Publications

    C. Voglis, P.E. Hadjidoukas, D. G. Papageorgiou, and I. E. Lagaris. 2013. “A parallel hybrid optimization algorithm for fitting interatomic potentials.” Applied Soft Computing, 13, 12, Pp. 4481–4492. Publisher's VersionAbstract
    A parallel hybrid optimization algorithm for fitting interatomic potentials
    In this work we present the parallel implementation of a hybrid global optimization algorithm assembled specifically to tackle a class of time consuming interatomic potential fitting problems. The resulting objec- tive function is characterized by large and varying execution times, discontinuity and lack of derivative information. The presented global optimization algorithm corresponds to an irregular, two-level execu- tion task graph where tasks are spawned dynamically. We use the OpenMP tasking model to express the inherent parallelism of the algorithm on shared-memory systems and a runtime library which imple- ments the execution environment for adaptive task-based parallelism on multicore clusters. We describe in detail the hybrid global optimization algorithm and various parallel implementation issues. The pro- posed methodology is then applied to a specific instance of the interatomic potential fitting problem for the metal titanium. Extensive numerical experiments indicate that the proposed algorithm achieves the best parallel performance. In addition, its serial implementation performs well and therefore can also be used as a general purpose optimization algorithm.
    Samantha K Ammons. 2013. “Work-family boundary strategies: Stability and alignment between preferred and enacted boundaries.” Journal of Vocational Behavior, 82, 1, Pp. 49-58. Publisher's VersionAbstract

    Are individuals bounding work and family the way they would like? Much of the work–family boundary literature focuses on whether employees are segmenting or integrating work with family, but does not explore the boundaries workers would like to have, nor does it examine the fit between desired and enacted boundaries, or assess boundary stability. In this study, 23 respondents employed at a large Fortune 500 company were interviewed about their work–family boundaries before and after their teams underwent a cultural change initiative that sought to loosen workplace norms and allow employees more autonomy to decide when and where they performed their job tasks. Four distinct boundary strategies emerged from the data, with men and parents of young children having better alignment between preferred and enacted boundaries than women and those without these caregiving duties. Implications for boundary theory and research are discussed.

    2013. A Revolution for All: Women’s Rights in the New Libya. Human Rights Watch. Publisher's VersionAbstract

    http://www.hrw.org/reports/2013/05/27/revolution-all

    This 40-page report highlights key steps that Libya should take to meet its international obligations by firmly rejecting gender-based discrimination in both law and practice. The report calls on Libya’s parliament, the General National Congress (GNC), to ensure that women are involved on equal terms with men in the entire constitution drafting process, including active participation in the Constituent Assembly tasked with preparing the draft.

    Towfique Raj, Manik Kuchroo, Joseph M Replogle, Soumya Raychaudhuri, Barbara E Stranger, and Philip L De Jager. 2013. “Common risk alleles for inflammatory diseases are targets of recent positive selection.” Am J Hum Genet, 92, 4, Pp. 517-29. Publisher's VersionAbstract
    Genome-wide association studies (GWASs) have identified hundreds of loci harboring genetic variation influencing inflammatory-disease susceptibility in humans. It has been hypothesized that present day inflammatory diseases may have arisen, in part, due to pleiotropic effects of host resistance to pathogens over the course of human history, with significant selective pressures acting to increase host resistance to pathogens. The extent to which genetic factors underlying inflammatory-disease susceptibility has been influenced by selective processes can now be quantified more comprehensively than previously possible. To understand the evolutionary forces that have shaped inflammatory-disease susceptibility and to elucidate functional pathways affected by selection, we performed a systems-based analysis to integrate (1) published GWASs for inflammatory diseases, (2) a genome-wide scan for signatures of positive selection in a population of European ancestry, (3) functional genomics data comprised of protein-protein interaction networks, and (4) a genome-wide expression quantitative trait locus (eQTL) mapping study in peripheral blood mononuclear cells (PBMCs). We demonstrate that loci for inflammatory-disease susceptibility are enriched for genomic signatures of recent positive natural selection, with selected loci forming a highly interconnected protein-protein interaction network. Further, we identify 21 loci for inflammatory-disease susceptibility that display signatures of recent positive selection, of which 13 also show evidence of cis-regulatory effects on genes within the associated locus. Thus, our integrated analyses highlight a set of susceptibility loci that might subserve a shared molecular function and has experienced selective pressure over the course of human history; today, these loci play a key role in influencing susceptibility to multiple different inflammatory diseases, in part through alterations of gene expression in immune cells.
    Katherine P Liao, Fina Kurreeman, Gang Li, Grant Duclos, Shawn Murphy, Raul Guzman, Tianxi Cai, Namrata Gupta, Vivian Gainer, Peter Schur, Jing Cui, Joshua C Denny, Peter Szolovits, Susanne Churchill, Isaac Kohane, Elizabeth W Karlson, and Robert M Plenge. 2013. “Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls.” Arthritis Rheum, 65, 3, Pp. 571-81. Publisher's VersionAbstract
    OBJECTIVE: The significance of non-rheumatoid arthritis (RA) autoantibodies in patients with RA is unclear. The aim of this study was to assess associations of autoantibodies with autoimmune risk alleles and with clinical diagnoses from the electronic medical records (EMRs) among RA cases and non-RA controls. METHODS: Data on 1,290 RA cases and 1,236 non-RA controls of European genetic ancestry were obtained from the EMRs of 2 large academic centers. The levels of anti-citrullinated protein antibodies (ACPAs), antinuclear antibodies (ANAs), anti-tissue transglutaminase antibodies (AGTAs), and anti-thyroid peroxidase (anti-TPO) antibodies were measured. All subjects were genotyped for autoimmune risk alleles, and the association between number of autoimmune risk alleles present and number of types of autoantibodies present was studied. A phenome-wide association study (PheWAS) was conducted to study potential associations between autoantibodies and clinical diagnoses among RA cases and non-RA controls. RESULTS: The mean ages were 60.7 years in RA cases and 64.6 years in non-RA controls. The proportion of female subjects was 79% in each group. The prevalence of ACPAs and ANAs was higher in RA cases compared to controls (each P < 0.0001); there were no differences in the prevalence of anti-TPO antibodies and AGTAs. Carriage of higher numbers of autoimmune risk alleles was associated with increasing numbers of autoantibody types in RA cases (P = 2.1 × 10(-5)) and non-RA controls (P = 5.0 × 10(-3)). From the PheWAS, the presence of ANAs was significantly associated with a diagnosis of Sjögren's/sicca syndrome in RA cases. CONCLUSION: The increased frequency of autoantibodies in RA cases and non-RA controls was associated with the number of autoimmune risk alleles carried by an individual. PheWAS of EMR data, with linkage to laboratory data obtained from blood samples, provide a novel method to test for the clinical significance of biomarkers in disease.
    Hyun Soo Lee, Simona Schlereth, Payal Khandelwal, and Daniel R Saban. 2013. “Ocular allergy modulation to hi-dose antigen sensitization is a Treg-dependent process.” PLoS One, 8, 9, Pp. e75769.Abstract
    A reproducible method to inhibit allergic immune responses is accomplished with hi-dose Ag sensitization, via intraperitoneal (IP) injection. However, the role of CD4+ CD25+ FoxP3+ T regulatory cells (Treg) in this process is unknown, as is whether such modulation extends to ocular allergy. We therefore determined herein whether hi-dose sensitization modulates ocular allergy, and whether CD4+ CD25+ FoxP3+ Treg are involved. C57BL/6 mice were IP sensitized via low-dose (100 µg) versus hi-dose (1000 µg) ovalbumin (OVA), in aluminum hydroxide (1 mg) and pertussis-toxin (300 ng). Other mice received anti-CD25 Ab (PC61) to ablate Treg during sensitization. In another experiment, Treg from hi-dose sensitized mice were adoptively transferred into low-dose sensitized mice. Once daily OVA challenges were administered. Clinical signs, IgE, T cell cytokines, and eosinophils were assessed. Data revealed that hi-dose, but not low-dose, sensitization led to allergy modulation, indicated by decreased clinical signs, serum IgE levels, Th2 recall responses, and eosinophil recruitment. T cells from hi-dose sensitized mice showed a robust increase in TGF-b production, and Treg from these mice were able to efficiently suppress effector T cell proliferation in vitro. In addition, in vivo Treg ablation in hi-dose sensitized mice revoked allergy modulation. Lastly, Treg from hi-dose sensitized mice were able to adoptively transfer allergy modulation to their low-dose sensitized counterparts. Collectively, these findings indicate that modulation to hi-dose sensitization, which is extended to ocular allergy, occurs in a Treg-dependent manner. In addition, our data suggest that hi-dose sensitization may henceforth facilitate the further examination of CD4+ CD25+ FoxP3+ Treg in allergic disease.
    Nariman Nassiri, Medi Eslani, Nekoo Panahi, Shiva Mehravaran, Alireza Ziaei, and Ali R Djalilian. 2013. “Ocular graft versus host disease following allogeneic stem cell transplantation: a review of current knowledge and recommendations.” J Ophthalmic Vis Res, 8, 4, Pp. 351-8.Abstract
    Graft versus host disease (GVHD) is a common complication of allogeneic stem cell transplantation (allo-SCT). Ocular GVHD develops in approximately 40-60% of patients following allo-SCT and its most common clinical manifestations include keratoconjunctivitis sicca and cicatricial conjunctivitis. Ocular GVHD may lead to severe ocular surface disease, which can significantly diminish quality of life and restrict daily activities. It is thus important to monitor the condition closely since with timely diagnosis, irreversible damage can be avoided. The current review will focus on updated information regarding ocular GVHD.
    Yureeda Qazi and Pedram Hamrah. 2013. “Corneal Allograft Rejection: Immunopathogenesis to Therapeutics.” J Clin Cell Immunol, 2013, Suppl 9.Abstract
    Corneal transplantation is among the most successful solid organ transplants. However, despite low rejection rates of grafts in the 'low-risk' setting, rejection can be as high as 70% when grafted into 'high-risk' recipient beds. Under normal homeostatic conditions, the avascular cornea provides a unique environment that facilitates immune and angiogenic privilege. An imbalance in pro-inflammatory, angiogenic and lymphangiogenic mediators leads to a breakdown in corneal immune privilege with a consequent host response against the donor graft. Recent developments in lamellar and endothelial keratoplasties have reduced the rates of graft rejection even more, while providing improved visual outcomes. The corneal layer against which an immune response is initiated, largely determines reversibility of the acute episode. While epithelial and stromal graft rejection may be treated with topical corticosteroids with higher success, acute endothelial rejection mandates a more aggressive approach to therapy due to the lack of regenerative capacity of this layer. However, current immunosuppressive regimens come with the caveat of ocular and systemic side effects, making prolonged aggressive treatment undesirable. With the advent of biologics, efficacious therapies with a superior side effect profile are on the horizon. In our review we discuss the mediators of ocular immune privilege, the roles of cellular and molecular immune players in graft rejection, with a focus on human leukocyte antigen and antigen presenting cells. Furthermore, we discuss the clinical risk factors for graft rejection and compare rates of rejection in lamellar and endothelial keratoplasties to traditional penetrating keratoplasty. Lastly, we present the current and upcoming measures of therapeutic strategies to manage and treat graft rejection, including an overview of biologics and small molecule therapy.
    The allure of order : high hopes, dashed expectations, and the troubled quest to remake American schooling
    Jal Mehta. 2013. The allure of order : high hopes, dashed expectations, and the troubled quest to remake American schooling. Oxford University Press.Abstract

    "Ted Kennedy and George W. Bush agreed on little, but united behind the No Child Left Behind Act (NCLB). Passed in late 2001, it was hailed as a dramatic new departure in school reform. It would make the states set high standards, measure student progress, and hold failing schools accountable. A decade later, NCLB has been repudiated on both sides of the aisle. According to Jal Mehta, we should have seen it coming. Far from new, it was the same approach to school reform that Americans have tried before. In The Allure of Order, Mehta recounts a century of attempts at revitalizing public education, and puts forward a truly new agenda to reach this elusive goal. Not once, not twice, but three separate times-in the Progressive Era, the 1960s and '70s, and NCLB-reformers have hit upon the same idea for remaking schools.

    How Reason Almost Lost Its Mind: The Strange Career of Cold War Rationality
    Rebecca Lemov. 2013. How Reason Almost Lost Its Mind: The Strange Career of Cold War Rationality, Pp. 272. Chicago: University of Chicago Press. Publisher's VersionAbstract
    In the United States at the height of the Cold War, roughly between the end of World War II and the early 1980s, a new project of redefining rationality commanded the attention of sharp minds, powerful politicians, wealthy foundations, and top military brass. Its home was the human sciences—psychology, sociology, political science, and economics, among others—and its participants enlisted in an intellectual campaign to figure out what rationality should mean and how it could be deployed.
               
    How Reason Almost Lost Its Mind brings to life the people—Herbert Simon, Oskar Morgenstern, Herman Kahn, Anatol Rapoport, Thomas Schelling, and many others—and places, including the RAND Corporation, the Center for Advanced Study in the Behavioral Sciences, the Cowles Commission for Research and Economics, and the Council on Foreign Relations, that played a key role in putting forth a “Cold War rationality.” Decision makers harnessed this picture of rationality—optimizing, formal, algorithmic, and mechanical—in their quest to understand phenomena as diverse as economic transactions, biological evolution, political elections, international relations, and military strategy. The authors chronicle and illuminate what it meant to be rational in the age of nuclear brinkmanship.
    Johanna Mårtensson, Markus Nilsson, Freddy Ståhlberg, Pia C Sundgren, Christer Nilsson, Danielle van Westen, Elna-Marie Larsson, and Jimmy Lätt. 2013. “Spatial analysis of diffusion tensor tractography statistics along the inferior fronto-occipital fasciculus with application in progressive supranuclear palsy.” MAGMA, 26, 6, Pp. 527-37.Abstract
    BACKGROUND: The purpose of the study was to develop a method for analysis of diffusion parameters along white matter (WM) tracts, using spatial normalization based on anatomical landmarks, and to introduce the apparent area coefficient (AAC). The method's applicability was tested in the inferior fronto-occipital fasciculus (IFO) in patients with progressive supranuclear palsy (PSP) and healthy controls (HCs). METHODS: A framework for analysis of diffusion parameters was developed. Spatial normalization of the tracts was performed using anatomical landmarks, to avoid deformations caused by cerebral atrophy. Initially, 38 HCs were used to optimize a threshold for the minimal size of regions that differ between groups. The fractional anisotropy, mean diffusivity, AAC, and the hemispheric asymmetry index (AI), were compared between 11 PSP patients and 15 HCs. RESULTS: The method was feasible for analysis of PSP patients and HCs. The AI showed that the observed hemispheric asymmetry of AAC was significantly larger in PSP patients compared with HCs in small regions of the IFO. CONCLUSIONS: The method was successfully employed for analysis of diffusion parameters along the IFO in a patient group. This method can be potentially useful in studies of WM diseases, with or without cerebral atrophy.
    Henry Córdova, Raúl San José Estépar, Antonio Rodríguez-D'Jesús, Graciela Martínez-Pallí, Pedro Arguis, Cristina Rodríguez de Miguel, Ricard Navarro-Ripoll, Juan M Perdomo, Miriam Cuatrecasas, Josep Llach, Kirby G Vosburgh, and Gloria Fernández-Esparrach. 2013. “Comparative study of NOTES alone versus NOTES guided by a new image registration system for navigation in the mediastinum: a study in a porcine model.” Gastrointest Endosc, 77, 1, Pp. 102-7.Abstract
    BACKGROUND: Natural orifice transluminal endoscopic surgery (NOTES) mediastinoscopy (MED) through the esophagus has proved to be feasible in the animal model. However, injury of the adjacent pleura and pneumothorax has been reported as a frequent adverse event when using a blind access. OBJECTIVE: To assess the utility and safety of a CT-based image registration system (IRS) for navigation in the mediastinum. DESIGN: Prospective, randomized, controlled trial in 30 Yorkshire pigs. Thirty-minute MEDs were performed: 15 MEDs were performed with IRS guidance (MED-IRS), and 15 MEDs were performed with a blind access. SETTING: Animal research laboratory. INTERVENTIONS: In both groups, the mediastinum was accessed through a 10-cm submucosal tunnel in the esophageal wall. Timed exploration was performed with identification of 8 mediastinal structures. MAIN OUTCOME MEASUREMENTS: Technical feasibility, adverse events, and the number of mediastinal structures identified. RESULTS: Thirty animals weighing 31.5 ± 3.5 kg were included in this study. MED was not possible in 2 animals in the "MED with blind access" group but was possible in all MEDs performed with IRS. The mean number of identified organs was slightly higher in "with IRS-MED" (6.13 ± 1.3) than with MED with blind access (4.7 ± 2.3; P = .066). Moreover, the right atrium and vena cava were identified in more cases with IRS-MED than in MED with blind access (13 vs 3 and 15 vs 11, P = .000 and P = .03, respectively). There were 3 (23%) adverse events with IRS-MED and 4 (27%) with "MED with blind access" (P = not significant), with pneumothorax being the most frequent (2 and 3, respectively). LIMITATIONS: Nonsurvival animal study. CONCLUSIONS: This study demonstrates that the IRS system appears feasible in natural orifice transluminal endoscopic surgery MED and suggests that IRS guidance might be useful for selected procedures.

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