Optimality and Construction of Designs with Generalized Group Divisible Structure

This thesis is an investigation of the optimality and construction problems attendant to the assignment of v treatments to experimental units in b blocks of size k, paying special attention to settings for which equal replication of the treatments is not possible. The model is that of one way elimination of heterogeneity, in which the expectation of an observation on treatment i in block j is Ti + βj (treatment effect + block effect), where Ti and βj are unknown constants, 1 ≤ i ≤ v and 1 ≤ j ≤ b. All observations are assumed to be uncorrelated with same variance. The generalized group divisible design with s groups, or GGDD(s), is defined in terms of the elements of the information matrix, instead of in terms of the elements of the concurrence matrix as done by Adhikary (1965) and extended by Jacroux (1982). This definition extends the class of designs to include non-binary members, and allows for broader optimality results. Some sufficient conditions are derived for GGDD(s) to be E- and MV-optimal. It is also shown how augmentation of addition blocks to certain GGDD(s)s produces other nonbinary, unequally replicated E- and MV-optimal block designs. Where nonbinary designs are found, they are generally preferable to binary designs in terms of interpretability, and often in terms of one or more formal optimality criteria as well. The class of generalized nearly balanced incomplete block designs with maximum concurrence range l, or NBBD(l), is defined. This class extends the nearly balance incomplete block designs as defined by Cheng & Wu (1981), and the semi-regular graph designs as defined by Jacroux (1985), to cases where off-diagonal entries of the concurrence matrix differ by at most the positive integer l. Sufficient conditions are derived for a NBBD(2) to be optimal under a given type-I criterion. The conditions are used to establish the A- and D-optimality of an infinite series of NBBD(2)s having unequal numbers of replicates. Also, a result from Jacroux (1985) is used to establish the A-optimality of a new series of NBBD(1)s. Several methods of construction of GGDD(s)s are developed from which many infinite series of designs are derived. Generally these designs satisfy the obtained sufficient conditions for E- and MV-optimality. Finally, in the nested row-column setting, the necessary conditions for existence of 2 x 2 balanced incomplete block designs with nested rows and columns (BIBRCs) are found to be sufficient. It is also shown that, sufficient for a BIBRC with p=q to generally balanced, is that the row and column classifications together form a balanced incomplete block design, as does the block classification. All of the 2 x 2 BIBRCs are constructed to have this property

On the Type-1 optimality of nearly balanced incomplete block designs with small concurrence range

Abstract: The class of nearly balanced incomplete block designs with concurrence range l, or NBBD(l), is defined. This extends previous notions of "most balanced" designs to cover settings where off-diagonal entries of the concurrence matrix must differ by a positive integer l ≥ 2. Sufficient conditions are found for optimality of NBBD(2)'s under type-1 criteria, then used to establish A-and D-optimality in settings where optimal designs were previously unknown. Some NBBD(3)'s are also found to be uniquely A-and D-optimal. Included is a study of settings where the necessary conditions for balanced incomplete block designs are satisfied, but no balanced design exists

Simian Immunodeficiency Virus Infection Mediated Changes in Jejunum and Peripheral SARS-CoV-2 Receptor ACE2 and Associated Proteins or Genes in Rhesus Macaques

Angiotensin converting enzyme-2 (ACE2) and associated proteins play a pivotal role in various physiological and pathological events, such as immune activation, inflammation, gut barrier maintenance, intestinal stem cell proliferation, and apoptosis. Although many of these clinical events are quite significant in SIV/HIV infection, expression profiling of these proteins has not been well reported. Considering the different pathological consequences in the gut after HIV infection, we hypothesized that the expression of ACE2 and associated proteins of the Renin-angiotensin system (RAS) could be compromised after SIV/HIV infection. We quantified the gene expression of ACE2 as well as AGTR1/2, ADAM17, and TMPRSS2, and compared between SIV infected and uninfected rhesus macaques (Macaca mulatta; hereafter abbreviated RMs). The gene expression analysis revealed significant downregulation of ACE2 and upregulation of AGTR2 and inflammatory cytokine IL-6 in the gut of infected RMs. Protein expression profiling also revealed significant upregulation of AGTR2 after infection. The expression of ACE2 in protein level was also decreased, but not significantly, after infection. To understand the entirety of the process in newly regenerated epithelial cells, a global transcriptomic study of enteroids raised from intestinal stem cells was performed. Interestingly, most of the genes associated with the RAS, such as DPP4, MME, ANPEP, ACE2, ENPEP, were found to be downregulated in SIV infection. HNFA1 was found to be a key regulator of ACE2 and related protein expression. Jejunum CD4+ T cell depletion and increased IL-6 mRNA, MCP-1 and AGTR2 expression may signal inflammation, monocyte/macrophage accumulation and epithelial apoptosis in accelerating SIV pathogenesis. Overall, the findings in the study suggested a possible impact of SIV/HIV infection on expression of ACE2 and RAS-associated proteins resulting in the loss of gut homeostasis. In the context of the current COVID-19 pandemic, the outcome of SARS-CoV-2 and HIV co-infection remains uncertain and needs further investigation as the significance profile of ACE2, a viral entry receptor for SARS-CoV-2, and its expression in mRNA and protein varied in the current study. There is a concern of aggravated SARS-CoV-2 outcomes due to possible serious pathological events in the gut resulting from compromised expression of RAS- associated proteins in SIV/HIV infection

PCR-free method detects high frequency of genomic instability in prostate cancer

Most studies of tumor instability are PCR-based. PCR-based methods may underestimate mutation frequencies of heterogeneous tumor genomes. Using a novel PCR-free random cloning/sequencing method, we analyzed 100 kb of total genomic DNA from blood lymphocytes, normal prostate and tumor prostate taken from six individuals. Variations were identified by comparison of the sequence of the cloned fragments with the nr-database in Genbank. After excluding known polymorphisms (by comparison to the NCBI dbSNP), we report a significant over-representation of variants in the tumors: 0.66 variations per kilobase of sequence, compared with the corresponding normal prostates (0.14 variations/kb) or blood (0.09 variations/kb). Extrapolating the observed difference between tumor and normal prostate DNA, we estimate 1.8 million somatic (de novo) alterations per tumor cell genome, a much higher frequency than previous measurements obtained by mostly PCR-based methods in other tumor types. Moreover, unlike the normal prostate and blood, most of the tumor variations occur in a specific motif (P = 0.046), suggesting common etiology. We further report high tumor cell-to-cell heterogeneity. These data have important implications for selecting appropriate technologies for cancer genome projects as well as for understanding prostate cancer progression

Intensive care unit course of infants and children after cranial vault reconstruction for craniosynostosis

<p>Abstract</p> <p>Background</p> <p>Craniosynostosis (CSS) results from the premature closure of one or more cranial sutures, leading to deformed calvaria at birth. It is a common finding in children with an incidence of one in 2000 births. Surgery is required in order to release the synostotic constraint and promote normal calvaria growth. Cranial vault remodeling is the surgical approach to CSS repair at our institution and it involves excision of the frontal, parietal, and occipital bones. The purpose of this article is to describe the post-operative course of infants and children admitted to our PICU after undergoing cranial vault remodeling for primary CSS.</p> <p>Findings</p> <p>Complete data was available for analyses in only 82 patients, 44 males (M) and 38 females (F); M: F ratio was 1:1.2. Patients (pts) age in months (mo) ranged from 2 mo to 132 mo, mean 18.2 ±-24.9 mo and weights (wt) ranged from 4.7 kg to 31.4 kg, mean 10.24 ± 5.5 Kg.. Duration of surgery (DOS) ranged from 70 minutes to 573 minutes mean 331.6 ± 89.0 minutes. No significant correlation exist between duration of surgery, suture category, patient's age or use of blood products (P > 0.05). IOP blood loss was higher in older pts (P < 0.05) and it correlates with body temperature in the PICU (P < .0001). Post-op use of FFP correlated with intra-operative PRBC transfusion (P < 0.0001). More PRBC was transfused within 12 hrs-24 hrs in PICU compared to other time periods (P < 0.05). LOS in PICU was < 3 days in 68% and > 3 days in 32%. Pts with fever had prolonged LOS (P < 0. 05); re-intubation rate was 2.4% and MVD were 1.83 days. Repeat operation for poor cosmetic results occurred in 9.7% of pts.</p> <p>Conclusions</p> <p>Post-op morbidities from increased use of blood products can be minimized if cranial vault remodeling is done at a younger age in patients with primary CSS. PICU length of stay is determined in part by post-op pyrexia and it can be reduced if extensive evaluations of post-op fever are avoided.</p

Expanding Research Capacity in Sub-Saharan Africa Through Informatics, Bioinformatics, and Data Science Training Programs in Mali

Bioinformatics and data science research have boundless potential across Africa due to its high levels of genetic diversity and disproportionate burden of infectious diseases, including malaria, tuberculosis, HIV and AIDS, Ebola virus disease, and Lassa fever. This work lays out an incremental approach for reaching underserved countries in bioinformatics and data science research through a progression of capacity building, training, and research efforts. Two global health informatics training programs sponsored by the Fogarty International Center (FIC) were carried out at the University of Sciences, Techniques and Technologies of Bamako, Mali (USTTB) between 1999 and 2011. Together with capacity building efforts through the West Africa International Centers of Excellence in Malaria Research (ICEMR), this progress laid the groundwork for a bioinformatics and data science training program launched at USTTB as part of the Human Heredity and Health in Africa (H3Africa) initiative. Prior to the global health informatics training, its trainees published first or second authorship and third or higher authorship manuscripts at rates of 0.40 and 0.10 per year, respectively. Following the training, these rates increased to 0.70 and 1.23 per year, respectively, which was a statistically significant increase (p &lt; 0.001). The bioinformatics and data science training program at USTTB commenced in 2017 focusing on student, faculty, and curriculum tiers of enhancement. The program’s sustainable measures included institutional support for core elements, university tuition and fees, resource sharing and coordination with local research projects and companion training programs, increased student and faculty publication rates, and increased research proposal submissions. Challenges reliance of high-speed bandwidth availability on short-term funding, lack of a discounted software portal for basic software applications, protracted application processes for United States visas, lack of industry job positions, and low publication rates in the areas of bioinformatics and data science. Long-term, incremental processes are necessary for engaging historically underserved countries in bioinformatics and data science research. The multi-tiered enhancement approach laid out here provides a platform for generating bioinformatics and data science technicians, teachers, researchers, and program managers. Increased literature on bioinformatics and data science training approaches and progress is needed to provide a framework for establishing benchmarks on the topics

On the class of t-designs

The necessary and sufficient condition for a t-design satisfying v=2k to be a resolvable t-design is derived. Construction of some series of resolvable 3-designs are also given. Finally, a simple and general method for constructing balanced incomplete block designs from symmetrical balanced incomplete block designs are shown. Using this method many known infinite series of balanced incomplete block designs can easily be obtained.Pairwise balanced design Balanced incomplete block design Symmetric balanced incomplete block design Resolvable designs

Divergent Cytokine and Chemokine Responses at Early Acute Simian Immunodeficiency Virus Infection Correlated with Virus Replication and CD4 T Cell Loss in a Rhesus Macaque Model

Cytokine and chemokine levels remain one of the significant predictive factors of HIV pathogenesis and disease outcome. Understanding the impact of cytokines and chemokines during early acute infection will help to recognize critical changes during HIV pathogenesis and might assist in establishing improved HIV treatment and prevention methods. Sixty-one cytokines and chemokines were evaluated in the plasma of an SIV-infected rhesus macaque model. A substantial change in 11 cytokines/growth factors and 9 chemokines were observed during acute infection. Almost all the cytokines/chemokines were below the baseline values for an initial couple of days of infection. We detected six important cytokines/chemokines, such as IL-18, IP-10, FLT3L, MCP-1, MCP-2, and MIP-3β, that can be used as biomarkers to predict the peripheral CD4+ T cell loss and increased viral replication during the acute SIV/HIV infection. Hence, regulating IL-18, IP-10, FLT3L, MCP-1, MCP-2, and MIP-3β expression might provide an antiviral response to combat acute SIV/HIV infection

On the E-optimality of certain class of block designs

In this paper we consider the problem of determining and constructing E-optimal block designs within an experimental setting where v treatments are arranged in b blocks of size kConnected block design Generalized group divisible design Non-binary design E-optimality