 2D fragments and combining this approach with a good understanding of the literature, bespoke 2D structural alerts have been written. These SARs form the beginning of a tool for screening novel chemicals to establish the kind of interactions that they may be able to make in humans. These SARs have been run through an internal validation to test their quality, and the results of this are also discussed. MIEs have proven to be difficult to find and characterize, but we believe we have taken a key first step with this work.

Studies have shown that American Sign Language (ASL) fluency has a positive impact on deaf individuals' English reading, but the cognitive and cross-linguistic mechanisms permitting the mapping of a visual-manual language onto a sound-based language have yet to be elucidated. Fingerspelling, which represents English orthography with 26 distinct hand configurations, is an integral part of ASL and has been suggested to provide deaf bilinguals with important cross-linguistic links between sign language and orthography. Using a hierarchical multiple regression analysis, this study examined the relationship of age of ASL exposure, ASL fluency, and fingerspelling skill on reading fluency in deaf college-age bilinguals. After controlling for ASL fluency, fingerspelling skill significantly predicted reading fluency, revealing for the first-time that fingerspelling, above and beyond ASL skills, contributes to reading fluency in deaf bilinguals. We suggest that both fingerspelling--in the visual-manual modality--and reading--in the visual-orthographic modality--are mutually facilitating because they share common underlying cognitive capacities of word decoding accuracy and automaticity of word recognition. The findings provide support for the hypothesis that the development of English reading proficiency may be facilitated through strengthening of the relationship among fingerspelling, sign language, and orthographic decoding en route to reading mastery, and may also reveal optimal approaches for reading instruction for deaf and hard of hearing children.

Consumer and environmental safety decisions are based on exposure and hazard data, interpreted using risk assessment approaches. The adverse outcome pathway (AOP) conceptual framework has been presented as a logical sequence of events or processes within biological systems which can be used to understand adverse effects and refine current risk assessment practices in ecotoxicology. This framework can also be applied to human toxicology and is explored on the basis of investigating the molecular initiating events (MIEs) of compounds. The precise definition of the MIE has yet to reach general acceptance. In this work we present a unified MIE definition: an MIE is the initial interaction between a molecule and a biomolecule or biosystem that can be causally linked to an outcome via a pathway. Case studies are presented, and issues with current definitions are addressed. With the development of a unified MIE definition, the field can look toward defining, classifying, and characterizing more MIEs and using knowledge of the chemistry of these processes to aid AOP research and toxicity risk assessment. We also present the role of MIE research in the development of in vitro and in silico toxicology and suggest how, by using a combination of biological and chemical approaches, MIEs can be identified and characterized despite a lack of detailed reports, even for some of the most studied molecules in toxicology.

The "moral wound," rendered symbolically in the form of the tiger in Life of Pi, is a complex trauma in which the victim, in order to survive in life-threatening circumstances, commits an ethical transgression against his or her deeply held values. Pi experiences such a trauma and deals with it by dissociating it in the form of the tiger and then has to simultaneously both preserve the tiger and wish it to disappear. Jonathan Shay's work relating the experiences of returning Vietnam veterans to Homer's Odyssey is used to further an understanding of both Life of Pi and American soldiers returning from the wars in Iraq and Afghanistan. Reasons are considered for the possible delayed effect of trauma as a factor in the increased suicide rate of older veterans. Finally, the concept of the "moral wound" is discussed, with an eye to its treatment., (© 2014 by the American Psychoanalytic Association.)

Brief review is provided of recent research on the impact of early visual language exposure on a variety of developmental outcomes, including literacy, cognition, and social adjustment. This body of work points to the great importance of giving young deaf children early exposure to a visual language as a critical precursor to the acquisition of literacy. Four analyses of data from the Visual Language and Visual Learning (VL2) Early Education Longitudinal Study are summarized. Each confirms findings from previously published laboratory findings and points to the positive effects of early sign language on, respectively, letter knowledge, social adaptability, sustained visual attention, and cognitive-behavioral milestones necessary for academic success. The article concludes with a consideration of the qualitative similarity hypothesis and a finding that the hypothesis is valid, but only if it can be presented as being modality independent.

Background: This article briefly summarizes not only the history of physician health programs, including their singular success, but also their struggle to maintain the ethical integrity of the programs, their appropriate autonomy, and the privacy of physicians enrolled in them., Method: We review the history of the Maryland Physicians Health Program, how it initially developed and was funded, how the program became funded by the state, how this ultimately caused serious problems, and how these were eventually resolved., Results: Maryland was able to achieve a 2-program solution that protected both the voluntary participants while meeting the needs of the state licensing board for participants mandated by the state licensing board. This result has been well received by both the physician community and the state licensing board., Conclusions: How the problems were solved and the ultimate agreement provide a model for others to use.

This article investigated to what extent age, use of a cochlear implant, parental hearing status, and use of sign in the home determine language of instruction for profoundly deaf children. Categorical data from 8,325 profoundly deaf students from the 2008 Annual Survey of Deaf and Hard-of-Hearing Children and Youth were analyzed using chi-square automated interaction detector, a stepwise analytic procedure that allows the assessment of higher order interactions among categorical variables. Results indicated that all characteristics were significantly related to classroom communication modality. Although younger and older students demonstrated a different distribution of communication modality, for both younger and older students, cochlear implantation had the greatest effect on differentiating students into communication modalities, yielding greater gains in the speech-only category for implanted students. For all subgroups defined by age and implantation status, the use of sign at home further segregated the sample into communication modality subgroups, reducing the likelihood of speech only and increasing the placement of students into signing classroom settings. Implications for future research in the field of deaf education are discussed.

Four critical responses to an article, "The Role of Phonology and Phonologically Related Skills in Reading Instruction for Students Who Are Deaf or Hard of Hearing" (Wang, Trezek, Luckner, & Paul, 2008), are presented. Issue is taken with the conclusions of the article by Wang and colleagues regarding the "necessary" condition of phonological awareness for the development of reading skills among deaf readers. Research findings (not cited by Wang and colleagues) are pointed out that reveal weak correlations between phonemic awareness and reading comprehension, and stronger correlations between other variables such as overall language skill and early exposure to a visual language.

Purpose: CTL-associated antigen 4 (CTLA-4) can inhibit T-cell activation and helps maintain peripheral self-tolerance. Previously, we showed immune-related adverse events (IRAE) and objective, durable clinical responses in patients with metastatic melanoma treated with CTLA-4 blockade. We have now treated 139 patients in two trials and have sufficient follow-up to examine factors associated with clinical response., Experimental Design: A total of 139 patients with metastatic melanoma were treated: 54 patients received ipilimumab in conjunction with peptide vaccinations and 85 patients were treated with intra-patient dose escalation of ipilimumab and randomized to receive peptides in accordance with HLA-A*0201 status., Results: Three patients achieved complete responses (CR; ongoing at 29+, 52+, and 53+ months); an additional 20 patients achieved partial responses (PR) for an overall objective response rate of 17%. The majority of patients (62%, 86 of 139) developed some form of IRAE, which was associated with a greater probability of objective antitumor response (P = 0.0004); all patients with CR had more severe IRAEs. Prior therapy with IFNalpha-2b was a negative prognostic factor, whereas prior high-dose interleukin-2 did not significantly affect the probability of response. There were no significant differences in the rate of clinical response or development of IRAEs between the two trials. The duration of tumor response was not affected by the use of high-dose steroids for abrogation of treatment-related toxicities (P = 0.23). There were no treatment-related deaths., Conclusion: In patients with metastatic melanoma, ipilimumab can induce durable objective clinical responses, which are related to the induction of IRAEs.

Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial and 16 archaeal organisms using wavelet analysis. Pattern strength was found to correlate with organism-specific features such as genome size, overall GC content, and the occurrence of known motility and chromosomal binding proteins. Given additional functional data for Escherichia coli, we found significant correlations among chromosome position dependent patterns in numerous properties, some of which are consistent with previously experimentally identified chromosome macrodomains. These results demonstrate that the large-scale organization of most sequenced genomes is significantly nonrandom, and, moreover, that this organization is likely linked to genome size, nucleotide composition, and information transfer processes. Constraints on genome evolution and design are thus not solely dependent upon information content, but also upon an intricate multi-parameter, multi-length-scale organization of the chromosome.

The genome-wide location of RNA polymerase binding sites was determined in Escherichia coli using chromatin immunoprecipitation and microarrays (chIP-chip). Cross-linked chromatin was isolated in triplicate from rifampin-treated cells, and DNA bound to RNA polymerase was precipitated with an antibody specific for the beta' subunit. The DNA was amplified and hybridized to "tiled" oligonucleotide microarrays representing the whole genome at 25-bp resolution. A total of 1,139 binding sites were detected and evaluated by comparison to gene expression data from identical conditions and to 961 promoters previously identified by established methods. Of the detected binding sites, 418 were located within 1,000 bp of a known promoter, leaving 721 previously unknown RNA polymerase binding sites. Within 200 bp, we were able to detect 51% (189/368) of the known sigma70-specific promoters occurring upstream of an expressed open reading frame and 74% (273/368) within 1,000 bp. Conversely, many known promoters were not detected by chIP-chip, leading to an estimated 26% negative-detection rate. Most of the detected binding sites could be associated with expressed transcription units, but 299 binding sites occurred near inactive transcription units. This map of RNA polymerase binding sites represents a foundation for studies of transcription factors in E. coli and an important evaluation of the chIP-chip technique.

Maedi visna virus (MVV) vertical transmission in sheep via infected colostrums is a very important route of infection in lambs. To verify colostral transmission and to study early viral entry in lambs, colostrum samples, and small intestine and mesenteric lymph nodes of lambs born from experimentally infected ewes were examined by histopathology, immunohistochemistry (IHC) and in situ hybridisation (ISH) studies. In particular, newborn lambs were naturally fed maternal colostrum and humanely killed at 10, 24, 48, 72, 96 h and 7 and 10 days after birth; two caesarian-derived lambs served as uninfected controls. No lesions suggestive of MVV infection were found, but marked immunoreactions for MVV capsid antigen (CA, p28) were detected in lambs fed maternal colostrum and in macrophages cultured from colostrum. IHC results in lambs suggest an initial viral absorption by intestinal epithelial cells at the tip of the villi, passage to mononuclear cells in the lamina propria and involvement of ileum Peyers' patches and mesenteric lymph nodes, with different staining patterns depending on infection times. ISH on intestinal sections of the 72 h lamb revealed the presence of proviral DNA in epithelial cells at the tip of the villi, suggesting a role for these cells in early MVV replication. The results contribute to knowledge about the pathogenesis of ovine lentivirus infection suggesting that the small intestine and mesenteric nodes are the sites of entry and propagation of MVV in lambs fed colostrums from infected ewes.

The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to study the expression state of the entire Escherichia coli genome. The resulting in silico analysis of the expression state highlighted three facets of gene expression in E. coli: (i) the metabolic resources required for genome expression and protein synthesis were found to be relatively invariant under the conditions tested; (ii) effective promoter strengths were estimated at the genome scale by using global mRNA abundance and half-life data, revealing genes subject to regulation under the experimental conditions tested; and (iii) large-scale genome location-dependent expression patterns with approximately 600-kb periodicity were detected in the E. coli genome based on the 49 expression data sets analyzed. These results support the notion that a structured model-driven analysis of expression data yields additional information that can be subjected to commonly used statistical analyses. The integration of heterogeneous genome-scale data (i.e., sequence, expression data, and mRNA half-life data) is readily achieved in the context of an in silico model.

The composition of the editosome, a multi-protein complex that catalyzes uridine insertion and deletion RNA editing to produce mature mitochondrial mRNAs in trypanosomes, was analyzed by mass spectrometry. The editosomes were isolated by column chromatography, glycerol gradient sedimentation, and monoclonal antibody affinity purifications. At least 16 proteins form the catalytic core of the editosome, and additional associated proteins were identified. Analyses of mitochondrial fractions identified several non-editosome proteins and multi-protein complexes. These studies contribute to the functional annotation of T. brucei genome.

Constraints-based models for microbial metabolism can currently be constructed on a genome-scale. These models do not account for RNA and protein synthesis. A scalable formalism to describe translation and transcription that can be integrated with the existing metabolic models is thus needed. Here, we developed such a formalism. The fundamental protein synthesis network described by this formalism was analysed via extreme pathway and flux balance analyses. The protein synthesis network exhibited one extreme pathway per messenger RNA synthesized and one extreme pathway per protein synthesized. The key parameters in this network included promoter strengths, messenger RNA half-lives, and the availability of nucleotide triphosphates, amino acids, RNA polymerase, and active ribosomes. Given these parameters, we were able to calculate a cell's material and energy expenditures for protein synthesis using a flux balance approach. The framework provided herein can subsequently be integrated with genome-scale metabolic models, providing a sequence-based accounting of the metabolic demands resulting from RNA and protein polymerization., (Copyright 2003 Elsevier Science Ltd.)

Ovine pulmonary adenocarcinoma, caused by jaagsiekte sheep retrovirus (JSRV), is a naturally occurring retrovirus-induced pulmonary neoplasm of sheep. We report here that expression of the JSRV env gene is sufficient to transform an avian embryo fibroblast cell line, DF-1. DF-1 cells transfected with an avian sarcoma-leukaemia retroviral expression vector containing the JSRV env gene [pRCASBP(A)-J:env] exhibited changes consistent with transformation, including contraction and rounding of cells with formation of dense foci. Transfection with a reporter construct expressing the green fluorescent protein did not induce morphological changes in DF-1 cells, eliminating the possibility that the vector, the transfection protocol or culturing techniques were responsible for the transformed phenotype. When pRCASBP(A)-J:env-transfected cells were inoculated into nude mice, tumours formed, verifying that the DF-1 cells were tumorigenic. Analysis of the JSRV env gene revealed a conserved tyrosine (597) and methionine (600) residue in the cytoplasmic tail within the transmembrane domain of the envelope, which creates a known binding site of SH2 domains in the p85 subunit of phosphatidylinositol 3-kinase. However, when this tyrosine residue was mutated to serine or alanine, transformation was not affected. Furthermore, mutation of the methionine residue to valine or leucine also failed to eliminate JSRV env-mediated transformation. These results are in contrast to mutational analysis performed in JSRV env-transformed murine NIH-3T3 cells in which both the tyrosine and methionine residues are necessary for transformation. These findings suggest that more than one mechanism may be involved in JSRV env-mediated transformation.