Phase transition for cutting-plane approach to vertex-cover problem

We study the vertex-cover problem which is an NP-hard optimization problem and a prototypical model exhibiting phase transitions on random graphs, e.g., Erdoes-Renyi (ER) random graphs. These phase transitions coincide with changes of the solution space structure, e.g, for the ER ensemble at connectivity c=e=2.7183 from replica symmetric to replica-symmetry broken. For the vertex-cover problem, also the typical complexity of exact branch-and-bound algorithms, which proceed by exploring the landscape of feasible configurations, change close to this phase transition from "easy" to "hard". In this work, we consider an algorithm which has a completely different strategy: The problem is mapped onto a linear programming problem augmented by a cutting-plane approach, hence the algorithm operates in a space OUTSIDE the space of feasible configurations until the final step, where a solution is found. Here we show that this type of algorithm also exhibits an "easy-hard" transition around c=e, which strongly indicates that the typical hardness of a problem is fundamental to the problem and not due to a specific representation of the problem.Comment: 4 pages, 3 figure

Kearns-sayre syndrome with reduced plasma and cerebrospinal fluid folate

A young woman with Kearns-Sayre syndrome and progressive central nervous system deterioration over 15 years had decreased plasma and cerebrospinal fluid folate levels while receiving phenytoin for a seizure disorder. A muscle biopsy showed a “ragged red fiber” myopathy with reduced muscle carnitine and mitochondrial enzymes. Computed tomographic brain scans showed cerebral white matter hypodensities and bilateral calcification of the basal ganglia. The mechanism for the folate deficiency and altered ratio of plasma to cerebrospinal fluid folate is unknown, but the deficiency may be responsive to replacement therapy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50301/1/410130620_ftp.pd

Presence of antiphospholipid antibodies is associated with increased implantation failure following in vitro fertilization technique and embryo transfer: A systematic review and meta-analysis

PURPOSE: A systematic review and meta-analysis was conducted comparing the presence of anti-phospholipid (anti-PL) antibodies between women of reproductive age, without diagnosis of antiphospholipid syndrome, who experienced at least two implantation failures following in vitro fertilization and embryo transfer (IVF-ET), and either women who had a successful implantation after IVF-ET or women with at least one successful spontaneous pregnancy or unselected healthy fertile women with no history of IVF-ET. METHODS: Systematic search of the literature and meta-analysis of the relevant studies studying presence of antiphospholipid antibodies in women experiencing at least two implantation failures in IVF-ET as compared to either women who had a successful implantation after IVF-ET or/and women with at least one successful spontaneous pregnancy or unselected healthy fertile women with no history of IVF-ET. Six hundred ninety-four published reports were retrieved; 17 of them fulfilled the inclusion criteria set. RESULTS: Presence of either any type of anti-phospholipid or anticardiolipin antibodies or lupus-anticoagulant in women experiencing at least two implantation failures in IVF-ET was associated with increased implantation failure compared to women who had a successful implantation after IVF-ET (relative risk, RR: 3.06, 5.06 and 5.81, respectively). Presence of either anticardiolipin or lupus-anticoagulant or anti-beta(2) glycoprotein-I or anti-phosphatidylserine antibodies in women experiencing at least two implantation failures in IVF-EΤ was associated with increased implantation failure compared to unselected healthy fertile women with no history of IVF-ET (RR:13.92, 6.37, 15.04 and 164.58, respectively). CONCLUSION: The prevalence of antiphospholipid antibodies, particularly that of anti-beta(2) glycoprotein-I and anti-phosphatidylserine antibodies, in women experiencing at least two implantation failures in IVF-ET without diagnosis of antiphospholipid syndrome is significantly greater than either in women who had a successful implantation after IVF-ET or women with at least one successful spontaneous pregnancy or unselected healthy fertile women with no history of IVF-ET. TRIAL REGISTRATION NUMBER: PROSPERO ID: CRD4201808145

Flip Distance Between Triangulations of a Planar Point Set is APX-Hard

In this work we consider triangulations of point sets in the Euclidean plane, i.e., maximal straight-line crossing-free graphs on a finite set of points. Given a triangulation of a point set, an edge flip is the operation of removing one edge and adding another one, such that the resulting graph is again a triangulation. Flips are a major way of locally transforming triangular meshes. We show that, given a point set $S$ in the Euclidean plane and two triangulations $T_1$ and $T_2$ of $S$, it is an APX-hard problem to minimize the number of edge flips to transform $T_1$ to $T_2$.Comment: A previous version only showed NP-completeness of the corresponding decision problem. The current version is the one of the accepted manuscrip

Holography and Brane-bulk Energy Exchange

The five-dimensional description of generalized Randall-Sundrum cosmology is mapped via holography to a generalization of the Starobinsky model. This provides a holographic dual description of the cosmological brane-bulk energy exchange processes studied previously. Some simple solutions are presented in four dimensions.Comment: 41 pages, LaTe

Statistical mechanics of the vertex-cover problem

We review recent progress in the study of the vertex-cover problem (VC). VC belongs to the class of NP-complete graph theoretical problems, which plays a central role in theoretical computer science. On ensembles of random graphs, VC exhibits an coverable-uncoverable phase transition. Very close to this transition, depending on the solution algorithm, easy-hard transitions in the typical running time of the algorithms occur. We explain a statistical mechanics approach, which works by mapping VC to a hard-core lattice gas, and then applying techniques like the replica trick or the cavity approach. Using these methods, the phase diagram of VC could be obtained exactly for connectivities $c<e$, where VC is replica symmetric. Recently, this result could be confirmed using traditional mathematical techniques. For $c>e$, the solution of VC exhibits full replica symmetry breaking. The statistical mechanics approach can also be used to study analytically the typical running time of simple complete and incomplete algorithms for VC. Finally, we describe recent results for VC when studied on other ensembles of finite- and infinite-dimensional graphs.Comment: review article, 26 pages, 9 figures, to appear in J. Phys. A: Math. Ge

Canalization Leads to Similar Whole Bone Mechanical Function at Maturity in Two Inbred Strains of Mice

Previously, we showed that cortical mineralization is coordinately adjusted to mechanically offset external bone size differences between A/J (narrow) and C57BL/6J (wide) mouse femora to achieve whole bone strength equivalence at adulthood. The identity of the genes and their interactions that are responsible for establishing this homeostatic state (ie, canalization) remain unknown. We hypothesize that these inbred strains, whose interindividual differences in bone structure and material properties mimic that observed among humans, achieve functional homeostasis by differentially adjusting key molecular pathways regulating external bone size and mineralization throughout growth. The cortices of A/J and C57BL/6J male mouse femora were phenotyped and gene expression levels were assessed across growth (ie, ages 2, 4, 6, 8, 12, 16 weeks). A difference in total cross‐sectional area (p < 0.01) and cortical tissue mineral density were apparent between mouse strains by age 2 weeks and maintained at adulthood (p < 0.01). These phenotypic dissimilarities corresponded to gene expression level differences among key regulatory pathways throughout growth. A/J mice had a 1.55‐ to 7.65‐fold greater expression among genes inhibitory to Wnt pathway induction, whereas genes involved in cortical mineralization were largely upregulated 1.50‐ to 3.77‐fold to compensate for their narrow diaphysis. Additionally, both mouse strains showed an upregulation among Wnt pathway antagonists corresponding to the onset of adult ambulation (ie, increased physiological loads). This contrasts with other studies showing an increase in Wnt pathway activation after functionally isolated, experimental in vivo loading regimens. A/J and C57BL/6J long bones provide a model to develop a systems‐based approach to identify individual genes and the gene‐gene interactions that contribute to trait differences between the strains while being involved in the process by which these traits are coordinately adjusted to establish similar levels of mechanical function, thus providing insight into the process of canalization. © 2017 American Society for Bone and Mineral Research.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136753/1/jbmr3093.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136753/2/jbmr3093_am.pd

Global network of computational biology communities: ISCB's regional student groups breaking barriers [version 1; peer review: Not peer reviewed]

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: “Nurture the new generation of computational biologists”.Fil: Shome, Sayane. University of Iowa; Estados UnidosFil: Parra, Rodrigo Gonzalo. European Molecular Biology Laboratory; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fatima, Nazeefa. Uppsala Universitet; SueciaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Cuypers, Bart. Universiteit Antwerp; BélgicaFil: Moosa, Yumna. University of KwaZulu Natal; SudáfricaFil: Da Rocha Coimbra, Nilson. Universidade Federal de Minas Gerais; BrasilFil: Assis, Juliana. Universidade Federal de Minas Gerais; BrasilFil: Giner Delgado, Carla. Universitat Autònoma de Barcelona; EspañaFil: Dönertaş, Handan Melike. European Molecular Biology Laboratory. European Bioinformatics Institute; Reino UnidoFil: Cuesta Astroz, Yesid. Universidad de Antioquia; Colombia. Universidad Ces. Facultad de Medicina.; ColombiaFil: Saarunya, Geetha. University of South Carolina; Estados UnidosFil: Allali, Imane. Universite Mohammed V. Rabat; Otros paises de África. University of Cape Town; SudáfricaFil: Gupta, Shruti. Jawaharlal Nehru University; IndiaFil: Srivastava, Ambuj. Indian Institute of Technology Madras; IndiaFil: Kalsan, Manisha. Jawaharlal Nehru University; IndiaFil: Valdivia, Catalina. Universidad Andrés Bello; ChileFil: Olguín Orellana, Gabriel José. Universidad de Talca; ChileFil: Papadimitriou, Sofia. Vrije Unviversiteit Brussel; Bélgica. Université Libre de Bruxelles; BélgicaFil: Parisi, Daniele. Katholikie Universiteit Leuven; BélgicaFil: Kristensen, Nikolaj Pagh. Technical University of Denmark; DinamarcaFil: Rib, Leonor. Universidad de Copenhagen; DinamarcaFil: Guebila, Marouen Ben. University of Luxembourg; LuxemburgoFil: Bauer, Eugen. University of Luxembourg; LuxemburgoFil: Zaffaroni, Gaia. University of Luxembourg; LuxemburgoFil: Bekkar, Amel. Universite de Lausanne; SuizaFil: Ashano, Efejiro. APIN Public Health Initiatives; NigeriaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Moreyra, Nicolás Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure