Gene Expression Commons: an open platform for absolute gene expression profiling.

Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000) of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/) which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples

Tipping Points in Adolescent Adjustment: Predicting Social Functioning from Adolescents’ Conflict with Parents and Friends

©American Psychological Association, 2012. This paper is not the copy of record and may not exactly replicate the authoritative document published in the APA journal. The final article is available, upon publication, at: https://doi.org/10.1037/a0029868Despite widespread interest in examining the role of conflict for adolescent development, researchers only rarely have examined adolescents' experiences of conflict across relationships. The present study examined how adolescents' experiences of conflict with parents and friends were linked to their social functioning. Adolescents (n = 189) and their mothers and fathers participated in semistructured discussions about areas of parent-adolescent conflict in the laboratory. In addition, adolescents reported about conflict in their best friendships, and peers reported about adolescents' social acceptance and behavior in social settings. Parent–adolescent conflict was associated with peer-reported aggression and delinquency, and friendship conflict was associated with delinquency and prosocial behavior. In addition, significant Parent–Adolescent Conflict × Friend–Adolescent Conflict interactions revealed that parent–adolescent conflict was associated with poor social functioning only when conflict with best friends was also high. The findings suggest that consideration of conflict across relationships may yield insight into the specific contexts in which conflict is associated with negative outcomes for adolescents. (PsycInfo Database Record (c) 2020 APA, all rights reserved)https://doi.org/10.1037/a002986

Reporter Discrepancies Among Parents, Adolescents, and Peers: Adolescent Attachment and Informant Depressive Symptoms as Explanatory Factors

This is the peer reviewed version of the following article: Ehrlich, K.B., Cassidy, J. and Dykas, M.J. (2011), Reporter Discrepancies Among Parents, Adolescents, and Peers: Adolescent Attachment and Informant Depressive Symptoms as Explanatory Factors. Child Development, 82: 999-1012., which has been published in final form at https://doi.org/10.1111/j.1467-8624.2010.01530.x . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.The issue of informant discrepancies about child and adolescent functioning is an important concern for clinicians, developmental psychologists, and others who must consider ways of handling discrepant reports of information, but reasons for discrepancies in reports have been poorly understood. Adolescent attachment and informant depressive symptoms were examined as 2 explanations for absolute and directional discrepancies about adolescent symptoms, relationships, and social behavior in a sample of 189 eleventh-grade students (mean age = 16.5 years). Adolescent attachment predicted absolute discrepancies, with greater attachment coherence associated with fewer discrepancies in reports of adolescent depressive symptoms, parent–adolescent conflict, and adolescent externalizing behavior. Parents’ but not adolescents’ depressive symptoms sometimes predicted absolute discrepancies. Mothers’ depressive symptoms and adolescent attachment predicted the direction of discrepancies for mother–peer reports only.https://doi.org/10.1111/j.1467-8624.2010.01530.

Do Adolescents and Parents Reconstruct Memories About Their Conflict as a Function of Adolescent Attachment?

This is the peer reviewed version of the following article: Dykas, M.J., Woodhouse, S.S., Ehrlich, K.B. and Cassidy, J. (2010), Do Adolescents and Parents Reconstruct Memories About Their Conflict as a Function of Adolescent Attachment?. Child Development, 81: 1445-1459., which has been published in final form at https://doi.org/10.1111/j.1467-8624.2010.01484.x . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.This study examined whether 17-year-old adolescents (n = 189) and their parents reconstructed their memory for an adolescent–parent laboratory conflict over a 6-week period as a function of adolescent attachment organization. It also compared participants’ perceptions of conflict over time to observational ratings of the conflict to further characterize the nature of the attachment-related memory biases that emerged. Secure adolescents reconstructed interactions with each parent more favorably over time, whereas insecure adolescents showed less favorable reconstructive memory. Likewise, mothers of secure girls reconstructed conflicts more favorably over time, whereas mothers of insecure boys showed less favorable reconstructive memory. Participant ratings were associated with observational ratings in theoretically consistent ways. Contrary to expectations, fathers showed no attachment-related memory biases.https://doi.org/10.1111/j.1467-8624.2010.01484.

Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Epigenetic modifications must underlie lineage-specific differentiation as terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Haematopoiesis provides a well-defined model to study epigenetic modifications during cell-fate decisions, as multipotent progenitors (MPPs) differentiate into progressively restricted myeloid or lymphoid progenitors. Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 hypomorphs, a comprehensive DNA methylation map of haematopoietic progenitors, or of any multipotent/oligopotent lineage, does not exist. Here we examined 4.6 million CpG sites throughout the genome for MPPs, common lymphoid progenitors (CLPs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and thymocyte progenitors (DN1, DN2, DN3). Marked epigenetic plasticity accompanied both lymphoid and myeloid restriction. Myeloid commitment involved less global DNA methylation than lymphoid commitment, supported functionally by myeloid skewing of progenitors following treatment with a DNA methyltransferase inhibitor. Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. Many examples of genes and pathways not previously known to be involved in choice between lymphoid/myeloid differentiation have been identified, such as Arl4c and Jdp2. Several transcription factors, including Meis1, were methylated and silenced during differentiation, indicating a role in maintaining an undifferentiated state. Additionally, epigenetic modification of modifiers of the epigenome seems to be important in haematopoietic differentiation. Our results directly demonstrate that modulation of DNA methylation occurs during lineage-specific differentiation and defines a comprehensive map of the methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions

Eye health and quality of life: an umbrella review protocol.

INTRODUCTION: Vision impairment and eye disease are major global health concerns and have been associated with increased morbidity and mortality, and lower quality of life. Quality of life, whether generic, vision-specific or disease-specific, is an important measure of the impact of eye health on people's daily activities, well-being and visual function, and is increasingly used to evaluate the impact of ophthalmic interventions and new devices. While many studies and reviews have examined the relationship between vision or eye health and quality of life across different contexts, there has yet to be a synthesis of the impact of vision impairment, eye disease and ophthalmic interventions on quality of life globally and across the lifespan. METHODS AND ANALYSIS: An umbrella review of systematic reviews will be conducted to address these two questions: (1) What is the association of vision impairment and eye disease with quality of life? (2) What is the impact of ophthalmic interventions on quality of life? A search of related literature will be performed on the 11 February 2020 in Medline Ovid, Embase.com, Cochrane Database of Systematic Reviews, Proquest Dissertations and Theses Global, and the grey literature, and repeated at the synthesis stage. Title/abstract and full-text screening, methodological quality assessment and data extraction will be conducted by reviewers working independently and in duplicate. Assessment of methodological quality and data extraction will be performed using Joanna Briggs Institute standard forms. Findings from the systematic reviews and their methodological quality will be summarised qualitatively in the text and using tables. ETHICS AND DISSEMINATION: No ethical approval is required. Results of this umbrella review will be published in a peer-reviewed journal and summarised in the Lancet Global Health Commission on Global Eye Health. TRIAL REGISTRATION NUMBER: This protocol was registered in the Open Science Framework Registries (https://osf.io/qhv9g/)

Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution

Contains fulltext : 172169.pdf (publisher's version ) (Open Access)The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ss-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored

Tethered balloon-borne profile measurements of atmospheric properties in the cloudy atmospheric boundary layer over the Arctic sea ice during MOSAiC: Overview and first results

The tethered balloon-borne measurement system BELUGA (Balloon-bornE moduLar Utility for profilinG the lower Atmosphere) was deployed over the Arctic sea ice for 4 weeks in summer 2020 as part of the Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition. Using BELUGA, vertical profiles of dynamic, thermodynamic, aerosol particle, cloud, radiation, and turbulence properties were measured from the ground up to a height of 1,500 m. BELUGA was operated during an anomalously warm period with frequent liquid water clouds and variable sea ice conditions. Three case studies of liquid water phase, single-layer clouds observed on 3 days (July 13, 23, and 24, 2020) are discussed to show the potential of the collected data set to comprehensively investigate cloud properties determining cloud evolution in the inner Arctic over sea ice. Simulated back-trajectories show that the observed clouds have evolved within 3 different air masses (“aged Arctic,” “advected over sea ice,” and “advected over open ocean”), which left distinct fingerprints in the cloud properties. Strong cloud top radiative cooling rates agree with simulated results of previous studies. The weak warming at cloud base is mostly driven by the vertical temperature profile between the surface and cloud base. In-cloud turbulence induced by the cloud top cooling was similar in strength compared to former studies. From the extent of the mixing layer, it is speculated that the overall cloud cooling is stronger and thus faster in the warm oceanic air mass. Larger aerosol particle number concentrations and larger sizes were observed in the air mass advected over the sea ice and in the air mass advected over the open ocean

Lost Opportunities to Reduce Periconception HIV Transmission: Safer Conception Counseling By South African Providers Addresses Perinatal but not Sexual HIV Transmission

Introduction: Safer conception strategies create opportunities for HIV-serodiscordant couples to realize fertility goals and minimize periconception HIV transmission. Patient–provider communication about fertility goals is the first step in safer conception counseling. Methods: We explored provider practices of assessing fertility intentions among HIV-infected men and women, attitudes toward people living with HIV (PLWH) having children, and knowledge and provision of safer conception advice. We conducted in-depth interviews (9 counselors, 15 nurses, 5 doctors) and focus group discussions (6 counselors, 7 professional nurses) in eThekwini District, South Africa. Data were translated, transcribed, and analyzed using content analysis with NVivo10 software. Results: Among 42 participants, median age was 41 (range, 28–60) years, 93% (39) were women, and median years worked in the clinic was 7 (range, 1–27). Some providers assessed women's, not men's, plans for having children at antiretroviral therapy initiation, to avoid fetal exposure to efavirenz. When conducted, reproductive counseling included CD4 cell count and HIV viral load assessment, advising mutual HIV status disclosure, and referral to another provider. Barriers to safer conception counseling included provider assumptions of HIV seroconcordance, low knowledge of safer conception strategies, personal feelings toward PLWH having children, and challenges to tailoring safer sex messages. Conclusions: Providers need information about HIV serodiscordance and safer conception strategies to move beyond discussing only perinatal transmission and maternal health for PLWH who choose to conceive. Safer conception counseling may be more feasible if the message is distilled to delaying conception attempts until the infected partner is on antiretroviral therapy. Designated and motivated nurse providers may be required to provide comprehensive safer conception counseling