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3. Back Cover

Author

Collins, Jim

Published
2010

4. Cover

Author

Collins, Jim

Published
2010

5. Index

Author

Collins, Jim

Published
2010

21. Invasive Nontypeable Haemophilus influenzae Disease Outbreak at an Elementary School--Michigan, May 2023

Author

Weinberg, Meghan M., Akel, Kaitlyn, Akinyemi, Oluwaseun, Balasubramanian, Thrishika, Blankenship, Heather M., Collins, Jennifer P., Collins, Jim, Henderson, Tiffany, Johnson, Shannon, Lai, Joyce, McNamara, Lucy A., Richardson, Claudia, Sharma, Shalabh, and Sheth, Darsheen

Subjects
Michigan. Department of Health and Human Services, Health care reform, Epidemics -- Michigan, Diseases -- Michigan, Households, Rifampin, Health care industry, Hemophilus infections, Public health, Vaccines, Health care industry, Health
Abstract

Introduction After the introduction and widespread use of vaccines against Haemophilus influenzae (Hi) type b (Hib) in the United States for the last 30 years, the incidence of invasive Hi [...]

Published
2024

27. Update : Characteristics of Health Care Personnel with COVID-19 — United States, February 12–July 16, 2020

Author

Hughes, Michelle M., Groenewold, Matthew R., Lessem, Sarah E., Xu, Kerui, Ussery, Emily N., Wiegand, Ryan E., Qin, Xiaoting, Do, Tuyen, Thomas, Deepam, Tsai, Stella, Davidson, Alexander, Latash, Julia, Eckel, Seth, Collins, Jim, Ojo, Mojisola, McHugh, Lisa, Li, Wenhui, Chen, Judy, Chan, Jonathan, Wortham, Jonathan M., Reagan-Steiner, Sarah, Lee, James T., Reddy, Sujan C., Kuhar, David T., Burrer, Sherry L., and Stuckey, Matthew J.

Published
2020

28. SARS-CoV-2–Associated Deaths Among Persons Aged

Author

Pediatric Mortality Investigation Team, Bixler, Danae, Miller, Allison D., Mattison, Claire P., Taylor, Burnestine, Komatsu, Kenneth, Pompa, Xandy Peterson, Moon, Steve, Karmarkar, Ellora, Liu, Caterina Y., Openshaw, John J., Plotzker, Rosalyn E., Rosen, Hilary E., Alden, Nisha, Kawasaki, Breanna, Siniscalchi, Alan, Leapley, Andrea, Drenzek, Cherie, Tobin-D’Angelo, Melissa, Kauerauf, Judy, Reid, Heather, Hawkins, Eric, White, Kelly, Ahmed, Farah, Hand, Julie, Richardson, Gillian, Sokol, Theresa, Eckel, Seth, Collins, Jim, Holzbauer, Stacy, Kollmann, Leslie, Larson, Linnea, Schiffman, Elizabeth, Kittle, Theresa S., Hertin, Kimberly, Kraushaar, Vit, Raman, Devin, LeGarde, Victoria, Kinsinger, Lindsey, Peek-Bullock, Melissa, Lifshitz, Jenna, Ojo, Mojisola, Arciuolo, Robert J, Davidson, Alexander, Huynh, Mary, Lash, Maura K., Latash, Julia, Lee, Ellen H., Li, Lan, McGibbon, Emily, McIntosh-Beckles, Natasha, Pouchet, Renee, Ramachandran, Jyotsna S., Reilly, Kathleen H., Dufort, Elizabeth, Pulver, Wendy, Zamcheck, Ariela, Wilson, Erica, de Fijter, Sietske, Naqvi, Ozair, Nalluswami, Kumar, Waller, Kirsten, Bell, Linda J., Burch, Anna-Kathryn, Radcliffe, Rachel, Fiscus, Michelle D., Lewis, Adele, Kolsin, Jonathan, Pont, Stephen, Salinas, Andrea, Sanders, Kelsey, Barbeau, Bree, Althomsons, Sandy, Atti, Sukhshant, Brown, Jessica S., Chang, Arthur, Clarke, Kevin R., Datta, S. Deblina, Iskander, John, Leitgeb, Brooke, Pindyck, Talia, Priyamvada, Lalita, Reagan-Steiner, Sarah, Scott, Nigel A., Viens, Laura J., Zhong, Jonathan, and Koumans, Emilia H.

Published
2020

29. Characteristics of Persons Who Died with COVID-19 — United States, February 12–May 18, 2020

Author

Wortham, Jonathan M., Lee, James T., Althomsons, Sandy, Latash, Julia, Davidson, Alexander, Guerra, Kevin, Murray, Kenya, McGibbon, Emily, Pichardo, Carolina, Toro, Brian, Li, Lan, Paladini, Marc, Eddy, Meredith L., Reilly, Kathleen H., McHugh, Lisa, Thomas, Deepam, Tsai, Stella, Ojo, Mojisola, Rolland, Samantha, Bhat, Maya, Hutchinson, Katherine, Sabel, Jennifer, Eckel, Seth, Collins, Jim, Donovan, Catherine, Cope, Anna, Kawasaki, Breanna, McLafferty, Sarah, Alden, Nisha, Herlihy, Rachel, Barbeau, Bree, Dunn, Angela C., Clark, Charles, Pontones, Pamela, McLafferty, Meagan L., Sidelinger, Dean E., Krueger, Anna, Kollmann, Leslie, Larson, Linnea, Holzbauer, Stacy, Lynfield, Ruth, Westergaard, Ryan, Crawford, Richard, Zhao, Lin, Bressler, Jonathan M., Read, Jennifer S., Dunn, John, Lewis, Adele, Richardson, Gillian, Hand, Julie, Sokol, Theresa, Adkins, Susan H., Leitgeb, Brooke, Pindyck, Talia, Eure, Taniece, Wong, Karen, Datta, Deblina, Appiah, Grace D., Brown, Jessica, Traxler, Rita, Koumans, Emilia H., and Reagan-Steiner, Sarah

Published
2020

31. Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains

Author

Mostafavi, Sara, Ortiz-Lopez, Adriana, Bogue, Molly A, Hattori, Kimie, Pop, Cristina, Koller, Daphne, Mathis, Diane, Benoist, Christophe, Blair, David A, Dustin, Michael L, Shinton, Susan A, Hardy, Richard R, Shay, Tal, Regev, Aviv, Cohen, Nadia, Brennan, Patrick, Brenner, Michael, Kim, Francis, Rao, Tata Nageswara, Wagers, Amy, Heng, Tracy, Ericson, Jeffrey, Rothamel, Katherine, Kreslavsky, Taras, Fletcher, Anne, Elpek, Kutlu, Bellemare-Pelletier, Angelique, Malhotra, Deepali, Turley, Shannon, Miller, Jennifer, Brown, Brian, Merad, Miriam, Gautier, Emmanuel L, Jakubzick, Claudia, Randolph, Gwendalyn J, Monach, Paul, Best, Adam J, Knell, Jamie, Goldrath, Ananda, Jojic, Vladimir, Laidlaw, David, Collins, Jim, Gazit, Roi, Rossi, Derrick J, Malhotra, Nidhi, Sylvia, Katelyn, Kang, Joonsoo, Bezman, Natalie A, Sun, Joseph C, Min-Oo, Gundula, Kim, Charlie C, and Lanier, Lewis L

Subjects
Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Animals, CD4-Positive T-Lymphocytes, Chromosome Mapping, Cluster Analysis, Computational Biology, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, Genetic Variation, Genotype, Humans, Immunity, Mice, Mice, Inbred Strains, Neutrophils, Quantitative Trait Loci, Reproducibility of Results, Transcriptome, Immunological Genome Consortium, Immunology
Abstract

To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others.

Published
2014

33. Detection of a Human Adenovirus Outbreak, Including Some Critical Infections, Using Multipathogen Testing at a Large University, September 2022–January 2023.

Author

Montgomery, JoLynn P, Marquez, Juan Luis, Nord, Jennifer, Stamper, Aleksandra R, Edwards, Elizabeth A, Valentini, Nicholas, Frank, Christopher J, Washer, Laraine L, Ernst, Robert D, Park, Ji In, Price, Deanna, Collins, Jim, Smith-Jeffcoat, Sarah E, Hu, Fang, Knox, Christine L, Khan, Rebia, Lu, Xiaoyan, Kirking, Hannah L, and Hsu, Christopher H

Subjects
ADENOVIRUS diseases, STUDENT health services, ADENOVIRUSES, ELECTRONIC health records, EMERGENCY medical services, HUMAN adenoviruses
Abstract

Background Human adenoviruses (HAdVs) can cause outbreaks of flu-like illness in university settings. Most infections in healthy young adults are mild; severe illnesses rarely occur. In Fall 2022, an adenovirus outbreak was identified in university students. Methods HAdV cases were defined as university students 17–26 years old who presented to the University Health Service or nearby emergency department with flu-like symptoms (eg, fever, cough, headache, myalgia, nausea) and had confirmed adenovirus infections by polymerase chain reaction (PCR). Demographic and clinical characteristics were abstracted from electronic medical records; clinical severity was categorized as mild, moderate, severe, or critical. We performed contact investigations among critical cases. A subset of specimens was sequenced to confirm the HAdV type. Results From 28 September 2022 to 30 January 2023, 90 PCR-confirmed cases were identified (51% female; mean age, 19.6 years). Most cases (88.9%) had mild illness. Seven cases required hospitalization, including 2 critical cases that required intensive care. Contact investigation identified 44 close contacts; 6 (14%) were confirmed HAdV cases and 8 (18%) reported symptoms but never sought care. All typed HAdV-positive specimens (n = 36) were type 4. Conclusions While most students with confirmed HAdV had mild illness, 7 otherwise healthy students had severe or critical illness. Between the relatively high number of hospitalizations and proportion of close contacts with symptoms who did not seek care, the true number of HAdV cases was likely higher. Our findings illustrate the need to consider a wide range of pathogens, even when other viruses are known to be circulating. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Characteristics and Outcomes Among Adults Aged ≥60 Years Hospitalized with Laboratory-Confirmed Respiratory Syncytial Virus — RSV-NET, 12 States, July 2022–June 2023

Author

Havers, Fiona P., primary, Whitaker, Michael, additional, Melgar, Michael, additional, Chatwani, Bhoomija, additional, Chai, Shua J., additional, Alden, Nisha B., additional, Meek, James, additional, Openo, Kyle P., additional, Ryan, Patricia A., additional, Kim, Sue, additional, Lynfield, Ruth, additional, Shaw, Yomei P., additional, Barney, Grant, additional, Tesini, Brenda L., additional, Sutton, Melissa, additional, Talbot, H. Keipp, additional, Olsen, Kristen P., additional, Patton, Monica E., additional, Coates, Ashley, additional, Hall, Brenna, additional, Napoles, Monica, additional, Roland, Jeremy, additional, Rothrock, Gretchen, additional, Armistead, Isaac, additional, Strayhorn, Nina, additional, Desiato, Julia, additional, Labazzo, Noelle, additional, Sorosindi, Hazhia, additional, Szajai, Melanie, additional, Yousey-Hindes, Kimberly, additional, Zmek, Emily, additional, Bacon, Emily, additional, Cantey, Meghann, additional, Ceaser, Rayna, additional, Clausen, Alyssa, additional, Fawcett, Emily, additional, Hagley-Alexander, Sydney, additional, Hendrick, Sabrina, additional, Hernandez, Johanna, additional, Joseph, Asmith, additional, Patterson, Annabel, additional, Roebling, Allison, additional, Servais, MaCayla, additional, Turner, Emma Grace, additional, Wilson, Hope, additional, Brooks, Alicia, additional, Brown, Chloe, additional, Collins, Jim, additional, Falkowski, Anna, additional, Henderson, Justin, additional, Johnson, Shannon, additional, Leigh, Lindsay, additional, Meda, Sanchitha, additional, McCormick, Elizabeth, additional, Melicor, Alyanna, additional, Nunez, Val Tellez, additional, Reeg, Libby, additional, Alfath, Sumaya, additional, Bye, Erica, additional, Como-Sabetti, Kathy, additional, Hershberger, Angela, additional, Zipprich, Jennifer, additional, Montoya, Mark, additional, Plymesser, Kelly, additional, Ropp, Susan, additional, Smelser, Chad, additional, Sosin, Daniel, additional, Eisenberg, Nancy, additional, Khanlian, Sarah, additional, Pacheco, Francesca, additional, Salazar-Sanchez, Yadira, additional, Anderson, Bridget, additional, Engesser, Kerianne, additional, McGuire, Suzanne, additional, Rowlands, Jemma, additional, Spina, Nancy, additional, Bushey, Sophrena, additional, Felsen, Christina, additional, Gaitan, Maria, additional, Licherdell, Erin, additional, Popham, Kevin, additional, St George, Katherine, additional, Billings, Kathy, additional, Dyer, Katie, additional, Leib, Karen, additional, Markus, Tiffanie, additional, McMinn, Terri, additional, Ndi, Danielle, additional, Sackey, Emmanuel, additional, Bruno, Ashton, additional, Carter, Amanda, additional, Chatelain, Ryan, additional, Crossland, Melanie, additional, George, Andrea, additional, Gonzalez, Rosie, additional, Haraghey, Andrew, additional, Hill, Mary, additional, Mendez, Emma, additional, Price, Andrea, additional, Reyes, Isabella, additional, Sacco, Courtney H., additional, Staten, Holly, additional, Swain, Ashley, additional, Zahid, Hafsa, additional, Kirley, Pam Daily, additional, Austin, Elizabeth, additional, Kim, Daewi, additional, Surell, Chandler, additional, Monroe, Maya, additional, Leegwater, Lauren, additional, Mumm, Erica, additional, Bleecker, Molly, additional, Rowe, Adam, additional, Novak, Arilene, additional, and Schaffner, William, additional

Published
2023
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45. Differential splicing across immune system lineages

Author

Ergun, Ayla, Doran, Graeme, Costello, James C, Paik, Henry H, Collins, James J, Mathis, Diane, Benoist, Christophe, Blair, David A, Dustin, Michael L, Shinton, Susan A, Hardy, Richard R, Shay, Tal, Regevc, Aviv, Cohen, Nadia, Brennan, Patrick, Brenner, Michael, Kim, Francis, Rao, Tata Nageswara, Wagers, Amy, Heng, Tracy, Ericson, Jeffrey, Rothamel, Katherine, Ortiz-Lopez, Adriana, Kreslavsky, Taras, Fletcher, Anne, Elpek, Kutlu, Bellemare-Pelletier, Angelique, Malhotra, Deepali, Turley, Shannon, Miller, Jennifer, Brown, Brian, Merad, Miriam, Gautier, Emmanuel L, Jakubzick, Claudia, Randolph, Gwendalyn J, Monach, Paul, Best, Adam J, Knell, Jamie, Goldrath, Ananda, Jojic, Vladimir, Koller, Daphne, Laidlaw, David, Collins, Jim, Gazit, Roi, Rossi, Derrick J, Malhotra, Nidhi, Sylvia, Katelyn, Kang, Joonsoo, Bezman, Natalie A, Sun, Joseph C, Min-Oo, Gundula, Kim, Charlie C, and Lanier, Lewis L

Subjects
Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Inflammatory and immune system, Alternative Splicing, B-Lymphocytes, Cell Lineage, Humans, T-Lymphocytes, ImmGen Consortium
Abstract

Alternative splicing (AS) allows increased diversity and orthogonal regulation of the transcriptional products of mammalian genomes. To assess the distribution and variation of alternative splicing across cell lineages of the immune system, we comprehensively analyzed RNA sequencing and microarray data generated by the Immunological Genome Project Consortium. AS is pervasive: 60% of genes showed frequent AS isoforms in T or B lymphocytes, with 7,599 previously unreported isoforms. Distinct cell specificity was observed, with differential exon skipping in 5% of genes otherwise coexpressed in both B and T cells. The distribution of isoforms was mostly all or none, suggesting on/off switching as a frequent mode of AS regulation in lymphocytes. From the identification of differential exon use in the microarray data, clustering of exon inclusion/exclusion patterns across all Immunological Genome Project cell types showed that ∼70% of AS exons are distributed along a common pattern linked to lineage differentiation and cell cycling. Other AS events distinguished myeloid from lymphoid cells or affected only a small set of exons without clear lineage specificity (e.g., Ptprc). Computational analysis predicted specific associations between AS exons and splicing regulators, which were verified by detection of the hnRPLL/Ptprc connection.

Published
2013

46. The transcriptional landscape of αβ T cell differentiation.

Author

Mingueneau, Michael, Kreslavsky, Taras, Gray, Daniel, Heng, Tracy, Cruse, Richard, Ericson, Jeffrey, Bendall, Sean, Spitzer, Matthew H, Nolan, Garry P, Kobayashi, Koichi, von Boehmer, Harald, Mathis, Diane, Benoist, Christophe, Immunological Genome Consortium, Best, Adam J, Knell, Jamie, Goldrath, Ananda, Joic, Vladimir, Koller, Daphne, Shay, Tal, Regev, Aviv, Cohen, Nadia, Brennan, Patrick, Brenner, Michael, Kim, Francis, Nageswara Rao, Tata, Wagers, Amy, Rothamel, Katherine, Ortiz-Lopez, Adriana, Bezman, Natalie A, Sun, Joseph C, Min-Oo, Gundula, Kim, Charlie C, Lanier, Lewis L, Miller, Jennifer, Brown, Brian, Merad, Miriam, Gautier, Emmanuel L, Jakubzick, Claudia, Randolph, Gwendalyn J, Monach, Paul, Blair, David A, Dustin, Michael L, Shinton, Susan A, Hardy, Richard R, Laidlaw, David, Collins, Jim, Gazit, Roi, Rossi, Derrick J, Malhotra, Nidhi, Sylvia, Katelyn, Kang, Joonsoo, Fletcher, Anne, Elpek, Kutlu, Bellemare-Pelletier, Angelique, Malhotra, Deepali, and Turley, Shannon

Subjects
Immunological Genome Consortium, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Cells, Cultured, Animals, Mice, Inbred C57BL, Mice, Lectins, C-Type, Receptors, Antigen, T-Cell, alpha-beta, Antigens, CD, Antigens, Differentiation, T-Lymphocyte, Histocompatibility Antigens, Oligonucleotide Array Sequence Analysis, Flow Cytometry, Cluster Analysis, Cell Differentiation, Cell Proliferation, Phosphorylation, Cell Lineage, Male, Transcriptome, Thymocytes, Immunology
Abstract

The differentiation of αβT cells from thymic precursors is a complex process essential for adaptive immunity. Here we exploited the breadth of expression data sets from the Immunological Genome Project to analyze how the differentiation of thymic precursors gives rise to mature T cell transcriptomes. We found that early T cell commitment was driven by unexpectedly gradual changes. In contrast, transit through the CD4(+)CD8(+) stage involved a global shutdown of housekeeping genes that is rare among cells of the immune system and correlated tightly with expression of the transcription factor c-Myc. Selection driven by major histocompatibility complex (MHC) molecules promoted a large-scale transcriptional reactivation. We identified distinct signatures that marked cells destined for positive selection versus apoptotic deletion. Differences in the expression of unexpectedly few genes accompanied commitment to the CD4(+) or CD8(+) lineage, a similarity that carried through to peripheral T cells and their activation, demonstrated by mass cytometry phosphoproteomics. The transcripts newly identified as encoding candidate mediators of key transitions help define the 'known unknowns' of thymocyte differentiation.

Published
2013

47. Identification of transcriptional regulators in the mouse immune system.

Author

Jojic, Vladimir, Shay, Tal, Sylvia, Katelyn, Zuk, Or, Sun, Xin, Kang, Joonsoo, Regev, Aviv, Koller, Daphne, Immunological Genome Project Consortium, Best, Adam J, Knell, Jamie, Goldrath, Ananda, Joic, Vladimir, Cohen, Nadia, Brennan, Patrick, Brenner, Michael, Kim, Francis, Rao, Tata Nageswara, Wagers, Amy, Heng, Tracy, Ericson, Jeffrey, Rothamel, Katherine, Ortiz-Lopez, Adriana, Mathis, Diane, Benoist, Christophe, Bezman, Natalie A, Sun, Joseph C, Min-Oo, Gundula, Kim, Charlie C, Lanier, Lewis L, Miller, Jennifer, Brown, Brian, Merad, Miriam, Gautier, Emmanuel L, Jakubzick, Claudia, Randolph, Gwendalyn J, Monach, Paul, Blair, David A, Dustin, Michael L, Shinton, Susan A, Hardy, Richard R, Laidlaw, David, Collins, Jim, Gazit, Roi, Rossi, Derrick J, Malhotra, Nidhi, Kreslavsky, Taras, Fletcher, Anne, Elpek, Kutlu, Bellemarte-Pelletier, Angelique, Malhotra, Deepali, and Turley, Shannon

Subjects
Immunological Genome Project Consortium, T-Lymphocytes, Immune System, Animals, Humans, Mice, DNA-Binding Proteins, Trans-Activators, Receptors, Antigen, T-Cell, gamma-delta, Transcription Factors, Repressor Proteins, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Cell Differentiation, Transcription, Genetic, Gene Expression Regulation, Cell Lineage, Algorithms, Gene Regulatory Networks, Transcriptome, Receptors, Antigen, T-Cell, gamma-delta, Transcription, Genetic, Immunology
Abstract

The differentiation of hematopoietic stem cells into cells of the immune system has been studied extensively in mammals, but the transcriptional circuitry that controls it is still only partially understood. Here, the Immunological Genome Project gene-expression profiles across mouse immune lineages allowed us to systematically analyze these circuits. To analyze this data set we developed Ontogenet, an algorithm for reconstructing lineage-specific regulation from gene-expression profiles across lineages. Using Ontogenet, we found differentiation stage-specific regulators of mouse hematopoiesis and identified many known hematopoietic regulators and 175 previously unknown candidate regulators, as well as their target genes and the cell types in which they act. Among the previously unknown regulators, we emphasize the role of ETV5 in the differentiation of γδ T cells. As the transcriptional programs of human and mouse cells are highly conserved, it is likely that many lessons learned from the mouse model apply to humans.

Published
2013

50. Perception of Local COVID-19 Transmission and Use of Preventive Behaviors Among Adults with Recent SARS-CoV-2 Infection--Illinois and Michigan, June 1-July 31, 2022

Author

Czeisler, Mark E., Lane, Rashon I., Orellana, Robert C., Lundeen, Kristen, Macomber, Kathryn, Collins, Jim, Varma, Prerna, Booker, Lauren A., Rajaratnam, Shantha M.W., Howard, Mark E., Czeisler, Charles A., Flannery, Brendan, and Weaver, Matthew D.

Subjects
Infection, Adults, Resveratrol, Health
Abstract

During the early stages of the COVID-19 pandemic, use of preventive behaviors was associated with perceived risk for contracting SARS-CoV-2 infection (1,2). Over time, perceived risk has declined along with [...]

Published
2022

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