Miracle-dz/UniFAR-FTUs huggingface dataset:
Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings

Covering a directed graph by a Hamiltonian path or a set of words by a superstring belong to well studied optimisation problems that prove difficult to approx-imate. Indeed, the Maximum Asymmetric Travelling Salesman Problem (Max-ATSP), which asks for a Hamiltonian path of maximum weight covering a digraph, and the Shortest Superstring Problem (SSP), which, for a finite language P := {s 1 , . , s p }, searches for a string of minimal length having each input word as a substring, are both Max-SNP hard. Finding a short superstring requires to choose a permutation of words and the associated overlaps to minimise the superstring length or to maximise the compression of P . Hence, a strong relation exists between Max-ATSP and SSP since solving Max-ATSP on the Overlap Graph for P gives a shortest superstring. Numerous works have designed algorithms that improve the approximation ratio but are increasingly complex. Often, these rely on solving the pendant problems where the cover is made of cycles instead of single path (Max-CC and SCCS). Finally, the greedy algorithm remains an attractive solution for its simplicity and ease of implementation. Its approximation ratios have been obtained by different approaches. In a seminal but complex proof, Tarhio and Ukkonen showed that it achieves 1/2 compression ratio for Max-CC. Here, using the full power of subset systems, we provide a unified approach for proving simply the approximation ratio of a greedy algorithm for these four prob-lems. Especially, our proof for Maximal Compression shows that the Monge property suffices to derive the 1/2 tight bound.
The antioxidant, anticancer and anticoagulant activities of Acanthus ilicifolius L. roots and Lumnitzera racemosa Willd. leaves, from southeast coast of India. -

The present study was designed to evaluate and determine the phytochemical composition, antioxidant, anticancer and anticoagulant activities of the aqueous extracts of Acanthus ilicifolius roots and Lumnitzera racemosa leaves from Pichavaram mangrove forest, Tamil Nadu, India based on folklore knowledge. The preliminary phytochemical screening revealed the presence of the following classes of bioactive compounds: phenols, flavonoids, alkaloids, terpenoids, sterols, tannins, carbohydrates, cardiac glycosides, saponins and quinones. The total phenolic content was reported much higher as compared to the total flavonoid content mainly in the leaf extract of L.racemosa. This mostly contributes to the antioxidant power of the extracts, which is affirmed by the IC50 values of the crude extracts in the DPPH assay, which was lower than the ABTS assay. The FRAP assay also exhibited a consistent increase in reducing ability with increase in the concentration which is indicative of the extractâ€™s antioxidant potential. The extracts were also reported to exhibit in vitro cytotoxicity and apoptosis inducing ability in Hep G2 cancer cells. And the anticoagulant study conducted provided a first hand report for the plants exhibiting the property. However, further studies must be conducted for secondary metabolite profiling to decipher and clarify the compound(s) responsible for the reported activities of the plant crude extracts.
Laboratory confirmation of meningococcal disease in Scotland, 1993-9.

AIMS To describe the laboratory confirmation of meningococcal disease, using culture and non-culture based techniques, between 1993 and 1999 as part of a national service in Scotland. METHODS Samples from patients with suspected meningococcal disease in Scotland were analysed by culture and non-culture based techniques to gain a laboratory confirmation of disease. Data were analysed to establish the number of disease cases, the serogroups of the organisms involved, and the importance of the techniques used. RESULTS Between 1993 and 1999, there was a total of 1749 notified cases of meningococcal disease in Scotland. Culture based methods provided a laboratory confirmation of 788 cases whereas non-culture techniques confirmed 461 cases. CONCLUSIONS Non-culture techniques were a useful addition to culture based techniques in Scotland and improved the dataset required for public health management, disease surveillance, and vaccine policy.
Characterization of the late-gene regulatory region of phage 21

A segment of Escherichia coli bacteriophage 21 DNA encoding the late-gene regulator, Q21, and the late-gene leader RNA segment was sequenced; its structure is similar to those of the related phages lambda and 82. The leader RNA is about 45 nucleotides long and consists essentially entirely of sequences encoding the p-independent terminator that is the putative target of the antitermination activity of Q21. Like the corresponding regions of lambda and 82, the 21 late-gene promoter segment encodes an early transcription pause in vitro, at about nucleotide 18, during which Q21 presumably acts to modify RNA polymerase. The 21 Q gene, cloned in isolation, is active on the late-gene leader segment in trans, and its purified product is active as an antiterminator in vitro; Q21 represents a third late-gene antiterminator, in addition to those of lambda and 82. There is little evident similarity in the primary sequences of the three Q genes.
The vascularly and luminally perfused small intestine in vitro: dissection technique and model system

The quantitative study in vitro of a wide range of intestinal functions is best achieved by perfusing the intestine simultaneously by the luminal and vascular routes. A comprehensive description is given of the dissections involved in preparing a selected segment of jejunum for such simultaneous perfusions. Attention is drawn to a number of occasional aberrant vascular structures which require special attention if successful perfusions are to be established. It is essential to restore the ATP and diphosphoglycerate concentrations of erythrocytes, and to assess their deformability, before incorporating them in the vascular perfusion medium. The perfusion equipment, the perfusion media and the general conduct of a perfusion experiment, are described.
Standardized and weighted time-dependent receiver operating characteristic curves to evaluate the intrinsic prognostic capacities of a marker by taking into account confounding factors

Time-dependent receiver operating characteristic curves allow to evaluate the capacity of a marker to discriminate between subjects who experience the event up to a given prognostic time from those who are free of this event. In this article, we propose an inverse probability weighting estimator of a standardized and weighted time-dependent receiver operating characteristic curve. This estimator provides a measure of the prognostic capacities by taking into account potential confounding factors. We illustrate the robustness of the estimator by a simulation-based study and its usefulness by two applications in kidney transplantation.
Topological dynamics of holins in programmed bacterial lysis

The fate of phage-infected bacteria is determined by the holin, a small membrane protein that triggers to disrupt the membrane at a programmed time, allowing a lysozyme to attack the cell wall. S2168, the holin of phage 21, has two transmembrane domains (TMDs) with a predicted N-in, C-in topology. Surprisingly, TMD1 of S2168 was found to be dispensable for function, to behave as a SAR (“signal-anchor-release”) domain in exiting the membrane to the periplasm, and to engage in homotypic interactions in the soluble phase. The departure of TMD1 from the bilayer coincides with the lethal triggering of the holin and is accelerated by membrane depolarization. Basic residues added at the N terminus of S2168 prevent the escape of TMD1 to the periplasm and block hole formation by TMD2. Lysis thus depends on dynamic topology, in that removal of the inhibitory TMD1 from the bilayer frees TMD2 for programmed formation of lethal membrane lesions.
Fetal exposure to excess glucocorticoid is unlikely to explain the effects of periconceptional undernutrition in sheep

Periconceptional undernutrition alters fetal growth, metabolism and endocrinology in late gestation. The underlying mechanisms remain uncertain, but fetal exposure to excess maternal glucocorticoids has been hypothesized. We investigated the effects of periconceptional undernutrition on maternal hypothalamic–pituitary–adrenal axis function and placental 11β‐hydroxysteroid dehydrogenase type 2 (11βHSD2) activity. Ewes received maintenance feed (N, n= 20) or decreased feed from −60 to +30 days from mating to achieve 15% weight loss after an initial 2‐day fast (UN, n= 21). Baseline plasma samples and arginine vasopressin (AVP)–corticotrophin‐releasing hormone (CRH) challenges were performed on days −61, −57, −29, −1, +29, 33, and 49 from mating (day 0). Maternal adrenal and placental tissue was collected at 50 days. Baseline plasma levels of adrenocorticotrophic hormone (ACTH) and cortisol decreased in the UN group (P < 0.0001). ACTH response to AVP–CRH was greater in UN ewes during undernutrition (P= 0.03) returning to normal levels after refeeding. Cortisol response to AVP–CRH was greater in UN ewes after the initial 2‐day fast, but thereafter decreased and was lower in UN ewes from mating until the end of the experiment (P= 0.007). ACTH receptor, StAR and p450c17 mRNA levels were down‐regulated in adrenal tissue from UN ewes. Placental 11βHSD2 activity was lower in UN than N ewes at 50 days (P= 0.014). Moderate periconceptional undernutrition results in decreased maternal plasma cortisol concentrations during undernutrition and after refeeding, and adrenal resistance to ACTH for at least 20 days after refeeding. Fetal exposure to excess maternal cortisol is unlikely during the period of undernutrition, but could occur later in gestation if maternal plasma cortisol levels return to normal while placental 11βHSD2 activity remains low.
Metabolic Syndrome Is Correlated With Carotid Atherosclerosis in Patients With Lupus Nephritis

Background:To investigate the prevalence of metabolic syndrome (MS) in patients with lupus nephritis (LN), and its correlation with carotid atherosclerosis. Methods:Two hundred ten patients with LN (age: 38.83 ± 12.41 years, 92.86% women) were enrolled. The control group included 150 lupus patients without nephritis and 200 age-matched healthy persons. The improved criteria in 2009 were used to calculate the prevalence of MS, and carotid artery ultrasound was used to detect plaque and intima-media thickness (IMT). The correlation between MS and carotid atherosclerosis in patients with LN was analyzed. Results:The prevalence of MS in patients with LN was 41.90%, which was significantly higher than that in lupus patients without nephritis (30.67%) and healthy controls (11.50%). LN patients with MS showed a significantly increased carotid plaque ratio (28.41% versus 17.21%, P < 0.05) and IMT value (0.74 ± 0.25 mm versus 0.64 ± 0.18 mm, P < 0.01). Stepwise multiple regression further confirmed that age (&bgr; = 0.026, P = 0.033), duration of disease (&bgr; = 0.057, P = 0.025) and MS (&bgr; = 0.074, P < 0.001) were independent risk factors that affected the carotid IMT value in patients with LN. Conclusions:The prevalence of MS was comparatively high in patients with LN and was significantly correlated with carotid atherosclerosis, indicating that MS screening might be useful in the prevention and treatment of carotid atherosclerosis in patients with LN.
Tumor‐inhibiting platinum(II) complexes with aminoalcohol ligands: Comparison of the mode of action by capillary electrophoresis and electrospray ionization‐mass spectrometry

Capillary electrophoresis (CE) was used as an assay for studying the interaction of (SP‐4‐2)‐bis[(R)‐(–)‐2‐aminobutanol)dichloroplatinum(II) (1) and (SP‐4‐2)bis(4‐aminobutanol)dichloroplatinum(II) (2) with guanosine 5'‐monophosphate (GMP). CE kinetic measurements carried out at two physiological pH levels indicated that upon increasing the pH, 1 showed an appreciable change in binding behavior, with the rate of binding increased for more than 10 times as expressed by apparent half‐life values of GMP (6.1 and 62.2 h at pH 6.0 and 7.4, respectively). The rate of GMP binding for 2 remained comparatively less affected by pH (half‐lives of 8.5 and 10.6 h, respectively). Regardless of the nature of platinum complex and pH, the reaction with GMP tends to be decelerated at increased chloride concentrations in solution, this effect being particularly pronounced when changing from 4 mM (intracellular level) to 100 mM (extracellular level). The kinetic differences of platinum complexes were characterized in terms of the respective GMP‐adducts structure, independently identified by means of off‐line electrospray ionization‐mass spectrometry. Also addressed was the interpretation of binding behavior as based on the structural features of the intact complexes, namely differing inclination to intramolecular chelation.
Hybrid Recommendation System

Recommendation systems are widely used in e-commerce companies like Amazon and Netflix to help users discover items that might interest them. Due to their wide applicability, recommendation systems have become an area of active research. We do a comparative study on the different algorithms used to do recommendation popularly and build a hybrid model out of them. Introduction Various algorithms for recommending choices to users have been used by companies involved in selling products and services online like E-commerce sites, movie renting sites, housing and restaurant recommendation sites etc. These algorithms can be majorly classified into two types content-based techniques and collaborative-filtering based techniques. The former rely on the computing the similarity of items based on the meta data provided about the items i.e. incase of movies data like the genre, date of release, IMDB rating etc. For example if the user has watched a lot of comic thrillers, he is recommended a suitable comic thriller. There are also demographic content based techniques which compute similar users based on their same demography to do recommendation. The collaborative filtering techniques rely on computing the similarity based upon similarity of the user ratings for multiple items i.e. if two users have liked similar movies in the past they are likely to have same preferences. In collaborative filtering, we will also look at the latest techniques which incorporate the factor of time while recommending products. This is very essential especially, in todays time when the users have way too many choices and their preferences change frequently over time. Dataset Used We will be using the MovieLens 100k dataset for testing and training purposes. The reason for using this particular dataset is that the data is made available by a reputed and trustworthy source (University of Minnesota) and contains the information about the movies and the demographic data for users which we require in our content-based analysis. Also, each of the user-item ratings has a timestamp as the ratings have been collected over a period of 7 months. The dataset contains 100,000 ratings from 943 MovieLens users on 1682 movies from September 19, 1997 through April 22, 1998. We will use 80k for training and 20k for validation wherever such a partition is required.
Efficient Multicore Algorithms For Identifying Biconnected Components

In this paper we design and implement an algorithm for finding the biconnected components of a given graph. Our algorithm is based on experimental evidence that finding the bridges of a graph is usually easier and faster in the parallel setting. We use this property to first decompose the graph into independent and maximal 2-edge-connected subgraphs. To identify the articulation points in these 2-edge connected subgraphs, we again convert this into a problem of finding the bridges on an auxiliary graph. It is interesting to note that during the conversion process, the size of the graph may increase. However, we show that this small increase in size and the run time is offset by the consideration that finding bridges is easier in a parallel setting. We implement our algorithm on an Intel i7 980X CPU running 12 threads. We show that our algorithm is on average 2.45x faster than the best known current algorithms implemented on the same platform. Finally, we extend our approach to dense graphs by applying the sparsification technique suggested by Cong and Bader in [7]. Â
HVLP: Hybrid visible light positioning of a mobile robot

In recent years energy efficient LEDs have become a commonplace lighting solution. It is possible to create an indoor positioning system (IPS) from existing lighting infrastructure by making minor modifications to the luminaire drivers. In this paper we develop and implement an IPS by augmenting the luminaires with collocated Zigbee radios. The Hybrid Visible Light Positioning (HVLP) system utilizes a two-stage process where it first localizes which room a mobile robot resides in, followed by estimating the robot's position within the room itself. Experimental results conducted in two adjacent rooms with dimensions 4.8 × 5.7 × 2.5, 4.8 × 3.3 × 2.5 show that the HVLP system attains a median error of 5.8 cm, which is a significant improvement on existing approaches.
A Fast Full Search Scheme for Rate-Distortion Optimization of Variable Block Size and Multi-frame Motion Estimation

Two new fast full search (FFS) methods are proposed which can improve the performance of the rate- distortion optimized video encoding process. The first method combines the concepts of both conventional sum of absolute difference (SAD) reuse method and row-based partial distortion search (PDS) together to make the performance largely better than these two conventional methods for variable block size motion estimation. The second method speeds up the multi-frame motion estimation process by using the previous results obtained in considered reference frames to set extra thresholds for rejecting search points sooner in reference frames. Furthermore, these two proposed methods can be easily combined to form a very effective motion compensation scheme. On average, a 62% and 52% reduction in terms of computational complexity of integer variable block size and multi-frame motion estimation can be achieved without any video quality degradation as compared with that of the conventional PDS and conventional SAD reuse method respectively.
Influence of HumDN1 VNTR polymorphism on DNASE1 expression in systemic lupus erythematosus and rheumatoid arthritis

The purpose of this study was to analyze the effect of the HumDN1 VNTR polymorphism on DNASE1 mRNA expression and enzyme activity in lupus (SLE) and rheumatoid arthritis (RA) compared to healthy control (HC). Kuwait subjects (n = 500) matched by age/gender/ethnicity were genotyped by fragment-analysis. DNASE1 expression was analysed using quantitative Real-Time-PCR and sera from subjects were screened for DNase1 reduction activity by ELISA. Allele and genotype distribution of HumDN1 VNTR revealed a significant association with susceptibility to SLE and RA (p < 0.05, OR > 1). Relative expression analysis revealed a significant increase in DNASE1 mRNA in SLE (p = 0.0001) and RA (p = 0.002) compared to HC. Stratification of subjects revealed, increased DNASE1 expression in SLE with 5/5 (p = 0.0001), 3/4 (p = 0.0001) and 3/5 genotype (p = 0.01). A reduction in DNASE1 expression was specifically observed in SLE with 4,4 genotype (p = 0.0004). RA patients with 3/4 genotype (p = 0.02) showed a significant increase in DNASE1 expression. Similarly a significant association was observed between DNase1 reduction activity and SLE (p = 0.0001). SLE patients with 3,4 (p = 0.0001) and 5,5 genotype (p = 0.0001) showed increased DNase1 reduction activity, while a lack of association was observed with RA. The present study is the first to reveal the effect of HumDN1 VNTR on DNASE1 expression in SLE and RA.
Temporal expression of cytokines and their receptors mRNAs in a neuropathic pain model

Proinflammatory mediators, such as tumor necrosis factor (TNF) &agr;, interleukin (IL)-1&bgr; and IL-6 have been found to play a key role in the propagation of persistent pain states. We investigated the temporal expressions of the mRNAs and the receptor mRNAs of TNF&agr;, IL-1&bgr; and IL-6 in rat dorsal root ganglia and spinal cord in a chronic constriction injury model of neuropathic pain. Our results show that the maximal induction of IL-6 mRNA occurred later and was more sustained than those of TNF&agr; and IL-1&bgr; mRNAs in the dorsal root ganglia and spinal cord following chronic injury. Receptors mRNAs, except TNF receptor 2 and gp130 mRNAs, showed temporal profiles that were similar to those of their cytokine mRNAs. Additionally, the induction of the mRNAs of cytokines and of their receptors in the dorsal root ganglia was more rapid than in the spinal cord.
Multilocus Sequence Typing of Campylobacter jejuni Isolates from Humans, Chickens, Raw Milk, and Environmental Water in Quebec, Canada

ABSTRACT Molecular strain typing is essential for deciphering the epidemiology of Campylobacter jejuni infections. We applied two different methods, multilocus sequence typing (MLST) and analysis of the flaA short variable repeat (SVR), to 289 isolates (163 human, 56 chicken, 34 raw milk, and 36 environmental water isolates) collected in the province of Québec, Canada, over 3 years; in addition, the analysis included the pulsed-field gel electrophoresis (PFGE) typing results for a subset of 131 isolates studied previously. MLST defined 96 sequence types (STs) and 20 clonal complexes (CCs), including 49 STs (73 isolates, 25%) and 39 alleles not previously documented in an international database. The frequency of new STs was significantly higher among water isolates than among isolates from other sources (18/36 [50%] and 55/253 [22%], respectively; P < 0.001). Nine of the 10 most prevalent CCs included isolates from humans and at least one other source; five CCs comprised exclusively or mostly human and chicken isolates. However, water and milk were the predominant nonhuman sources among the remaining CCs, suggesting that sporadic C. jejuni infections in humans may frequently arise from sources other than chickens. All three typing systems were discriminatory (discriminatory index > 0.9). Among 131 isolates analyzed by PFGE, each of the 20 types represented by two or more isolates corresponded to a single CC. In contrast, among the 14 most prevalent types detected by analysis of the flaA SVR (5 to 27 isolates each), 8 (57%) included isolates that represented multiple different CCs. The basis for these discordant results was uncertain. Antimicrobial resistance was randomly distributed among the CCs and appeared to be more closely related to the source of an isolate than its genotype. Although MLST is labor-intensive and expensive, it remains the single best method for the genotyping of C. jejuni isolates and deciphering the epidemiologic relationships among isolates.