Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards an abstract recursive agent

Current business trends, policy markets, production requirements, etc., have created the need for integrating pre-existing Multi Agent Systems (MAS). In the agent-specialized literature, we have found very little work about agent architectures and methodologies that allow us to carry out recursive and dynamic analysis, design, and implementation of MASs. Several difficult challenges for automated systems can be tackled by giving full meaning to the agent concept: adopting a recursive definition of agents and allowing for the dynamic creation of agents by the agents themselves. In this work, we propose a definition of an abstract recursive agent and an initial formalization of its behaviour in terms of the behaviour of its constituent agents.
Intramolecular CH…O Hydrogen Bonds in the AI and BI DNA-like Conformers of Canonical Nucleosides and their Watson-Crick Pairs. Quantum Chemical and AIM Analysis

Abstract The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-crick pairs, which were regarded as the simplest models of the double- stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH…O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2′H…O5′, C1′H…O2, C6H…O5′, C8H…O5′, and C6H…O4′. The energy values of H-bonds occupy the range of 2.3–5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH…O hydrogen bonds appeared to “survive” turns of bases against the sugar, sometimes in rather large ranges of the angle χ values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H…O4 and N1…N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H…O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH…O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.
Determination of the Deacetylation Degree of Chitooligosaccharides

The methods for determination of chitosan content recommended in the Chinese Pharmacopoeia and the European Pharmacopoeia are not applicable for evaluation of the extent of deacetylation (deacetylation degree, DD) in chitooligosaccharides (COS). This study explores two different methods for assessment of DD in COS having relatively high and low molecular weights: an acid-base titration with bromocresol green indicator and a first order derivative UV spectrophotometric method for assessment of DD in COS. The accuracy of both methods as a function of molecular weight was also investigated and compared to results obtained using 1H NMR spectroscopy. Our study demonstrates two simple, fast, widely adaptable, highly precise, accurate, and inexpensive methods for the effective determination of DD in COS, which have the potential for widespread commercial applications in developing country.
Two spatially distinct genetic elements constitute a bipartite DNA replication origin in the minute virus of mice genome

Mutations were introduced into plasmid pMM984, a full-length infectious clone of the fibrotropic strain of minute virus of mice, to identify cis-acting genetic elements required for the excision and replication of the viral genome. The replicative capacity of these mutants was measured directly, using an in vivo transient DNA replication assay following transfection of plasmids into murine A9 cells and primate COS-7 cells. Experiments with subgenomic constructs indicated that both viral termini must be present on the same DNA molecule for replication to occur and that the viral nonstructural protein NS-1 must be provided in trans. The necessary sequences were located within 1,084 and 807 nucleotides of the 3' and 5' ends of the minute virus of mice genome, respectively. The inhibitory effect of deletions within the 206-bp 5'-terminal palindrome demonstrated that these sequences comprise a cis-acting genetic element that is absolutely essential for the excision and replication of viral DNA. The results further indicated a requirement for a stem-plus-arms T structure as well as for the formation of a simple hairpin. In addition, the removal of one copy of a tandemly arranged 65-bp repeat found 94 nucleotides inboard of the 5'-terminal palindrome inhibited viral DNA replication in cis by 10- and just greater than 100-fold in A9 and COS-7 cells, respectively. The latter results define a novel genetic element within the 65-bp repeated sequence, distinct from the terminal palindrome, that is capable of regulating minute virus of mice DNA replication in a species-specific manner.
Building a high-performance communication layer over virtual interface architecture on Linux clusters

The Virtual Interface Architecture (VIA) is an industry standard user-level communication architecture for cluster or system area networks. The VIA provides a protected, directly-accessible interface to a network hardware, removing the operating system from the critical communication path. Although the VIA enables low-latency high-bandwidth communication, the application programming interface defined in the VIA specification lacks many high-level features. In this paper, we develop a high performance communication layer over VIA, named SOVIA (Sockets Over VIA). Our goal is to make the SOVIA layer as efficient as possible so that the performance of native VIA can be delivered to the application, while retaining the portable Sockets semantics. We find that the single-threaded implementation with conditional sender-side buffering is effective in reducing latency. To increase bandwidth, we implement a flow control mechanism similar to the TCP's sliding window protocol. Our flow control mechanism is enhanced further by adding delayed acknowledgments and the ability to combine small messages. With these optimizations, SOVIA realizes comparable performance to native VIA, showing the latency of 10.5 µsec for 4-byte messages and the peak bandwidth of 814Mbps on Giganet's cLAN. The functional validity of SOVIA is verified by porting FTP (File Transfer Protocol) application over SOVIA.
Low-rank matrix factorization with attributes

We develop a new collaborative filtering (CF) method that combines both previously known users' preferences, i.e. standard CF, as well as product/user attributes, i.e. classical function approximation, to predict a given user's interest in a particular product. Our method is a generalized low rank matrix completion problem, where we learn a function whose inputs are pairs of vectors -- the standard low rank matrix completion problem being a special case where the inputs to the function are the row and column indices of the matrix. We solve this generalized matrix completion problem using tensor product kernels for which we also formally generalize standard kernel properties. Benchmark experiments on movie ratings show the advantages of our generalized matrix completion method over the standard matrix completion one with no information about movies or people, as well as over standard multi-task or single task learning methods.
Développement d'outils de caractérisation de la mécanique pulmonaire en ventilation liquidienne totale

An unsteady flowmeter was developed for implementation in the Inolivent-4 total liquid ventilator prototype. The proposed design consists of a symmetrical venturi tube com­ prising three pressure sensors and in which flow measurement is obtained by numerically solving a slightly modified version of the unsteady Bernoulli equation. A prototype was validated experimentally by applying zero-mean sinusoidal flows. Low-frequency characte­ rization determined the venturi discharge coefficient as a function of the Reynolds number, and higher-frequency (<4 Hz) measurements determined the applicable bandwidth of the device. The velocity profiles were measured in the venturi by particle image velocimetry (PIV), and the device was calibrated experimentally by comparison with an ultrasonic flowmeter and measurements from a piston pump. Results showed that quasi-steady flows could be accurately measured in the 5 ml/s-60 ml/s range, while low-amplitude (<10 ml/s) oscillatory flows were well measured for frequencies below 3 Hz. Finally, PIV experiments showed that the flat velocity profile assumption required for a simple solution of the flow­ meter equation was valid within the operating range.
Asymptomatic serum cryptococcal antigenemia and early mortality during antiretroviral therapy in rural Uganda

Objective To evaluate the association between a positive serum cryptococcal antigen (CRAG) test at baseline and mortality during the first 12 weeks on antiretroviral therapy (ART). Cryptococcal meningitis is a leading cause of HIV‐related mortality in Africa, but current guidelines do not advocate CRAG testing as a screening tool.
DNA-Salmonella enterica Serovar Typhimurium Primer-Booster Vaccination Biases towards T Helper 1 Responses and Enhances Protection against Leishmania major Infection in Mice

ABSTRACT Successful resolution of infections by intracellular pathogens requires gamma interferon (IFN-γ). DNA vaccines promote T helper 1 (Th1) responses by triggering interleukin-12 (IL-12) release by dendritic cells (DC) through Toll-like receptor 9 (TLR9). In humans TLR9 is restricted to plasmacytoid DC. Here we show that DNA-Salmonella enterica serovar Typhimurium primer-booster vaccination, which provides alternative ligands to bind TLR4 on myeloid DC, strongly biases towards Th1 responses compared to vaccination with DNA alone. This results in higher immunoglobulin G2a (IgG2a) responses compared to IgG1 responses, higher IFN-γ responses compared to IL-10 CD4+-T-cell responses, and enhanced protection against Leishmania major infection in susceptible BALB/c mice.
A BIOFACIE STUDY OF AN OUTCROPPING UNIT AT IBII QUARRY SITE, AFIKPO BASIN, SOUTH EASTERN NIGERIA

A Biofacie study of an outcropping unit at the Ibii quarry site, Afikpo Basin, South Eastern Nigeria was carried out to determine the fossil assemblage of the samples in relation to its lithological variations in order to determine the age and paleoenvironment of deposition, using a total of ten samples obtained from the field. The samples were further subjected to lithological/Sedimentological and palynological analysis respectively. The results for the lithological/Sedimentological analysis which cuts across both processes of lithological description, lithofacie and wet sieve analysis showed that the samples were highly calcareous, and the lithofacie analysis showed the presence of authigenic minerals such as quartz, heavy minerals, muscovite, gypsum, and mica flakes respectively while the wet sieve analysis showed a high value of shale to sand ratio all of which further depicts a marginal marine to marine depositional environment. The palynological analysis yielded practically no Palynomorph to very scanty to low quantity of palynomorphs. The palynomorphs include; Psilatricolporites sp, Laevigasporites discordatus, Diatom and Fungal spore. Although the analysis yielded no environmentally significant Palynomorph, the presence of Diatom and fungal spore in most of the samples portray that the samples were probably deposited in a marine setting.
Using Very Simple Statistics for Review Search: An Exploration

We report on work in progress on using very simple statistics in an unsupervised fashion to re-rank search engine results when review-oriented queries are issued; the goal is to bring opinionated or subjective results to the top of the results list. We find that our proposed technique performs comparably to methods that rely on sophisticated pre-encoded linguistic knowledge, and that both substantially improve the initial results produced by the Yahoo! search engine.
Modelling the cost-effectiveness of PCSK9 inhibitors vs. ezetimibe through LDL-C reductions in a Norwegian setting

Abstract Aims Despite the success of statins, there remains unmet clinical need in cardiovascular disease (CVD) prevention. New proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors reduce low-density lipoprotein cholesterol (LDL-C) by 55–65%. Two PCSK9 inhibitors, evolocumab, and alirocumab, were approved for use in Norway but not yet for reimbursement through public national insurance. We aim to explore the cost-effectiveness of these compared with available treatments in a Norwegian setting. Methods and results A state transition Markov model was developed to model the cost-effectiveness of PCSK9 inhibitors for prevention of coronary heart disease, ischaemic strokes, and death among high-risk patient subpopulations in Norway, in both primary and secondary settings. Evolocumab and alirocumab are compared against ezetimibe and standard treatment. Risk of CVD is based on population incidence rates and adjusted according to baseline risk factors. Preventative effect of treatment was modelled according to absolute reduction in LDL-C. PCSK9 inhibitors were never found to be cost-effective in primary prevention. In secondary prevention they were cost-effective only for older, high-risk patients. The lowest cost-effectiveness ratios were for heterozygous familial hypercholesterolaemia patients and high-risk diabetics, with €63 200 and €68 400 per quality-adjusted life-year, respectively. Conclusion High lifetime costs of PCSK9 inhibitors may not be offset by estimated health gains for most eligible patients. PCSK9 inhibitors are found in the model only to be cost-effective in secondary prevention for older patients with high absolute risk of CVD. This picture is likely to change as price decreases. Future research is needed to determine the long-term preventative effects of PCSK9 inhibitors.
Dependency Grammar Induction with Neural Lexicalization and Big Training Data

We study the impact of big models (in terms of the degree of lexicalization) and big data (in terms of the training corpus size) on dependency grammar induction. We experimented with L-DMV, a lexicalized version of Dependency Model with Valence (Klein and Manning, 2004) and L-NDMV, our lexicalized extension of the Neural Dependency Model with Valence (Jiang et al., 2016). We find that L-DMV only benefits from very small degrees of lexicalization and moderate sizes of training corpora. L-NDMV can benefit from big training data and lexicalization of greater degrees, especially when enhanced with good model initialization, and it achieves a result that is competitive with the current state-of-the-art.
The Influence of AHI1 Variants on the Diagnosis and Treatment Outcome in Schizophrenia

The present study aimed to explore whether four single nucleotide polymorphisms (SNPs) within the AHI1 gene could be associated with schizophrenia (SCZ) and whether they could predict the clinical outcomes in SCZ patients treated with antipsychotics. Four hundred twenty-six (426) in-patients with SCZ and 345 controls were genotyped for four AHI1 SNPs (rs11154801, rs7750586, rs9647635 and rs9321501). Baseline and clinical measures for SCZ patients were assessed through the Positive and Negative Syndrome Scale (PANSS). Allelic and genotypic frequencies in SCZ subjects were compared with those of controls using the χ2 statistics. The repeated-measure ANOVA was used for the assessment of treatment outcomes measured by PANSS changes. The case-control analysis did not show any difference in the genotypic distribution of the SNPs, while in the allelic analysis, a weak association was found between the rs9647635 A allele and SCZ. Furthermore, in the haplotype analysis, three haplotypes resulted in being associated with SCZ. On the other hand, two SNPs (rs7750586 and rs9647635) were associated with clinical improvement of negative symptoms in the allelic analysis, although in the genotypic analysis, only trends of association were found for the same SNPs. Our findings suggest a possible influence of AHI1 variants on SCZ susceptibility and antipsychotic response, particularly concerning negative symptomatology. Subsequent well-designed studies would be mandatory to confirm our results due to the methodological shortcomings of the present study.
REWIND: Recovery Write-Ahead System for In-Memory Non-Volatile Data-Structures

Recent non-volatile memory (NVM) technologies, such as PCM, STT-MRAM and ReRAM, can act as both main memory and storage. This has led to research into NVM programming models, where persistent data structures remain in memory and are accessed directly through CPU loads and stores. Existing mechanisms for transactional updates are not appropriate in such a setting as they are optimized for block-based storage. We present REWIND, a user-mode library approach to managing transactional updates directly from user code written in an imperative general-purpose language. REWIND relies on a custom persistent in-memory data structure for the log that supports recoverable operations on itself. The scheme also employs a combination of non-temporal updates, persistent memory fences, and lightweight logging. Experimental results on synthetic transactional workloads and TPC-C show the overhead of REWIND compared to its non-recoverable equivalent to be within a factor of only 1.5 and 1.39 respectively. Moreover, REWIND outperforms state-of-the-art approaches for data structure recoverability as well as general purpose and NVM-aware DBMS-based recovery schemes by up to two orders of magnitude.
Generating Affective Natural Language for Parents of Neonatal Infants

This paper presents several affective NLG strategies for generating medical texts for parents of pre-term neonates. Initially, these were meant to be personalised according to a model of the recipient's level of stress. However, our evaluation showed that all recipients preferred texts generated with the affective strategies, regardless of predicted stress level.
Negative symptoms in schizophrenia—A review

Negative symptoms refer to the weakening or lack of normal thoughts, emotions or behaviour in schizophrenia patients. Their prevalence in first-episode psychosis is high, 50–90%, and 20–40% of schizophrenia patients have persisting negative symptoms. Severe negative symptoms during the early stages of treatment predict poor prognosis. The aim of the study was to review the current literature on the negative symptoms of schizophrenia. In June 2007, the following databases were searched: Web of Science, PubMed, PsycINFO, Medline (Ovid) and Scopus. The search included articles written in English and no time limit was determined. The studies were manually screened by one of the authors according to the title and abstract. About one in three schizophrenia patients suffer from significant negative symptoms. In these patients, negative symptoms constitute a key element of overall symptoms, weakening their ability to cope with everyday activities, affecting their quality of life and their ability to manage without significant outside help. About one in three schizophrenia patients suffer from significant negative symptoms. Attention should be focused on negative symptoms during the early phase of treatment, because they cause significant impairment to patients’ quality of life. So far, no treatment appears to substantially improve negative symptoms narrowly defined. However, according to clinical experience, when treating negative symptoms, the best effect is achieved by optimizing the dose of medication and by complementing it with psychosocial therapies.
Neonatal Cerebral Infarction Diagnosed by Diffusion-Weighted MRI: Pseudonormalization Occurs Early

Background— Seizures in the neonatal period may be the single symptom of acute ischemic cerebral infarction. It may be difficult to establish the diagnosis in the acute phase by the use of ultrasound, CT, and conventional MRI because of the high water content of the immature brain. Diffusion-weighted (DW) MRI is a very sensitive and fast imaging modality to visualize acute ischemic stroke in infants even before conventional MR images become abnormal. Signal abnormality in DW MRI, however, seems to follow a different time course than in older patients. Case Description— DW MRI became falsely negative 1 week after stroke (pseudonormalization) in 2 newborn patients during persistence of signal abnormalities on turbo spin-echo images, whereas the so-called pseudonormalization in adults normally occurs within 10 to 14 days. Conclusions— T2-weighted sequences should supplement DW images to reliably detect subacute ischemic infarctions in the neonatal period.
Avoiding the Disk Bottleneck in the Data Domain Deduplication File System

Disk-based deduplication storage has emerged as the new-generation storage system for enterprise data protection to replace tape libraries. Deduplication removes redundant data segments to compress data into a highly compact form and makes it economical to store backups on disk instead of tape. A crucial requirement for enterprise data protection is high throughput, typically over 100 MB/sec, which enables backups to complete quickly. A significant challenge is to identify and eliminate duplicate data segments at this rate on a low-cost system that cannot afford enough RAM to store an index of the stored segments and may be forced to access an on-disk index for every input segment. This paper describes three techniques employed in the production Data Domain deduplication file system to relieve the disk bottleneck. These techniques include: (1) the Summary Vector, a compact in-memory data structure for identifying new segments; (2) Stream-Informed Segment Layout, a data layout method to improve on-disk locality for sequentially accessed segments; and (3) Locality Preserved Caching, which maintains the locality of the fingerprints of duplicate segments to achieve high cache hit ratios. Together, they can remove 99% of the disk accesses for deduplication of real world workloads. These techniques enable a modern two-socket dual-core system to run at 90% CPU utilization with only one shelf of 15 disks and achieve 100 MB/sec for single-stream throughput and 210 MB/sec for multi-stream throughput.