Miracle-dz/UniFAR-FTUs huggingface dataset:
Shapes of tree representations of spin-glass landscapes

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure—a barrier tree—the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their 'depth' in the tree.
Online Decision-Making in General Combinatorial Spaces

We study online combinatorial decision problems, where one must make sequential decisions in some combinatorial space without knowing in advance the cost of decisions on each trial; the goal is to minimize the total regret over some sequence of trials relative to the best fixed decision in hindsight. Such problems have been studied mostly in settings where decisions are represented by Boolean vectors and costs are linear in this representation. Here we study a general setting where costs may be linear in any suitable low-dimensional vector representation of elements of the decision space. We give a general algorithm for such problems that we call low-dimensional online mirror descent (LDOMD); the algorithm generalizes both the Component Hedge algorithm of Koolen et al. (2010), and a recent algorithm of Suehiro et al. (2012). Our study offers a unification and generalization of previous work, and emphasizes the role of the convex polytope arising from the vector representation of the decision space; while Boolean representations lead to 0-1 polytopes, more general vector representations lead to more general polytopes. We study several examples of both types of polytopes. Finally, we demonstrate the benefit of having a general framework for such problems via an application to an online transportation problem; the associated transportation polytopes generalize the Birkhoff polytope of doubly stochastic matrices, and the resulting algorithm generalizes the PermELearn algorithm of Helmbold and Warmuth (2009).
Award Number: W81XWH-05-1-0314 TITLE: Early Life Processes, Endocrine Mediators and Number of Susceptible Cells in Relation to Breast Cancer Risk

Introduction Oestrogen exposure is a central factor in the development of breast cancer. Oestrogen receptor alpha (ESR1) is the main mediator of oestrogen effect in breast epithelia and has also been shown to be activated by epidermal growth factor (EGF). We sought to determine if common genetic variation in the ESR1 and EGF genes affects breast cancer risk, tumour characteristics or breast cancer survival. Methods We genotyped 157 single nucleotide polymorphisms (SNPs) in ESR1 and 54 SNPs in EGF in 92 Swedish controls and selected haplotype tagging SNPs (tagSNPs) that could predict both single SNP and haplotype variation in the genes with an R2 of at least 0.8. The tagSNPs were genotyped in 1,590 breast cancer cases and 1,518 controls, and their association with breast cancer risk, tumour characteristics and survival were assessed using unconditional logistic regression models, Cox proportional hazard models and haplotype analysis. Results The single tagSNP analysis did not reveal association evidence for breast cancer risk, tumour characteristics, or survival. A multi-locus analysis of five adjacent tagSNPs suggested a region in ESR1 (between rs3003925 and rs2144025) for association with breast cancer risk (p = 0.001), but the result did not withstand adjustment for multiple comparisons (p = 0.086). A similar region was also implicated by haplotype analyses, but its significance needs to be verified by follow-up analysis. Conclusion Our results do not support a strong association between common variants in the ESR1 and EGF genes and breast cancer risk, tumour characteristics or survival. Introduction Breast cancer is the most common cancer in women overall worldwide. Oestrogen exposure is a central factor in the development and progression of this cancer [1-3] and its effects on the breast epithelium is primarily mediated by oestrogen receptor alpha (ESR1) [4]. In addition to being activated by oestrogen, the ESR1 protein can be activated by growth factors such as epidermal growth factor (EGF) [3], which acts as a potent mitogen for epithelial cells, including mammary epithelia [5]. Variation in the ESR1 (MIM 133430) and EGF (MIM 131530) genes affecting the function or expression of their respective proteins could thus potentially affect the risk of developing breast cancer, characteristics of the tumour or the risk of dying from the disease. With regard to breast cancer risk or survival, a number of single nucleotide polymorphisms (SNPs) have been studied in the ESR1 gene, yet none have previously been investigated in the EGF gene. As far as we are aware, no attempt to capture the common genetic variation in the ESR1 gene in its entirety has yet been published. One group, who genotyped 17 SNPs in the ESR1 gene, found a decreased risk of breast cancer for carriers of three common haplotypes in the gene and an
Soluble Cytokine Receptors (sIL-2Rα, sIL-2Rβ) Induce Subunit-Specific Behavioral Responses and Accumulate in the Cerebral Cortex and Basal Forebrain

Soluble cytokine receptors are normal constituents of body fluids that regulate peripheral cytokine and lymphoid activity. Levels of soluble IL-2 receptors (sIL-2R) are elevated in psychiatric disorders linked with autoimmune processes, including ones in which repetitive stereotypic behaviors and motor disturbances are present. However, there is no evidence that sIL-2Rs (or any peripheral soluble receptor) induce such behavioral changes, or that they localize in relevant brain regions. Here, we determined in male Balb/c mice the effects of single peripheral injections of sIL-2Rα or sIL-2Rβ (0–2 µg/male Balb/c mouse; s.c.) on novelty-induced ambulatory activity and stereotypic motor behaviors. We discovered that sIL-2Rα increased the incidence of in-place stereotypic motor behaviors, including head up head bobbing, rearing/sniffing, turning, and grooming behavior. A wider spectrum of behavioral changes was evident in sIL-2Rβ-treated mice, including increases in vertical and horizontal ambulatory activity and stereotypic motor movements. To our knowledge, this is the first demonstration that soluble receptors induce such behavioral disturbances. In contrast, soluble IL-1 Type-1 receptors (0–4 µg, s.c.) didn't appreciably affect these behaviors. We further demonstrated that sIL-2Rα and sIL-2Rβ induced marked increases in c-Fos in caudate-putamen, nucleus accumbens and prefrontal cortex. Anatomical specificity was supported by the presence of increased activity in lateral caudate in sIL-2Rα treated mice, while sIL-2Rβ treated mice induced greater c-Fos activity in prepyriform cortex. Moreover, injected sIL-2Rs were widely distributed in regions that showed increased c-Fos expression. Thus, sIL-2Rα and sIL-2Rβ induce marked subunit- and soluble cytokine receptor-specific behavioral disturbances, which included increases in the expression of ambulatory activity and stereotypic motor behaviors, while inducing increased neuronal activity localized to cortex and striatum. These findings suggest that sIL-2Rs act as novel immune-to- brain messengers and raise the possibility that they contribute to the disease process in psychiatric disorders in which marked increases in these receptors have been reported.
Maternal weight gain during the first half of pregnancy and offspring obesity at 16 years: a prospective cohort study

Please cite this paper as: Laitinen J, Jääskeläinen A, Hartikainen A, Sovio U, Vääräsmäki M, Pouta A, Kaakinen M, Järvelin M. Maternal weight gain during the first half of pregnancy and offspring obesity at 16 years: a prospective cohort study. BJOG 2012;119:716–723.
Electrocardiographic Notching in Rats Deficient in Essential Fatty Acids

A notch has been seen in the electrocardiograms of rats who were fed diets deficient in essential fatty acids. This notching occurs consistently at a point 37 percent through the QRS-complex. It can be prevented by the addition of small amounts of linoleate, linolenate, or arachidonate to the diet of these rats.
Ecological & Profitable Carsharing Business: emission Limits & Heterogeneous Fleets

Carsharing is a mobility concept that addresses the world’s growing interest in sustainability. It reduces CO2 emissions, traffic congestion, and noise in cities. Including electric and hybrid vehicles in the carsharing fleet supports these aspects even more. For a station-based carsharing organization (CSO), the distribution and availability of vehicles play a crucial role to satisfy the customers’ needs as well as to obtain profits. We developed a tactical optimization model to determine the size and composition of a heterogeneous carsharing fleet while considering different emission limits with time-depended demand profiles. Different propulsion modes and vehicle classes represent the heterogeneity of the fleet. Using the application example of the city of San Francisco, results are presented, discussed, and analyzed. Our benchmarks for two different demand scenarios reveal the strong influence of a preset maximum level of CO2 emissions on fleet composition and monthly net profit. The optimization model allows CSOs to provide a sustainable and profitable mobility concept; city planners are supported to evaluate influences of CO2 emission thresholds on CSOs. The model thereby represents a Green IS approach, as it contributes to supporting a society’s path towards a low emission and noise-reduced environment in urban areas where carsharing is feasible.
Plasmon-assisted controllable excitation of single quantum dots on a metal nanowire

The hybrid systems of multiple quantum emitters coupled with plasmonic waveguides provide promising building blocks for the future integrated quantum nanophotonic circuits. The techniques that can selectively excite adjacent quantum emitters in a diffraction-limited area are of great importance for studying the plasmon-mediated interaction between quantum emitters and manipulating the generation and propagation of single plasmons in nanophotonic circuits. We show that by modulating the electric field on the nanowire using the interference of surface plasmons, multiple quantum dots coupled with a silver nanowire can be controllably excited. We experimentally demonstrate the selective excitation of two quantum dots with a separation distance of about 100 nm. Our work provides a new kind of optical excitation and characterization method overcoming the diffraction limit, and adds a new tool for studying and manipulating single quantum emitters and single plasmons for quantum plasmonic circuitry applications.
Lattice Boltzmann Formulation for Linear Viscoelastic Fluids Using an Abstract Second Stress

The kinetic theory of gases implies an independent evolution equation for the momentum flux tensor that closely resembles an evolution equation for the elastic stress in continuum descriptions of viscoelastic liquids. However, kinetic theory leads to a nonobjective convected derivative for the evolution of the deviatoric stress, and a fixed relation between the stress relaxation rate and the viscosity. We show that simulations of freely decaying shear flow using the standard two-dimensional lattice Boltzmann kinetic model develop a tangential stress consistent with this nonobjective convected derivative, and this fixed relation between parameters. By contrast, viscoelastic liquids are typically modeled by an upper convected derivative, and with two independent parameters for the viscosity and stress relaxation rate. Although we are unable to obtain an upper convected derivative from kinetic theory with a scalar distribution function, we show that introducing a general linear coupling to a second stress te.
TAFII105 mediates activation of anti‐apoptotic genes by NF‐κB

The transcription factor NF‐κB is important for expression of genes involved in immune responses, viral infections, cytokine signaling and stress. In addition NF‐κB plays a crucial role in protecting cells from TNF‐α‐induced apoptotic stimuli, presumably by activating anti‐apoptotic genes. Here we report that the sub‐stoichiometric TFIID subunit TAFII105 is essential for activation of anti‐apoptotic genes in response to TNF‐α, serving as a transcriptional coactivator for NF‐κB. The putative coactivator domain of TAFII105 interacts with the activation domain of the p65/RelA member of the NF‐κB family, and further stimulates p65‐induced transcription in human 293 cells. Moreover, inhibition of TAFII105 activity by overexpression of a dominant negative mutant of TAFII105 decreased NF‐κB transcriptional activity and severely reduced cell survival in response to TNF‐α. Similarly, expression of anti‐sense TAFII105 RNA sensitized the cells to TNF‐α cytotoxicity. These results suggest that TAFII105 is involved in activation of anti‐apoptotic genes by NF‐κB.
Comparisons of aerosol optical properties derived from Sun photometry to estimates inferred from surface measurements in Big Bend National Park , Texas

As a part of the Big Bend Regional Aerosol and Visibility Observational Study (BRAVO, July–October 1999), aerosol physical, optical and chemical properties were measured continuously in an effort to characterize visibility in Big Bend National Park. Surface-based estimates of aerosol extinction coefficients derived from size distribution data were compared to aerosol optical properties retrieved independently from ground-based remote sensing measurements from the United States Department of Agriculture (USDA) UVB radiometer network site. Comparisons suggested that for the majority of the study, surface visibility was a good indicator of the column aerosol optical depth, with a correlation coefficient of r 1⁄4 0:77: The average (and one standard deviation) aerosol optical depth from the USDA network was 0.1370. 06 at a wavelength of 500 nm. Ångstrom wavelength exponents were computed for both data sets to characterize the spectral variations of aerosol optical properties over the wavelength range of 415–860 nm. Variations in Ångstrom exponents corresponded to changing aerosol properties as seen in the ground-based composition and size distribution data sets. The average Ångstrom exponent from in situ measurements was 1.570. 4 compared to column estimates of 1.370. 4. The root mean square of the difference between the estimates of Ångstrom exponents was 0.20 ( 12%) and on average the estimates were highly correlated (r 1⁄4 0:89). Aerosol optical depths and ambient surface aerosol extinction coefficients were positively correlated with PM2.5 sulfate mass concentrations (r 2 1⁄4 0:68 and r 1⁄4 0:79; respectively), suggesting that sulfate aerosols were a major contributor to visibility degradation and column aerosol loading during the study. r 2004 Elsevier Ltd. All rights reserved.
Research into poultry meat quality

1. Research in the field of poultry meat quality has become more varied during the last 50 years. Besides meat content and microbial condition, animal welfare issues during the slaughter process, muscle morphology, physiology of meat ripening, impact of slaughter process on meat quality, sensory attributes of meat and meat processing have come into focus. 2. The present review summarizes findings and developments in the fields of muscle physiology, meat ripening and meat quality aberrations (like PSE), nutrient composition and sensory qualities, effect of the slaughter process on carcass and meat quality, hygienic conditions and product safety during slaughtering, all based on selected papers published in British Poultry Science during the last 50 years. 3. Some special findings and conclusions are lifted out of the whole results presented in the papers to indicate their importance and to show their contribution to the development of knowledge in the respective field.
Virtual Systems Workload Characterization: An Overview

Virtual systems and virtualization technology are taking the momentum nowadays in data centers and IT infrastructure models.Performance analysis of such systems is very invaluable for enterprises but yet is not a deterministic process. Single-workload benchmark is useful in quantifying the virtualization overhead within a single VM, but not useful in whole virtualized environment with multiple isolated VM and varying workload on each and can’t capture the system behavior. We need a common workload model and methodology for virtualized systems so that benchmark results can be compared across different platforms. In this paper we will present an overview of the key requirements and characteristics of virtual systems performance metrics and workload characterization which can be considered one step further in implementing virtual systems benchmark and performance model that describe the effect of the applications, host operating system and the hypervisor layer on the performance metrics of virtual workloads. An overview of Intel® vCon modeland VMware VMmark will be introduced as examples for the consolidated servers’ workload evaluation.
The Genericity Theorem and the Notion of Parametricity in the Polymorphic λ-calculus

This paper focuses on how terms of second order λ-calculus, which may take types as inputs, depend on types. These terms are generally understood to have an “essentially” constant meaning, in all models, on input types. We show how the proof theory of second order λ-calculus suggests a clear syntactic description of this phenomenon. Namely, under a reasonable condition, we show that identity of two polymorphic functions on a single type implies identity of the functions (equivalently, every type is a generic input).
Load Handling and Repetitive Movements Are Associated with Chronic Low Back Pain among Jute Mill Workers in India

Introduction. WHO recognizes low back pain as one of the most important ergonomic stressors. Therefore, the present study was designed to find out the magnitude of the problem among jute mill workers in India and identify possible associations. Methodology. This cross-sectional workplace based study was conducted among eight (8) selected jute mills of India. Subjects with self-reported back pain for at least last 12 weeks were included and n = 717 male jute mill workers actively engaged in work entered the study and completed all assessments. Results. Among all participants 55% (n = 392) had current chronic low back pain. Age was an important association with subjects in the age group of 40–59 years more likely to have pain (p = 0.02, OR 1.44). Regarding ergonomic risk factors lifting of load of more than 20 kg (p = 0.04, OR 1.42) and repetitive movements of limbs (p = 0.03, OR 0.67) were significant associations of chronic low back pain. Conclusion. This study identified a significant prevalence of current chronic low back pain among jute mill workers. Regarding ergonomic risk factors the present study has identified two significant associations: lifting of load above 20 kg and repetitive movements of limbs. Therefore, this study has identified need for workplace interventions in this occupational group employing approximately 3,50,000 workers in India.
The sensitivity of clinical isolates of Leishmania from Peru and Nepal to miltefosine.

Clinical isolates of Leishmania, from visceral leishmaniasis (VL) cases in Nepal and from cutaneous leishmaniasis (CL) cases in Peru, were cultured using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to type species and strain. Promastigotes from 38 isolates, within eight passages from isolation, were used to infect mouse peritoneal macrophage cultures in vitro, and the amastigote sensitivity to miltefosine was determined. The concentration required to kill 50% of intracellular amastigotes from Nepalese VL isolates, all typed as Leishmania (L.) donovani (N = 24) from both Sbv responders and nonresponders, ranged from 8.7 to 0.04 microg/mL. In contrast, the concentration required to kill 50% intracellular amastigotes from isolates from Peru, typed as L. (V.) braziliensis (N = 8), was > 30 to 8.4 microg/mL, L. (V.) guyanensis (N = 2) > 30 to 1.9 microg/mL, L. (L.) mexicana (N = 1) > 30 microg/mL, and L. (V.) lainsoni (N = 4) was 3.4 to 1.9 microg/mL. This demonstrates a notable difference in the intrinsic sensitivity of Leishmania species to miltefosine in vitro. If this model can be correlated to therapeutic outcome, it may have implications for the interpretation of clinical trials.
Role of the left interventricular sulcus in formation of the interventricular septum and crista supraventricularis in normal human cardiogenesis

Serial sections of normal human embryos were studied and three‐dimensional images reconstructed to determine the early development of the interventricular septum. The position of the interventricular septum is determined in stage 9 of normal development by the formation of the left interventricular sulcus. As a result of unknown properties of the cells of the myocardial layer, the left interventricular sulcus persists while the right disappears, producing the initial lateral asymmetry of the primary heart tube. By stage 14, the left interventricular sulcus forms a spiral which is continuous with the developing interventricular septum. The dorsal limb of the spiral passes to the right between the atrioventricular canal and the origin of the outflow tract, and is lost in the wall of the trabeculated right ventricle. It appears that this dorsal limb of the spiral is the precursor of part of the cirsta supraventricularis. The midportion of the sulcus, the bulboventricular groove, becomes the socalled fibrous continuity between the aortic and mitral valves. The ventral limb of the spiral passes caudally in the anterior interventricular groove and then dorsally and cranially toward the dorsal cushion of the atrioventricular canal. The ventral limb of the spiral is continuous with the crest of the muscular interventricular septum, which develops by apposition of tissue from the expanding right and left ventricles. From stage 14 to stage 19, the muscular interventricular septum, the atrioventricular endocardial cushions, and the ventricular end of the spiral ridges of the outflow tract appose and fuse. Subsequent formation of the membranous interventricular septum completes the physical separation of the right and left ventricles.