Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic gains of COL1A1‐PDFGB occur in the histologic evolution of giant cell fibroblastoma into dermatofibrosarcoma protuberans

Giant cell fibroblastoma (GCF) is a subcutaneous mesenchymal neoplasm characterized by the chromosomal t(17;22), which results in the formation of the fusion gene COL1A1‐PDGFB. This same fusion gene is also seen in the supernumerary ring chromosome of dermatofibrosarcoma protuberans (DFSP). Several studies have addressed the molecular genetics of DFSP but molecular cytogenetic characterization of individual areas and cell components in pure GCF and GCF/DFSP hybrids have not been performed. Herein, we studied the frequency and genomic copy number of COL1A1‐PDGFB in pure GCF and GCF/DFSP hybrids, and identified the molecular cytogenetic signatures in individual cells in each component. Four pure GCF and nine GCF/DFSP hybrids were studied. All tumors exhibited classical histological features and CD34 expression. COL1A1 and PDGFB rearrangements were evaluated by fluorescence in situ hybridization (FISH) using probes for COL1A1 and PDGFB on paraffin‐embedded thin tissue sections. All GCF and GCF/DFSP hybrids showed unbalanced rearrangements of COL1A1‐PDGFB at the molecular cytogenetic level. Genomic gains of COL1A1‐PDGFB were found predominantly in the DFSP component of GCF/DFSP hybrids but in none of the pure GCF, suggesting that these gains are associated with the histologic evolution of GCF into DFSP. The molecular cytogenetic abnormalities were found not only in the spindle/stellated cells but also in individual nuclei of the multinucleated giant cells, suggesting that these cells may result from the fusion of individual neoplastic cells. © 2007 Wiley‐Liss, Inc.
Influence of sex, reproductive status and foetal number on erythrocyte osmotic fragility, haematological and physiologic parameters in goats during the hot-dry season.

The current study was aimed at evaluating the effect of heat stress (during the hot-dry period) on some physiological variables, haematology and erythrocyte osmotic fragility (EOF) in bucks, pregnant (single and twin) and lactating Red Sokoto (RS) goats. Forty apparently healthy adult goats were used for the study and were allotted to four groups (bucks ( n = 10), pregnant ( n = 10) dry (n = 10), and lactating ( n = 10) does). The pregnant goats were further re-grouped according to number of foetuses (single foetus, n = 5 and twins, n = 5). corpuscular haemoglobin (MCH) and total leucocyte counts than dry does. Pregnant does exhibited significantly lower ( P < 0.05) packed cell volume, but significantly higher ( P < 0.05) MCH and mean corpuscular haemoglobin concentrations (MCHC) than lactating does. Does with a single foetus had significantly lower ( P < 0.05) MCV, but higher MCHC than does with twin pregnancies. Using EOF as a biomarker of oxidative stress, erythrocytes of bucks were significantly more resistant to hypotonic haemolysis than those of dry, pregnant and lactating does, with no significant difference in EOF between does of different groups. The erythrocytes of single and twin preg - nancies showed similar haemolysis pattern. In conclusion, sex, lactation, and the number of foetuses carried by pregnant does significantly influences physiological and haematological variables in RS goats during the hot-dry season. Also, during heat stress, the changes in physiological variables seem to enhance favourable adaptation by preventing an increase in rectal temperature even in twin pregnancies.
Increased Pulsatility Index Is Associated with Intracranial Arterial Calcification

Background/Aims: An increase in the pulsatility index (PI) has been suggested to reflect distal vascular resistance. The purpose of the present study was to investigate the association between intracranial arterial calcification and intracranial PIs. Methods: Consecutive patients with acute ischemic stroke or transient ischemic attack were included. The PIs of both middle cerebral arteries (MCAs) were measured by transcranial Doppler ultrasonography. Intracranial carotid artery calcification (ICAC) was assessed on computed tomography angiography, and then compared with the mean PI of both MCAs. Patients with internal carotid artery steno-occlusion were excluded from this study. Results: A total of 156 patients were finally enrolled. The prevalence of diabetes increased as the PI value increased (p for trends; p = 0.025). PI was correlated with ICAC score (r = 0.413, p < 0.001) and age (r = 0.507, p < 0.001). Multiple linear regression analysis indicated that aging and ICAC were independent determinants of the PI of MCA after adjusting for sex, systolic blood pressure, smoking, and the presence of diabetes. Conclusions: This study shows that an increase in PI was correlated with the severity of ICAC, which suggests calcification-related vascular resistance might have a role in the elevation of PI.
Quantifying Biofilm Structure: Facts and Fiction

There is no doubt among biofilm researchers that biofilm structure is important to many biofilm processes, such as the transport of nutrients to deeper layers of the biofilm. However, biofilm structure is an elusive term understood only qualitatively, and as such it cannot be directly correlated with any measurable parameters characterizing biofilm performance. To correlate biofilm structure with the parameters characterizing biofilm performance, such as the rate of nutrient transport within the space occupied by the biofilms, biofilm structure must first be quantified and expressed numerically on an appropriate scale. The task of extracting numerical parameters quantifying biofilm structure relies on using biofilm imaging and image analysis. Although defining parameters characterizing biofilm structure is relatively straightforward, and multiple parameters have been described in the computer science literature, interpreting the results of such analyses is not trivial. Existing computer software developed by several research groups, including ours, for the sole purpose of analyzing biofilm images helps quantify parameters from biofilm images but does nothing to help interpret the results of such analyses. Although computing structural parameters from biofilm images permits correlating biofilm structure with other biofilm processes, the meaning of the results is not obvious. The first step to understanding the quantification of biofilm structure, developing image analysis, methods to quantify information from biofilm images, has been made by several research groups. The next step is to explain the meaning of these analyses. This presentation explains the meanings of several parameters commonly used to characterize biofilm structure. It also reviews the authors' research and experience in quantifying biofilm structure and their attempts to quantitatively relate biofilm structure to fundamental biofilm processes.
Diagnostic architectural and dynamic features at breast MR imaging: multicenter study.

PURPOSE To prospectively determine the prevalence and predictive value of three-dimensional (3D) and dynamic breast magnetic resonance (MR) imaging and contrast material kinetic features alone and as part of predictive diagnostic models. MATERIALS AND METHODS The study protocol was approved by the institutional review board or ethics committees of all participating institutions, and informed consent was obtained from all participants. Although study data collection was performed before HIPAA went into effect, standards that would be compliant with HIPAA were adhered to. Data from the International Breast MR Consortium trial 6883 were used in the analysis. Women underwent 3D (minimum spatial resolution, 0.7 x 1.4 x 3 mm; minimal temporal resolution, 4 minutes) and dynamic two-dimensional (temporal resolution, 15 seconds) MR imaging examinations. Readers rated enhancement shape, enhancement distribution, border architecture, enhancement intensity, presence of rim enhancement or internal septations, and the shape of the contrast material kinetic curve. Regression was performed for each feature individually and after adjustment for associated mammographic findings. Multivariate models were also constructed from multiple architectural and dynamic features. Areas under the receiver operating characteristic curve (Az values) were estimated for all models. RESULTS There were 995 lesions in 854 women (mean age, 53 years +/- 12 [standard deviation]; range, 18-80 years) for whom pathology data were available. The absence of enhancement was associated with an 88% negative predictive value for cancer. Qualitative characterization of the dynamic enhancement pattern was associated with an Az value of 0.66 across all lesion architectures. Focal mass margins (Az = 0.76) and signal intensity (Az = 0.70) were highly predictive imaging features. Multivariate models were constructed with an Az value of 0.880. CONCLUSION Architectural and dynamic features are important in breast MR imaging interpretation. Multivariate models involving feature assessment have a diagnostic accuracy superior to that of qualitative characterization of the dynamic enhancement pattern.
Rheological properties and biocompatibility of endodontic sealers.

AIM To determine the flow characteristics and subcutaneous tissue reactions to five endodontic sealers. METHODOLOGY The materials used were Procosol, AH26, Endomethasone, Sealapex and Endion. The sealers were prepared following the manufacturers' instructions, and 0.075 mL of each material was placed on a glass surface, which was then rotated 90 degrees. The samples were stored at 37 degrees C and 95% humidity. The displacement of the sealer was recorded by measuring the difference between its original position and the position recorded at 15 and 60 min. Three samples of each material were used. Two pockets were created in the back of Wistar rats, and one silicone tube, 1 mm in diameter and 1 cm in length, was implanted in each. One was filled with one of the materials under study, and the other empty tube was implanted as a control. Fourteen days after implantation, the animals were sacrificed, and samples of the skin containing the tubes were histologically processed. Histological and histomorphometric evaluations of the tissues adjacent to the open end of the tube were carried out the volume of tissue reaction was measured histomorphometrically according to standard stereological principles. Results were statistically analysed using analysis of variance and Duncan's test. RESULTS The highest flow values were obtained with Sealapex and AH26. Time significantly affected the flow and the material (P < (1001). Procosol and Endion produced the most severe histological reactions: these were outlined by fibrous tissue; AH26. Endomethasone and Sealapex produced reactions of smaller size and with more moderately defined limits. CONCLUSIONS The flow did not correlate with the degree of inflammatory response. Procosol and Endion produced the most severe tissue reactions, whereas Endomethasone, Sealapex and AH26 produced only minimum reactions.
libDAI: A Free and Open Source C++ Library for Discrete Approximate Inference in Graphical Models

This paper describes the software package libDAI, a free & open source C++ library that provides implementations of various exact and approximate inference methods for graphical models with discrete-valued variables. libDAI supports directed graphical models (Bayesian networks) as well as undirected ones (Markov random fields and factor graphs). It offers various approximations of the partition sum, marginal probability distributions and maximum probability states. Parameter learning is also supported. A feature comparison with other open source software packages for approximate inference is given. libDAI is licensed under the GPL v2+ license and is available at http://www.libdai. org.
Review of terahertz photoconductive antenna technology

Abstract. Photoconductive antennas (PCAs) have been extensively utilized for the generation and detection of both pulsed broadband and single frequency continuous wave terahertz (THz) band radiation. These devices form the basis of many THz imaging and spectroscopy systems, which have demonstrated promising applications in various industries and research fields. The development of THz PCA technology through the last 30 years is reviewed. The key modalities of improving device performance are identified, and literature is reviewed to summarize the progress made in these areas. The goal of this review is to provide a collection of all relevant literature to bring researchers up to date on the current state and remaining challenges of THz PCA technology.
Endothelial MMP14 is required for endothelial-dependent growth support of human airway basal cells

ABSTRACT Human airway basal cells are the stem (or progenitor) population of the airway epithelium, and play a central role in anchoring the epithelium to the basement membrane. The anatomic position of basal cells allows for potential paracrine signaling between them and the underlying non-epithelial stromal cells. In support of this, we have previously demonstrated that endothelial cells support growth of basal cells during co-culture through vascular endothelial growth factor A (VEGFA)-mediated signaling. Building on these findings, we found, by RNA sequencing analysis, that basal cells expressed multiple fibroblast growth factor (FGF) ligands (FGF2, FGF5, FGF11 and FGF13) and that only FGF2 and FGF5 were capable of functioning in a paracrine manner to activate classical FGF receptor (FGFR) signaling. Antibody-mediated blocking of FGFR1 during basal-cell–endothelial-cell co-culture significantly reduced the endothelial-cell-dependent basal cell growth. Stimulation of endothelial cells with basal-cell-derived growth factors induced endothelial cell expression of matrix metallopeptidase 14 (MMP14), and short hairpin RNA (shRNA)-mediated knockdown of endothelial cell MMP14 significantly reduced the endothelial-cell-dependent growth of basal cells. Overall, these data characterize a new growth-factor-mediated reciprocal ‘crosstalk’ between human airway basal cells and endothelial cells that regulates proliferation of basal cells. Summary: Basal cell and endothelial cell crosstalk might play a substantial role in maintaining normal airway structure, with alteration of this crosstalk contributing towards smoking-dependent airway remodeling.
Regulation of Hepatocyte Engraftment and Proliferation after Cytotoxic Drug-Induced Perturbation of the Rat Liver

Background. Perturbations in specific liver cell compartments benefit transplanted cell engraftment and/or proliferation. We analyzed whether cytotoxic drugs interfering with the integrity of genomic DNA or cell division could be useful for liver cell transplantation. Methods. We used dipeptidyl peptidase IV deficient (DPPIV-) rats as recipients of syngeneic F344 rat hepatocytes. Rats were pretreated with doxorubicin, irinotecan, or vincristine prior to cell transplantation and synergistic liver perturbations were induced by drug administration followed by partial hepatectomy or carbon tetrachloride treatments. Transplanted cells were identified by DPPIV histochemistry and cell engraftment and proliferation were analyzed morphometrically. Perturbations in endothelial, Kupffer cell, and hepatocyte compartments were analyzed by electron microscopy, carbon incorporation, and blood tests, respectively. Results. Cell engraftment was improved in rats treated with doxorubicin but not with irinotecan or vincristine. Doxorubicin disrupted endothelial cells for up to seven days without causing Kupffer cell or hepatocellular toxicity. Neither doxorubicin nor vincristine induced liver repopulation in animals up to three months, including after partial hepatectomy or carbon tetrachloride-induced additional liver injury. Conclusions. Doxorubicin-induced hepatic endothelial damage enhanced cell engraftment, which should be useful in cell therapy strategies.
Alkali therapy in renal tubular acidosis: who needs it?

Pines and Mudge ([1][1]) coined the term “renal tubular acidosis” (RTA) to denote a renal tubular disorder that causes acidosis by restricting the reduction of urinary pH and thereby the titration of urinary buffers and excretion of acid. In extensive earlier studies of this “specific form of
Culture Age, Temperature, and pH Affect the Polyol and Trehalose Contents of Fungal Propagules

The growth and conidial physiology of the entomopathogenic fungi Beauveria bassiana, Metarhizium anisopliae, and Paecilomyces farinosus were studied under different conditions. The effects of culture age (up to 120 days), temperature (5 to 35(deg)C), and pH (2.9 to 11.1) were determined. Growth was optimal at pH 5 to 8 for each isolate and between 20 and 35(deg)C, depending on the isolate. The predominant polyol in conidia was mannitol, with up to 39, 134, and 61 mg g of conidia(sup-1) for B. bassiana, M. anisopliae, and P. farinosus, respectively. Conidia of M. anisopliae contained relatively small amounts of lower-molecular-weight polyols and trehalose (less than 25 mg g(sup-1) in total) in all treatments. Conidia of B. bassiana and P. farinosus contained up to 30, 32, and 25 mg of glycerol, erythritol, and trehalose, respectively, g(sup-1), depending on the treatment. Conidia of P. farinosus contained unusually high amounts of glycerol and erythritol at pH 2.9. The apparent effect of pH on gene expression is discussed in relation to the induction of a water stress response. To our knowledge, this is the first report of polyols and trehalose in fungal propagules produced over a range of temperature or pH. Some conditions and harvesting times were associated with an apparent inhibition of synthesis or accumulation of polyols and trehalose. This shows that culture age and environmental conditions affect the physiological quality of inoculum and can thereby determine its potential for biocontrol.
Geographic distribution and ecological studies of inflammatory bowel disease in southeastern Norway in 1990–1993

Background: The purpose was to study the spatial distribution of cases of inflammatory bowel disease (IBD) and characterize municipalities with high incidences in a search for environmental risk factors. Methods: Spatial clustering of patients diagnosed with IBD during 1990–1993 were studied in 4 counties in southeastern Norway, and an ecological analysis was conducted to study the relationship between risk of IBD in the municipalities and their characteristics such as population, health care, urban/rural change, and socioeconomic change. Results: One cluster consisting of 4 municipalities was identified for IBD in ϕstfold county (P = 0.011). The ecological analysis showed that the incidence rate of IBD was 33% (95% confidence interval [CI]: 2%–75%) higher in municipalities with the highest level of education compared to the lowest level of education and 35% (2%–78%) higher in urban than rural municipalities. The incidence rate was 11% (1%–20%) lower in municipalities with a high urban/rural change compared to municipalities with low urban/rural change. Individuals living in high‐risk municipalities were 3 times (1.57–5.45) more likely to have a first‐degree family member with IBD than individuals living in normal‐risk municipalities. Conclusions: The geographic distribution of cases with IBD is not uniformly distributed and is related to urbanization, level of education, and moving pattern. Geographic distribution may be explained by either changes in environment–host relationships or neurobiological mechanisms due to stress and economic frustration. These factors and genetic predisposition might also explain increased familial clustering. Spatial clustering was significant neither for Crohn's disease CD nor ulcerative colitis (UC) but showed a stronger tendency within the CD group.
SKIN OPTICS AND PHOTOTHERAPY OF JAUNDICE

Abstract The Kubelka–Munk theory of radiation transfer is applied to determine the influence of skin optical losses on the efficiency of phototherapy of jaundice. Using a multi‐layer model of the skin the photon absorption rate of bilirubin molecules is calculated for spectrally Gaussian light sources and fluorescent lamps used in phototherapy. Light absorption and scattering processes in the skin layers shift the optimum value of the peak excitation wavelength from λ= 453 nm (absorption maximum of bilirubin in vitro) to λ= 480 nm. This suggests the clinical investigation of narrow‐spectrum lamps emitting in the blue‐green region of the spectrum.
Micrococci and Peptidoglycan Activate TLR2→MyD88→IRAK→TRAF→NIK→IKK→NF-κB Signal Transduction Pathway That Induces Transcription of Interleukin-8

ABSTRACT This study was done to elucidate the signal transduction pathway of interleukin-8 (IL-8) induction by gram-positive bacteria. Bacteria (micrococci) and peptidoglycan (PGN) induced transcription of IL-8 in HEK293 cells expressing Toll-like receptor 2 (TLR2) and CD14 but not in those expressing TLR1 or TLR4. A mutation within the NF-κB site in the IL-8 promoter abrogated transcriptional induction of IL-8 by the two stimulants. Dominant negative myeloid differentiation protein (MyD88), IL-1 receptor-associated kinase (IRAK), NFκB-inducing kinase (NIK), and IκB kinase (IKK) mutant forms completely inhibited micrococcus- and PGN-induced activation of NF-κB and expression of the gene for IL-8. Induction of NF-κB was partially inhibited by dominant negative tumor necrosis factor receptor-associated kinase 6 (TRAF6) but not TRAF2, whereas induction of IL-8 gene was partially inhibited by both TRAF6 and TRAF2. These data indicate that micrococci and PGN induce TLR2-dependent activation of the gene for IL-8 and that this activation requires MyD88, IRAK, NIK, IKK, and NF-κB and may also utilize TRAF6 and, to a lesser extent, TRAF2.
Assessment of Mercury Detoxification Potentiality of Isolated Streptococcus sp. MTCC 9724 under Different Environmental Conditions

The objectives of the present study were to isolate and identify a suitable mercury resistance bacterial strain and to explore their detoxification potentiality of mercury in different environmental conditions. A strain of Streptococcus sp. MTCC 9724 was isolated from the soil of waste dumping site adjacent to East Calcutta wetlands, West Bengal, India. Minimum inhibitory concentration of mercury was estimated. The bacteria were resistant to lead, arsenic, chromium and copper and antibiotics like Tetracycline, Ofloxacin, Amoxicillin, Ampicillin, Chloramphenicol and Cefadroxil. The bacteria were exposed containing 2, 5 and 10 mg/l of mercury containing media with variable pH, phenol and chloride ions as co-pollutants. It was observed that acidic pH was not suitable for bacterial growth and also for mercury detoxification. The presence of phenol in wastewater actually supported bacterial population growth and also mercury removal within 16 hours time periods, which indicated that utilization of phenol as a sole carbon source for bacterial metabolism, where as chloride ions up to 21 g/l did not inhibit the bacterial growth but significantly decreased the detoxification potentiality of Streptococcus sp. MTCC 9724.