Miracle-dz/UniFAR-FTUs huggingface dataset:
Rational Live Oral Carrier Vaccine Design by Mutating Virulence-Associated Genes of Yersinia enterocolitica

ABSTRACT Three different Yersinia enterocolitica serotype O8 strains harboring mutations in virulence-associated genes coding forYersinia adhesin A (YadA), Mn-cofactored superoxide dismutase (SodA), and high-molecular-weight protein 1 were analyzed for their ability to colonize and persist in tissues after orogastric immunization of C57BL/6 mice. We demonstrated that all threeYersinia mutant strains were markedly impaired in their ability to disseminate into the spleens and livers of immunized mice but were able to colonize the Peyer’s patches for at least 12 days, resulting in the induction of significant antibody titers againstYersinia outer proteins (Yops) and in the priming ofYersinia antigen-specific CD4+ Th1 cells isolated from spleens. The high level of attenuation did not diminish the immunogenic properties of the mutant strains. In fact, mice immunized with a single oral dose of any of the mutant strains were protected against a lethal oral-challenge infection with wild-typeY. enterocolitica. Moreover, adoptive transfer ofYersinia-specific antibodies from sera of mice immunized with the mutant WAP-314 sodA revealed that this protection could be mediated by Yersinia-specific immunoglobulins.
Learning and reasoning in logic tensor networks: theory and application to semantic image interpretation

This paper presents a revision of Real Logic and its implementation with Logic Tensor Networks and its application to Semantic Image Interpretation. Real Logic is a framework where learning from numerical data and logical reasoning are integrated using first order logic syntax. The symbols of the signature of Real Logic are interpreted in the data-space, i.e, on the domain of real numbers. The integration of learning and reasoning obtained in Real Logic allows us to formalize learning as approximate satisfiability in the presence of logical constraints, and to perform inference on symbolic and numerical data. After introducing a refined version of the formalism, we describe its implementation into Logic Tensor Networks which uses deep learning within Google's TensorFlow™. We evaluate LTN on the task of classifying objects and their parts in images, where we combine state-of-the-art-object detectors with a part-of ontology. LTN outperforms the state-of-the-art on object classification, and improves the performances on part-of relation detection with respect to a rule-based baseline.
Loss of endothelial pertussis toxin-sensitive G protein function in atherosclerotic porcine coronary arteries.

Pertussis toxin, an irreversible inhibitor of some G proteins, inhibits endothelium-dependent relaxations to certain agonists in porcine coronary arteries. In the present study, the effects of the toxin were examined on endothelium-dependent and -independent relaxations of hypercholesterolemic and atherosclerotic porcine coronary arteries to assess the functional state of the endothelial pertussis toxin-sensitive G protein. Male Yorkshire pigs were maintained on either a regular diet (control group, n = 7) or a 2% high-cholesterol diet (cholesterol-fed group, n = 7) for 10 weeks. After the initial 2 weeks of maintenance, animals in both groups underwent balloon catheter removal of the endothelium of the left anterior descending or left circumflex coronary arteries. Endothelium-dependent responses were examined in vitro after 10 weeks of maintenance; at this time, a full lining of endothelial cells in both left coronary arteries was confirmed histologically. In arteries with endothelium of the control group (normal responses), pertussis toxin significantly inhibited the endothelium-dependent relaxations to serotonin, UK14304 (a selective alpha 2-adrenergic receptor agonist), and thrombin but not those to ADP, bradykinin, or the calcium ionophore A23187. In previously denuded arteries of the control group (effects of endothelial regeneration alone) or intact arteries of the cholesterol-fed group (effects of hypercholesterolemia alone), the relaxations to serotonin, UK14304, and thrombin were impaired significantly; those relaxations were impaired further in previously denuded arteries of the cholesterol-fed group (effects of atherosclerosis). The inhibitory effects of pertussis toxin were significantly reduced after endothelial regeneration and in hypercholesterolemia and were almost absent in atherosclerosis. (ABSTRACT TRUNCATED AT 250 WORDS)
Prevalence and Antimicrobial Susceptibility Pattern of Methicillin-resistant Staphylococcus Aureus [MRSA] Isolates at a Tertiary Care Hospital in Mangalore, South India

Background/Aim: Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of nosocomial infections worldwide. The aim of this study was to determine the prevalence of MRSA and their antimicrobial susceptibility pattern in our hospital located in Mangalore, India. Materials and Methods: The bacterial isolates from various clinical specimens of patients admitted in our hospital were cultured as per standard protocol and all isolates of Staphylococcus aureus obtained were included in the study. The isolates were identified by standard methods like catalase test, slide and tube coagulase tests, and growth on Mannitol salt agar (HiMedia Lab, Mumbai). The antimicrobial susceptibility testing was performed by Kirby–Bauer disc diffusion method. The D-test for inducible clindamycin resistance was performed. The isolates were tested for methicillin resistance by using oxacillin disc by disc diffusion method and confirmed by agar screen test (oxacillin 6 μgm/ml). The results were interpreted according to CLSI criteria. Results: During a period of one year, a total of 237 isolates of S. aureus were studied and 69 (29.1%) were found to be methicillin-resistant. MRSA isolates showed greater resistance to multiple drugs than methicillin sensitive Staphylococcus aureus MSSA isolates. Inducible clindamycin resistance was 18.8% in MRSA as against 3.5% in MSSA. About 40–50% of MRSA were resistant to erythromycin, gentamicin, and chloramphenicol, while less than 30% were resistant to ciprofloxacin and amikacin. However, all strains were sensitive to vancomycin. Conclusion: The regular surveillance of hospital-acquired infections of MRSA may be helpful in formulating and monitoring the antibiotic policy. This may also help in preserving antibiotics like vancomycin, only for life-threatening staphylococcal diseases.
A Novel Coordinated Spectrum Assignment Scheme for Densely Deployed Enterprise LTE Femtocells

With the emergence of femtocells, the complexity and heterogeneity of the mobile radio networks have been dramatically increased, which lead to more operational tasks such as self-configuration and optimization of the new distributed wireless system. The allocation of spectrum and avoidance of inter-cell interference are some of the more urgent challenges that operators have to face before femtocells become widely deployed. However, considering the small cell radius and irregular coverage area of the femto BS, the typical ICIC (Inter-Cell Interference Coordination) technologies such as FFR (Fractional Frequency Reuse) in current LTE network are not suitable for femtocells. In this paper, a novel coordinated spectrum assignment scheme is proposed for inter-femtocell interference coordination of densely deployed enterprise LTE femtocells. The proposed scheme is mainly composed of an autonomous selection process of dedicated subband for basic connectivity and a cooperated allocation process of shared subband for high data capacity. It works in a distributed and localized manner, showing a high level of scalability and feasibility.
Serum Fetuin A and Chemerin Levels Correlate with Hepatic Steatosis and Regional Adiposity in Maintenance Hemodialysis Patients

Background A deficiency of fetuin A is linked to cardiovascular calcification and mortality in dialysis patients. But, high levels of fetuin A and chemerin correlate with hepatic steatosis and regional adiposity in general population. The association between hepatic steatosis and fetuin A/chemerin levels in hemodialysis (HD) remains unclear. Methods We performed a cross-sectional, observational study; 216 prevalent HD patients from a single center were enrolled. Baseline serum fetuin A, chemerin levels, conicity index and anthropometric parameters were checked. Presence of hepatic steatosis was qualified by liver ultrasound and quantified by the hepato-renal index (HRI); central obesity defined by waist circumference (WC). ROC analyses and multivariate logistic regression analyses for prediction of hepatic steatosis and central obesity on the basis of fetuin A/chemerin levels, anthropometric parameters, and other relevant covariates were performed. Results Data from 103 women and 113 men (mean age 60±12 years) were analyzed. Eighty subjects had hepatic steatosis and their HRIs were significantly higher than those without hepatic steatosis (P<0.001). Serum fetuin A levels were positively associated with HRIs (P<0.001) and chemerin levels (P<0.001). Fetuin A, chemerin and WC were predictors for hepatic steatosis and central obesity by ROC curve. In multivariate logistic regression analysis, fetuin A and WC independently predicted hepatic steatosis defined by HRIs. And chemerin predicted central obesity and regional adiposity after covariate adjustments (all P<0.05). Conclusions Serum fetuin A levels were higher in prevalent HD patients with hepatic steatosis, and positively correlated with chemerin levels. Chemerin levels predicted central obesity as well as regional adiposity in the HD patients.
Abnormal dendritic spine characteristics in the temporal and visual cortices of patients with fragile-X syndrome: a quantitative examination.

Fragile-X syndrome is a common form of mental retardation resulting from the inability to produce the fragile-X mental retardation protein. Qualitative examination of human brain autopsy material has shown that fragile-X patients exhibit abnormal dendritic spine lengths and shapes on parieto-occipital neocortical pyramidal cells. Similar quantitative results have been obtained in fragile-X knockout mice, that have been engineered to lack the fragile-X mental retardation protein. Dendritic spines on layer V pyramidal cells of human temporal and visual cortices stained using the Golgi-Kopsch method were investigated. Quantitative analysis of dendritic spine length, morphology, and number was carried out on patients with fragile-X syndrome and normal age-matched controls. Fragile-X patients exhibited significantly more long dendritic spines and fewer short dendritic spines than did control subjects in both temporal and visual cortical areas. Similarly, fragile-X patients exhibited significantly more dendritic spines with an immature morphology and fewer with a more mature type morphology in both cortical areas. In addition, fragile-X patients had a higher density of dendritic spines than did controls on distal segments of apical and basilar dendrites in both cortical areas. Long dendritic spines with immature morphologies and elevated spine numbers are characteristic of early development or a lack of sensory experience. The fact that these characteristics are found in fragile-X patients throughout multiple cortical areas may suggest a global failure of normal dendritic spine maturation and or pruning during development that persists throughout adulthood.
Corticosteroids as adjunctive therapy for severe Pneumocystis carinii pneumonia in the acquired immunodeficiency syndrome. A double-blind, placebo-controlled trial.

BACKGROUND Preliminary reports suggest that patients with the acquired immunodeficiency syndrome (AIDS) and Pneumocystis carinii pneumonia may benefit from the addition of corticosteroid treatment to antibiotic therapy. METHODS We conducted a double-blind, placebo-controlled trial to assess the efficacy of adjunctive corticosteroids in patients with AIDS and severe P. carinii pneumonia. Patients with marked abnormalities in gas exchange who had been treated with antibiotics for less than 72 hours were randomly assigned to receive either methylprednisolone (40 mg) or placebo every 6 hours for 7 days, in addition to treatment for 21 days with trimethoprim-sulfamethoxazole. The primary outcome measures were survival until hospital discharge and the development of respiratory failure. RESULTS Twenty-three patients were enrolled in the study; there were no significant differences in base-line clinical or laboratory measures between the two treatment groups. Of 12 patients treated with corticosteroids, 9 (75 percent) survived until hospital discharge, as compared with only 2 of 11 placebo recipients (18 percent) (P less than 0.008). Respiratory failure developed in nine placebo recipients, as compared with only three patients treated with corticosteroids (P less than 0.008). No patient required the interruption or discontinuation of corticosteroid or antibiotic treatment because of toxicity or a complicating event. Because of the marked difference in survival, it was deemed unethical to continue the trial, and the study was terminated. CONCLUSIONS Early adjunctive corticosteroid therapy can improve survival and decrease the occurrence of respiratory failure in patients with AIDS and severe P. carinii pneumonia.
A Compiler to Implement Lotos Specifications on Distributed Environments

In this paper, we propose a method to implement distributed systems using the formal description language LOTOS. First, we give a sub-class of LOTOS for specifying distributed systems. In the sub-class, each system's behavior is described as a set of interacting processes where each process is assigned to a specific node of a distributed system and inter-node process interaction is specified with LOTOS operators such as choice, disabling and multi-way synchronization. We propose a method to implement such a LOTOS specification as a set of programs which run on the corresponding nodes cooperating with each other by exchanging messages. In the proposed method, we transform processes assigned to a node into a multi-threaded executable program, and implement LOTOS operators specified among processes on distributed nodes with total-order broadcast communication. We have developed a LOTOS compiler based on the proposed method. Some experimental results show that programs generated from distributed systems' specifications can be used as prototypes for practical use or for performance evaluation/analysis.
Study of metamemory in patients with chronic alcoholism using a feeling-of-knowing episodic memory task.

BACKGROUND Alcoholism affects various cognitive processes, including components of memory. Metamemory, though of particular interest for patient treatment, has not yet been extensively investigated. METHODS A feeling-of-knowing (FOK) measure of metamemory was administered to 28 alcoholic patients and 28 healthy controls during an episodic memory task including the learning of 20 pairs of items, followed by a 20-minute delayed recall and a recognition task. Prior to recognition, participants rated their ability to recognize each nonrecalled word among 4 items. This episodic FOK measure served to compare predictions of future recognition performance and actual recognition performance. Furthermore, a subjective measure of metamemory, the Metamemory In Adulthood (MIA) questionnaire, was completed by patients and controls. This assessment of alcoholic patients' metamemory profile was accompanied by an evaluation of episodic memory and executive functioning. RESULTS FOK results revealed deficits in accuracy, with the alcoholic patients providing overestimations. There were also links between FOK inaccuracy, executive decline, and episodic memory impairment in patients. MIA results showed that although alcoholics did display memory difficulties, they did not differ from controls on questions about memory capacity. CONCLUSIONS Chronic alcoholism affects both episodic memory and metamemory for novel information. Patients were relatively unaware of their memory deficits and believed that their memory was as good as that of the healthy controls. The monitoring measure (FOK) and the subjective measure of metamemory (MIA) showed that patients with chronic alcoholism overestimated their memory capacities. Episodic memory deficit and executive dysfunction would explain metamemory decline in this clinical population.
Assessing the Efficacy of Nano- and Micro-Sized Magnetic Particles as Contrast Agents for MRI Cell Tracking

Iron-oxide based contrast agents play an important role in magnetic resonance imaging (MRI) of labelled cells in vivo. Currently, a wide range of such contrast agents is available with sizes varying from several nanometers up to a few micrometers and consisting of single or multiple magnetic cores. Here, we evaluate the effectiveness of these different particles for labelling and imaging stem cells, using a mouse mesenchymal stem cell line to investigate intracellular uptake, retention and processing of nano- and microsized contrast agents. The effect of intracellular confinement on transverse relaxivity was measured by MRI at 7 T and in compliance with the principles of the ‘3Rs’, the suitability of the contrast agents for MR-based cell tracking in vivo was tested using a chick embryo model. We show that for all particles tested, relaxivity was markedly reduced following cellular internalisation, indicating that contrast agent relaxivity in colloidal suspension does not accurately predict performance in MR-based cell tracking studies. Using a bimodal imaging approach comprising fluorescence and MRI, we demonstrate that labelled MSC remain viable following in vivo transplantation and can be tracked effectively using MRI. Importantly, our data suggest that larger particles might confer advantages for longer-term imaging.
Subject-Verb Agreement in Respective Coordinations and Context Freeness

This fact leads directly to a demonstration that there is, after all, a cross-serial dependency involving the grammatical number of subject NPs and verbs in respectively constructions. However, it is not clear at present how representative such speakers are, and so instead of making claims about English in general, we will confine them to just those varieties of the language that stigmatize examples like (2), which will be denoted as English1, leaving to one side any varieties of which this may not be true (English2). I In English1, a verb that formally distinguishes singular from plural, i.e., a non-auxiliary present tense verb, cannot occur in a respectively construction if the corresponding subject NP is singular. This cannot be accounted for merely by barring marked singular verbs from occurring in coordinate predicates of respectively constructions. Such a move would correctly exclude examples like (1), but it would allow sentences like (2), with plural verbs corresponding to singular subjects. Nor is it possible to simply bar singular subjects from occurring in respectively constructions, since they are perfectly possible provided the corresponding verb is either a past tense, as in (3a), or an auxiliary, as in (3b).
Skiplist-based concurrent priority queues

This paper addresses the problem of designing scalable concurrent priority queues for large scale multiprocessors machines with up to several hundred processors. Priority queues are fundamental in the design of modern multiprocessor algorithms, with many classical applications ranging from numerical algorithms through discrete event simulation and expert systems. While highly scalable approaches have been introduced for the special case of queues with a fixed set of priorities, the most efficient designs for the general case are based on the parallelization of the heap data structure. Though numerous intricate heap-based schemes have been suggested in the literature, their scalability seems to be limited to small machines in the range of ten to twenty processors. This paper proposes an alternative approach: to base the design of concurrent priority queues on the probabilistic skiplist data structure, rather than on a heap. To this end, we show that a concurrent skiplist structure, following a simple set of modifications, provides a concurrent priority queue with a higher level of parallelism and significantly less contention than the fastest known heap-based algorithms. Our initial empirical evidence, collected on a simulated 256 node shared memory multiprocessor architecture similar to the MIT Alewife, suggests that the new skiplist based priority queue algorithm scales significantly better than heap based schemes throughout most of the concurrency range. With 256 processors, they are about twice as fast in performing deletions and up to 8 times faster in performing insertions.
GenoType® MTBDRplus compared with conventional drug-susceptibility testing of Mycobacterium tuberculosis in a low-resistance locale.

AIM To determine the diagnostic accuracy of Geno Type® MTBDRplus compared with conventional proportional method (PM) drug susceptibility testing (DST) for detecting drug resistance of Mycobacterium tuberculosis (MTB) clinical isolates derived from the University Hospital of Heraklion, Crete, Greece. METHODS All MTB clinical isolates obtained between January 2000 and May 2009 were tested prospectively using the PM DST. All isolates were also tested either prospectively (strains isolated after January 2006; n = 140) or retrospectively (January 2000-December 2005; n = 81) using MTBDRplus. RESULTS Among the 221 MTB isolates tested, 19 were resistant to isoniazid based on PM DST. The MTBDRplus assay identified 18 INH-resistant strains. Of these, 12 strains gave positive hybridization results with the mutation-specific probe katG Ser315Thr. The other six INH-resistant strains carried the mutation 15C→T in the inhA promoter region. One INH-sensitive strain, as determined by PM DST, had a katG gene mutation. The sensitivity, specificity, and positive and negative predictive values of MTBDRplus for INH were 89.5, 99.5, 94.7 and 99%, respectively. The single rifampicin-resistant strain that was also the only multidrug resistance isolate gave a positive hybridization result with the mutation-specific probe MUT1: D516V, which confers resistance to rifampicin. CONCLUSION Despite the advantages of MTBDRplus (turn-around time of only 1 working day) compared with PM DST, the latter is still required in every case of a MTB clinical isolate, as the molecular assay does not detect 100% of drug resistance, especially INH resistance.
Targeted Mutation: Efficient Mutation Analysis for Testing Non-Functional Properties

Mutation analysis has proven to be a strong technique for software testing. Unfortunately, it is also computationally expensive and researchers have therefore proposed several different approaches to reduce the effort. None of these reduction techniques however, focuses on non-functional properties. Given that our goal is to create a strong test suite for testing a certain non-functional property, which mutants should be used? In this paper, we introduce the concept of targeted mutation, which focuses mutation effort to those parts of the code where a change can make a difference with respect to the targeted non-functional property. We show how targeted mutation can be applied to derive efficient test suites for estimating the Worst-Case Execution Time (WCET). We use program slicing to direct the mutations to the parts of the code that are likely to have the strongest influence on execution time. Finally, we outline an experimental procedure for how to evaluate the technique.