Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkless and flat embeddings in 3-space and the unknot problem

We consider piecewise linear embeddings of graphs in 3-space ℜ3. Such an embbeding is linkless if every pair of disjoint cycles forms a trivial link (in the sense of knot theory). Robertson, Seymour and Thomas [47] showed that a graph has a linkless embedding in ℜ3 if, and only if, it does not contain as a minor any of seven graphs in Petersen's family (graphs obtained from K6 by a series of YΔ and ΔY operations). They also showed that a graph is linklessly embeddable in ℜ3 if, and only if, it admits a flat embedding into ℜ3, i.e. an embedding such that for every cycle C of G there exists a closed 2-disk D ⊆ ℜ3 with D ∩ G = ∂D = C. Clearly, every flat embeddings is linkless, but the converse is not true. We first consider the following algorithmic problem associated with embeddings in ℜ3: Flat Embedding: For a given graph G, either detect one of Petersen's family graphs as a minor in G or return a flat (and hence linkless) embedding in ℜ3. The first outcome is a certificate that G has no linkless and no flat embeddings. Our first main result is to give an O(n2) algorithm for this problem. While there is a known polynomial-time algorithm for constructing linkless embeddings [20], this is the first polynomial time algorithm for constructing flat embeddings in 3-space and we thereby settle a problem proposed by Lovasz [29]. We also consider the following classical problem in topology. The Unknot Problem: Decide if a given knot is trivial or not. This is a fundamental problem in knot theory and low dimensional topology, whose time complexity is unresolved. It has been extensively studied by researchers working in computational geometry. A related problem is: The Link Problem: Decide if two given knots form a link. Hass, Lagarias and Pippenger [16] observed that a polynomial time algorithm for the link problem yields a polynomial time algorithm for the unknot problem. We relate the link problem to the following problem that was proposed independently by Lovasz and by Robertson et al. Conjecture. (Lovasz [29]; Robertson, Seymour and Thomas [48]) There is a polynomial time algorithm to decide whether a given embedding of a graph in the 3-space is linkless. Affirming this conjecture would clearly yield a polynomial-time solution for the link problem. We prove that the converse is also true by providing a polynomial-time solution for the above conjecture, if we are given a polynomial time oracle for the link problem.
Human hand impedance characteristics during reaching movements

The dynamic characteristics of human arm are usually expressed by mechanical impedance which includes inertia, viscosity and stiffness. This paper aimed to investigate human impedance during maintained posture and reaching movements for the purpose of clarifying human impedance changes depending on different conditions as a first step to realize impedance training for sports and rehabilitation. In this study, a subject was asked to do reaching movements in a virtual sports system to estimate the hand impedance during movements. The experimental results for all 3 subjects in different conditions demonstrate that people may optimally regulate hand impedance properties according to environmental constraints and the desired tasks.
Laparoscopic cholecystectomy in childhood: a review of twenty-four consecutive cases

Background. The experience with laparoscopic cholecystectomy in children remains limited. Therefore, we aimed to present our experience with this procedure. Methods. Between April 2011 and June 2016, retrospectively, data points of children who underwent laparoscopic cholecystectomy reviewed included demographics properties, indication for cholecystectomy, surgical technique, operative time, complications, and length of hospital stay. Results. Twenty-four children (5 were males with ages ranging from 2 to 17 years, mean: 10.5 years) underwent laparoscopic cholecystectomy. The indication for surgery was associated to symptomatic gallstones in all patients. The surgery was performed under general anesthesia and classical 4-port approach was done in twenty-two patients, and 2-port approach in combination with 2 portless 2.3-mm percutaneous graspers was used in two patients. The operating time ranged between 45 and 90 minutes (mean: 60 minutes). Two patients ended by open surgery. No complications occurred. Hospital stays ranged from 1-3 days. Conclusion. Laparoscopic cholecystectomy is safe and effective in children, and shows the same advantages reported in adults series.
Stimulation of the Calcitonin Gene-Related Peptide Enhancer by Mitogen-Activated Protein Kinases and Repression by an Antimigraine Drug in Trigeminal Ganglia Neurons

Calcitonin gene-related peptide (CGRP) is involved in the underlying pathophysiology of all vascular headaches, including migraines. Elevated levels of CGRP during migraine are restored to normal coincident with headache relief after treatment with the antimigraine drug sumatriptan. We have used primary cultures of trigeminal neurons under conditions simulating migraine pathology and therapy to study the mechanisms controlling the CGRP promoter. Using reporter genes in transient transfection assays, we demonstrate that an 18 bp enhancer containing a helix–loop–helix element is both necessary and sufficient for full promoter activity. NGF treatment and cotransfection with an upstream activator of the extracellular signal-regulated MAP kinases (MAPKs) activated the enhancer. Treatment with sumatriptan repressed NGF- and MAPK-stimulated CGRP promoter activity. Repression was also observed using a synthetic MAPK-responsive reporter gene. Sumatriptan regulation of CGRP gene expression did not couple to a Gi/Gopathway, but rather caused a prolonged increase in intracellular calcium. The importance of the prolonged calcium signal in repression of MAPK activity was demonstrated by using the ionophore ionomycin to mimic sumatriptan action. We propose that activation of MAPK pathways may increase CGRP gene expression during migraine, and that sumatriptan can diametrically oppose that activation via a prolonged elevation of intracellular calcium.
Sparsity-aware, channel order-blind pilot placement with channel estimation in orthogonal frequency division multiplexing systems

Equispaced pilot arrangement is the most popular scheme for pilot-aided transmission in orthogonal frequency division multiplexing systems. In this study, the authors argue that a non-equispaced pilot pattern may outperform its equispaced counterpart, if they fully take into account the sparsity of the channel impulse response which is inherent in wireless channels. More specifically, a sparsity-aware pilot arrangement scheme based on the coherence criterion is investigated in this study. To address the resulting non-deterministic polynomial (NP)-hard combinatorial optimisation problem, they propose an efficient local search algorithm. For channel estimation, they convert it to a sparse recovery problem. To enhance the applicability of the authors scheme, that is, when there is no prior knowledge about the channel order, they propose to employ the Bayesian information criterion to estimate the channel order first and then recover the sparse channel vector via existing low-complexity methods, for example, orthogonal matching pursuit. By combining the above pilot arrangement scheme with channel estimation, their scheme exhibits substantially better performance in comparison with the conventional equispaced schemes with linear (or spline) interpolation, in terms of total number of pilot symbols and bit error rate.
The GABRIEL Advanced Surveys: study design, participation and evaluation of bias.

Exposure to farming environments has been shown to protect substantially against asthma and atopic disease across Europe and in other parts of the world. The GABRIEL Advanced Surveys (GABRIELA) were conducted to determine factors in farming environments which are fundamental to protecting against asthma and atopic disease. The GABRIEL Advanced Surveys have a multi-phase stratified design. In a first-screening phase, a comprehensive population-based survey was conducted to assess the prevalence of exposure to farming environments and of asthma and atopic diseases (n = 103,219). The second phase was designed to ascertain detailed exposure to farming environments and to collect biomaterial and environmental samples in a stratified random sample of phase 1 participants (n = 15,255). A third phase was carried out in a further stratified sample only in Bavaria, southern Germany, aiming at in-depth respiratory disease and exposure assessment including extensive environmental sampling (n = 895). Participation rates in phase 1 were around 60% but only about half of the participating study population consented to further study modules in phase 2. We found that consenting behaviour was related to familial allergies, high parental education, wheeze, doctor diagnosed asthma and rhinoconjunctivitis, and to a lesser extent to exposure to farming environments. The association of exposure to farm environments with asthma or rhinoconjunctivitis was not biased by participation or consenting behaviour. The GABRIEL Advanced Surveys are one of the largest studies to shed light on the protective 'farm effect' on asthma and atopic disease. Bias with regard to the main study question was able to be ruled out by representativeness and high participation rates in phases 2 and 3. The GABRIEL Advanced Surveys have created extensive collections of questionnaire data, biomaterial and environmental samples promising new insights into this area of research.
Altered functions of plasmacytoid dendritic cells and reduced cytolytic activity of natural killer cells in patients with chronic HBV infection.

BACKGROUND & AIMS Hepatitis B virus (HBV) modulates the immune system to escape clearance. Plasmacytoid dendritic cells (pDCs) initiate antiviral immunity and might determine outcomes of HBV infections. Functional defects in pDCs and natural killer (NK) cells have been reported in patients with chronic HBV infection. However, the mechanisms of these immune dysfunctions and the interactions between pDCs and NK cells have not been determined. We investigated features of pDCs from patients with chronic HBV infection and their interactions with NK cells. METHODS We used flow cytometry and cytokine assays to analyze pDCs from patients with chronic HBV infection (118 aviremic and 67 viremic) and compared them with pDCs from uninfected individuals (controls). We performed coculture assays to analyze the ability of pDCs to activate heterologous NK cells. RESULTS Circulating and hepatic pDCs from patients with chronic HBV infection had higher levels of activation than pDCs from controls and defective responses to stimulation with Toll-like receptor 9 ligand (TLR9-L), regardless of the patient's viral load. TLR9-L-activated pDCs from viremic patients with HBV did not induce cytolytic activity of NK cells. This altered function of pDCs was associated with reduced expression of OX40L and could be reproduced by incubating control pDCs with plasma from viremic patients with HBV. A high level of interferon-induced protein 10 (IP-10 or CXCL10) and hepatitis B surface and e antigens might induce these defective pDC functions. CONCLUSIONS HBV escapes antiviral immunity by altering pDC functions, to disrupt interactions between pDC and NK cells. This could reduce immune control of HBV and lead to chronic infection.
Quantitative Near Infrared Spectroscopy Measurement of Cerebral Hemodynamics in Newborn Piglets

Severely premature infants are often at increased risk of cerebral hemorrhage and/or ischemic injury caused by immature autoregulatory control of blood flow to the brain. If blood flow is too high, the infant is at risk of hemorrhage, whereas too little blood flow can result in ischemic injury. The development of a noninvasive, bedside means of measuring cerebral hemodynamics would greatly facilitate both diagnosis and monitoring of afflicted individuals. It is to this end that we have developed a near infrared spectroscopy (NIRS) system that allows for quantitative, bedside measurement of cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT). The technique requires an i.v. injection of the near infrared chromophore indocyanine green. Six newborn piglets, median age of 18 h (range 6–54 h), median weight of 1.75 kg (range 1.5–2.1 kg), were studied. Measurements of CBF, CBV, and MTT were made at normocapnia, hypocapnia, and hypercapnia to test the technique over a range of hemodynamic conditions. The accuracy of our new approach has been determined by direct comparison with measurements made using a previously validated computed tomography technique. Paired t tests showed no significant difference between computed tomography and NIRS measurements of CBF, CBV, and MTT, and mean biases between the two methods were −2.05 mL·min−1·100 g−1, −0.18 mL·100 g−1, and 0.43 s, respectively. The precision of NIRS CBF, CBV, and MTT measurements, as determined by repeated-measures ANOVA, was 9.71%, 13.05%, and 7.57%, respectively.
T-Cell Activation Independently Associates With Immune Senescence in HIV-Infected Recipients of Long-term Antiretroviral Treatment.

BACKGROUND Aging-associated noncommunicable comorbidities are more prevalent among human immunodeficiency virus type 1 (HIV)-infected individuals than among HIV-uninfected individuals. Residual HIV-related chronic immune activation and senescence may increase the risk of developing comorbidities. METHODS Immune phenotyping, thymic output, and telomere length were assessed in 94 HIV-infected individuals who were aged >45 years and receiving antiretroviral therapy (ART; cases) and 95 age-matched uninfected controls. RESULTS Cases had lower CD4(+) T-cell counts, higher CD8(+) T-cell counts, and increased levels of immune activation (ie, increased soluble CD14 [sCD14] level and increased percentages of CD38(+)HLA-DR(+) cells among both CD4(+) and CD8(+) T cells), regulatory T cells, and percentage of programmed cell death 1 (PD-1)-expressing cells among CD4(+) T cells. Immune senescence levels (ie, percentages of CD27(-)CD28(-) cells or CD57(+) cells) were comparable between cases and controls. Peripheral blood mononuclear cells from cases had shorter telomeres but increased single-joint T-cell receptor excision circle content and CD31(+) naive CD4(+) T cells. Although cytomegalovirus (CMV) antibody titers were higher in cases, CMV-specific T-cell responses were comparable between cases and controls. T-cell senescence in cases was independently associated with T-cell activation but not with CMV-specific immune responses. CONCLUSIONS Despite long-term receipt of ART, HIV-infected adults had higher levels of immune activation, regulatory T cells, and PD-1-expressing CD4(+) cells and shorter telomeres. The increased soluble CD14 levels and percentage of CD38(+)HLA-DR(+) cells among CD4(+) T cells correlated with shorter telomeres and increased regulatory T-cell levels. This suggests that HIV influences immune function irreversibly, with several pathways that are persistently abnormal during effective ART. Therapies aimed at improving immune health during ART are needed.
Effect of stress on female-specific ornamentation

SUMMARY Signal honesty is theorized to be maintained by condition-dependent trait expression. However, the mechanisms mediating the condition dependence of sexually selected traits are often unknown. New work suggests that elevated glucocorticoid levels during physiological stress may play a role in maintaining signal honesty. Here, we experimentally examine the effect of both chronic and acute stress on the expression of the condition-dependent ornamentation of female striped plateau lizards, Sceloporus virgatus. Females were stressed either chronically via corticosterone implants or relatively acutely via autotomy, were sham manipulated or were left unmanipulated. Both stressors resulted in elevations in corticosterone within physiologically relevant levels, though the implants resulted in significantly higher levels than did autotomy. Corticosterone-implanted females were less likely to produce a clutch of eggs, but those individuals that did reproduce had reproductive output similar to that of females from other treatment groups. Compared with females in other groups, the corticosterone-implanted females tended to develop smaller ornaments that had less UV and orange-to-red wavelength reflectance relative to medium wavelength reflectance. The sex steroid hormones testosterone and estradiol were correlated to corticosterone levels, but did not appear to underlie the effect on ornament expression; of the steroids measured, only corticosterone levels were negatively related to ornament size and coloration. Thus, the condition-dependent ornamentation of female lizards is sensitive to chronic elevations in stress hormones, supporting their importance in the maintenance of signal honesty.
Differential Control of Wnt Target Genes Involves Epigenetic Mechanisms and Selective Promoter Occupancy by T-Cell Factors

ABSTRACT Canonical Wnt signaling and its nuclear effectors, β-catenin and the family of T-cell factor (TCF) DNA-binding proteins, belong to the small number of regulatory systems which are repeatedly used for context-dependent control of distinct genetic programs. The apparent ability to elicit a large variety of transcriptional responses necessitates that β-catenin and TCFs distinguish precisely between genes to be activated and genes to remain silent in a specific context. How this is achieved is unclear. Here, we examined patterns of Wnt target gene activation and promoter occupancy by TCFs in different mouse cell culture models. Remarkably, within a given cell type only Wnt-responsive promoters are bound by specific subsets of TCFs, whereas nonresponsive Wnt target promoters remain unoccupied. Wnt-responsive, TCF-bound states correlate with DNA hypomethylation, histone H3 hyperacetylation, and H3K4 trimethylation. Inactive, nonresponsive promoter chromatin shows DNA hypermethylation, is devoid of active histone marks, and additionally can show repressive H3K27 trimethylation. Furthermore, chromatin structural states appear to be independent of Wnt pathway activity. Apparently, cell-type-specific regulation of Wnt target genes comprises multilayered control systems. These involve epigenetic modifications of promoter chromatin and differential promoter occupancy by functionally distinct TCF proteins, which together determine susceptibility to Wnt signaling.
Computer Use and Its Effect on the Memory Process in Young and Adults

This work investigates the effect of computer use in the memory process in young and adults under the Perceptual and Memory experimental conditions. The memory condition involved the phases acquisition of information and recovery, on time intervals (2 min, 24 hours and 1 week) on situations of pre and post-test (before and after the participants took part on a Basic Computing course), in which the participants studied the map of Brazil during 7 minutes and the estimates of different areas of Brazilian states were performed according to the magnitude estimation method, without the presence of the map. On the Perceptual condition, the estimates were made in the pres- ence of the Brazilian map. The study made possible to verify that the use of a computer, as a new activity enables a differentiation on the memory process in relation to the different experimental conditions proposed and to the time intervals used between acquisition, processing and information recovery, showing that the use of a computer as a pedagogical tool may promote the improvement of the memory process in academic activities.
The "art" of programming gossip-based systems

How does one best go about building actual gossip-based protocols? Trying to answer this question has brought us to address two preliminary questions, namely (1) what the intrinsics of such systems or protocols are, and (2) what kind of applications would in the end be built on top of such protocols. We address the first question by arguing that gossip-based protocols are all built following one and the same pattern, and describing three building blocks which we claim are used to support this recurrent pattern---most notably a source of randomness. We validate these claims by devising simplified versions of well-known protocols, in a layered fashion, on top of a conceptual interface describing these basic services. The second question is addressed by arguing that gossip-based protocols exhibit some probabilistic or imperfect flavor (e.g., probabilistic or partial completion), and by proposing to take such probabilistic behavior into account when devising interfaces for applications building on top of gossip-based protocols. We argue for inherent support for these probabilities in the programming model.
Extensible algebraic datatypes with defaults

A major problem for writing extensible software arises when recursively defined datatypes and operations on these types have to be extended simultaneously without modifying existing code. This paper introduces Extensible Algebraic Datatypes with defaults, which promote a simple programming pattern to solve this well-known problem. We show that it is possible to encode extensible algebraic datatypes in an object-oriented language, using a new design pattern for extensible visitors. Extensible algebraic datatypes have been successfully applied in the implementation of an extensible Java compiler. Our technique allows for the reuse of existing components in compiler extensions without the need for any adaptations.
Psychotherapy for social phobia: How do alliance and cognitive process interact to produce outcome?

Abstract The purpose of this study was to ascertain whether and how alliance and specific cognitive process may interact to influence outcome. Eighty social phobic patients were randomized to 10-week residential cognitive or interpersonal therapy, conducted mostly in groups. They completed process and outcome measures weekly. The ratings were analyzed with mixed models. It was found that initial patient-rated alliance predicted the course of social anxiety throughout therapy and that this effect was indirect through the cognitive process. However, this indirect effect did not interact with treatment. There was a trend toward an indirect effect of weekly variations in alliance rated by the individual therapist through weekly variations in subsequent cognitive process on weekly variations in subsequent social anxiety. Thus, the results support a facilitative rather than an active ingredient perspective on the role of alliance.
Recognition of exon/intron boundaries using dynamic ensembles

Many studies have been carried out in recognition of exon/intron boundaries. For example, PROCRUSTES uses similarity-based approach to gene recognition. Other examples include GRAIL (Gene Recognition and Assembly Internet Link) http://compbio.ornl. gov/Grail-1.3/help/(1996) and Glimmer (Gene Locator and Interpolated Markov Modeler). Since the problem of recognition of exon/intron boundaries can be cast as a classification task, ensemble learning can be applied. An ensemble consists of a set of organized individual trained classifiers whose individual decisions are combined in a certain way for classification purpose. However, existing studies typically take static approaches which hampered flexibility for improved accuracy. To overcome this problem we have proposed the concept of dynamic ensemble and developed a new algorithm, BAGA, which combines bagging and genetic algorithm techniques.