Miracle-dz/UniFAR-FTUs huggingface dataset:
The probabilistic analysis of a greedy satisfiability algorithm

On input a random 3‐CNF formula of clauses‐to‐variables ratio r3 applies repeatedly the following simple heuristic: Set to True a literal that appears in the maximum number of clauses, irrespective of their size and the number of occurrences of the negation of the literal (ties are broken randomly; 1‐clauses when they appear get priority). We prove that for r3 < 3.42 this heuristic succeeds with probability asymptotically bounded away from zero. Previously, heuristics of increasing sophistication were shown to succeed for r3 < 3.26. We improve up to r3 < 3.52 by further exploiting the degree of the negation of the evaluated to True literal. © 2005 Wiley Periodicals, Inc. Random Struct. Alg. , 2006
Using re-ranking to boost deep learning based community question retrieval

The current study presents a two-stage question retrieval approach which, in the first phase, retrieves similar questions for a given query using a deep learning based approach and in the second phase, re-ranks initially retrieved questions on the basis of inter-question similarities. The suggested deep learning based approach is trained using several surface features of texts and the associated weights are pre-trained using a deep generative model for better initialization. The proposed retrieval model outperforms standard baseline question retrieval approaches. The proposed re-ranking approach performs inference over a similarity graph constructed with the initially retrieved questions and re-ranks the questions based on their similarity with other relevant questions. Suggested re-ranking approach significantly improves the precision for the retrieval task.
Revealing information while preserving privacy

We examine the tradeoff between privacy and usability of statistical databases. We model a statistical database by an n-bit string d1,. ,dn, with a query being a subset q ⊆ [n] to be answered by Σiεq di. Our main result is a polynomial reconstruction algorithm of data from noisy (perturbed) subset sums. Applying this reconstruction algorithm to statistical databases we show that in order to achieve privacy one has to add perturbation of magnitude (Ω√n). That is, smaller perturbation always results in a strong violation of privacy. We show that this result is tight by exemplifying access algorithms for statistical databases that preserve privacy while adding perturbation of magnitude Õ(√n). For time-T bounded adversaries we demonstrate a privacypreserving access algorithm whose perturbation magnitude is ≈ √T.
The surface structure of Escherichia coli.

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Cell Cycle Defects Contribute to a Block in Hormone-induced Mammary Gland Proliferation in CCAAT/Enhancer-binding Protein (C/EBPβ)-null Mice*

In contrast to hormone-dependent breast cancer, steroid hormone-induced proliferation in the normal mammary gland does not occur in the steroid-receptor positive cells but rather in adjacent cells via paracrine signaling involving several local growth factors. To help elucidate the mechanisms involved in the block in proliferation in hormone-receptor positive cells, we have utilized a CCAAT/enhancer binding protein (C/EBPβ)-null mouse model. Loss of this transcription factor results in increased steroid and prolactin receptor expression concomitant with a 10-fold decrease in proliferation in response to pregnancy hormones. To determine the basis for this decrease, several markers of cell cycle progression were analyzed in wild type and C/EBPβ-null mammary epithelial cells (MECs). These studies indicated that cell cycle progression in C/EBPβ-null MECs is blocked at the G1/S transition. C/EBPβ-null mammary glands display substantially increased levels of the activated form of transforming growth factor β, a potent inhibitor of epithelial cell proliferation, as well as increased downstream Smad2 expression and signaling. While cyclin D1 levels were equivalent, cyclin E expression was markedly reduced in C/EBPβ-null as compared with wildtype MECs. In addition, increased p27 stability and retention in the nucleus and decreased levels of the cdc25a phosphatase contributed to a significant loss of cdk2 kinase activity. Collectively, these changes prevent C/EBPβ-null mammary epithelial cells from responding to hormone-induced proliferative signals.
Context Effects in Word Recognition

This study investigated whether a prior context influenced lexical access as indexed by participants' electrophysiological response in the N1 from 132 to 192 ms poststimulus. Ambiguous, high-frequency (HF), and low-frequency (LF) words were presented in neutral and biasing contexts. Event-related potentials (ERPs) for ambiguous words were compared with those for unambiguous HF (word form) and LF (word meaning) control words. Word frequency effects in the N1 extended previous ERP findings. A marginal effect of context for LF words provided electrophysiological support for the context-by-frequency interaction shown in reaction time paradigms. In neutral context, responses to ambiguous words were comparable to responses to HF words, and in biasing context (where context instantiated the subordinate sense), responses to ambiguous words were comparable to responses to LF words. The results establish temporal parameters for the early operation of context in lexical access. These constraints are more consistent with an interactive than a modular account.
Avenues for entry of peripherally administered protein to the central nervous system in mouse, rat, and squirrel monkey

Pathways traversed by peripherally administered protein tracers for entry to the mammalian brain were investigated by light and electron microscopy. Native horseradish peroxidase (HRP) and wheat germ agglutinin (WGA) conjugated to peroxidase were administered intranasally, intravenously, or intraventricularly to mice; native HRP was delivered intranasally or intravenously to rats and squirrel monkeys. Unlike WGA‐HRP, native HRP administered intranasally passed freely through intercellular junctions of the olfactory epithelia to reach the olfactory bulbs of the CNS extracelluarly within 45–90 minutes in all species. The olfactory epithelium labeled with intravenously delivered HRP, which readily escaped vasculature supplying this epithelium. Blood‐borne peroxidase also exited fenestrated vessels of the dura mater and circumventricular organs. This HRP in the mouse, but not in the other species, passed from the dura mater through patent intercellular junctions within the arachnoid mater; in time, peroxidase reaction product in the mouse brain was associated with the pial surface, the Virchow‐Robin spaces of vessels penetrating the pial surface, perivascular clefts, and with phagocytic pericytes located on the abluminal surface of superficial and deep cerebral microvasculature. Blood‐borne HRP was endocytosed avidly at the luminal face of the cerebral endothelium in all species. WGA‐HRP and native HRP delivered intraventricularly to the mouse were not endocytosed appreciably at the abluminal surface of the endothelium; hence, the endocytosis of protein and internalization of cell surface membrane within the cerebral endothelium are vectorial. The low to non‐existent endocytic activity and internalization of membrane from the abluminal endothelial surface suggests that vesicular transport through the cerebral endothelium from blood to brain and from brain to blood does not occur. The extracellular pathways through which probe molecules enter the mammalian brain offer potential routes of passage for blood‐borne and airborne toxic, carcinogenic, infectious, and neurotoxic agents and addictive drugs, and for the delivery of chemotherapeutic agents to combat CNS infections and deficiency states. Methodological considerations are discussed for the interpretation of data derived from application of peroxidase to study the blood brain barrier.
A new control volume method for calculating valvular regurgitation.

BACKGROUND The purpose of the present study was to develop a new method of measuring heart valvular regurgitation based on control volume theory and to verify its accuracy in vitro and in vivo. Current methods of quantifying valvular regurgitation rely too much on assumptions about the flow field and therefore are difficult to apply in vivo. In particular, the proximal isovelocity surface area (PISA) method oversimplifies the proximal velocity field by assuming hemispherical isovelocity contours proximal to the orifice. This severely limits the applicability of the PISA method. Use of the basic control volume theory, however, removes the need to assume the manner in which the proximal flow accelerates toward the regurgitant orifice, the shape and size of the orifice, the shape of the orifice plate, and the non-newtonian behavior of the fluid. Apart from a correction that is necessary if the orifice plate is moving, the control volume method assumes only the incompressibility of the fluid and therefore is a potentially more accurate approach. In addition, the use of magnetic resonance imaging (MRI) precludes the need for an acoustic window. METHODS AND RESULTS MRI has been used to measure the three-dimensional velocity field proximal to regurgitant orifices, including single and multiple orifices and a cone-shaped orifice plate. Both steady (0 to 7.5 L/min) and pulsatile (2 and 3 L/min) flows were used. By intergrating this velocity over a control volume surrounding the orifice, we calculated the flow rate through the orifice. As a validation, the cardiac output of a 50-kg pig also was measured and was compared with thermodilution measurements. It was found that MRI could be used to measure the three-dimensional flow proximal to regurgitant orifices. This enabled the calculation of the flow rate through the orifice by integrating the velocity over the surface of a control volume covering the orifice. This flow rate correlated well with the actual rate (0.992; correlation line slope, 1.01). Care had to be taken, however, to exclude from the integration regions of aliased velocity. The cardiac output of the pig measured using MRI was in close agreement with the themodilution measurements. CONCLUSIONS Our new method of measuring valvular regurgitation has been shown to be very accurate in vitro and in vivo and therefore is a potentially accurate way to quantify valvular regurgitation.
Reasons Underlying Treatment Preferences Between Sertraline and Prolonged Exposure in Posttraumatic Stress Disorder

Individuals with posttraumatic stress disorder (PTSD) often wait years before seeking treatment. Improving treatment initiation and adherence requires a better understanding of patient beliefs that lead to treatment preferences. Using a treatment-seeking sample (N = 200) with chronic PTSD, qualitative reasons underlying treatment preferences for either prolonged exposure (PE) or sertraline (SER) were examined. Reasons for treatment preference primarily focused on how the treatment was perceived to reduce PTSD symptoms rather than practical ones. The patients were more positive about PE than SER. Individual differences did not reliably predict underlying preference reasons, suggesting that what makes a treatment desirable is not strongly determined by current functioning, treatment, or trauma history. Taken together, this information is critical for treatment providers, arguing for enhancing psychoeducation about how treatment works and acknowledging preexisting biases against pharmacotherapy for PTSD that should be addressed. This knowledge has the potential to optimize and better personalize
The changing accretion states of the intermediate polar MU Camelopardalis

Aims. We study the timing and spectral properties of the intermediate polar MU Camelopardalis (1RXS J062518.2+733433) to determine the accretion modes and the accretion geometry from multi-wavelength, multi-epoch observational data. Methods. Light curves in different observed energy ranges (optical, UV, X-ray) are extracted. The timescales of variability in these light curves are determined using Analysis of Variance. Phase-resolved X-ray spectra are created with respect to the most prominent detected periodicities and each fitted with an identical model, to quantify the differences in the fitted components. Results. The published tentative value for the spin period is unambiguously identified with the rotation period of the white dwarf. We detect a distinct soft X-ray component that can be reproduced well by a black body. The analysis of data obtained at different epochs demonstrates that the system is changing its accretion geometry from disk-dominated to a combination of disk- plus stream-dominated, accompanied with a significant change in brightness at optical wavelengths.
Rapid early-stage microarchitecture design using predictive models

The early-stage design of a new microprocessor involves the evaluation of a wide range of benchmarks across a large number of architectural configurations. Several methods are used to cut down on the required simulation time. Typically, however, existing approaches fail to capture true program behaviour accurately and require a non-negligible number of training simulations to be run. We address these problems by developing a machine learning model that predicts the mean of any given metric, e.g. cycles or energy, across a range of programs, for any microarchitectural configuration. It works by combining only the most representative programs from the benchmark suite based on their behaviour in the design space under consideration. We use our model to predict the mean performance, energy, energy-delay (ED) and energy-delay-squared (EDD) of the SPEC CPU 2000 and MiBench benchmark suites within our design space. We achieve the same level of accuracy as two state-of-the-art prediction techniques but require five times fewer training simulations. Furthermore, our technique is scalable and we show that, asymptotically, it requires an order of magnitude fewer simulations than these existing approaches.
Carbohydrate and lignin partitioning in switchgrass (Panicum virgatum L.) biomass as a bioenergy feedstock.

Approaching switchgrass (Panicum virgatum L.) as a multifunctional energy plant, it is important to comprehensively study the composition and partitioning of organic substances in the biomass. The character of carbohydrates and lignin concentration variation was assessed in switchgrass biomass cut at two maturity stages (heading and seed filling) in the first and second harvest years. Quality components partitioning in the biomass of aboveground plant parts was examined in leaves, stems and panicles of the most productive switchgrass accessions cut at seed filling. The concentrations of lignocellulose (NDF), cellulose (Cel), sum of structural carbohydrates (holocellulose – HoCel), sum of nonstructural and structural carbohydrates (ΣCH2O) and lignin in switchgrass biomass of both plant development stages in the second harvest year were significantly higher, whereas an average hemicellulose (HCel) concentration was significantly lower compared with the respective parameters in the first harvest year. The concentrations of nonstructural carbohydrates (NSC) and their individual fractions (water soluble carbohydrates (WSC) and starch) in biomass were similar both in the first and second harvest years. The concentrations of NDF, Cel, HoCel and ΣCH2O and particularly lignin at seed filling were significantly higher compared with the respective data at heading in both harvest years. High lignin concentration (105 g kg-1 dry matter (DM)) in switchgrass biomass at seed filling in the second harvest year showed its great suitability for solid biofuel production. Considerable amount of ΣCH2O (693–742 g kg -1 DM) indicated that switchgrass biomass at this stage fits for the second-generation bioethanol production. At heading, switchgrass in the second harvest year produced quite a high NSC yield (an average 28.4 g plant-1) and low lignin output (an average 19.3 g plant-1), which is a favourable feature of feedstock for biogas production, biomass at seed filling is less suitable for that than at heading. Switchgrass plant part significantly (P < 0.01) affected the concentration of all biomass quality attributes tested, but did not affect HCel concentration. Accessions’ DM yield correlated positively with NDF (r = 0.781, P < 0.05), Cel (r = 0.882, P < 0.01) and lignin (r = 0.517) and negatively with WSC and NSC (r = −0.982, −0.959; P < 0.01).
Automatic Fuzzy Rules Generation Using Fuzzy Genetic Algorithm

To solve the problem which is hard to avoid the local optimal solution or slower population diversity when using genetic algorithm to generate the fuzzy rules in a fuzzy system, this paper proposes an automatic rule generation using fuzzy genetic algorithm. This algorithm utilizes the rules population diversity and evolutionary speed to automatically adjust the crossover rate and mutation rate based on fuzzy logic, which leads to the automatic control rules generation of a genetic fuzzy system. In addition, the performance indices of control system and how to evaluate the fitness function in genetic algorithm are also presented. Finally, simulation results demonstrate the proposed algorithm is practical and effective in applications.
Sensitivity of Candida albicans Germ Tubes and Biofilms to Photofrin-Mediated Phototoxicity

ABSTRACT Treatment of mucocutaneous and cutaneous Candida albicans infections with photosensitizing agents and light, termed photodynamic therapy (PDT), offers an alternative to conventional treatments. Initial studies using the clinically approved photosensitizer Photofrin demonstrated the susceptibility of C. albicans to its photodynamic effects. In the present study, we have further refined parameters for Photofrin-mediated photodynamic action against C. albicans and examined whether mechanisms commonly used by microorganisms to subvert either antimicrobial oxidative defenses or antimicrobial therapy, including biofilm formation, were operative. In buffer and defined medium, germ tubes preloaded with Photofrin retained their photosensitivity for up to 2 hours, indicating the absence of degradation or export of Photofrin by the organism. The addition of serum resulted in a gradual loss of photosensitivity over 2 hours. In contrast to an adaptive response by germ tubes to oxidative stress by hydrogen peroxide, there was no adaptive response to singlet oxygen-mediated stress by photodynamic action. C. albicans biofilms were sensitive to Photofrin-mediated phototoxicity in a dose-dependent manner. Finally, the metabolic activity of C. albicans biofilms following photodynamic insult was significantly lower than that of biofilms treated with amphotericin B for the same time period. These results demonstrate that several of the mechanisms microorganisms use to subvert either antimicrobial oxidative defenses or antimicrobial therapy are apparently not operative during Photofrin-mediated photodynamic treatment of C. albicans. These observations provide support and rationale for the continued investigation of PDT as an adjunctive, or possibly alternative, mode of therapy against cutaneous and mucocutaneous candidiasis.
Social setting, intuition and experience in laboratory experiments interact to shape cooperative decision-making

Recent studies suggest that cooperative decision-making in one-shot interactions is a history-dependent dynamic process: promoting intuition versus deliberation typically has a positive effect on cooperation (dynamism) among people living in a cooperative setting and with no previous experience in economic games on cooperation (history dependence). Here, we report on a laboratory experiment exploring how these findings transfer to a non-cooperative setting. We find two major results: (i) promoting intuition versus deliberation has no effect on cooperative behaviour among inexperienced subjects living in a non-cooperative setting; (ii) experienced subjects cooperate more than inexperienced subjects, but only under time pressure. These results suggest that cooperation is a learning process, rather than an instinctive impulse or a self-controlled choice, and that experience operates primarily via the channel of intuition. Our findings shed further light on the cognitive basis of human cooperative decision-making and provide further support for the recently proposed social heuristics hypothesis.
Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes

The incidence of the autoimmune disease, type 1 diabetes (T1D), has increased dramatically over the last half century in many developed countries and is particularly high in Finland and other Nordic countries. Along with genetic predisposition, environmental factors are thought to play a critical role in this increase. As with other autoimmune diseases, the gut microbiome is thought to play a potential role in controlling progression to T1D in children with high genetic risk, but we know little about how the gut microbiome develops in children with high genetic risk for T1D. In this study, the early development of the gut microbiomes of 76 children at high genetic risk for T1D was determined using high-throughput 16S rRNA gene sequencing. Stool samples from children born in the same hospital in Turku, Finland were collected at monthly intervals beginning at 4–6 months after birth until 2.2 years of age. Of those 76 children, 29 seroconverted to T1D-related autoimmunity (cases) including 22 who later developed T1D, the remaining 47 subjects remained healthy (controls). While several significant compositional differences in low abundant species prior to seroconversion were found, one highly abundant group composed of two closely related species, Bacteroides dorei and Bacteroides vulgatus, was significantly higher in cases compared to controls prior to seroconversion. Metagenomic sequencing of samples high in the abundance of the B. dorei/vulgatus group before seroconversion, as well as longer 16S rRNA sequencing identified this group as Bacteroides dorei. The abundance of B. dorei peaked at 7.6 months in cases, over 8 months prior to the appearance of the first islet autoantibody, suggesting that early changes in the microbiome may be useful for predicting T1D autoimmunity in genetically susceptible infants. The cause of increased B. dorei abundance in cases is not known but its timing appears to coincide with the introduction of solid food.