Miracle-dz/UniFAR-FTUs huggingface dataset:
Representation and Processing of Structures with Binary Sparse Distributed Codes

The schemes for compositional distributed representations include those allowing on-the-fly construction of fixed dimensionality codevectors to encode structures of various complexity. Similarity of such codevectors takes into account both structural and semantic similarity of represented structures. We provide a comparative description of sparse binary distributed representation developed in the framework of the associative-projective neural network architecture and the more well known holographic reduced representations of T.A. Plate (1995) and binary spatter codes of P. Kanerva (1996). The key procedure in associative-projective neural networks is context-dependent thinning which binds codevectors and maintains their sparseness. The codevectors are stored in structured memory array which can be realized as distributed auto-associative memory. Examples of distributed representation of structured data are given. Fast estimation of the similarity of analogical episodes by the overlap of their codevectors is used in the modeling of analogical reasoning both for retrieval of analogs from memory and for analogical mapping.
Unexpected Inhibition of Peptidoglycan LD-Transpeptidase from Enterococcus faecium by the β-Lactam Imipenem*

The β-lactam antibiotics mimic the d-alanyl4-d-alanine5 extremity of peptidoglycan precursors and act as “suicide” substrates of the dd-transpeptidases that catalyze the last cross-linking step of peptidoglycan synthesis. We have previously shown that bypass of the dd-transpeptidases by the ld-transpeptidase of Enterococcus faecium (Ldtfm) leads to high level resistance to ampicillin. Ldtfm is specific for the l-lysyl3-d-alanine4 bond of peptidoglycan precursors containing a tetrapeptide stem lacking d-alanine5. This specificity was proposed to account for resistance, because the substrate of Ldtfm does not mimic β-lactams in contrast to the d-alanyl4-d-alanine5 extremity of pentapeptide stems used by the dd-transpeptidases. Here, we unexpectedly show that imipenem, a β-lactam of the carbapenem class, totally inhibited Ldtfm at a low drug concentration that was sufficient to inhibit growth of the bacteria. Peptidoglycan cross-linking was also inhibited, indicating that Ldtfm is the in vivo target of imipenem. Stoichiometric and covalent modification of Ldtfm by imipenem was detected by mass spectrometry. The modification was mapped into the trypsin fragment of Ldtfm containing the catalytic Cys residue, and the Cys to Ala substitution prevented imipenem binding. The mass increment matched the mass of imipenem, indicating that inactivation of Ldtfm is likely to involve rupture of the β-lactam ring and acylation of the catalytic Cys residue. Thus, the spectrum of activity of β-lactams is not restricted to transpeptidases of the dd-specificity, as previously thought. Combination therapy with imipenem and ampicillin could therefore be active against E. faecium strains having the dual capacity to manufacture peptidoglycan with transpeptidases of the ld- and dd-specificities.
Risk factors for the rising rates of primary liver cancer in the United States.

BACKGROUND A recent increase in the incidence of hepatocellular carcinoma was reported in the United States. The cause of this witnessed rise remains unknown. METHODS We examined the temporal changes in both age-specific and age-standardized hospitalization rates of primary liver cancer associated with hepatitis C, hepatitis B, and alcoholic cirrhosis in the Department of Veterans Affairs Medical Center's Patient Treatment File. RESULTS A total of 1605 patients were diagnosed with primary liver cancer between 1993 and 1998. The overall age-adjusted proportional hospitalization rate for primary liver cancer increased from 36.4 per 100,000 (95% confidence interval [CI], 34.0-38.9) between 1993 and 1995 to 47.5 per 100,000 (95% CI, 44.6-50.1) between 1996 and 1998. There was a 3-fold increase in the age-adjusted rates for primary liver cancer associated with hepatitis C virus, from 2.3 per 100,000 (95% CI, 1. 8-3.0) between 1993 and 1995 to 7.0 per 100,000 (95% CI, 5.9-8.1) between 1996 and 1998. Concomitant with this rise, the age-specific rates for primary liver cancer associated with hepatitis C also shifted toward younger patients. During the same periods, the age-adjusted rates for primary liver cancer associated with either hepatitis B virus (2.2 vs 3.1 per 100,000) or alcoholic cirrhosis (8. 4 vs 9.1 per 100,000) remained stable. The rates for primary liver cancer without risk factors also remained without a statistically significant change, from 17.5 (95% CI, 15.8-19.1) between 1993 and 1995 to 19.0 per 100,000 (95% CI, 17.3-20.7) between 1996 and 1998. CONCLUSIONS Hepatitis C virus infection accounts for most of the increase in the number of cases of primary liver cancer among US veterans. The rates of primary liver cancer associated with alcoholic cirrhosis and hepatitis B virus infection have remained stable. Arch Intern Med. 2000;160:3227-3230.
Density‐based clustering

Clustering refers to the task of identifying groups or clusters in a data set. In density‐based clustering, a cluster is a set of data objects spread in the data space over a contiguous region of high density of objects. Density‐based clusters are separated from each other by contiguous regions of low density of objects. Data objects located in low‐density regions are typically considered noise or outliers. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 231–240 DOI: 10.1002/widm.30
Does Diabetes Double the Risk of Depression?

PURPOSE In this study, we compared the rate of depression diagnoses in adults with and without diabetes mellitus, while carefully controlling for number of primary care visits. METHODS We matched adults with incident diabetes (n = 2,932) or prevalent diabetes (n = 14,144) to nondiabetic control patients based on (1) age and sex, or (2) age, sex, and number of outpatient primary care visits. Logistic regression analysis was used to assess the association between various predictors and a diagnosis of depression in each diabetes cohort relative to matched nondiabetic control patients. RESULTS With matching for age and sex alone, patients with prevalent diabetes having few primary care visits were significantly more likely to have a new depression diagnosis than matched control patients (odds ratio [OR] = 1.46, 95% confidence interval [CI], 1.19–1.80), but this relationship diminished when patients made more than 10 primary care visits (OR = 0.95, 95% CI, 0.77–1.17). With additional matching for number of primary care visits, patients with prevalent diabetes mellitus with few primary care visits were more likely to have a new diagnosis of depression than those in control group (OR = 1.32, 95% CI, 1.07–1.63), but this relationship diminished and reversed when patients made more than 4 primary care visits (OR = 0.99, 95% CI, 0.80–1.23). Similar results were observed in the subset of patients with incident diabetes and their matched control patients. CONCLUSIONS Patients with diabetes have little or no increase in the risk of a new diagnosis of depression relative to nondiabetic patients when analyses carefully control for the number of outpatient visits. Studies showing such an association may have inadequately adjusted for comorbidity or for exposure to the medical care system.
Transcranial magnetic stimulation

This work gives an overview of the articles contained in the theme section of an issue of IEEE Engineering in Medicine and Biology Magazine. The manuscripts found in this magazine are from a series of presentations given as part of the "Uncovering the Mechanisms of Movement and Sensation using Transcranial Magnetic Stimulation (TMS)" symposium held during the XVth Congress of the International Society of Electrophysiology and Kinesology, Boston, USA, 18-21 June 2004. This symposium was conceived as an effort to strengthen communication and integration among movement scientists from the subdisciplines of neurology, clinical neurophysiology, basic and clinical neuroscience, physical therapy, biomechanics, biomedical engineering, robotics, and clinical care. Specifically, the symposium's aim was to generate a novel synthesis of basic science and clinical mechanisms of motor cortex plasticity and thus facilitate the design of rehabilitation programs.
Administration of dihydrotestosterone to rhesus monkeys inhibits gonadotropin-stimulated ovarian steroidogenesis.

Androgens, in addition to serving as a substrate for estrogen biosynthesis, exert autocrine/paracrine actions on ovarian function. However, much of the information regarding the actions of androgens on the ovary has been obtained using rodents, and the extent to which these results can be extrapolated to higher primates is uncertain. The current study was initiated to determine the effects of dihydrotestosterone (DHT) and testosterone (T) on the responsiveness of the rhesus monkey ovary to exogenous FSH and LH in vivo. Rhesus monkeys whose spontaneous gonadotropin secretion was interrupted with a GnRH antagonist received s. implants of either DHT or T for 5 d before and continuing throughout a 15-d i.v. infusion of human FSH and LH. Neither T nor DHT treatment synergized with FSH/LH to stimulate estrogen production or increases in ovarian weight. Rather, administration of DHT significantly reduced estrogen secretion and the augmentation of ovarian weight in response to exogenously administered FSH and LH. These results indicate that high concentrations of DHT are antagonistic to gonadotropin-stimulated ovarian function in primates.
Alternative approach in generating cancellable fingerprint by using matrices operations

A cancellable biometric system aims to revote a biometric feature of an authorized person when his biometric information is misused by improper. In this system, an established biometric image is transformed to a different feature to distinguish it from the original one. Moreover, this revocable system can regenerate a new transformed cancellable biometric feature if the previous transformed feature is known by someone. These basic concepts are similar with the idea of inverse matrix and elementary row operation in matrices domain. Biometric image as a digital image definitely can be processed in matrices domain. It means that the image is able to be imposed by matrices operations such as inverse matrix operation, elementary row operation, and Kronecker product operation. In matrix, these operations are used for several objectives whether inverting matrix elements, changing rows or columns, or enlarging size of the matrix. On the other hand, the combination of these operations even can produce a non-inversed matrix.
A mouse Model of Focal Vascular Injury Induces Astrocyte Reactivity, Tau Oligomers, and Aberrant Behavior

Neuropsychiatric symptom development has become more prevalent with 270,000 blast exposures occurring in the past 10 years in the United States. How blast injury leads to neuropsychiatric symptomology is currently unknown. Preclinical models of blast-induced traumatic brain injury have been used to demonstrate blood-brain barrier disruption, degenerative pathophysiology, and behavioral deficits. Vascular injury is a primary effect of neurotrauma that can trigger secondary injury cascades and neurodegeneration. Here we present data from a novel scaled and clinically relevant mouse blast model that was specifically developed to assess the outcome of vascular injury. We look at the biochemical effects and behavioral changes associated with blast injury in young-adult male BALB/c mice. We report that blast exposure causes focal vascular injury in the Somatosensory Barrel Field cortex, which leads to perivascular astrocyte reactivity, as well as acute aberrant behavior. Biochemical analysis revealed that mild blast exposure also invokes tauopathy, neuroinflammation, and oxidative stress. Overall, we propose our model to be used to evaluate focal blood-brain barrier disruption and to discover novel therapies for human neuropsychiatric symptoms.
Virulence-associated 15- to 17-kilodalton antigens in Rhodococcus equi: temperature-dependent expression and location of the antigens

Virulent Rhodococcus equi showing 15- to 17-kDa antigens, which is virulent in mice, was found to harbor an 85-kbp plasmid, and the 15- to 17-kDa antigens were found to be associated with possession of the 85-kbp plasmid of R. equi (S. Takai, T. Sekizaki, T. Ozawa, T. Sugawara, Y. Watanabe, and S. Tsubaki, Infect. Immun. 59:4056-4060, 1991). The expression of these antigens was temperature regulated: when cells were grown at a low temperature (25 to 32 degrees C), they did not express them, whereas they expressed them in large amounts when the cells were grown at a higher temperature (34 to 41 degrees C). The antigens were expressed on the cell surface, as evidenced by their susceptibility to proteolysis by a trypsin and by the biotin-avidin protein-blotting technique.
Measuring Congestion for Dynamic Task Allocation in Distributed Simulation

An important factor affecting the performance of distributed simulations running on parallel-processing computers is the allocation of logical processes to the available physical processors. An inefficient allocation can result in excessive communication times and unfavorable load conditions. This leads to long run times, possibly giving performance worse than that with a uniprocessor sequential event-list implementation. But the efficiency of any allocation strategy is dependent on the metric, or measure, it uses to characterize the load in the distributed system. This paper presents a simple and intuitive way of measuring and reallocating the load when the objective is to minimize simulation run time. The metric, based on estimating measures of message utilization at each processor, has been used in an adaptive scheme for load allocation, and experiments on an iPSC/2 Hypercube indicate that it successfully characterizes the load for purposes of reducing simulation run time. INFORMS Journal on Computing , ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
A woman and her canary: a tale of chlamydiae and lymphomas.

JNCI Vol. 99, Issue 18 | September 19, 2007 Fig. 1 . Radiologic and histopathologic features of the diffuse large B-cell lymphoma of the bronchus and immunohistochemical features in the canary’s liver. A ) Contrasted total-body computed tomography scan showing a neoplastic mass surrounding the right bronchus ( open arrow ) and multiple mediastinal lymphadenopathies of up to 5 cm ( white arrow ); the esophagus is encircled by a dotted line . B ) Treatment with doxycycline was followed by complete lymphoma regression, with the persistence of a small (<1 cm) mediastinal lymph node ( white arrow ). C ) Cross section of a bronchial biopsy stained with hematoxylin and eosin showing monotonous and diffuse infi ltration of large neoplastic lymphoid cells. Note the neoplastic lymphocyte size compared with the endothelial cell size ( arrow ); areas of low-grade MALT lymphoma were not detected (magnifi cation = ×400). D ) Immunostaining with Ki67 monoclonal antibody of bronchial biopsy shows a high proliferation rate (near 50%) in the large cell population. The size of Ki67+ cells was at least equal to bronchial epithelial nuclei ( arrows ). Magnifi cation = ×630. E ) Immunostaining by anti-chlamydial lipopolysaccharide monoclonal antibody (Imagen Chlamydia test, code number K6101, dilution 1 : 150, Dako, Glostrup, Denmark) in formalin-fi xed, paraffi n-embedded 4μ m sections of the canary’s liver (×630). The antibody stained scattered parasinusoidal cells with macrophage-like morphology (Kupffer cells; arrows ), which displayed a granular and predominantly intracytoplasmatic immunoreactivity. These features were consistent with the detection of Cp DNA, including Cp heat shock protein 60, by polymerase chain reaction in the same samples. A Woman and Her Canary: A Tale of Chlamydiae and Lymphomas
When are they old enough to drink? Outcomes of an Australian social marketing intervention targeting alcohol initiation

INTRODUCTION AND AIMS This paper reports on the evaluation of an Australian whole-of-community social marketing intervention targeting social norms, which aimed to reduce inflated perceptions of the prevalence of underage drinking and increase the age at which alcohol initiation is considered acceptable. DESIGN AND METHODS A community-wide intervention was delivered in a single community over a period of 2 years, targeting adolescents, parents and community members. Pre-and post-intervention computer-assisted telephone interview surveys were conducted in the intervention and a matched comparison (control) community. A total of 417 respondents completed both surveys (215 in the intervention community and 202 in the control community). RESULTS The intervention community saw an increase of 6 months in the average age at which it is perceived to be acceptable for young people to have a sip/taste of alcohol and 5 months in the average age at which it is perceived to be acceptable to have weak/watered down alcohol. Furthermore, there was a reduction in the perception of the prevalence of alcohol consumption by young people to a level consistent with actual underage drinking rates. In comparison, the control community saw no change in any of these variables. DISCUSSION AND CONCLUSIONS This study provides preliminary evidence that a whole-of-community social marketing intervention can change perceptions of the prevalence, and acceptability, of underage drinking. Given the central role of social norms in decisions regarding alcohol consumption, these changes have the potential to reduce parental supply and thus underage drinking.
A simple finite element method for non-divergence form elliptic equation

We develop a simple finite element method for solving second order elliptic equations in non-divergence form by combining least squares concept with discontinuous approximations. This simple method has a symmetric and positive definite system and can be easily analyzed and implemented. Also general meshes with polytopal element and hanging node can be used in the method. We prove that our finite element solution approaches to the true solution when the mesh size approaches to zero. Numerical examples are tested that demonstrate the robustness and flexibility of the method.
Treatment of Diesel‐ and Kerosene‐Contaminated Water by B. subtilis SPB1 Biosurfactant‐Producing Strain

This study investigated the efficiency of hydrocarbon utilization by B. subtilis SPB1, a biosurfactant‐producing strain. Microbial growth, biosurfactant production, and hydrocarbon biodegradation were studied in a liquid mineral medium, supplemented with 2% hydrocarbons in both the absence and in the presence of 0.1% yeast extract. Preliminary studies showed that maximum growth was registered with a 2% hydrocarbon solution. Results showed that the addition of yeast extract greatly stimulated microbial growth and thus induced biosurfactant production. Furthermore, biodegradation efficiencies were higher in the presence of yeast extract. Kerosene fuel was more recalcitrant to biodegradation than diesel oil. This study's findings suggest that the addition of an organic nitrogen source stimulates tension‐active agents' production, which emulsifies hydrophobic compounds and enhances their biodegradation and microbial growth.
Assessment of the Degree of Coronary Stenosis Based on Forensic Pathological Autopsy

Aims: The purpose of this project was to determine the percentage of the lumen area to the whole vessel area of normal coronary and stenotic coronary in humans at postmortem, to compare the difference between the value of measurement to coronary samples and slices, and finally to provide a reference for assessing the coronary stenosis severity . Methods and Results: Image Analyze software was used to measure the circumference of 82 human normal coronary artery samples, and then the percentage of the lumen area to the whole vessel area was calculated. Total 134 human coronary artery samples and slices were imaged using camera and microscope. The lumen area sizes were measured using Motic Imanges Advanced 3.2 software, yield R S1 and R S2 . The percentage of the lumen area to the whole vessel area of normal coronary artery is 52.1%±3.3%. There were obviously differences between R S1 and R S2 . Conclusions: The percentage of lumen area to the whole vessel area could be measured and calculated exactly using image analysis software, which can avoid the variability inherent in subjective estimates. The lumen area sizes of coronary slices measured with the image analyze software overestimated that of coronary samples by 7.9%±5.8 %.
Biomineralization: linking the fossil record to the production of high value functional materials

The microbial cell offers a highly efficient template for the formation of nanoparticles with interesting properties including high catalytic, magnetic and light‐emitting activities. Thus biomineralization products are not only important in global biogeochemical cycles, but they also have considerable commercial potential, offering new methods for material synthesis that eliminate toxic organic solvents and minimize expensive high‐temperature and pressure processing steps. In this review we describe a range of bacterial processes that can be harnessed to make precious metal catalysts from waste streams, ferrite spinels for biomedicine and catalysis, metal phosphates for environmental remediation and biomedical applications, and biogenic selenides for a range of optical devices. Recent molecular‐scale studies have shown that the structure and properties of bionanominerals can be fine‐tuned by subtle manipulations to the starting materials and to the genetic makeup of the cell. This review is dedicated to the late Terry Beveridge who contributed much to the field of biomineralization, and provided early models to rationalize the mechanisms of biomineral synthesis, including those of geological and commercial potential.
Antibody diversity in amphibians: inheritance of isoelectric focusing antibody patterns in isogenic frogs

Anti‐sheep red cell, anti‐dinitrophenyl, anti‐phosphorylcholine antibody responses have been followed in isogenic frogs of the genus Xenopus. Isoelectric focusing antibody patterns show a high degree of overlap for all antigens studied, and a heterogeneity that is lower than in mammals for the same antigens. Inheritance of antibody isoelectric focusing spectrotypes was demonstrated for sheep red cells and dinitrophenyl in two clones of isogenic animals.
Modeling of a 150W DCDC series-parallel resonant converter with integrated magnetic component

A 150W series-parallel resonant converter dedicated for audio-video equipment is proposed. The converter utilizes an integrated magnetic component that allows for easier inductor design and improvement in size and efficiency. A performance analysis focusing converter losses is conducted followed by creation of a simulation model, that includes various sources of losses is presented. The simulation model includes a simplified method for calculating core losses based on the common core parameters and the value of the flux flowing through that core. Lastly the converter simulation model is verified with measurement from a physical model. The establishment of this kind of model will useful in the future for predicting performance when different control schemes are applied.