Miracle-dz/UniFAR-FTUs huggingface dataset:
Transaction Repair: Full Serializability Without Locks

Transaction Repair is a method for lock-free, scalable transaction processing that achieves full serializability. It demonstrates parallel speedup even in inimical scenarios where all pairs of transactions have significant read-write conflicts. In the transaction repair approach, each transaction runs in complete isolation in a branch of the database; when conflicts occur, we detect and repair them. These repairs are performed efficiently in parallel, and the net effect is that of serial processing. Within transactions, we use no locks. This frees users from the complications and performance hazards of locks, and from the anomalies of sub-SERIALIZABLE isolation levels. Our approach builds on an incrementalized variant of leapfrog triejoin, a worst-case optimal algorithm for $\exists_1$ formulae, and on well-established techniques from programming languages: declarative languages, purely functional data structures, incremental computation, and fixpoint equations.
Computing Maximized Effectiveness Distance for Recall-Based Metrics

Given an effectiveness metric <inline-formula><tex-math notation="LaTeX">$M(\cdot)$</tex-math><alternatives> <inline-graphic xlink:href="moffat-ieq1-2754371.gif"/></alternatives></inline-formula>, two ordered document rankings <inline-formula><tex-math notation="LaTeX">$X_1$</tex-math><alternatives> <inline-graphic xlink:href="moffat-ieq2-2754371.gif"/></alternatives></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$X_2$</tex-math><alternatives><inline-graphic xlink:href="moffat-ieq3-2754371.gif"/> </alternatives></inline-formula> generated by a score-based information retrieval activity, and relevance labels in regard to some subset (possibly empty) of the documents appearing in the two rankings, Tan and Clarke's Maximized Effectiveness Distance (MED) computes the greatest difference in metric score that can be achieved that is consistent with all provided information, crystallized via a set of relevance assignments to the unlabeled documents such that <inline-formula><tex-math notation="LaTeX">$|M(X_1)-M(X_2)|$</tex-math><alternatives> <inline-graphic xlink:href="moffat-ieq4-2754371.gif"/></alternatives></inline-formula> is maximized. The closer the maximized effectiveness distance is to zero, the more similar <inline-formula><tex-math notation="LaTeX">$X_1$ </tex-math><alternatives><inline-graphic xlink:href="moffat-ieq5-2754371.gif"/></alternatives></inline-formula> and <inline-formula><tex-math notation="LaTeX">$X_2$</tex-math><alternatives> <inline-graphic xlink:href="moffat-ieq6-2754371.gif"/></alternatives></inline-formula> can be considered to be from the point of view of the metric <inline-formula><tex-math notation="LaTeX">$M(\cdot)$</tex-math><alternatives> <inline-graphic xlink:href="moffat-ieq7-2754371.gif"/></alternatives></inline-formula>. Here, we consider issues that arise when Tan and Clarke's definitions are applied to recall-based metrics, notably normalized discounted cumulative gain (NDCG), and average precision (AP). In particular, we show that MED can be applied to NDCG without requiring an <italic>a priori</italic> assumption in regard to the total number of relevant documents; we also show that making such an assumption leads to different outcomes for both NDCG and average precision (AP) compared to when no such assumption is made.
Polynomial-time Algorithm for Isomorphism of Graphs with Clique-width at most 3

The clique-width is a measure of complexity of decomposing graphs into certain tree-like structures. The class of graphs with bounded clique-width contains bounded tree-width graphs. While there are many results on the graph isomorphism problem for bounded treewidth graphs, very little is known about isomorphism of bounded cliquewidth graphs. We give the first polynomial-time graph isomorphism algorithm for graphs with clique-width at most 3.
A Simple and Effective Scheme of Ciphertext-Policy ABE

Since more sensitive data are stored and shared on third-party sites, we may need a system capable of one-to-many communication and data encryption without knowing specific recipients. However, the traditional public key crypto system and broadcast encryption system can't solve both of the problems at the same time. Attribute-Based Encryption (ABE) offers both of the desired abilities. In this paper, we present a simple and effective scheme of Cipher text-Policy Attribute-Based Encryption (CP-ABE), where access structures are single AND gates on positive and negative attributes and the size of access structure is fixed. Our scheme can be proven chosen plaintext attack (CPA) secure under the decisional bilinear Diffie-Hellman (DBDH) assumption. In addition, we provide an implementation of our scheme and give performance measurements.
AngularJS in the wild: a survey with 460 developers

To implement modern web applications, a new family of JavaScript frameworks has emerged, using the MVC pattern. Among these frameworks, the most popular one is ANGULARJS, which is supported by Google. In spite of its popularity, there is not a clear knowledge on how ANGULARJS design and features affect the development experience of Web applications. Therefore, this paper reports the results of a survey about ANGULARJS, including answers from 460 developers. Our contributions include the identification of the most appreciated features of ANGULARJS (e.g., custom interface components, dependency injection, and two-way data binding) and the most problematic aspects of the framework (e.g., performance and implementation of directives).
Robust Learning under Uncertain Test Distributions: Relating Covariate Shift to Model Misspecification

Many learning situations involve learning the conditional distribution p(y|x) when the training instances are drawn from the training distribution ptr(x), even though it will later be used to predict for instances drawn from a different test distribution pte(x). Most current approaches focus on learning how to reweigh the training examples, to make them resemble the test distribution. However, reweighing does not always help, because (we show that) the test error also depends on the correctness of the underlying model class. This paper analyses this situation by viewing the problem of learning under changing distributions as a game between a learner and an adversary. We characterize when such reweighing is needed, and also provide an algorithm, robust covariate shift adjustment (RCSA), that provides relevant weights. Our empirical studies, on UCI datasets and a real-world cancer prognostic prediction dataset, show that our analysis applies, and that our RCSA works effectively.
Prevalence and predictors of fatigue in glioblastoma: a prospective study.

BACKGROUND The main goal of this study was to assess frequency, clinical correlates, and independent predictors of fatigue in a homogeneous cohort of well-defined glioblastoma patients at baseline prior to combined radio-chemotherapy. METHODS We prospectively included 65 glioblastoma patients at postsurgical baseline and assessed fatigue, sleepiness, mean bedtimes, mood disturbances, and clinical characteristics such as clinical performance status, presenting symptomatology, details on neurosurgical procedure, and tumor location and diameter as well as pharmacological treatment including antiepileptic drugs, antidepressants, and use of corticosteroids. Data on fatigue and sleepiness were measured with the Fatigue Severity Scale and the Epworth Sleepiness Scale, respectively, and compared with 130 age- and sex-matched healthy controls. RESULTS We observed a significant correlation between fatigue and sleepiness scores in both patients (r = 0.26; P = .04) and controls (r = 0.36; P < .001). Only fatigue appeared to be more common in glioblastoma patients than in healthy controls (48% vs 11%; P < .001) but not the frequency of sleepiness (22% vs 19%; P = .43). Female sex was associated with increased fatigue frequency among glioblastoma patients but not among control participants. Multiple linear regression analyses identified depression, left-sided tumor location, and female sex as strongest associates of baseline fatigue severity. CONCLUSIONS Our findings indicate that glioblastoma patients are frequently affected by fatigue at baseline, suggesting that factors other than those related to radio- or chemotherapy have significant impact, particularly depression and tumor localization.
Extending the Knowledge Discovery Metamodel for architecture-driven simulation modernization

With the rapid improvement of hardware, the constant evaluation of simulation development methodologies and environments has brought us a new challenge: simulations modernization. This paper presents a simulation knowledge discovery metamodel that extends the Object Management Group’s knowledge discovery metamodel by adding a simulation model package for enabling architecture-driven simulation modernization. While there are some endeavors that propose integration methods, modernization of legacy simulations has not been investigated. Architecture-driven modernization has been introduced as a process of comprehending and transforming existing software assets. It advocates a model-based approach to software modernization in which the knowledge extracted from software assets is captured in models that conform to a metamodel, namely the knowledge discovery metamodel. It specifies an ontology of software assets. Model transformations are then recommended as means of modernization of legacy assets. But diversity in methodologies and approaches to specify simulation modeling assets prohibits the Knowledge Discovery Metamodel from providing adequate meta definitions to capture knowledge in simulations. System Entity Structure has long been used for knowledge representation by the simulation community. It provides formalism for composition, taxonomy and coupling relations. Hence, System Entity Structure is proposed as an intermediate metamodel to capture the meta-constructs and their relations. It is then made available to define particular metamodels for particular simulation modeling methodologies or approaches. The promoted methodology is exercised with samples in order to collect evidence of its applicability. Metamodel segments are presented for knowledge discovery for discrete event systems specification and Modelica simulation programming language. A complete metamodel is then introduced for the real-time distributed simulation domain model of the German Aerospace Center (DLR) Institute of Flight Systems. Finally, this metamodel is used to introduce discovery artifacts. These samples provide valuable indications that the methodology works.
K-Anonymization using Multidimensional Suppression for Data De-identification

searching methods have advanced the increased risk of privacy disclosure makes it important to protect privacy of user during data publishing. Many of the algorithms used for the data de-identification are not efficient because resulted dataset can easily linked with the public database and it reveals the users identity. One of the method uses for protecting the privacy of user is to apply anonymization algorithms. TDS and TDR using generalization of method to anonymized the dataset. Major drawback as these algorithm is they requires a manually generated domain hierarchy taxonomy for every quasi-identifier in the data set on which k- anonymity has to be performed. Therefore, in this paper we propose new approach which will makes use of suppression based k-anonymization method to allow data publisher to de- identify datasets and in this method only certain attributes from record are suppressed based on values other attributes. As suppression method is used in algorithm, it does not required manually created taxonomy tree of quasi-identifiers. We applied this algorithm on 3 different data sets to evaluate its accuracy as compared to other k-anonymity generalization algorithms. It is found that predicative performance of this algorithm is better than existing generalization methods. This method is expected to provide privacy and accuracy measures to data publishers.
Neurocognitive Sequelae of Scaphocephaly

Objective. Early cranioplasty for scaphocephaly has become routine in most countries. In addition to normalizing the shape of the skull, it has been found to decrease intracranial hypertension. Whether corrective surgery benefits the child's cognitive outcome has been poorly documented. Design. Eighteen children whose sagittal suture showed premature fusion at birth or soon thereafter were operated on at age 1 week to 7 months. All patients healed without complications and were followed-up at regular intervals. At the age of 7.8 to 16.3 years they were examined to clarify their neurocognitive development and to compare the results with their age- and gender-matched healthy controls. Results. Originally scaphocephalic children, although operated on, had mild deficiencies in auditory short-term memory and language development when examined with the general comprehension, similarities, and digit span subscales of the Wechsler Intelligence Scale for Children–Revised. In all other respects their developmental outcome was equal to that of the controls. Conclusions. Despite relative early correction of the skull shape, originally scaphocephalic children's neurocognitive performances do not reach the same level in all of the neurocognitive domains as their matched controls at school age. Early operation (≤1 month) may decrease this developmental delay. This implies that impairment of brain function has already taken place in utero. For the same reason an early operation seems to be justified not only for correction of the skull shape, but also to allow unrestricted development for the brain. Postponement of the operation would not serve either of these aims.
Post-Translational Modifications of TRP Channels

Transient receptor potential (TRP) channels constitute an ancient family of cation channels that have been found in many eukaryotic organisms from yeast to human. TRP channels exert a multitude of physiological functions ranging from Ca2+ homeostasis in the kidney to pain reception and vision. These channels are activated by a wide range of stimuli and undergo covalent post-translational modifications that affect and modulate their subcellular targeting, their biophysical properties, or channel gating. These modifications include N-linked glycosylation, protein phosphorylation, and covalent attachment of chemicals that reversibly bind to specific cysteine residues. The latter modification represents an unusual activation mechanism of ligand-gated ion channels that is in contrast to the lock-and-key paradigm of receptor activation by its agonists. In this review, we summarize the post-translational modifications identified on TRP channels and, when available, explain their physiological role.
[Effects of insertional inactivation of gacS gene on two secondary metabolites in Psedomonas chlororaphis G-05].

UNLABELLED Phenazine-1-carboxylic acid biosynthesized and secreted by Pseudomonas chlororaphis G-05 isolated from the rhizosphere of pepper in greenhouse (Huaian, China), contributes to its biological suppression of R. solani growth. OBJECTIVE Our aim is to elucidate its biocontrol function and regulation mechanism. METHODS We first identified the strain with biochemical method and homology comparison of 16S rDNA. A conservative DNA fragment of gacS gene was then obtained from the genomic DNA of the wild type strain G-05 by polymerase chain reaction (PCR). According to homologous recombination technology, a mutant G-05S was then created with insertional inactivation of gentamycin resistance cassette (aacC1). RESULTS In comparison with the wild type strain G-05, the gacS-deficient mutant G-05S produced trace amount of phenazine-1-carboxylic acid in King's B ( KMB ) or Pigment Production Medium( PPM) medium, respectively. However, it produced indole-3-acetic acid (IAA) in the same way as the wild type strain. When the gacS gene was introduced with the shuttle vector pME6032, the mutant G-05S produced the same phenazine-1-carboxylic acid as the wild type strain. CONCLUSION The regulation mediated by gacS gene on secondary metabolites is specific and differential in some biocontrol agents.
Stress-Dependent Elastic Properties of Anisotropic Sedimentary Rocks: Uniaxial and Triaxial Experiments and Theoretical Modelling

In this section is described application of the porosity deformation approach (PDA) to the experimentally obtained data. This enables a direct comparison of laboratory measurements with the numerical modelling for validation and further analysis. As intermediate product were obtained and compared experimentally measured and theoretically modeled compliance tensors, ultrasonic velocities and anisotropy parameters. The modelling of the orthorhombic medium is carried out using equations set 2.53 and modelling of the VTI medium performed using equations set 2.50. Theoretical background and a description of the PDA can be found in section 2.5. For the sake of simplicity the data bank is divided in two parts and described separately. The first part includes two VTI shales: BaZ-VTI and DH06-VTI. They are compared and analyzed. Based on this the general trends are described for uniaxially loaded VTI samples. An individual influence of the mineralogical composition and genesis on the stress sensitivity is analyzed. In the second part are compared two samples with similar mineralogy but with different anisotropy: one sample has a VTI symmetry (DR-VTI) and another sample is seismically orthorhombic (DR-ORT). Their stress-dependencies are compared and the influence of uniaxially applied stress is described, taking into account orientation of the layering. Algorithm The porosity deformation approach is designed for the application on the complete data set of stressdependent elastic constants. Below, is shown the algorithm of the procedure: 1. Computation of the stress-dependent compliance tensor based on measured velocities 2. Modelling of the stress-dependent compliance tensor, using PDA 3. Comparison of measured and modelled compliances and ultrasonic velocities
Barrier spraying to control the malaria vector Anopheles albimanus: laboratory and field evaluation in the Dominican Republic

Abstract. To develop a new strategy for control of exophilic/exophagic malaria vectors which rest on peridomestic foliage, Anopheles albimanus was used for laboratory bioassays of mosquito adulticides applied to various vegetation types. Of the three classes of insecticide tested, the pyrethroid (permethrin at 112 g/ha) showed greater foliar persistence than either the carbamate (bendiocarb at 340g/ha) or the organophosphorus compound (malathion at 277g/ha).
A Mammalian patched Homolog Is Expressed in Target Tissues of sonic hedgehog and Maps to a Region Associated with Developmental Abnormalities (*)

Drosophila patched is a segment polarity gene required for the correct patterning of larval segments and imaginal discs during fly development and has a close functional relationship with hedgehog. We have isolated a complete human PATCHED cDNA sequence, which encodes a putative protein of 1296 amino acids, and displays 39% identity and 60% similarity to the Drosophila PATCHED protein. Hydropathy analysis suggests that human PATCHED is an integral membrane protein with a pattern of hydrophobic and hydrophilic stretches nearly identical to that of Drosophila patched. In the developing mouse embryo, patched is initially detected within the ventral neural tube and later in the somites and limb buds. Expression in the limb buds is restricted to the posterior ectoderm surrounding the zone of polarizing activity. The results show that patched is expressed in target tissues of sonic hedgehog, a murine homolog of Drosophila hedgehog suggesting that patched/hedgehog interactions have been conserved during evolution. Human PATCHED maps to human chromosome 9q22.3, the candidate region for the nevoid basal cell carcinoma syndrome. Patched expression is compatible with the congenital defects observed in the nevoid basal cell carcinoma syndrome.
Negative Regulation of Superoxide Dismutase-1 Promoter by Thyroid Hormone

The role of thyroid hormone [l-3,5,3′-triiodothyronine (T3)] and the thyroid hormone receptor (TR) in regulating growth, development, and metabolic homeostasis is well established. It is also emerging that T3 is associated with oxidative stress through the regulation of the activity of superoxide dismutase-1 (SOD-1), a key enzyme in the metabolism of oxygen free radicals. We found that T3 reverses the activation of the SOD-1 promoter caused by the free radical generators paraquat and phorbol 12-myristate 13-acetate through the direct repression of the SOD-1 promoter by liganded TR. Conversely, the SOD-1 promoter is significantly stimulated by unliganded TRs. This regulation requires the DNA-binding domain of the TR, which is recruited to an inhibitory element between -157 and +17 of the SOD-1 promoter. TR mutations, which abolish recruitment of coactivator proteins, block repression of the SOD-1 promoter. Conversely, a mutation that inhibits corepressor binding to the TR prevents activation. Together, our findings suggest a mechanism of negative regulation in which TR binds to the SOD-1 promoter but coactivator and corepressor binding surfaces have an inverted function. This effect may be important in T3 induction of oxidative stress in thyroid hormone excess.
A protocol for self-organizing peer-to-peer network supporting content-based search

For a peer-to-peer(P2P) content sharing network holding large amount of data, an efficient semantic based search mechanism is a key requisite. Semantic based search should generate as little traffic (messages) possible while achieving precision and recall rates comparable to those of correspondent centralized system. In this paper protocols for self-organizing P2P networks that arranges links between peers according to peer's content are developed and tested. Peers organize themselves into "semantic communities" without losing links to other semantic communities. Proposed network requires no prior knowledge of the semantics of documents that are to be shared in the system. Through simulations, it is shown that proposed network is resilient to membership changes and achieves high recall rates.
TRANSIT - A Software Tool for Himar1 TnSeq Analysis

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit