Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Evaluation on State of the Art Sequential Pattern Mining Algorithms

Data mining refers to extracting or mining knowledge from large amounts of data. Among the various data mining tasks sequential pattern mining is one of the most important tasks. It has broad applications in several domains such as the analysis of customer purchase patterns, web access patterns, seismologic data, and weather observations. Sequential pattern mining consists of mining subsequences that appear frequently in a set of sequences. Sequential pattern mining was first introduced by Rakesh Agarwal and Ramakrishnan Srikant in 1995. Many novel approaches for sequential pattern mining were proposed like Apriori, AprioriALL, GSP, SPADE, SPAM and PrefixSpan. In this paper, the performance of state-of-the-art sequential pattern mining algorithms PrefixSpan and SPAM is evaluated. "From the comprehensive experiments what have been done several phenomena were observed which are different from the traditional standpoint will be explained in this paper. "
Distribution and diversity of amphibians in Albania: New data and foundations of a comprehensive database

Albania is part of the Mediterranean biodiversity hotspot. Yet its amphibian fauna is poorly known due to little scientific exploration during the long political isolation of the country. To fill this gap, we constructed a georeferenced database with occurrences of all known amphibian species based on records from published sources and personal data collected during expeditions to poorly known areas. Our database includes 1097 records of 16 species collected between 1920 and 2017. Based on aggregated records, we analysed richness patterns of amphibians in 10 × 10 km grid cells as a function of altitude, climate, land cover diversity and distance from the sea. The mean number of species per cell was 1.8 ± 0.11 S.E. (maximum: 10 species) and at least one species occurred in 238 of the 349 cells. Sampling effort was uneven and sampling hotspots were mostly in popular sites of natural heritage. Cells with high amphibian diversity were near the Prokletije Mountains in the North-West, near Lura, Korab and Grammos Mountains and Ohrid and Prespa Lakes in the East, and near Cikes Mountains and in coastal areas of Vlore in the South-West. General linear models showed that the most important predictors of presence and diversity of amphibian species are land cover diversity and precipitation. Our study presents the largest database of amphibian occurrences in Albania to date that will be useful for biogeographical and ecological studies and for conservation purposes.
Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.
Bilexical Embeddings for Quality Estimation

This paper describes the SHEF submissions for the three sub-tasks of the Quality Estimation shared task of WMT17, namely: (i) a word-level prediction sys-tem using bilexical embeddings, (ii) a phrase-level labelling approach based on the word-level predictions, (iii) a sentence-level prediction system using word embeddings and handcrafted baseline features. Results are promising for the sentence-level approach, but still very pre-liminary for the other two levels.
The association of polymorphisms in nucleotide excision repair genes with ovarian cancer susceptibility

Nucleotide excision repair (NER), the core mechanism of DNA repair pathway, was commonly used to maintain genomic stability and prevent tumorigenesis. Previous investigations have demonstrated that single nucleotide polymorphisms (SNPs) of NER pathway genes were associated with various types of cancer. However, there was no research elucidating the genetic association of entire NER pathway with ovarian cancer susceptibility. Therefore, we conducted genotyping for 17 SNPs of six NER core genes (XPA, XPC, XPG, ERCC1, ERCC2, and ERCC4) in 89 ovarian cancer cases and 356 cancer-free controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to describe the strength of association. The result showed that both ERCC1 rs11615 and XPC rs2228000 were significantly associated with reduced risk of ovarian cancer under dominant genetic model (adjusted OR = 0.35, 95% CI = 0.20–0.61, P=0.0002 and adjusted OR = 0.49, 95% CI = 0.30–0.81, P=0.005 respectively). In addition, XPC rs2228001 and ERCC2 rs238406 had statistically significant association with the increased risk of ovarian cancer under dominant genetic model (adjusted OR = 1.72, 95% CI = 1.02–2.92, P=0.043 and adjusted OR = 2.07, 95% CI = 1.07–4.01, P=0.032 respectively). ERCC1 rs3212986 were related with the increased risk of ovarian cancer under recessive model (adjusted OR = 2.40, 95% CI = 1.30–4.44, P=0.005). In conclusion, our results indicated that ERCC1, XPC and ERCC2 might influence ovarian cancer susceptibility. Further research with large sample size is warranted to validate the reliability and accuracy of our results.
A surface plasmon resonance assay for characterisation and epitope mapping of anti‐GLP‐1 antibodies

The incretin hormone glucagon‐like peptide‐1 (GLP‐1) has been subject to substantial pharmaceutical research regarding the treatment of type 2 diabetes mellitus. However, quantification of GLP‐1 levels remains complicated due to the low circulation concentration and concurrent existence of numerous metabolites, homologous peptides, and potentially introduced GLP‐1 receptor agonists. Surface plasmon resonance (SPR) facilitates real‐time monitoring allowing a more detailed characterisation of the interaction compared with conventional enzyme‐linked immunosorbent assays (ELISA). In this paper, we describe the development of the first SPR assays for characterisation of anti‐GLP‐1 antibodies for ELISA purposes. Binding responses were obtained on covalently immobilised anti‐GLP‐1 antibodies at 12°C, 25°C, and 40°C and fitted to a biomolecular (1:1) interaction model showing association rates of 1.01 × 103 to 4.54 × 103 M−1 s−1 and dissociation rates of 3.56 × 10−5 to 1.56 × 10−3 s−1 leading to affinities of 35.2 to 344 nM, depending on the temperature. Determination of thermodynamic properties revealed an enthalpy driven interaction (ΔH < ΔS < 0) with higher affinities at lower temperatures due to the formation and stabilisation of hydrogen bonds within the binding site primarily composed of polar amino acids (ΔCp < 0). Pair‐wise epitope mapping was performed on captured anti‐GLP‐1 antibodies followed by subsequent interaction with GLP‐1 (7‐36) and other anti‐GLP‐1 antibodies. A global evaluation of every binding response led to an epitope map elucidating the potential of various anti‐GLP‐1 antibody pairs for sandwich ELISA and hence pinpointing the optimal antibody combinations. The SPR assays proved capable of providing vital information for ELISA development endorsing it as a useful optimisation tool.
Local yield stress statistics in model amorphous solids.

We develop and extend a method presented by Patinet, Vandembroucq, and Falk [Phys. Rev. Lett. 117, 045501 (2016)PRLTAO0031-900710.1103/PhysRevLett.117. 045501] to compute the local yield stresses at the atomic scale in model two-dimensional Lennard-Jones glasses produced via differing quench protocols. This technique allows us to sample the plastic rearrangements in a nonperturbative manner for different loading directions on a well-controlled length scale. Plastic activity upon shearing correlates strongly with the locations of low yield stresses in the quenched states. This correlation is higher in more structurally relaxed systems. The distribution of local yield stresses is also shown to strongly depend on the quench protocol: the more relaxed the glass, the higher the local plastic thresholds. Analysis of the magnitude of local plastic relaxations reveals that stress drops follow exponential distributions, justifying the hypothesis of an average characteristic amplitude often conjectured in mesoscopic or continuum models. The amplitude of the local plastic rearrangements increases on average with the yield stress, regardless of the system preparation. The local yield stress varies with the shear orientation tested and strongly correlates with the plastic rearrangement locations when the system is sheared correspondingly. It is thus argued that plastic rearrangements are the consequence of shear transformation zones encoded in the glass structure that possess weak slip planes along different orientations. Finally, we justify the length scale employed in this work and extract the yield threshold statistics as a function of the size of the probing zones. This method makes it possible to derive physically grounded models of plasticity for amorphous materials by directly revealing the relevant details of the shear transformation zones that mediate this process.
Biofilm infections between Scylla and Charybdis: interplay of host antimicrobial peptides and antibiotics

Purpose The aim of this study is to improve the anti-biofilm activity of antibiotics. We hypothesized that the antimicrobial peptide (AMP) complex of the host’s immune system can be used for this purpose and examined the assumption on model biofilms. Methods FLIP7, the AMP complex of the blowfly Calliphora vicina containing a combination of defensins, cecropins, diptericins and proline-rich peptides was isolated from the hemolymph of bacteria-challenged maggots. The complex interaction with antibiotics of various classes was studied in biofilm and planktonic cultures of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Acinetobacter baumannii by the checkerboard method using trimethyl tetrazolium chloride cell viability and crystal violet biofilm eradication assays supplemented with microscopic analysis. Results We found that FLIP7 demonstrated: high synergy (fractional inhibitory concentration index <0.25) with meropenem, amikacin, kanamycin, ampicillin, vancomycin and cefotaxime; synergy with clindamycin, erythromycin and chloramphenicol; additive interaction with oxacillin, tetracycline, ciprofloxacin and gentamicin; and no interaction with polymyxin B. The interaction in planktonic cell models was significantly weaker than in biofilms of the same strains. The analysis of the dose–effect curves pointed to persister cells as a likely target of FLIP7 synergistic effect. The biofilm eradication assay showed that the effect also caused total destruction of S. aureus and E. coli biofilm materials. The effect allowed reducing the effective anti-biofilm concentration of the antibiotic to a level well below the one clinically achievable (2–3 orders of magnitude in the case of meropenem, ampicillin, cefotaxime and oxacillin). Conclusion FLIP7 is a highly efficient host antimicrobial system helping antibiotics to overcome biofilm barriers through persisters’ sensitization and biofilm material destruction. It is promising for the treatment of biofilm infections as an adjuvant of various small-molecule antibiotics.
Estrogenic Activity of Persistent Organic Pollutants and Parabens Based on the Stably Transfected Human Estrogen Receptor-α Transcriptional Activation Assay (OECD TG 455)

Screening of estrogenic activity on dichloro diphenyl trichloroethane (DDT), dichloro diphenyl dichloro ethylene (DDE), dieldrin, heptachlor, aldrin, chlordane, lindane, polybrominated diphenyl ethers (PBDE) and parabens was compared using Organization for Economic Cooperation and Development (OECD) test guideline 455 (TG455). The estrogenic activity of DDT was 58,000-fold (PC_50, 1.67 × 10^−6M) less than 17ß-estradiol(E_2) (PC_50, 2.88×10^−11M) but DDE, dieldrin, heptachlor, aldrin, chlordane, lindane and PBDE did not show any estrogenic activity in this assay system. In the case of paraben compounds, the rank of relative transcriptional activation (logRTA) was butyl paraben −1.63752 (PC_50, 1.25 × 10^−7M) > isobutyl paraben −2.34008 (PC_50, 6.3 × 10^−7M) > ethyl paraben -2.64016 (PC_50, 1.26 × 10^−6M) > isopro-pyl paraben −2.73993 (PC_50, 1.58 × 10^−6M) > propyl paraben -2.84164 (PC_50, 2.0 × 10^−6M). Our data suggest that OECD test guideline TG455 may be useful as a screening tool for potential endocrine disruptors.
Predictors of colorectal neoplasia after polypectomy: based on initial and consecutive findings.

BACKGROUND Colorectal adenoma patients are kept under surveillance because of the risk of developing metachronous neoplasia. The aim is to determine predictors of neoplasia development after polypectomy. METHODS It is an observational cohort study. 433 Patients who had ≥1 adenoma removed between 1988 and 2004 were included, with follow-up until 2010. Multivariate analysis of patient and adenoma characteristics was performed at initial colonoscopy and at consecutive positive examinations. The main outcome measured was the development of metachronous (advanced) adenomas during follow-up. RESULTS Median follow-up was 85 months. Multivariate analysis identified male sex, ≥3 adenomas, high-grade dysplasia and age ≥55 years as risk factors for metachronous lesions at first surveillance. Analysis using life expectancy as a timescale showed ≥3 adenomas to be the only predictive factor. The time to second or third metachronous adenoma did not depend on the number of adenomas. Patients with ≥3 adenomas were five years older at the time of their first polypectomy compared with those with fewer adenomas, but of the same age at the first recurrence. Prevalence of high-grade dysplasia was associated with age and high-grade dysplasia in the prior adenoma independent of time interval. CONCLUSIONS Adenoma development after polypectomy occurs in a regular and repetitive way. Our data suggest that only the interval between the initial colonoscopy and the first follow-up colonoscopy should be based on initial findings, i.e. number of adenomas, and that subsequent colonoscopies can be planned at predetermined intervals.
Unsupervised Grounding of Textual Descriptions of Object Features and Actions in Video

We propose a novel method for learning visual concepts and their correspondence to the words of a natural language. The concepts and correspondences are jointly inferred from video clips depicting simple actions involving multiple objects, together with corresponding natural language commands that would elicit these actions. Individual objects are first detected, together with quantitative measurements of their colour, shape, location and motion. Visual concepts emerge from the co-occurrence of regions within a measurement space and words of the language. The method is evaluated on a set of videos generated automatically using computer graphics from a database of initial and goal configurations of objects. Each video is annotated with multiple commands in natural language obtained from human annotators using crowd sourcing.
Nerve Root Compression Increases Spinal Astrocytic Vimentin in Parallel With Sustained Pain and Endothelial Vimentin in Association With Spinal Vascular Reestablishment

Study Design. Temporal immunohistochemistry analysis of spinal cord tissue from a rat model of cervical radiculopathy. Objective. The goal was to measure spinal endothelial and astrocytic vimentin expression after a painful nerve root compression to define spinal cellular expression of vimentin in the context of pain. Summary of Background Data. The intermediate filament, vimentin, is expressed in a variety of cell types in the spinal cord and is modulated in response to neural pathologies. Early after nerve root compression spinal astrocytes become activated and blood-spinal cord barrier (BSCB) breakdown occurs in parallel with development of pain-related behaviors; these spinal responses remain activated as does the presence of pain. In addition to vimentin, glial fibrillary acidic protein (GFAP) expression is a hallmark of astrocyte activation. In contrast, vascular endothelial cells down-regulate vimentin expression in parallel with vascular breakdown. It is not known whether spinal astrocytes and endothelial cells modulate their expression of vimentin in response to a painful neural injury. Methods. Mechanical hyperalgesia was measured and spinal cord tissue was harvested at days 1 and 7 after a unilateral nerve root compression in rats. Vimentin was coimmunolabeled with GFAP to label astrocytes and von Willebrand factor (VWF) for endothelial cells in the spinal cord on the side of injury. Results. Spinal astrocytic vimentin increases by day 7 after nerve root compression, corresponding to when mechanical hyperalgesia is maintained. Spinal endothelial vimentin increases as early as day 1 after a painful compression and is even more robust at day 7. Conclusion. The delayed elevation in spinal astrocytic vimentin corresponding to sustained mechanical hyperalgesia supports its having a relationship with pain maintenance. Further, since BSCB integrity has been shown to be reestablished by day 7 after a painful compression, endothelial expressed vimentin may help to fortify spinal vasculature contributing to BSCB stability. Level of Evidence: N/A
Origins of lifetime health around the time of conception: causes and consequences

Parental environmental factors, including diet, body composition, metabolism, and stress, affect the health and chronic disease risk of people throughout their lives, as captured in the Developmental Origins of Health and Disease concept. Research across the epidemiological, clinical, and basic science fields has identified the period around conception as being crucial for the processes mediating parental influences on the health of the next generation. During this time, from the maturation of gametes through to early embryonic development, parental lifestyle can adversely influence long-term risks of offspring cardiovascular, metabolic, immune, and neurological morbidities, often termed developmental programming. We review periconceptional induction of disease risk from four broad exposures: maternal overnutrition and obesity; maternal undernutrition; related paternal factors; and the use of assisted reproductive treatment. Studies in both humans and animal models have demonstrated the underlying biological mechanisms, including epigenetic, cellular, physiological, and metabolic processes. We also present a meta-analysis of mouse paternal and maternal protein undernutrition that suggests distinct parental periconceptional contributions to postnatal outcomes. We propose that the evidence for periconceptional effects on lifetime health is now so compelling that it calls for new guidance on parental preparation for pregnancy, beginning before conception, to protect the health of offspring.
Resilient large-scale cognitive radio ad hoc networking using path-time codes

Cognitive radio ad hoc networks (CRAHNs) emerge as a spectrum efficient networking technology to enable autonomous machine-to-machine communication among massive number of IoT devices. However, spectrum sharing results in opportunistic links and CRAHN becomes a kind of opportunistic networks. To reduce latency in CRAHN and to achieve overall spectrum efficiency by avoiding tremendous feedback signaling, CRAHNs of open-loop physical layer transmission open a new avenue under massive operations. The new technology challenge associated with such new CRAHNs lies in error control with only local networking information without relying on feedback control over each opportunistic link. Path-time codes virtually realizing multi-input-multi-output over network layer have been innovated to resolve such a dilemma. However, effective multipath routing considering interference remains unclear. In this paper, be taking network topological factors and interference into account, we analytically derive SINR approximations to design power control and multi-path greedy routing. By stochastic geometry analysis, we also show that the resilient operation for large-scale CRAHNs can be facilitated with the aid of path-time codes.
Loading Hydrogen and Helium in the Diamond Anvil Cell: the First 30 Years

The combination of three major innovations have helped the advent of current high pressure physics, which aims at revealing the properties of matter in the multi-100 GPa range as finely as if under ambient pressure. Namely: the invention of the diamond anvil cell in 1958, 1 the loading of helium in 1979, 2 and the use of third generation synchrotrons, in the mid 80’s. The results on dense hydrogen and helium certainly exemplify what hence has been achieved. I was very fortunate to do my research training under the supervision of J. M. Besson after he had just achieved the loading of helium in the DAC. At the end of the 80’s, I was initiated to the use of synchrotron by H. K. Mao to measure the structural properties of helium under pressure, using the NSLS facility. Later we have been among the first users of the 3rd generation synchrotron source, ESRF, to measure the equation of state of dense hydrogen. 3 In my presentation, I will review what have been the important questions motivating high pressure studies on hydrogen & helium during 30 years, what kind of technical developments were required, which results were disclosed by us and others and what are the challenges for the next ten years.