Miracle-dz/UniFAR-FTUs huggingface dataset:
A Tractable Walsh Analysis of SAT and its Implications for Genetic Algorithms

Walsh Transforms measure all sources of nonlinear interactions for functions that have a bit representation. There can be exponentially many nonlinear interactions and exactly computing all Walsh coefficients is usually intractable for non-trivial functions. In this paper we will show that SAT problems evaluated as MAXSAT functions have a highly restricted set of nonzero Walsh coefficients and those coefficients can be computed in linear time with respect to the number of clauses. This analysis suggests why standard simple genetic algorithms should perform poorly on MAXSAT problems.
CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Summary The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System) spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys’s functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.
Weighted SLNR-based precoding algorithm for downlink multi-stream CoMP-JP system

Signal to leakage and noise ratio (SLNR) based precoding algorithm is widely researched in CoMP-JP system. Nevertheless, the equivalent channel gain for each stream can be severely unbalanced in multi-stream transmission, and the overall performance is limited by the worst data stream. An improved SLNR based precoding algorithm is presented, which generates new precoding matrix with the method of weighting and linear transformation based on original SLNR vectors to eliminate the disparity of performance among streams, and optimize overall performance in multi-stream system. The simulation results demonstrate that our proposed algorithm can achieve considerable gains in error performance over the original SLNR and eliminate co-channel interference (CCI) among UEs at the same time for multi-stream transmission.
RAPID Automated Patient Selection for Reperfusion Therapy: A Pooled Analysis of the Echoplanar Imaging Thrombolytic Evaluation Trial (EPITHET) and the Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution (DEFUSE) Study

Background and Purpose— The aim of this study was to determine if automated MRI analysis software (RAPID) can be used to identify patients with stroke in whom reperfusion is associated with an increased chance of good outcome. Methods— Baseline diffusion- and perfusion-weighted MRI scans from the Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution study (DEFUSE; n=74) and the Echoplanar Imaging Thrombolytic Evaluation Trial (EPITHET; n=100) were reprocessed with RAPID. Based on RAPID-generated diffusion-weighted imaging and perfusion-weighted imaging lesion volumes, patients were categorized according to 3 prespecified MRI profiles that were hypothesized to predict benefit (Target Mismatch), harm (Malignant), and no effect (No Mismatch) from reperfusion. Favorable clinical response was defined as a National Institutes of Health Stroke Scale score of 0 to 1 or a ≥8-point improvement on the National Institutes of Health Stroke Scale score at Day 90. Results— In Target Mismatch patients, reperfusion was strongly associated with a favorable clinical response (OR, 5.6; 95% CI, 2.1 to 15.3) and attenuation of infarct growth (10±23 mL with reperfusion versus 40±44 mL without reperfusion; P<0.001). In Malignant profile patients, reperfusion was not associated with a favorable clinical response (OR, 0.74; 95% CI, 0.1 to 5.8) or attenuation of infarct growth (85±74 mL with reperfusion versus 95±79 mL without reperfusion; P=0.7). Reperfusion was also not associated with a favorable clinical response (OR, 1.05; 95% CI, 0.1 to 9.4) or attenuation of lesion growth (10±15 mL with reperfusion versus 17±30 mL without reperfusion; P=0.9) in No Mismatch patients. Conclusions— MRI profiles that are associated with a differential response to reperfusion can be identified with RAPID. This supports the use of automated image analysis software such as RAPID for patient selection in acute stroke trials.
Dietary restriction and Sirtuin 1 in metabolic health: connections and divergences

Aging is the major risk factor for a constellation of multifactorial diseases, including insulin resistance, diabetes and cardiovascular complications. Dietary restriction has been shown to delay or prevent the manifestation of age-related health decline, extending lifespan in most species tested to date. Given the scarce willingness of human subjects to adhere to chronic dietary restriction exercises, there has been an interest in deciphering the molecular mechanisms triggering the adaptations to dietary restriction. In this context, Sirtuin 1 (SIRT1), a NAD+-dependent deacetylase enzyme, has been proposed to act as a key mediator of the adaptations to nutrient deprivation in eukaryotes, and SIRT1 activating compounds have been often referred to as ‘dietary restriction mimetic’ molecules. Here, we will discuss the convergences and divergences between the effects of dietary restriction and SIRT1 activation, based on the recent advances in the field. As of now, most evidences indicate that SIRT1 is required, but not sufficient to trigger dietary-restriction induced adaptations.
Pharmacogenetics of SSRIs and Sexual Dysfunction

Sexual dysfunction (SD) is a common and disconcerting side effect of selective serotonin reuptake inhibitors (SSRIs) that often influences a patient’s desire to continue long-term antidepressant treatment. Studies specifically assessing changes in sexual well-being over time illustrate that the incidence of sexual side effects from SSRIs ranges from 20% to 70%, depending on the characteristics of the study sample assessed. Developing strategies to predict who may be at the highest risk for adverse changes in their sexual well-being is an important step in improving the quality of life and treatment of patients who require antidepressant therapy. Pharmacogenetic studies of SSRI-associated SD have identified associations between serotonin and glutamate system genes with aspects of SD. The results of studies investigating genetic variations in drug metabolism enzymes and their relationships to antidepressant-associated adverse effects have been mixed. Continued efforts to characterize the relationships between genetic markers and antidepressant outcomes, and to translate this knowledge to patient care, have the potential to significantly improve the empiric selection of antidepressant agents and to minimize the risk for intolerable side effects.
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This paper describes a new method to extract feature lines directly from a surface point cloud. No surface reconstruction is needed in advance, only the inexpensive computation of a neighbor graph connecting nearby points. The feature extraction is performed in two stages. The rst stage consists of assigning a penalty weight to each point that indicates the unlikelihood that the point is part of a feature and assigning these penalty weights to the edges of a neighbor graph. Extracting a sub-graph of the neighbor graph that minimizes the edge penalty weights then produces a set of feature patterns. The second stage is especially useful for noisy data. It recovers feature lines and junctions by tting wedges to the crease lines and corners to the junctions. As the method works on the local neighbor graph only, it is fast and automatically adapts to the sampling resolution. This makes the approach ideal as a preprocessing step in mesh generation.
Information to the patient : an attempt to satisfy the patient's need for information

Dissatisfaction with medical information is a common problem among patients. There is also evidence that patients lack information that physicians believe they have given to the patient. The aims of this study were to 1) survey patients' subjective need for, and satisfaction with, the information that they received during their hospital stay 2) develop and evaluate systematic routines for giving information to the patients and also communication and collaboration between the medical and nursing staff concerning the satisfaction of the patients' need for information.The study was an intervention project and the research perspective was organizational psychology.Survey study. The patients experienced a considerable need for medical information, especially about the examination results and prognosis. The patients' need for information regarding prognosis was the least satisfied.Intervention 1. A general improvement of the information to the patients occurred when the systematic routines were established. The patients' subjective need for information was unchanged throughout two years. Their satisfaction with information, after an initial improvement, did not increase throughout these two years. There was low correlation between the patients' and their physicians' estimations concerning the patients' need for information on diagnosis, prognosis and examination results. Likewise, concerning the adequacy of that information.Intervention 2. Communication and collaboration between the medical and nursing staff included a system for assessment and solution of the patients' information problems. Problem-solving took place at a multidisciplinary team conference (MTC). Medical problems were better elucidated than the patients' psychological problems. After training of registered nurses (RN) as conference chairpersons, the patients need for information was better understood. The staff reported 42 information problems after training compared to two before. For half of the information problems decisions were discussed on steps to be taken in order to satisfy the patients' need for information. A year after the system for assessment and solution of information problems was established, the patients were more satisfied with information about examinations and their results and on information about medication (p< 0.05). Further, new norms for the patients' need for information were established and a change was initiated.The results are discussed with regard to how and why patients' shall have information, by whom and to whom information shall be given, when and where information shall be given and which content it shall have.
Optical multi-mode interference devices based on self-imaging: principles and applications

This paper presents an overview of integrated optics routing and coupling devices based on multimode interference. The underlying self-imaging principle in multimode waveguides is described using a guided mode propagation analysis. Special issues concerning the design and operation of multimode interference devices are discussed, followed by a survey of reported applications. It is shown that multimode interference couplers offer superior performance, excellent tolerance to polarization and wavelength variations, and relaxed fabrication requirements when compared to alternatives such as directional couplers, adiabatic X- or Y-junctions, and diffractive star couplers. >
Probabilistic Logic and the Synthesis of Reliable Organisms from Unreliable Components

The paper that follows is based on notes taken by Dr. R. S. Pierce on five lectures given by the author at the California Institute of Technology in January 1952. They have been revised by the author but they reflect, apart from minor changes, the lectures as they were delivered. The subject-matter, as the title suggests, is the role of error in logics, or in the physical implementation of logics—–in automatasynthesis. Error is viewed, therefore, not as an extraneous and misdirected or misdirecting accident, but as an essential part of the process under consideration—–its importance in the synthesis of automata being fully comparable to that of the factor which is normally considered, the intended and correct logical structure. Our present treatment of error is unsatisfactory and ad hoc. It is the author’s conviction, voiced over many years, that error should be treated by thermodynamical methods, and be the subject of a thermodynamical theory, as information has been, by the work of L. Szilard and C. E. Shannon (cf. 5.2). The present treatment falls far short of achieving this, but it assembles, it is hoped, some of the building materials, which will have to enter into the final structure. The author wants to express his thanks to K. A. Brueckner and M. Gell-Mann, then at the University of Illinois, to whose discussions in 1951 he owes some important stimuli on this subject; to Dr. R. S. Pierce at the California Institute of Technology, on whose excellent notes this exposition is based; and to the California Institute of Technology, whose invitation to deliver these lectures combined with the very warm reception by the audience, caused him to write this paper in its present form, and whose cooperation in connection with the present publication is much appreciated.
Vadose Zone Modeling in a Small Forested Catchment: Impact of Water Pressure Head Sampling Frequency on 1D-Model Calibration

The characterization of vadose zone processes is a primary goal for understanding, predicting, and managing water resources. In this study, the issue of soil water monitoring on a vertical profile in the small forested Strengbach catchment (France) is investigated using numerical modeling with the long-term sequences 1D-Richards’ equation and parameter estimation through an inverse technique. Three matric potential sensors produce the observation data, and the meteorological data is monitored using an automatic weather station. The scientific questions address the selection of the calibration sequence, the initial starting point for inverse optimization and monitoring frequency used in the inverse procedure. As expected, our results show that the highly variable data period used for the calibration provides better estimations when simulating the long-term sequence. For the starting point of the initial parameters, handmade iterative initial parameters estimation leads to better results than a laboratory analysis or set of ROSETTA parameters. Concerning the frequency of monitoring, weekly and daily datasets provide efficient results compared to hourly data. As reported in other articles, the accuracy of the boundary conditions is important for estimating soil hydraulic parameters and accessing water stored in the layered profile.
Sampling based algorithms for quantile computation in sensor networks

We study the problem of computing approximate quantiles in large-scale sensor networks communication-efficiently, a problem previously studied by Greenwald and Khana [12] and Shrivastava et al [21]. Their algorithms have a total communication cost of O(k log2 n / ε) and O(k log u / ε), respectively, where k is the number of nodes in the network, n is the total size of the data sets held by all the nodes, u is the universe size, and ε is the required approximation error. In this paper, we present a sampling based quantile computation algorithm with O(√kh/ε) total communication (h is the height of the routing tree), which grows sublinearly with the network size except in the pathological case h=Θ(k). In our experiments on both synthetic and real data sets, this improvement translates into a 10 to 100-fold communication reduction for achieving the same accuracy in the computed quantiles. Meanwhile, the maximum individual node communication of our algorithm is no higher than that of the previous two algorithms.
Coalitions and Networks in Industrial Organization

This paper provides a selective survey of recent approaches to coalition and network formation in industrial organization, and offers a unified framework in which the different approaches can be compared. We focus on two extreme forms of cooperation--collusive agreements and cost-reducing alliances. We show that bilateral negotiations yield higher levels of cooperation than multilateral agreements, that the formation of a cartel depends on the sequentiality of the procedure of coalition formation, and that the size of alliances depends on the membership rule. Copyright 2002 by Blackwell Publishers Ltd and The Victoria University of Manchester
Observational Manifestations of Solar Magnetoconvection: Center-to-Limb Variation

We present the first center-to-limb G-band images synthesized from high-resolution simulations of solar magnetoconvection. Toward the limb the simulations show "hilly" granulation with dark bands on the far side, bright granulation walls, and striated faculae, similar to observations. At disk center G-band bright points are flanked by dark lanes. The increased brightness in magnetic elements is due to their lower density compared with the surrounding intergranular medium. One thus sees deeper layers where the temperature is higher. At a given geometric height, the magnetic elements are cooler than the surrounding medium. In the G band, the contrast is further increased by the destruction of CH in the low-density magnetic elements. The optical depth unity surface is very corrugated. Bright granules have their continuum optical depth unity 80 km above the mean surface, the magnetic elements 200-300 km below. The horizontal temperature gradient is especially large next to flux concentrations. When viewed at an angle, the deep magnetic elements' optical surface is hidden by the granules and the bright points are no longer visible, except where the "magnetic valleys" are aligned with the line of sight. Toward the limb, the low density in the strong magnetic elements causes unit line-of-sight optical depth to occur deeper in the granule walls behind than for rays not going through magnetic elements, and variations in the field strength produce a striated appearance in the bright granule walls.
The genus Salfacarus ( Acari : Opilioacarida ) in Madagascar

The opilioacarid genus Salfacarus in Madagascar is revised, with description of four new species, S. antsirananensis, S. kirindiensis, S. mahafaliensis, and S. ranobensis, and a new delimitation for the type species, S. legendrei. Salfacarus is widespread in Madagascar but individual species appear restricted to relatively small areas. A key to the adults of Salfacarus in Madagascar is provided.
The association of statin use with reduced incidence of venous thromboembolism: a population-based cohort study

Objectives Venous thromboembolism (VTE) continues to be a frequent medical emergency requiring rapid recognition so as to reach diagnosis and initiate anticoagulation therapy. The use of statins in addition to reducing the incidence of arterial thrombosis for decreasing the incidence and reoccurrence of VTE is reported. The aim of our study was to explore the association between statin usage and the incidence of new VTE at the population level during a 10-year follow-up. Design Population-based historic cohort. Setting The Health 2000 Survey was based on a nationally representative sample. Participants 8028 individuals aged 30 years or over in Finland. Primary and secondary outcome measures The primary end point event was the first ever hospitalisation due to one of the following causes: pulmonary embolism (International Classification of Diseases-10 I26), cerebral venous non-pyogenic thrombosis (I63.6), or venous thrombosis (I80.9–189). Results The preselected explanatory variables applied to the Poisson regression model were statin usage (no/yes) during follow-up (2000–2011) and several baseline data (age, sex; usage of blood glucose lowering drugs, vitamin K antagonists and antiplatelet agents). We observed 136 VTE events, the incidence of 1.72 (95% CI 1.44 to 2.04) per 1000 person-years. Current statin usage did not associate with the incidence of VTE according to the univariate model (rate ratio (RR) 0.93, 0.56 to 1.52), but when adjusted with baseline variables (age, sex, medications) the RR declined to 0.60 (0.36 to 1.00, p=0.04). Conclusions Statin use offers protection against first ever VTE events and appears as a primary prevention tool in patients without anticoagulation or antiplatelet medication.
Haemopoietic colony‐forming cells from peripheral blood stem cells harvests: cytokine requirements and lineage potential

Summary. We have measured the in vitro growth requirements of progenitor cells released into the blood of cancer patients following administration of chemotherapy and cytokines. In order to distinguish the direct effects of cytokines on progenitors from those activating acessory cells, we have comparied clonogenic grwoth before and after CD34‐positive selection of progenitors, in serum‐free conditions. CD34 selection had little effect on the cytokine requirements of erythroid colony‐forming cells and single cytokines, particularly interleukin‐3, could support considerable colony growth in both mononulear and CD34+ cell suspensions. Optimal erythroid colony grwoth, however, usually required the addition of a combination of stem cells factor and interleukin‐3, in addition to erythoropoietin, which was was always required. Maximal numbers of granulocyte monocyte progenitors in mononuclear cell cultures, could be achieved with a mixture of stem cell factros, ionterleukin‐3 and granulocyte‐monocyte colony stimulating factor. How ever, after CD34 selection, full myeloid colony growth was only achieved when granulocyte colony stimulating factor was added to the above mixture. This presumably reflects loss of accessory cells, during CD34 selection, which produced this cytokine. When transplanted after 8 d of culutre. 16/22 myeloid colonies from erythorpoietin‐free cultures of peripheral blood stem cell harvests, could generate secondary multipotential. However, surface marker analysis of individual erythroid colonies revealed only the occasional presence of granulocytes and monocytes. These date demonstrate that cytokine mixtures are required for optimal colony growth, particuarly after CD34 selection, a nd that most mobilizied, blood clonogenic cells are multipotential.