Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient core computation in data exchange

Data exchange deals with inserting data from one database into another database having a different schema. Fagin et al. [2005] have shown that among the universal solutions of a solvable data exchange problem, there exists—up to isomorphism—a unique most compact one, “the core”, and have convincingly argued that this core should be the database to be materialized. They stated as an important open problem whether the core can be computed in polynomial time in the general setting where the mapping between the source and target schemas is given by source-to-target constraints that are arbitrary tuple generating dependencies (tgds) and target constraints consisting of equality generating dependencies (egds) and a weakly acyclic set of tgds. In this article, we solve this problem by developing new methods for efficiently computing the core of a universal solution. This positive result shows that data exchange based on cores is feasible and applicable in a very general setting. In addition to our main result, we use the method of hypertree decompositions to derive new algorithms and upper bounds for query containment checking and computing cores of arbitrary database instances. We also show that computing the core of a data exchange problem is fixed-parameter intractable with respect to a number of relevant parameters, and that computing cores is NP-complete if the rule bodies of target tgds are augmented by a special predicate that distinguishes a null value from a constant data value.
Similarity search and locality sensitive hashing using ternary content addressable memories

Similarity search methods are widely used as kernels in various data mining and machine learning applications including those in computational biology, web search/clustering. Nearest neighbor search (NNS) algorithms are often used to retrieve similar entries, given a query. While there exist efficient techniques for exact query lookup using hashing, similarity search using exact nearest neighbors suffers from a "curse of dimensionality", i.e. for high dimensional spaces, best known solutions offer little improvement over brute force search and thus are unsuitable for large scale streaming applications. Fast solutions to the approximate NNS problem include Locality Sensitive Hashing (LSH) based techniques, which need storage polynomial in n with exponent greater than 1, and query time sublinear, but still polynomial in n, where n is the size of the database. In this work we present a new technique of solving the approximate NNS problem in Euclidean space using a Ternary Content Addressable Memory (TCAM), which needs near linear space and has O(1) query time. In fact, this method also works around the best known lower bounds in the cell probe model for the query time using a data structure near linear in the size of the data base. TCAMs are high performance associative memories widely used in networking applications such as address lookups and access control lists. A TCAM can query for a bit vector within a database of ternary vectors, where every bit position represents 0, 1 or *. The * is a wild card representing either a 0 or a 1. We leverage TCAMs to design a variant of LSH, called Ternary Locality Sensitive Hashing (TLSH) wherein we hash database entries represented by vectors in the Euclidean space into {0,1,*}. By using the added functionality of a TLSH scheme with respect to the * character, we solve an instance of the approximate nearest neighbor problem with 1 TCAM access and storage nearly linear in the size of the database. We validate our claims with extensive simulations using both real world (Wikipedia) as well as synthetic (but illustrative) datasets. We observe that using a TCAM of width 288 bits, it is possible to solve the approximate NNS problem on a database of size 1 million points with high accuracy. Finally, we design an experiment with TCAMs within an enterprise ethernet switch (Cisco Catalyst 4500) to validate that TLSH can be used to perform 1.5 million queries per second per 1Gb/s port. We believe that this work can open new avenues in very high speed data mining.
Early sensitivity to sound and musical preferences and enjoyment in adolescents with autism spectrum disorders.

Children with autism spectrum disorders (ASD) frequently display unusual reactions to sound, ranging from idiosyncratic responses to avoidances. This atypical sensitivity often decreases over time, but little is known about how early avoidance of sounds might affect later enjoyment of auditory stimuli such as music. We surveyed children and adolescents with ASD, and an age-matched group of typically developing (TD) adolescents and the parents of both groups about early auditory sensitivities and musical experience, preferences, and enjoyment in later childhood and adolescence using an adaptation of the Queen’s University Music Questionnaire and the Salk and McGill Musical Inventory (SAMMI). Results showed that, although the group with ASD experienced much more auditory hypersensitivity than the TD group during childhood, there were no differences between groups in musical ability, memory, reproduction, creativity, or interest and emotional responsivity to music in later childhood and adolescence; both groups displayed a similar variety of genres in their musical preferences, with the exception that more participants with ASD reported classical as their favorite musical genre. We suggest that this latter pattern may arise from their lesser use of music as a mark of social affiliation and peer-group bonding, or from the increased complexity of classical music relative to other genres. We conclude that early childhood hypersensitivities to sound do not have detrimental effects on later enjoyment of music, although children and adolescents with ASD may use music in ways that differ from their TD peers.
Excretion and folding of plasmalemma function to accommodate alterations in guard cell volume during stomatal closure in Vicia faba L.

Stomatal movement results in large and repetitive changes in cell volume and consequently surface area. While endocytosis has been extensively studied and is thought to be a major mechanism for accommodating the volume changes as evidenced mainly by fluorescent labelling and confocal imaging, studies at the ultrastructural level in intact guard cells of stomata regulated by natural factors have never been reported. Here, it is reported that excretion and folding of the plasmalemma are critical for accommodating the volume alterations in intact guard cells in Vicia faba L. Using transmission electron microscopy in combination with laser confocal microscopy, it was observed that in fully opened stomata the plasmalemma was smooth and tightly adhered to the cell walls while a whole large vacuole appeared in the cell. In the closed stomata, besides vacuole fragmentation, endocytosis of the tonoplast rather than the plasmalemma commonly occurred. Importantly, in stomata where pore closure was induced by circadian rhythm or CO2, numerous tiny vesicles were found outside the plasmalemma and, moreover, extensive folding of the plasmalemma could also be found in some regions of the cells. Additionally, an unknown structure was found at the interface between the plasmalemma and cell walls, especially in those areas of the cell where extensive folding occurred, suggesting that plasmalemma turnover is possibly associated with an interaction between the plasmalemma and cell walls. Collectively, the results strongly indicate that excretion and folding of the plasmalemma are critical for the accommodation of the cell volume alterations during stomatal movement.
The Association of Virulence Factors with Genomic Islands

Background It has been noted that many bacterial virulence factor genes are located within genomic islands (GIs; clusters of genes in a prokaryotic genome of probable horizontal origin). However, such studies have been limited to single genera or isolated observations. We have performed the first large-scale analysis of multiple diverse pathogens to examine this association. We additionally identified genes found predominantly in pathogens, but not non-pathogens, across multiple genera using 631 complete bacterial genomes, and we identified common trends in virulence for genes in GIs. Furthermore, we examined the relationship between GIs and clustered regularly interspaced palindromic repeats (CRISPRs) proposed to confer resistance to phage. Methodology/Principal Findings We show quantitatively that GIs disproportionately contain more virulence factors than the rest of a given genome (p<1E-40 using three GI datasets) and that CRISPRs are also over-represented in GIs. Virulence factors in GIs and pathogen-associated virulence factors are enriched for proteins having more “offensive” functions, e.g. active invasion of the host, and are disproportionately components of type III/IV secretion systems or toxins. Numerous hypothetical pathogen-associated genes were identified, meriting further study. Conclusions/Significance This is the first systematic analysis across diverse genera indicating that virulence factors are disproportionately associated with GIs. “Offensive” virulence factors, as opposed to host-interaction factors, may more often be a recently acquired trait (on an evolutionary time scale detected by GI analysis). Newly identified pathogen-associated genes warrant further study. We discuss the implications of these results, which cement the significant role of GIs in the evolution of many pathogens.
Exploring case-Based building design—CADRE

Case-based design promises important advantages over rule-based design systems. However, the actual implementation of the paradigm poses many problems which put the advantages into question. In our work on CADRE, a case-based building design system, we have encountered seven fundamental problems which we think are common to most case-based design systems. We describe the problems and the ways we either solved or worked around them in the CADRE system. This leads us to conclusions about the general applicability of case-based reasoning to building design.
Flow by mean curvature of convex surfaces into spheres

The motion of surfaces by their mean curvature has been studied by Brakke [1] from the viewpoint of geometric measure theory. Other authors investigated the corresponding nonparametric problem [2], [5], [9]. A reason for this interest is that evolutionary surfaces of prescribed mean curvature model the behavior of grain boundaries in annealing pure metal. In this paper we take a more classical point of view: Consider a compact, uniformly convex w-dimensional surface M = Mo without boundary, which is smoothly imbedded in R. Let Mo be represented locally by a diffeomorphism
Reliability and cost analysis of a rainwater harvesting system in peri-urban regions of Greater Sydney, Australia

In large cities, rainwater tanks are used to save mains water, but in peri-urban and rural areas, rainwater tanks are used as a sole water supply for many households, as these regions often do not have any other means of water supply. This paper investigates the performance of a rainwater harvesting system (RWHS) in peri-urban regions of Greater Sydney, Australia. Considering the daily rainfall data over the entire period of record at ten different locations, it has been found that a 5 kL tank can meet 96% to 99% of the demand for toilet and laundry use depending on the location in Greater Sydney regions. However, in the driest year, a 5 kL tank can meet 69% to 99% of toilet and laundry demand depending on the location. Based on the results of life cycle cost analysis, it has been found that a 5 kL tank has the highest benefit-cost ratio (ranging from 0.86 to 0.97) among the eight possible tank sizes examined in this study. Interestingly, for a 5 kL tank, with a combined use (i.e., toilet, laundry and irrigation), the current water price in Sydney needs to be increased by 3% to 16% to achieve a benefit-cost ratio exceeding one. A set of regression equations are developed which can be used to estimate reliability using the average annual rainfall data at any arbitrary location in the peri-urban regions of Greater Sydney. The method presented in this paper can also be applied to other Australian states and other countries to estimate water savings and reliability of a RWHS using daily rainfall data.
Soybean N2 fixation estimates, ureide concentration, and yield responses to drought

Increasing N2 fixation tolerance to drought has been hindered by the labor and costs of quantifying N2 fixation using 15N methodologies. The relative abundance of ureides (RAU) in plant tissues has been used for estimating N2 fixation in soybean [Glycine max (L.) Merr. ] grown under well-watered conditions, but it has not been evaluated for drought conditions. The present research evaluated the response of N accumulation to N fertilization, the ability of the RAU technique to predict N2 fixation under drought conditions, and the response of yield to N fertilization under well-watered and drought conditions. Under drought, shoot N accumulation rate during vegetative growth approximately doubled as the amount of N fertilizer was increased from 10 to 200 kg N ha(-1), indicating a greater sensitivity of N2 fixation to drought than uptake and assimilation of inorganic N. Under well-watered conditions, the relationship between estimates of N2 fixation made by 15N-dilution and RAU agreed within 15% of published reports. Under drought conditions, however, this relationship was greatly different (13 to 43%) from published reports. Fertilization with inorganic N in 1 yr increased grain yield 15 to 25% for the drought treatment and 12 to 15% for the well-watered treatment. In a second year, N fertilization increased yield of both drought and well-watered treatments approximately 9%. This research indicates that the RAU technique for estimating N2 fixation under drought conditions may be invalid without further refinement, that N2 fixation is more sensitive to drought than the uptake and assimilation of inorganic soil N, and that increasing the tolerance of N2 fixation to drought would likely result in yield increases.
AAV Recombineering with Single Strand Oligonucleotides

Adeno-associated virus (AAV) transduction initiates a signaling cascade that culminates in a transient DNA damage response. During this time, host DNA repair proteins convert the linear single-strand AAV genomes to double-strand circular monomers and concatemers in processes stimulated by the AAV inverted terminal repeats (ITRs). As the orientation of AAV genome concatemerization appears unbiased, the likelihood of concatemerization in a desired orientation is low (less than 1 in 6). Using a novel recombineering method, Oligo-Assisted AAV Genome Recombination (OAGR), this work demonstrates the ability to direct concatemerization specifically to a desired orientation in human cells. This was achieved by a single-strand DNA oligonucleotide (oligo) displaying homology to distinct AAV genomes capable of forming an intermolecular bridge for recombination. This DNA repair process results in concatemers with genomic junctions corresponding to the sequence of oligo homology. Furthermore, OAGR was restricted to single-strand, not duplexed, AAV genomes suggestive of replication-dependent recombination. Consistent with this process, OAGR demonstrated oligo polarity biases in all tested configurations except when a portion of the oligo targeted the ITR. This approach, in addition to being useful for the elucidation of intermolecular homologous recombination, may find eventual relevance for AAV mediated large gene therapy.
Cognitive-behavioural therapy for the symptoms of schizophrenia: systematic review and meta-analysis with examination of potential bias.

BACKGROUND Cognitive-behavioural therapy (CBT) is considered to be effective for the symptoms of schizophrenia. However, this view is based mainly on meta-analysis, whose findings can be influenced by failure to consider sources of bias. AIMS To conduct a systematic review and meta-analysis of the effectiveness of CBT for schizophrenic symptoms that includes an examination of potential sources of bias. METHOD Data were pooled from randomised trials providing end-of-study data on overall, positive and negative symptoms. The moderating effects of randomisation, masking of outcome assessments, incompleteness of outcome data and use of a control intervention were examined. Publication bias was also investigated. RESULTS Pooled effect sizes were -0.33 (95% CI -0.47 to -0.19) in 34 studies of overall symptoms, -0.25 (95% CI -0.37 to -0.13) in 33 studies of positive symptoms and -0.13 (95% CI -0.25 to -0.01) in 34 studies of negative symptoms. Masking significantly moderated effect size in the meta-analyses of overall symptoms (effect sizes -0.62 (95% CI -0.88 to -0.35) v. -0.15 (95% CI -0.27 to -0.03), P = 0.001) and positive symptoms (effect sizes -0.57 (95% CI -0.76 to -0.39) v. -0.08 (95% CI -0.18 to 0.03), P<0.001). Use of a control intervention did not moderate effect size in any of the analyses. There was no consistent evidence of publication bias across different analyses. CONCLUSIONS Cognitive-behavioural therapy has a therapeutic effect on schizophrenic symptoms in the 'small' range. This reduces further when sources of bias, particularly masking, are controlled for.
Komposisi Fitoplankton Pada Tambak Kerang

This study aims to determine to determine the species composition, abundance and community structure of phytoplankton in shellfish aquaculture ponds blood (Anadara granosa) in Menco, District Wedung, District Demak.Metode used in this study is Diskriptif method, determination of the location of the study is purposive sampling Methods, namely the determination of the sampling locations should be based on consideration, the station I to III of the sampling stations representing keseluruan research area. Marine research station is Blood Shellfish Farming in Hamlet Menco. Station is divided into three stations, with making four periods. Environmental parameters taken include: salinity, temperature, pH, DO, nitrate, phosphate, dissolved oxygen, organic materials. The results of the study, found 19 genera of phytoplankton. Phytoplankton abundance 2596-18844 cells / L. Diversity index (H ') based on the total period ranged from 1.098 to 1.837. On January 18-March 3, 2014, categorized into the diversity index medium. Uniformity index (e) the entire period ranged from 0.616 to 0.999. Fitoplankton atau mikroalga merupakan makanan utama kerang di tambak. Penelitian ini bertujuan untuk mengetahui komposisi jenis, kelimpahan, dan struktur komunitas fitoplankton pada tambak budidaya kerang darah ( Anadara granosa ) di Menco, Kecamatan Wedung, Kabupaten Demak. M etode yang digunakan dalam penelitian ini adalah metode Deskriptif. Sampel fitoplankton diambil dari Tambak Kerang Darah selama empat periode. Parameter lingkungan sebagai data penunjang adalah salinitas, suhu, pH, DO, nitrat, fosfat, oksigen terlarut, bahan organik. Hasil penelitian menjunjukkan terdapat 19 genus fitoplankton, dengan kelimpahan 2.5-18.8x10 3 sel.L -1 . Indeks keanekaragaman (H’) berdasarkan total keseluruhan periode berkisar antara 1,098-1,837. Pada tanggal 18 Januari-3 Maret 2014, dikategorikan masuk dalam indeks keanekaragaman sedang. Indeks keseragaman (e) keseluruhan periode berkisar antara 0,616–0,999.
Prospective follow-up of patients with acute hepatitis C virus infection in Brazil.

BACKGROUND The natural outcome of infection with hepatitis C virus (HCV) varies substantially among individuals. However, little is known about host and viral factors associated with a self-limiting or chronic evolution of HCV infection. METHODS From 1 January 2001 through 31 December 2008, a consecutive series of 65 patients from Rio de Janeiro, Brazil, with a well-documented diagnosis of acute HCV infection, acquired via various routes, were enrolled in this study. Patients were prospectively followed up for a median of 40 months after the estimated date of HCV infection with serial measurements of serum alanine aminotransferase, HCV RNA, and anti-HCV antibodies. Spontaneous viral clearance (SVC) was defined as undetectable levels of HCV RNA in serum, in the absence of treatment, for 3 consecutive HCV polymerase chain reaction tests within the first 6 months of follow-up. Cox proportional hazards regression was used to identify host and viral predictors of SVC. RESULTS The cumulative rate of SVC was 44.6% (95% confidence interval, 32.3%-57.5%). Compared with chronic HCV evolution, patients with self-limiting disease had significantly lower peak levels of anti-HCV antibodies (median, 109.0 vs 86.7 optical density-to-cutoff ratio [od/co]; P<.02), experienced disease symptoms more frequently (69.4% vs 100%; P<.001), and had lower viral load at first clinical presentation (median, 4.3 vs 0.0 log copies; P=.01). In multivariate analyses, low peak anti-HCV level (<93.5 od/co) was the only independent predictor for SVC; the hazard ratio compared with high anti-HCV levels (> or =93.5 od/co) was 2.62 (95% confidence interval, 1.11-6.19; P=.03). CONCLUSION Our data suggest that low levels of anti-HCV antibodies during the acute phase of HCV infection are independently related to spontaneous viral clearance.
CLiPS Stylometry Investigation (CSI) corpus: A Dutch corpus for the detection of age, gender, personality, sentiment and deception in text

We present the CLiPS Stylometry Investigation (CSI) corpus, a new Dutch corpus containing reviews and essays written by university students. It is designed to serve multiple purposes: detection of age, gender, authorship, personality, sentiment, deception, topic and genre. Another major advantage is its planned yearly expansion with each year’s new students. The corpus currently contains about 305,000 tokens spread over 749 documents. The average review length is 128 tokens; the average essay length is 1126 tokens. The corpus will be made available on the CLiPS website (www.clips.uantwerpen.be/datasets) and can freely be used for academic research purposes. An initial deception detection experiment was performed on this data. Deception detection is the task of automatically classifying a text as being either truthful or deceptive, in our case by examining the writing style of the author. This task has never been investigated for Dutch before. We performed a supervised machine learning experiment using the SVM algorithm in a 10-fold cross-validation setup. The only features were the token unigrams present in the training data. Using this simple method, we reached a state-of-the-art F-score of 72.2%.
INCIDENCE OF SCHIZOPHRENIA IN AN URBAN COMMUNITY IN MADRAS

SUMMARY The incidence rate of an illness is a vital epidemiological measure for investigating etiology. Incidence estimates of schizophrenia from different parts of the world have shown variations, due to differences in the diagnostic criteria, measurement techniques and operational definitions used. In contrast to the prevalence studies in India, incidence surveys haw been sparse and the rates obtained relatively higher as compared to the west. As part of an ICMR Longitudinal Study of Functional Psychoses in an urban community in Madras, the incidence of schizophrenia was estimated in the slums. The case finding methods included a door to door survey and a leakage study. Cases defined using standardized diagnostic criteria, were identified using IPSS and PSE. The incidence rate was 0.21/1,000 by the community survey and 0.41/1,000 by the leakage study. This paper describes the study and discusses its relevance in India.