Miracle-dz/UniFAR-FTUs huggingface dataset:
Cardinality-aware and purely relational implementation of an XQuery processor

With the rapid growth in the use of XML documents as a universal format for storage and interchange of the data on the Web, several efforts have been made in order to develop efficient techniques for storing and querying XML data. Since XQuery is becoming the standard XML query language, significant effort has been made in developing efficient implementations of XQuery query processor. This thesis describes a purely relational implementation of an XQuery processor which exploits the well-known maturity and performance acceleration techniques of the relational database technology to translate XQuery expressions into their equivalent SQL evaluation scripts. The generated SQL evaluation scripts are based on the XPath accelerator relational mapping scheme of the XML documents and can be executed on any conventional relational database management systems with no need for any changes in its kernel or any other special requirements. The translation process starts by compiling the input XQuery expression into an intermediate algebraic plan which is then translated into its equivalent SQL evaluation script by means of a predefined SQL translation template for each algebraic operator. In order to produce efficient and concise SQL queries, different XQuery to SQL translation approaches are proposed and different relational optimization techniques have been exploited. In addition, this thesis presents a novel framework for estimating the cardinality of XQuery expressions as well as its sub-expressions. Although cardinality size estimation is very important on its own, it is also very crucial for an effective query optimization process. This thesis presents an integrated framework for exploiting the available estimated cardinality information to provide the RDBMS query optimizers with hints for selecting the best alternative execution plan for the SQL evaluation scripts of the input XQuery expression. The experiments of this thesis demonstrate the efficiency and scalability of our purely relational approach in comparison to the native XML/XQuery functionality supported by conventional RDBMSs.
Chronic ethanol-induced subtype- and subregion-specific decrease in the mRNA expression of metabotropic glutamate receptors in rat hippocampus.

BACKGROUND Chronic ethanol consumption is known to induce adaptive changes in the hippocampal glutamatergic transmission and alter NMDA receptor binding and subunit expression. Metabotropic glutamate (mGlu) receptors have been shown to function as modulators of neuronal excitability and can fine tune glutamatergic transmission. This study was aimed to determine whether chronic ethanol treatment could change the messenger RNA (mRNA) expression of mGlu receptors in the hippocampus. METHODS Male Sprague Dawley rats were fed a Lieber-DeCarli liquid diet with 5% (w/v) ethanol or isocaloric amount of maltose for 2 months. Quantitative in situ hybridization was carried out using coronal brain sections through the hippocampus. RESULTS The results revealed decreases in mRNA expression of several mGlu receptors in different subregions of the hippocampus. In the dentate gyrus, mGlu3 and mGlu5 receptor mRNA levels were significantly lower in the ethanol-treated rats than in the control rats. In the CA3 region, the mRNA expression of mGlu1, mGlu5, and mGlu7 receptors showed substantial decreases after ethanol exposure. The mGlu7 receptor mRNA levels were also declined in the CA1 region and the polymorph layer of the dentate gyrus. No changes were found in mRNA expression of mGlu2, mGlu4, and mGlu8 receptors. CONCLUSIONS Considering the involvement of hippocampal mGlu receptors in learning and memory processes as well as in neurotoxicity and seizure production, the reduced expression of these receptors might contribute to ethanol withdrawal-induced seizures and also may play a role in cognitive deficits and brain damage caused by long-term ethanol consumption.
Rates of adverse reactions to first and second doses of BCG vaccination: results of a large community trial in Brazilian schoolchildren.

OBJECTIVE To evaluate the incidence of adverse reactions to first and second bacille Calmette-Guérin (BCG) vaccination in schoolchildren. SETTING AND DESIGN Enhanced surveillance in a Brazilian trial. Suspected reactions were reported to a nurse who visited cases and completed a standard form. RESULTS Among 71341 schoolchildren studied, 33 reactions were reported. Of these, 25 fulfilled the criteria, resulting in a rate of one per 2854 vaccinations, with no deaths or BCG-osis. Reactions to second doses were more common than to first BCG vaccinations, but this difference was not statistically significant. CONCLUSIONS Adverse reactions to a second dose of BCG may be more frequent than reactions to a first dose, but they are still rare events.
Infection with Leishmania infantum Inhibits Actinomycin D‐Induced Apoptosis of Human Monocytic Cell Line U‐937

Abstract. Modulation of host cell apoptosis has been observed in many bacterial, protozoal, and viral infections. The aim of this work was to investigate the effect of viscerotropic Leishmania (L.) infantum infection on actinomycin D‐induced apoptosis of the human monocytic cell line U‐937. Cells were infected with L. infantum promastigotes or treated with the surface molecule lipophosphoglycan (LPG) or with parasite‐free supernatant of Leishmania culture medium and submitted to action of actinomycin D as the apoptosis‐inducing agent. Actinomycin D‐induced apoptosis in U‐937 cells was inhibited in the presence of both viable L. infantum promastigotes and soluble factors contained in Leishmania culture medium or purified LPG. Leishmania infantum affected the survival of U‐937 cells via a mechanism involving inhibition of caspase‐3 activation. Furthermore, protein kinase C δ (PKC δ) cleavage was increased in actinomycin D‐treated U‐937 cells and was inhibited by the addition of LPG. Thus, inhibition of the PKC‐mediated pathways by LPG can be implicated in the enhanced survival of the parasites.
Spread of an epidemic Pseudomonas aeruginosa strain from a patient with cystic fibrosis (CF) to non-CF relatives

Colonisation with Pseudomonas aeruginosa is common in adults with cystic fibrosis (CF) and there is increasing evidence that transmissible strains may cross colonise patients. However, transmission of these strains by social contact to healthy non-CF individuals has not been described. A case is presented where an adult CF patient colonised by an epidemic P aeruginosa strain infected her parents with subsequent morbidity.
Bio-ethanol Production from Bamboo Residues with Lignocellulose Fractionation Technology (LFT) and Separate Hydrolysis Fermentation (SHF) by Zymomonas Mobilis

Combined lignocellulose fractionation technology (LFT) and separate hydrolysis fermentation (SHF) for the production of ethanol from bamboo residues and corn stover were investigated by using Zymomonas mobilis. In this process, the highest ethanol concentration reached 4.72 g/l from pretreated bamboo shoots shell fiber (BSSF) and the ethanol yield were 55.82% of the theoretical within 24 h at 30° C. However, during the SHF process at different conditions, about 25.0%-40.0% of the reducing sugar produced by enzymatic hydrolysis remained in the ferment medium. These results indicated that the combinated process of LFT and SHF is a useful method for lignocellulosic-to-ethanol. Bamboo residues are also not only an attractive feedstock for ethanol production like corn stover, but better, based on these results.
Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants.

The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2OGDs remains to be accomplished. We present a phylogenetic classification of 479 2OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes - DOXA, DOXB and DOXC - based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli AlkB, which is a prototype of 2OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4-hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC-class 2OGDs to 57 phylogenetic clades. 2OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm-specific clades were found to be involved in various lineage-specific specialized metabolisms, but 31 of the 57 DOXC-class clades were only found in a single species. Therefore, the evolution and diversification of DOXC-class 2OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants.
Combining machine-learning topic models and spatiotemporal analysis of social media data for disaster footprint and damage assessment

ABSTRACT Current disaster management procedures to cope with human and economic losses and to manage a disaster’s aftermath suffer from a number of shortcomings like high temporal lags or limited temporal and spatial resolution. This paper presents an approach to analyze social media posts to assess the footprint of and the damage caused by natural disasters through combining machine-learning techniques (Latent Dirichlet Allocation) for semantic information extraction with spatial and temporal analysis (local spatial autocorrelation) for hot spot detection. Our results demonstrate that earthquake footprints can be reliably and accurately identified in our use case. More, a number of relevant semantic topics can be automatically identified without a priori knowledge, revealing clearly differing temporal and spatial signatures. Furthermore, we are able to generate a damage map that indicates where significant losses have occurred. The validation of our results using statistical measures, complemented by the official earthquake footprint by US Geological Survey and the results of the HAZUS loss model, shows that our approach produces valid and reliable outputs. Thus, our approach may improve current disaster management procedures through generating a new and unseen information layer in near real time.
Evolution of Animal Neural Systems

Nervous systems are one of the most spectacular products of evolution. Their provenance and evolution have been an area of interest and often intense debate since the late 19th century. The genomics era has provided researchers with a new set of tools with which to study the early evolution of neurons, and recent progress on the molecular evolution of the first neurons has been both exciting and frustrating. It has become increasingly obvious that genomic data is often insufficient to reconstruct complex phenotypes in deep evolutionary time. We review this recent progress and its attendant challenges, and suggest ways forward.
The glutamic acid decarboxylase 65 immunoglobulin G subclass profile differs between adult‐onset type 1 diabetes and latent autoimmune diabetes in adults (LADA) up to 3 years after clinical onset

Autoantibodies against glutamic acid decarboxylase 65 (GADA) are found frequently in patients with autoimmune diabetes. Immunoglobulin (Ig)G1 is the most frequent subclass among the GADA IgG subclasses. IgG4 is a more common subclass in latent autoimmune diabetes in adults (LADA) at clinical onset compared to type 1 diabetes. The aim of this work was to study the different GADA‐IgG subclass profiles during a 3‐year follow‐up in these groups of autoimmune diabetes. Adult‐onset subjects, classified as either type 1 (n = 40) or LADA (n = 43), were included in the study. New samples were collected every year from these patients. In addition to conventional GADA analyses, GADA‐IgG subclasses were also analysed with a radioimmunoprecipitation assay using biotin‐conjugated antibodies (directed against human IgG subclasses and IgM) and streptavidin Sepharose. During 3 years' follow‐up, all the IgG subclass levels decreased in type 1 diabetes – IgG1: P < 0·001; IgG2: P < 0·001; IgG3: P < 0·001; IgG4: P < 0·05 (Friedman's’ test) – while levels remained stable for all four subclasses in LADA. GADA IgM, however, decreased in both groups (P < 0·001). Patients with LADA have higher GADA IgG3 and IgG4 at clinical onset and seem to maintain the levels and profile of their IgG subclasses up to 3 years after clinical onset, while all the GADA IgG subclass levels decrease in type 1 diabetic patients. This indicates a persistent different immune response in LADA compared to type 1 diabetes and further indicates the difference in pathogenesis.
Serial neurologic examination of hyperactive children.

Forty-four of 102 children undergoing pharmacologic treatment of hyperactivity received serial neurologic examinations on five separate occasions. The responses to three of the "soft" neurologic signs administered were analyzed: heel gait, toe gait, and diadochokinesis. A high degree of variability of response within individuals was documented. There was no evidence of interaction between treatment and the subjects' responses. The degree of variability was such that to have used these data as measures of "improvement" (i.e., drug effect) would have been misleading. The value of these signs for purposes of diagnosis or assessment of therapy is doubtful.
SWRLx: A New Formalism for Hybrid Ontology Reasoning

Although OWL Web Ontology Language and SWRL Semantic Web Rule Language add considerable expressiveness to the Semantic Web, they do have expressive limitations. For some reasoning problems, it is necessary to modify existing knowledge in an ontology. This kind of problem cannot be fully resolved by OWL and SWRL, as they only support monotonic inference. In this paper, the authors propose SWRLx Extended Semantic Web Rule Language as an extension to the SWRL rules. The set of rules obtained with SWRLx are posted to the Jess engine using rewrite meta-rules. The reason for this combination is that it allows the inference of new knowledge and storing it in the knowledge base. The authors propose a formalism for SWRLx along with its implementation through an adaptation of different object-oriented techniques. The Jess rule engine is used to transform these techniques to the Jess model. The authors include a demonstration that demonstrates the importance of this kind of reasoning. In order to verify their proposal, they use a case study inherent to interpretation of a preventive medical check-up.
H2 and Hinfinity Filtering Design Subject to Implementation Uncertainty

This paper presents new filtering design procedures for discrete-time linear systems. It provides a solution to the problem of linear filtering design, assuming that the filter is subject to parametric uncertainty. The problem is relevant, since the proposed filter design incorporates real world implementation constraints that are always present in practice. The transfer function and the state space realization of the filter are simultaneously computed. The design procedure can also handle plant parametric uncertainty. In this case, the plant parameters are assumed not to be exactly known but belonging to a given convex and closed polyhedron. Robust performance is measured by the H2 and H$_\infty$ norms of the transfer function from the noisy input to the filtering error. The results are based on the determination of an upper bound on the performance objectives. All optimization problems are linear with constraint sets given in the form of LMI (linear matrix inequalities). Global optimal solutions to these problems can be readily computed. Numerical examples illustrate the theory.
Exploring the sentence advantage in working memory: Insights from serial recall and recognition

Immediate serial recall of sentences has been shown to be superior to that of unrelated words. This study was designed to further explore how this effect might emerge in recall and to establish whether it also extends to serial recognition, a different form of response task that has relatively reduced output requirements. Using auditory or visual presentation of sequences, we found a substantial advantage for sentences over lists in serial recall, an effect shown on measures of recall accuracy, order, intrusion, and omission errors and reflected in transposition gradients. In contrast however, recognition memory based on a standard change detection paradigm gave only weak and inconsistent evidence for a sentence superiority effect. However, when a more sensitive staircase procedure imported from psychophysics was used, a clear sentence advantage was found although the effect sizes were smaller than those observed in serial recall. These findings suggest that sentence recall benefits from automatic processes that utilise long-term knowledge across encoding, storage, and retrieval.
Neurite branching on deformable substrates

The mechanical properties of substrates underlying cells can have profound effects on cell structure and function. To examine the effect of substrate deformability on neuronal cell growth, protein-laminated polyacrylamide gels were prepared with differing amounts of bisacrylamide to generate substrates of varying deformability with elastic moduli ranging from 500 to 5500 dyne/cm2. Mouse spinal cord primary neuronal cells were plated on the gels and allowed to grow and extend neurites for several weeks in culture. While neurons grew well on the gels, glia, which are normally co-cultured with the neurons, did not survive on these deformable substrates even though the chemical environment was permissive for their growth. Substrate flexibility also had a significant effect on neurite branching. Neurons grown on softer substrates formed more than three times as many branches as those grown on stiffer gels. These results show that mechanical properties of the substrate specifically direct the formation of neurite branches, which are critical for appropriate synaptic connections during development and regeneration.
Appetite regulatory hormone responses to various dietary proteins differ by body mass index status despite similar reductions in ad libitum energy intake.

CONTEXT Although dietary protein produces higher acute satiety relative to carbohydrate, the influence of protein source and body mass index (BMI) has not been clearly described. OBJECTIVE The objective of the study was to assess postprandial responses to different protein sources, compared with glucose, in males with normal and high BMI. DESIGN This was a randomized, crossover study of four preloads followed by blood sampling (+15, 30, 45, 60, 90, 120, 180 min) and buffet meal. SETTING The study was conducted at an outpatient clinic. PARTICIPANTS The study population included 72 men, with a BMI range 20.6-39.9 kg/m(2). INTERVENTIONS Interventions consisted of liquid preloads (1.1 MJ, 450 ml) containing 50 g whey, soy, gluten, or glucose. MAIN OUTCOME MEASURES Fasting and postprandial plasma glucose, insulin, ghrelin, glucagon-like peptide-1 (GLP-1) and cholecystokinin (n = 38), ad libitum energy intake, and appetite ratings were measured. RESULTS Energy intake was 10% lower after all protein preloads, compared with the glucose treatment (P < 0.05), independent of BMI status and protein type. All protein loads prolonged the postprandial suppression of ghrelin (P < 0.01) and elevation of GLP-1 (P < 0.01) and cholecystokinin (P < 0.05). Fasting GLP-1 concentrations [overweight, 17.5 +/- 1.3; lean, 14.7 +/- 0.1 pg/ml (5.2 +/- 0.4 and 4.4 +/- 0.1 pmol/liter, respectively); P < 0.001] and postprandial responses (P = 0.038) were higher in overweight subjects. CONCLUSIONS Whey, soy, and gluten similarly tend to reduce ad libitum food intake 3 h later in lean and overweight males relative to glucose. Postprandial ghrelin, GLP-1, insulin, and cholecystokinin may contribute to this higher satiety after protein consumption. GLP-1 concentrations are increased in overweight subjects, which may affect satiety responses in this group.
Localization of m-iodo(131I)benzylguanidine in neuroblastoma.

Patient survival and the therapeutic strategy for treatment of neuroblastoma are highly dependent on the stage of the tumor at presentation. For routine staging, the Children's Cancer Study group currently recommends a chest radiograph, abdominal CT scan, radionuclide bone scan, bone marrow biopsy, catecholamine metabolite estimations, and surgical determination of tumor extent. A noninvasive method for detectiton of neuroblastoma that avoids surgery and bone marrow biopsy would be a most welcome addition to the armamentarium of the pediatric oncologist. A case of neuroblastoma demonstrated with m-iodo(/sup 131/I)benzylguanidine (MIBG) scintigraphy is reported.
ISMRM Syllabus Contribution Dr Gina Brown Consultant Radiologist and Reader in Gastrointestinal Cancer Imaging The Royal Marsden NHS Foundation Trust

Dr Gina Brown Consultant Radiologist and Reader in Gastrointestinal Cancer Imaging The Royal Marsden NHS Foundation Trust Downs Road Sutton Surrey SM2 5PT Tel +44 208 6613964 Fax + 44 208 915 6721 gina.brown@rmh.nhs. uk How MRI became the Gold Standard in Rectal Cancer Abstract With the acceleration and ever increasing costs of technologies across the imaging modalities, any imaging technique proposed for improving the assessment of disease needs to undergo rigorous validation. Imaging validation is only accepted as a clinical gold standard if a priori assessment criteria are clearly defined before testing and then needs to be proven to be reproducible. Objective comparison by multivariate analysis against known standards and other clinical parameters enables the true added value of new techniques to be measured. Finally, for a staging method or technique to achieve acceptances as a gold standard prospective validation of predefined imaging criteria against clinically relevant outcomes such as disease free survival, overall survival and local recurrence is also necessary. The development and acceptance of high resolution MRI for assessment of patients with rectal cancer illustrate how such validations can lead to changes in practice.
Process monitoring oriented IC testing

The authors proposed the use of functional testing for the extraction of IC manufacturing defect characteristics. It is demonstrated, using an SRAM (static random-access memory) example, that such extraction is feasible if an appropriate methodology for the interpretation of testing results is applied. The methodology allows for the extraction of information about process disturbances and abnormalities causing IC malfunctions. In this methodology the Monte Carlo fault modeling technique, combined with circuit simulation, was applied to build a defect fault vocabulary. The simulation experiment conducted by using this methodology demonstrated that a spectrum of signatures can be created to represent process disturbances. It was also shown that such a spectrum of signatures can be sensitive enough to changes in the defect densities. <<ETX>>