“Enriching Lives within Sedimentary Geology”: Actionable Recommendations for Making SEPM a Diverse, Equitable and Inclusive Society for All Sedimentary Geologists

Innovative science benefits from diversity of thought and influence at all waypoints along the scientific journey, from early education to career-length contributions in research and mentorship. Scientific societies, like the Society for Sedimentary Geology (SEPM), steward their innovators and the direction of the science, thereby defining the societal impact and evolution of a discipline. They are uniquely positioned to promote the representation and success of all scientists, including those from minoritized populations, through proactive advocacy, and inclusive mentorship, awards, and leadership. We introspectively review available records of SEPM membership, leadership, awardees, and editorial boards to identify areas for growth and begin a dialogue about how the society and its members can work together to better reflect our community. In the last decade, SEPM has seen a decline in membership, while representation and recognition of scientists from minoritized groups has remained low. Awards and honors have overwhelmingly gone to men, even in the last ten years, and very few women or people of color are in leadership roles. SEPM has recently taken positive steps towards becoming more inclusive (e.g., the Code of Professional Conduct); however, much more work is needed. We provide recommendations for swift actions that SEPM and its members should undertake for the society to become a diverse, inclusive, and equitable environment where all scientists thrive. The systemic changes needed will take continuous effort, which must be shared by all of us, to build an enduring legacy that we can be proud of

Nostalgia as a psychological resource for people with dementia: A systematic review and meta-analysis of evidence of effectiveness from experimental studies

Objective: This review systematically examines evidence relating to the effect of nostalgia on psychological well-being through a meta-analysis of measures of social connectedness, self-esteem, meaning in life, self-continuity, optimism and positive and negative affect. Rationale: If nostalgia is to be used as a clinical intervention to boost well-being in dementia by reducing threat, then it is important to assess its therapeutic potential. Results: Searches carried out in July 2014 and updated in February 2018 identified 47 eligible experimental studies comparing nostalgic reminiscence and non-nostalgic reminiscence to be included in the meta-analysis. Nostalgic reminiscence had moderate effects on positive affect (0.51 (0.37, 0.65), p= 0.001), social connectedness (0.72 (0.57, 0.87), p= 0.001), self-esteem (0.50 (0.30, 0.70), p= 0.001), meaning in life (0.77 (0.47, 1.08), p= 0.001) and optimism (0.38 (0.28, 0.47), p= 0.001) and a large effect on self-continuity (0.81 (0.55, 1.07), p= 0.001). There was, however, no difference between the effect of nostalgic reminiscence and non-nostalgic reminiscence for negative affect (−0.06 (−0.20, 0.09), p= 0.443). Conclusion: This systematic review and meta-analysis provides an overview of the evidence base for nostalgia. This is an important stage in developing nostalgia as a clinical intervention for people with dementia which might be achieved, for instance, by adapting current reminiscence and life review techniques. This meta-analysis will therefore also serve as a valuable reference point for the continued exploration of nostalgia as an intervention

Observation of the superconducting proximity effect in Nb/InAs and NbNx/InAs by Raman scattering

URL:http://link.aps.org/doi/10.1103/PhysRevB.66.134530 DOI:10.1103/PhysRevB.66.134530High-quality thin Nb and NbN films (60-100 Å) are grown on (100) n+-InAs (n=1019cm-3) substrates by dc-magnetron sputter deposition. Studies of the electronic properties of interfaces between the superconductor and the semiconductor are done by Raman scattering measurements. The superconducting proximity effect at superconductor-semiconductor interfaces is observed through its impact on inelastic light scattering intensities originating from the near-interface region of InAs. The InAs longitudinal optical phonon LO mode (237cm-1) and the plasmon-phonon coupled modes L- (221cm-1) and L+ (1100 to 1350cm-1), for n+=1×1019-2×1019cm-3 are measured. The intensity ratio of the LO mode (associated with the near-surface charge accumulation region, in InAs) to that of the L- mode (associated with bulk InAs), is observed to increase by up to 40% below the superconducting transition temperature. This temperature-dependent change in light scattering properties is only observed with high quality superconducting films and when the superconductor and the semiconductor are in good electrical contact. A few possible mechanisms of the observed effect are proposed.We gratefully acknowledge support from the United States Department of Energy through Materials Research Laboratory~Grant No. DEFG02-96ER45439! ~I.V.R., A.C.A., L.H.G., T.A.T., J.F.D., P.W.B., J.F.K.!, and from the United States Department of Energy through Midwest Superconductivity Consortium ~MISCON! ~Grant No. DE FG02-90ER45427! and the NSF ~Grant No. DMR 96-23827! ~S.W.H., P.F.M.!. SEM, XRD, XPS, and RBS materials characterizations were performed at the Center for Microanalysis of Materials and Microfabrication Center at Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana- Champaign ~Grant No. DE FG02-96ER45439!. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin company, for the United States Department of Energy under Contract No. DE-AC04-94AL85000

Nasopharyngeal Colonization and Invasive Disease Are Enhanced by the Cell Wall Hydrolases LytB and LytC of Streptococcus pneumoniae

Background: Streptococcus pneumoniae is a common colonizer of the human nasopharynx and one of the major pathogens causing invasive disease worldwide. Dissection of the molecular pathways responsible for colonization, invasion, and evasion of the immune system will provide new targets for antimicrobial or vaccine therapies for this common pathogen. Methodology/Principal Findings: We have constructed mutants lacking the pneumococcal cell wall hydrolases (CWHs) LytB and LytC to investigate the role of these proteins in different phases of the pneumococcal pathogenesis. Our results show that LytB and LytC are involved in the attachment of S. pneumoniae to human nasopharyngeal cells both in vitro and in vivo. The interaction of both proteins with phagocytic cells demonstrated that LytB and LytC act in concert avoiding pneumococcal phagocytosis mediated by neutrophils and alveolar macrophages. Furthermore, C3b deposition was increased on the lytC mutant confirming that LytC is involved in complement evasion. As a result, the lytC mutant showed a reduced ability to successfully cause pneumococcal pneumonia and sepsis. Bacterial mutants lacking both LytB and LytC showed a dramatically impaired attachment to nasopharyngeal cells as well as a marked degree of attenuation in a mouse model of colonization. In addition, C3b deposition and phagocytosis was more efficient for the double lytB lytC mutant and its virulence was greatly impaired in both systemic and pulmonary models of infection. Conclusions/Significance: This study confirms that the CWHs LytB and LytC of S. pneumoniae are essential virulence factor

A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence.

BACKGROUND: The polysaccharide capsule is a major virulence factor of the important human pathogen Streptococcus pneumoniae. However, S. pneumoniae strains lacking capsule do occur. RESULTS: Here, we report a nasopharyngeal isolate of Streptococcus pneumoniae composed of a mixture of two phenotypes; one encapsulated (serotype 18C) and the other nonencapsulated, determined by serotyping, electron microscopy and fluorescence isothiocyanate dextran exclusion assay.By whole genome sequencing, we demonstrated that the phenotypes differ by a single nucleotide base pair in capsular gene cpsE (C to G change at gene position 1135) predicted to result in amino acid change from arginine to glycine at position 379, located in the cytoplasmic, enzymatically active, region of this transmembrane protein. This SNP is responsible for loss of capsule production as the phenotype is transferred with the capsule operon. The nonencapsulated variant is superior in growth in vitro and is also 117-fold more adherent to and more invasive into Detroit 562 human epithelial cells than the encapsulated variant.Expression of six competence pathway genes and one competence-associated gene was 11 to 34-fold higher in the nonencapsulated variant than the encapsulated and transformation frequency was 3.7-fold greater. CONCLUSIONS: We identified a new single point mutation in capsule gene cpsE of a clinical S. pneumoniae serotype 18C isolate sufficient to cause loss of capsule expression resulting in the co-existence of the encapsulated and nonencapsulated phenotype. The mutation caused phenotypic changes in growth, adherence to epithelial cells and transformability. Mutation in capsule gene cpsE may be a way for S. pneumoniae to lose its capsule and increase its colonization potential

Human Embryonic and Rat Adult Stem Cells with Primitive Endoderm-Like Phenotype Can Be Fated to Definitive Endoderm, and Finally Hepatocyte-Like Cells

Stem cell-derived hepatocytes may be an alternative cell source to treat liver diseases or to be used for pharmacological purposes. We developed a protocol that mimics mammalian liver development, to differentiate cells with pluripotent characteristics to hepatocyte-like cells. The protocol supports the stepwise differentiation of human embryonic stem cells (ESC) to cells with characteristics of primitive streak (PS)/mesendoderm (ME)/definitive endoderm (DE), hepatoblasts, and finally cells with phenotypic and functional characteristics of hepatocytes. Remarkably, the same protocol can also differentiate rat multipotent adult progenitor cells (rMAPCs) to hepatocyte-like cells, even though rMAPC are isolated clonally from cultured rat bone marrow (BM) and have characteristics of primitive endoderm cells. A fraction of rMAPCs can be fated to cells expressing genes consistent with a PS/ME/DE phenotype, preceding the acquisition of phenotypic and functional characteristics of hepatocytes. Although the hepatocyte-like progeny derived from both cell types is mixed, between 10–20% of cells are developmentally consistent with late fetal hepatocytes that have attained synthetic, storage and detoxifying functions near those of adult hepatocytes. This differentiation protocol will be useful for generating hepatocyte-like cells from rodent and human stem cells, and to gain insight into the early stages of liver development

Comparative Study of Hematopoietic Differentiation between Human Embryonic Stem Cell Lines

Directed differentiation of human embryonic stem cells (hESCs) into any desired cell type has been hailed as a therapeutic promise to cure many human diseases. However, substantial roadblocks still exist for in vitro differentiation of hESCs into distinct cell types, including T lymphocytes. Here we examined the hematopoietic differentiation potential of six different hESC lines. We compare their ability to develop into CD34+ or CD34+CD45+ hematopoietic precursor populations under several differentiation conditions. Comparison of lymphoid potential of hESC derived- and fetal tissue derived-hematopoietic precursors was also made. We found diverse hematopoietic potential between hESC lines depending on the culture or passage conditions. In contrast to fetal-derived hematopoietic precursors, none of the CD34+ precursors differentiated from hESCs were able to develop further into T cells. These data underscore the difficulties in the current strategy of hESC forward differentiation and highlight distinct differences between CD34+ hematopoietic precursors generated in vitro versus in vivo

Evolutionarily Conserved Transcriptional Co-Expression Guiding Embryonic Stem Cell Differentiation

Understanding the molecular mechanisms controlling pluripotency in embryonic stem cells (ESCs) is of central importance towards realizing their potentials in medicine and science. Cross-species examination of transcriptional co-expression allows elucidation of fundamental and species-specific mechanisms regulating ESC self-renewal or differentiation.We examined transcriptional co-expression of ESCs from pathways to global networks under the framework of human-mouse comparisons. Using generalized singular value decomposition and comparative partition around medoids algorithms, evolutionarily conserved and divergent transcriptional co-expression regulating pluripotency were identified from ESC-critical pathways including ACTIVIN/NODAL, ATK/PTEN, BMP, CELL CYCLE, JAK/STAT, PI3K, TGFbeta and WNT. A set of transcription factors, including FOX, GATA, MYB, NANOG, OCT, PAX, SOX and STAT, and the FGF response element were identified that represent key regulators underlying the transcriptional co-expression. By transcriptional intervention conducted in silico, dynamic behavior of pathways was examined, which demonstrate how much and in which specific ways each gene or gene combination effects the behavior transition of a pathway in response to ESC differentiation or pluripotency induction. The global co-expression networks of ESCs were dominated by highly connected hub genes such as IGF2, JARID2, LCK, MYCN, NASP, OCT4, ORC1L, PHC1 and RUVBL1, which are possibly critical in determining the fate of ESCs.Through these studies, evolutionary conservation at genomic, transcriptomic, and network levels is shown to be an effective predictor of molecular factors and mechanisms controlling ESC development. Various hypotheses regarding mechanisms controlling ESC development were generated, which could be further validated by in vitro experiments. Our findings shed light on the systems-level understanding of how ESC differentiation or pluripotency arises from the connectivity or networks of genes, and provide a "road-map" for further experimental investigation

Computational analysis of expression of human embryonic stem cell-associated signatures in tumors

<p>Abstract</p> <p>Background</p> <p>The cancer stem cell model has been proposed based on the linkage between human embryonic stem cells and human cancer cells. However, the evidences supporting the cancer stem cell model remain to be collected. In this study, we extensively examined the expression of human embryonic stem cell-associated signatures including core genes, transcription factors, pathways and microRNAs in various cancers using the computational biology approach.</p> <p>Results</p> <p>We used the class comparison analysis and survival analysis algorithms to identify differentially expressed genes and their associated transcription factors, pathways and microRNAs among normal vs. tumor or good prognosis vs. poor prognosis phenotypes classes based on numerous human cancer gene expression data. We found that most of the human embryonic stem cell- associated signatures were frequently identified in the analysis, suggesting a strong linkage between human embryonic stem cells and cancer cells.</p> <p>Conclusions</p> <p>The present study revealed the close linkage between the human embryonic stem cell associated gene expression profiles and cancer-associated gene expression profiles, and therefore offered an indirect support for the cancer stem cell theory. However, many interest issues remain to be addressed further.</p

Systems biology discoveries using non-human primate pluripotent stem and germ cells: novel gene and genomic imprinting interactions as well as unique expression patterns

The study of pluripotent stem cells has generated much interest in both biology and medicine. Understanding the fundamentals of biological decisions, including what permits a cell to maintain pluripotency, that is, its ability to self-renew and thereby remain immortal, or to differentiate into multiple types of cells, is of profound importance. For clinical applications, pluripotent cells, including both embryonic stem cells and adult stem cells, have been proposed for cell replacement therapy for a number of human diseases and disorders, including Alzheimer's, Parkinson's, spinal cord injury and diabetes. One challenge in their usage for such therapies is understanding the mechanisms that allow the maintenance of pluripotency and controlling the specific differentiation into required functional target cells. Because of regulatory restrictions and biological feasibilities, there are many crucial investigations that are just impossible to perform using pluripotent stem cells (PSCs) from humans (for example, direct comparisons among panels of inbred embryonic stem cells from prime embryos obtained from pedigreed and fertile donors; genomic analysis of parent versus progeny PSCs and their identical differentiated tissues; intraspecific chimera analyses for pluripotency testing; and so on). However, PSCs from nonhuman primates are being investigated to bridge these knowledge gaps between discoveries in mice and vital information necessary for appropriate clinical evaluations. In this review, we consider the mRNAs and novel genes with unique expression and imprinting patterns that were discovered using systems biology approaches with primate pluripotent stem and germ cells