Miracle-dz/UniFAR-FTUs huggingface dataset:
CECM: Adding pairwise constraints to evidential clustering

Fuzzy or hard partitioning methods aim at grouping objects according to their similarity. Recently, a new concept of partition based on belief function theory, called credal partition, has been proposed and has been shown to generate meaningful description of the data. Hard, fuzzy or credal partitions are generally obtained using unsupervised learning methods, using only the numeric description between two objects to compute their similarity. However, in some applications, some kind of background knowledge about the objects or about the clusters is available. To integrate this auxiliary information, constraint-based (or semi-supervised) methods have been proposed. A popular type of constraints specifies whether two objects are in the same cluster (must-link) or in different clusters (cannot-link). We propose here a new algorithm, called CECM, which computes a credal partition using a constrained clustering method. We show how to translate the available information into constraints, and how to integrate them in the search of the credal partition. The paper ends with some experimental results. Results of CECM are compared to other constrained clustering algorithms. Then an application in image segmentation is described.
Self-Organizing Map Neural Network-Based Depth-of-Interaction Determination for Continuous Crystal PET Detectors

For continuous crystal-based PET detectors, not only the two-dimensional (2D) plane coordinate of the interaction point, but also the depth-of-interaction (DOI) of the γ event could be precisely estimated by the single-end readout of the scintillation light. In this paper, we propose a practical method for DOI determination for continuous crystal PET detectors. By self-organizing map (SOM) neural network with unsupervised learning, the perpendicularly irradiated reference events in each reference position are classified into a certain number of groups, which are simultaneously used for the plane coordinate estimation and the DOI decoding. The reference events measured in an oblique irradiation are used to generate the initial weights of the SOM neurons and to calibrate the DOI decoding. Applying the new method to our experimental data, the SOM-based DOI estimation could achieve an average resolution of 2.56 mm over the whole thickness (0 - 10 mm) of the crystal. The DOI effect is also evaluated by comparing the plane position resolutions of the test beams in different incident angles with and without the DOI correction. The test results show that the DOI determination could seamlessly integrate into our previously proposed the SOM-based plane coordinate estimation scheme to realize the high performance real-time three-dimensional position estimation for continuous crystal-based PET detectors.
Rapid Diagnosis of Extrapulmonary Tuberculosis by PCR: Impact of Sample Preparation and DNA Extraction

ABSTRACT In cases of suspected extrapulmonary tuberculosis, rapid and accurate laboratory diagnosis is of prime importance, since traditional techniques of detecting acid-fast bacilli have limitations. The major difficulty with mycobacteria is achieving optimal cell lysis. Buffers used in commercial kits do not allow this complete lysis in a number of clinical specimens. A comparison of two sample preparation methods, pretreatment with proteinase K (PK-Roche) and complete DNA purification (cetyltrimethylammonium bromide [CTAB]-Roche), was conducted on 144 extrapulmonary specimens collected from 120 patients to evaluate the impact on the Cobas-Amplicor method. Thirty patients were diagnosed with tuberculosis, with 15 patients culture positive for Mycobacterium tuberculosis. Amplification and detection of the amplicons were impaired by a high number of inhibitory specimens (39 to 52%). CTAB-Roche allowed the detection of more culture-positive specimens by PCR than PK-Roche. Comparison with the final diagnoses of tuberculosis confirmed that CTAB-Roche produced the best sensitivity (53.8%) compared to culture (43.3%), PK-Roche (16%), and smear (13%). However, the specificity of the PCR assay with CTAB-Roche-extracted material was always lower (78.8%) than those with culture (100%) and PK-Roche (96.5%). False-positive specimens were lung biopsy material, lymph node biopsy material and aspirate, or bone marrow aspirate, mainly from immunocompromised patients. Despite the efficiency of complete DNA extraction for the rapid diagnosis by PCR of extrapulmonary tuberculosis, the false-positive results challenge our understanding of PCR results.
Lumped equivalent circuit model synthesis for a passive element with frequency-dependent and/or temperature-dependent characteristics for EMC simulation

This paper proposes a black box approach which synthesizes lumped circuit model of the Foster type for a frequency-dependent characteristic element by the least squares method systematically. However there are two numerical difficulties to model them. One is the numerical stability problem which comes from limitation of effective numerical digits of data especially for wide frequency band ranges. The other is the passivity problem of extracted lumped parameter models which often have negative element values. This paper proposes a new method which eliminates the problems. Furthermore a passive element usually has not only a frequency-dependent but also a temperature-dependent characteristics. This paper extends the above basic model to a modified one which can include both characteristics. The extended nonlinear model is based on a set of the basic models at sampled temperatures and is derived as interpolation of the basic models. The extended model is described in VHDL-AMS and is flexibly utilized as one of libraries. Finally synthesized model examples, for example, inductors, capacitors, an induction motor, and temperature-dependent elements, are demonstrated.
Quantification of anaerobic energy production during intense exercise.

Anaerobic energy production during supramaximal exercise has been estimated from muscle metabolic changes. Based on such measurements the anaerobic energy production was determined to be 63 and 189 mmol ATP x kg(-1) d.w. for 60 and 142 s of exhaustive cycling exercise, respectively. These estimations do not, however, include release of lactate from the exercising muscles. Furthermore, the anaerobic production cannot be related to the work performed since the muscle biopsy sample may not be representative for the muscles involved in the exercise, and the total anaerobic energy production during whole body exercise cannot be determined because the mass of the muscles used is unknown. When a single muscle is exercised, the problems are minimized. With a one-legged knee-extensor exercise model, which uses a defined muscle mass, the anaerobic energy production has been estimated to be 370 mmol ATP x kg(-1) d.w. for a 192-s exhaustive exercise period. Estimated pulmonary oxygen deficit based on an energy demand extrapolated from a linear relationship between exercise intensity and oxygen uptake at submaximal exercise does not appear to represent the anaerobic energy production during whole body exercise.
Exact action spectra for cellular responses relevant to phototherapy.

OBJECTIVE The aim of the present work is to analyze available action spectra for various biological responses of HeLa cells irradiated with monochromatic light of 580-860 nm. BACKGROUND DATA Phototherapy (low-level laser therapy or photobiomodulation) is characterized by its ability to induce photobiological processes in cells. Exact action spectra are needed for determination of photoacceptors as well as for further investigations into cellular mechanisms of phototherapy. METHODS Seven action spectra for the stimulation of DNA and RNA synthesis rate and cell adhesion to glass matrix are analyzed by curve fitting, followed by deconvolusion with Lorentzian fitting. Exact parameters of peak positions and bandwidths are presented. RESULTS The peak positions are between 613.5 and 623.5 nm (in one spectrum, at 606 nm), in the red maximum. The far-red maximum has exact peak positions between 667.5 and 683.7 nm in different spectra. Two near infrared maxima have peak positions in the range 750.7-772.3 nm and 812.5-846.0 nm, respectively. CONCLUSIONS In the wavelength range important for phototherapy (600-860 nm), there are four "active" regions, but peak positions are not exactly the same for all spectra.
Rhythm sequence through the olfactory bulb layers during the time window of a respiratory cycle

The mammalian olfactory bulb is characterized by prominent oscillatory activity of its local field potentials. Breathing imposes the most important rhythm. Other rhythms have been described in the β‐ and γ‐frequency ranges. We recorded unitary activities in different bulbar layers simultaneously with local field potentials in order to examine the different relationships existing between (i) breathing and field potential oscillations, and (ii) breathing and spiking activity of different cell types. We show that, whatever the layer, odour‐induced γ oscillations always occur around the transition point between inhalation and exhalation while β oscillations appear during early exhalation and may extend up to the end of inhalation. By contrast, unitary activities exhibit different characteristics according to the layer. They vary in (i) their temporal relationship with respect to the respiratory cycle; (ii) their spike rates; (iii) their temporal patterns defined according to the respiratory cycle. The time window of a respiratory cycle might thus be split into three main epochs based on the deceleration of field potential rhythms (from γ to β oscillations) and a simultaneous gradient of spike discharge frequencies ranging from 180 to 30 Hz. We discuss the possibility that each rhythm could serve different functions as priming, gating or tuning for the bulbar network.
It’s Not “All in Your Head”

Theorists and researchers in the psychology of religion have often focused on the mind as the locus of religion. In this article, we suggest an embodied cognition perspective as a new dimension in studies of religion as a complement to previous research and theorizing. In contrast to the Cartesian view of the mind operating distinctly from the body, an embodied cognition framework posits religion as being grounded in an integrated and dynamic sensorimotor complex (which includes the brain). We review relevant but disparate literature in cognitive and social psychology to demonstrate that embodied cognition shapes the way that people represent the divine and other spiritual beings, guides people’s moral intuitions, and facilitates bonding within religious groups. Moreover, commitments to a religious worldview are sometimes manifested in the body. We suggest several promising future directions in the study of religion from an embodied cognition perspective.
Pattern of Malformation in Offspring of Chronic Alcoholic Mothers

T identification of the characteristics defining fetal alcohol syndrome (FAS) is usually credited to observations made in this Jones and colleagues’ 1973 article. Although a previous re­ port in a French medical journal several years earlier recognized a similar pattern (Lemoine 1968), it was Jones and Smith who actually coined the label “fetal alcohol syn­ drome” in a followup paper to this seminal article by Jones and col­ leagues, entitled “Recognition of the fetal alcohol syndrome in early in­ fancy” (Jones and Smith 1973). Historically, it was considered c o mm o n kn o w l e d g e t h a t a l c o h o l consumption during pregnancy was hazardous, and women were warned accordingly; around the turn of the century, there were even a few clini­ cal and experimental reports pub­ lished that outlined negative effects of such consumption. However, the clinical inquisitiveness and astute di­ agnostic skills of Jones and the rest o f t h e t e a m o f p h y s i c i a n s a t t h e University of Washington, led by the late Dr. David W. Smith, was the im­ petus for the work published in this landmark article. T h e o b s e r v e d c h a r a c t e r i s t i c s caused by maternal drinking and re­ ported by Jones and colleagues in the article interested practicing clini­ cians around the world, stimulating many international case reports that f urther confirmed these findings. The observations in the article also had a monumental impact on the sci­ entific community. They demonstrat­ e d t h a t a l c o h o l i n g e s t e d b y t h e m o t h e r a d v e r s e l y a f f e c t e d f e t a l growth and development. Thus, as with thalidomide, alcohol was being implicated as a teratogen, or an agent c a p a b l e o f a l t e r i n g n o r m a l f e t a l growth and development, and this was an exciting development. Since the original identification of FAS in 1973, approximately 600 additional cases have been reported in the alcohol literature. Abel (1990) published a compendium of these cases. Basically, all the cardinal features of FAS described in the 1973 article by Jones and colleagues of low birth weight; small eye openings; joint, limb, and cardiac defects; developmental de­ lays; and mental retardation have withstood the test of time. In addition, some anomalies not initially included in the character­ istics they outlined, such as a thin upper lip (narrow vermilion border) and a broad flat area under the nose (long smooth philtrum), are now considered features of FAS. One area of science inadvertently stimulated by this article was that of behavioral teratology. In an attempt to develop ani­ mal models of FAS, researchers found that prenatal alcohol ex­ posure in rats was associated with behavioral anomalies in the absence of gross physical defects. This meant that the brain could be affected while other major organ systems appeared nor­ mal. As a result of this research, alcohol today is considered by
Synergistic Effects of NAT2 slow and GSTM1 null Genotypes on Carcinogen DNA Damage in the Lung

Background: Polymorphisms in carcinogen detoxification enzymes, NAT2 and GSTM1, have been suggested as susceptibility factors for DNA damage and lung cancer. However, little information is available on DNA adduct burden in the lung tissue and polymorphisms in NAT2 and GST genes. We investigated the independent and combined effects of the metabolic gene polymorphisms of NAT2 and GSTs on DNA adduct formation in different tissues (lung and blood) in lung cancer patients. Methods: DNA adducts were measured in lung and blood by the 32P-postlabeling assay. Multiple regression models were used to assess adjusted percent change in DNA adduct levels associated with GST and NAT2 genotypes. Results: After adjusting for potential confounders, as well as for other GST gene variants, lung adduct levels significantly increased by 150.3% [95% confidence interval (95% CI), 35.4-362.6%] for the GSTM1 null and by 73.9% (95% CI, −3.2% to 212.4%) for the NAT2 slow acetylator genotype, respectively. No association was seen with polymorphisms of other GST genes such as GSTT1 and GSTP1. The high-risk group, the combined GSTM1 null plus NAT2 slow, had significantly enhanced levels of lung adducts by 295% (95% CI, 72.7-803.5%) over those associated with single genes, suggesting a synergistic effect on DNA damage in the target lung tissue. Conclusions: The increase in DNA adduct levels in lung is associated with the GSTM1 null and NAT2 slow genotypes alone or in combination. Impact: These results suggest that GSTM1 and NAT2 genotypes play an independent and interactive role in the formation of carcinogen DNA adduct in the lung. Cancer Epidemiol Biomarkers Prev; 19(6); 1492–7. ©2010 AACR.
Claudin 28b and F-actin are involved in rainbow trout gill pavement cell tight junction remodeling under osmotic stress

SUMMARY Permeability of rainbow trout gill pavement cells cultured on permeable supports (single seeded inserts) changes upon exposure to freshwater or treatment with cortisol. The molecular components of this change are largely unknown, but tight junctions that regulate the paracellular pathway are prime candidates in this adaptational process. Using differential display polymerase chain reaction we found a set of 17 differentially regulated genes in trout pavement cells that had been exposed to freshwater apically for 24 h. Five genes were related to the cell–cell contact. One of these genes was isolated and identified as encoding claudin 28b, an integral component of the tight junction. Immunohistochemical reactivity to claudin 28b protein was concentrated in a circumferential ring colocalized to the cortical F-actin ring. To study the contribution of this isoform to changes in transepithelial resistance and Phenol Red diffusion under apical hypo-or hyperosmotic exposure we quantified the fluorescence signal of this claudin isoform in immunohistochemical stainings together with the fluorescence of phalloidin-probed F-actin. Upon hypo-osmotic stress claudin 28b fluorescence and epithelial tightness remained stable. Under hyperosmotic stress, the presence of claudin 28b at the junction significantly decreased, and epithelial tightness was severely reduced. Cortical F-actin fluorescence increased upon hypo-osmotic stress, whereas hyperosmotic stress led to a separation of cortical F-actin rings and the number of apical crypt-like pores increased. Addition of cortisol to the basolateral medium attenuated cortical F-actin separation and pore formation during hyperosmotic stress and reduced claudin 28b in junctions except after recovery of cells from exposure to freshwater. Our results showed that short-term salinity stress response in cultured trout gill cells was dependent on a dynamic remodeling of tight junctions, which involves claudin 28b and the supporting F-actin ring.
Measurements of water diffusion and T1 values in peritumoural oedematous brain

Using quantitative MR imaging, values for the mean water diffusivity (), the diffusion anisotropy and the longitudinal relaxation time (T1) were measured for tumour, oedematous and normal brain in a group of treatment-naive patients with high-grade glioma and low-grade meningioma. The mean values of and T1 for enhancing tumour and oedematous brain were significantly higher in high-grade glioma than meningioma, while the diffusion anisotropy was reduced. Values of and T1 were also positively correlated in oedematous brain in both pathologies. There was, however, no clear evidence of similar correlations in apparently normal contralateral white matter. Such results illustrate the potential of MR imaging to improve not only the characterization of brain oedema, but also the monitoring of treatment response.
The validity of estimating triceps brachii volume from single MRI cross-sectional area before and after resistance training

Abstract The aim of this study was to determine whether triceps brachii muscle volume can be adequately estimated from a single anatomical cross-sectional area (ACSA) and can the same model be used for prediction after training. Thirty-five healthy male non-athletes (age 21.6 ± 2.5 years, body mass index 24.8 ± 3.5 kg · m−2) volunteered for this study. The volumes of the upper arm extensors were calculated from magnetic resonance imaging (MRI) sequence scans and regression models were developed, which were used to predict muscle volumes from single MRI cross-sectional scans taken at different points along the humerus length. The same procedure was repeated after 12 weeks of maximal resistance training of the elbow extensors. Correlation coefficients were calculated for Model A with CSAmax, humerus length (HL), and body mass index (r = 0.919), a model with CSA50% and HL (r = 0.922), and a model with CSA60% and HL (r = 0.920) (P < 0.001). The standard error of estimate for Model A, Model CSA50%, and Model CSA60% was 8.0%, 7.7%, and 7.8% respectively. Thesame prediction formula can be used for the left arm (r = 0.904). If a single ACSA is used for triceps brachii volume prediction, the best fit is with Model CSA60% and HL, both before and after training (r = 0.941). By introducing humerus length into the calculation, we simplify the procedure for volume measurement, since it can be obtained during MRI scanning.
Evaluation of PAX8 Expression in Brain Tissue and Related Neoplasms

Undifferentiated brain tumors represent a diagnostic challenge, particularly in small biopsies, with regards to their primary versus metastatic origin. The latter may show overlapping morphologic features with primary high-grade brain tumors. In recent years several new antibodies have entered the realm of daily pathology practice. PAX8 (mammalian paired box genes 1 to 9 protein encoding gene) is among these new markers and is recognized as a differentiating marker of the primary site in epithelial tumors outside of the central nervous system. A review of the literature shows lack of site-specific studies with regards to the expression of PAX8 in the central nervous system and its neoplasms. Using this marker we investigated its immunohistochemical expression in normal brain tissue and glial tumors. The immunostain was performed on tissue microarrays of 71 cores from 24 cases. We also performed PAX8 immunostain on sections from cerebellum, pons, periventricular ependymal layer, choroid plexus, pituitary, and meninges of 3 autopsy cases. Our results indicate lack of PAX8 expression by benign brain tissue. Only 1 glioblastoma core (1/9 cores) showed focal nuclear reactivity with the antibody. Our results indicate that presence of PAX8 immunoreactivity in an undifferentiated brain tumor lacking gliofibrillary acidic protein expression should prompt consideration of a metastatic tumor.
Regulation of Biological Activity and Matrix Assembly of Laminin-5 by COOH-terminal, LG4–5 Domain of α3 Chain*

The basement membrane protein laminin-5 (LN5; α3β3γ2) undergoes specific proteolytic processing of the 190-kDa α3 chain to the 160-kDa form after the secretion, releasing its COOH-terminal, LG4–5 domain. To clarify the biological significance of this processing, we tried to express a recombinant precursor LN5 with a 190-kDa α3 chain (pre-LN5), in which the cleavage sequence Gln-Asp was changed to Ala-Ala by point mutation. When the wild-type and mutated LN5 heterotrimers were expressed in HEK293 cells, the wild-type α3 chain was completely cleaved, whereas the mutated α3 chain was partially cleaved at the same cleavage site (Ala-Ala). pre-LN5 was preferentially deposited on the extracellular matrix, but this deposition was effectively blocked by exogenous heparin. This suggests that interaction between the LG4–5 domain and heparan sulfate proteoglycans on the cell surface and/or extracellular matrix is important in the matrix assembly of LN5. Next, we purified both pre-LN5 and the mature LN5 with the processed, 160-kDa α3 chain (mat-LN5) from the conditioned medium of the HEK293 cells and compared their biological activities. mat-LN5 showed higher activities to promote cell adhesion, cell scattering, cell migration, and neurite outgrowth than pre-LN5. These results indicate that the proteolytic removal of LG4–5 from the 190-kDa α3 chain converts the precursor LN5 from a less active form to a fully active form. Furthermore, the released LG4–5 fragment stimulated the neurite outgrowth in the presence of mat-LN5, suggesting that LG4–5 synergistically enhances integrin signaling as it is released from the precursor LN5.