Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient DNA extraction from 25‐year‐old paraffin‐embedded tissues: study of 365 samples

Aims: Archival fixed paraffin‐embedded tissue (PET) is a valuable source for population‐based molecular genetic studies but the extraction of high quality DNA is still a problematic issue. The present study tested the grade of DNA fragmentation and the DNA adequacy for genetic investigations in a large series of tissue specimens that were formalin‐ or Bouin‐fixed and paraffin‐embedded between 1979 and 1983. Specific aims were to: (1) estimate the amount of archival tissue samples from which DNA is recoverable by conventional methods and the influence of variables (origin, fixative, section size) on DNA recovery; and (2) evaluate the feasibility of genetic investigations in large scale population studies. Methods: DNA was extracted in 2005 from 365 PET samples from Italy and Spain and subjected to PCR analysis targeting fragments of 152, 268 and 676 bp of the &bgr;‐globin gene. Results: Amplification of a 152 bp fragment was obtained in 252/365 (69%) PET samples, a 268 bp fragment in 62/365 (17%), a 676 bp fragment in 19/365 (5%) and no amplification for any fragment was obtained in 113/365 (31%). A second processing of newly cut sections performed in a 25% simple random sample gave comparable results, with substantial concordance between the first and second tests (kappa value 0.62 [95% CI 0.59–0.64]). Conclusions: The results of this study show that DNA can be efficiently extracted from PETs archived for more than 20 years, and that large scale population studies based on PCR amplification of short target sequences are feasible.
Gpos-mPLoc: a top-down approach to improve the quality of predicting subcellular localization of Gram-positive bacterial proteins.

In this paper, a new predictor called "Gpos-mPLoc", is developed for identifying the subcellular localization of Gram positive bacterial proteins by fusing the information of gene ontology, as well as the functional domain information and sequential evolution information. Compared with the old Gpos-PLoc, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins as indicated by the character "m" in front of "PLoc" of its name. For a newly-constructed stringent benchmark dataset in which none of included proteins has > 25% pairwise sequence identity to any other in a same subset (location), the overall jackknife success rate achieved by Gpos-mPLoc was 82.2%, which was about 10% higher than the corresponding rate by the Gpos-PLoc. As a user friendly web-server, Gpos-mPLoc is freely accessible at http://www.csbio. sjtu.edu. cn/bioinf/Gpos-multi/.
The Body-Machine Interface: A New Perspective on an Old Theme

ABSTRACT Body-machine interfaces establish a way to interact with a variety of devices, allowing their users to extend the limits of their performance. Recent advances in this field, ranging from computer interfaces to bionic limbs, have had important consequences for people with movement disorders. The authors provide an overview of the basic concepts underlying the body-machine interface with special emphasis on their use for rehabilitation and for operating assistive devices. They outline the steps involved in building such an interface and highlight the critical role of body-machine interfaces in addressing theoretical issues in motor control as well as their utility in movement rehabilitation.
Experimental transmission of Toxoplasma gondii in mice.

Toxoplasma gondii is widely spread over the world, occurring in many kinds of animals and man, as revealed by serological surveys. The mode of its infection, however, is not yet clearly demonstrated except the congenital cases. Transmission from man to man or from animal to man or vis versa must have been occurring, but no conclusive data on this respect have yet been obtained. Transmission by the ingestion of contaminated food or drink, inhala tion, contagion or through insect-vectors can be more or less possible. Toxoplasma gondii has two different stages in its life-cycle: proliferative form and cyst. It is possible that the latter plays more important role in the transmission than the former. In the present study, investigations were made into the experimental transmission through placenta, coinhabitation, feeding and contagion in wounds. Both proliferative and cyst forms were used as agents of transmission.
A HIGH-FREQUENCY SEARCH FOR PULSARS WITHIN THE CENTRAL PARSEC OF Sgr A*

We report results from a deep high-frequency search for pulsars within the central parsec of Sgr A* using the Green Bank Telescope. The observing frequency of 15 GHz was chosen to maximize the likelihood of detecting normal pulsars (i.e., with periods of ∼500 ms and spectral indices of ∼−1.7) close to Sgr A* that might be used as probes of gravity in the strong-field regime; this is the highest frequency used for such pulsar searches of the Galactic center (GC) to date. No convincing candidate was detected in the survey, with a 10σ detection threshold of ∼10 μJy achieved in two separate observing sessions. This survey represents a significant improvement over previous searches for pulsars at the GC and would have detected a significant fraction (≳5%) of the pulsars around Sgr A*, if they had properties similar to those of the known population. Using our best current knowledge of the properties of the Galactic pulsar population and the scattering material toward Sgr A*, we estimate an upper limit of 90 normal pulsars in orbit within the central parsec of Sgr A*.
Polypropylenimine dendrimer-induced gene expression changes: The effect of complexation with DNA, dendrimer generation and cell type

Polypropylenimine (PPI) dendrimers appear attractive non-viral vectors for the delivery of genes, antisense oligonucleotides, and small interfering RNA (siRNA). However, the effects of these synthetic gene delivery vectors on global gene expression are poorly understood. Here we have examined the toxicogenomics of generation 2 (DAB-8) and generation 3 (DAB-16) PPI dendrimers in two human cell lines. At concentrations and treatment protocols routinely used for gene and oligonucleotide transfection, PPI dendrimers alone elicited marked changes in endogenous gene expression in A431 epithelial cells. The extent of PPI-induced gene changes appeared to be dependant on the dendrimer generation as the number of genes affected was greater with G3 compared to G2 PPI dendrimers in A431 cells. The signature of DAB16-induced gene changes in A549 cells was different to those elicited in A431 cells implying a strong dependence on cell type. The DAB-16 polymer complexed with DNA (dendriplexes) also elicited marked gene expression changes in A549 cells but with a signature that was different from the polymer alone implying that dendriplexes are “recognised” by cells as chemical entities that are distinct from the polymer alone. Alterations in expression of a variety of gene ontologies were observed including those involved in defence responses, cell proliferation and apoptosis. Although there was a tendency for increased DNA damage in cells treated with DAB16 alone or its DNA dendriplexes as detected by the COMET assay, these differences were not statistically significant. These data show for the first time that PPI-dendrimers, separate from their capability as transfection reagents, can intrinsically alter the expression of many endogenous genes that could potentially lead to them exerting multiple biological effects in cells. The impact and consequences of polymer-induced gene changes should guide their rational use as delivery systems for gene-based therapeutics.
Morphometric Analysis in Breast Lesions A Rapid Conjunct to Intraoperative Imprint Smears

Background : Breast carcinoma is the most common malignant tumor and leading cause of cancer deaths in women. While fine needle aspiration cytology is highly accurate in the diagnosis of breast lesions, it possesses certain drawbacks. In those circumstances intraoperative imprint cytology assumes importance, however, imprint cytology is subjected to interpretative errors. Computer image analysis has become an important tool in the pathology laboratory for quantitative morphometric analysis. The purpose of this study was to compare the morphometric values of various breast lesions on intraoperative imprint smears with final histopathological sections. Methods : The study group comprised 30 cases of, borderline (suspicious), and malignant lesions. Intraoperative imprint smears were stained with hematoxylin and eosin, and toluidine blue. Morphometry was done on these smears and compared with morphometry on the histopathological sections, followed by statistical correlation. We studied the following five parameters: mean nuclear area, mean nuclear diameter, mean nuclear perimeter, feret circle, and nucleo-cytoplasmic ratio. Results : In the current work, all of the studied parameters with the exception of feret circle showed significantly lower values in benign ductal epithelial cells compared to malignant lesions and concentrate on the importance of morphometry as a diagnostic tool that could differentiate benign from malignant lesions, especially if it can be employed on imprint smears intraoperatively. Accurate assessment of intraoperative margins by imprint smears using image analysis automation can prevent multiple re- excision procedures in breast conservation surgery.
GABAergic Neurons and Their Modulatory Effects on GnRH3 in Zebrafish

γ-Aminobutyric acid (GABA) is a major amino acid neurotransmitter in the vertebrate brain. To provide detailed information on the distribution of the GABA in zebrafish (Danio rerio), neurons were labeled with mCherry driven by the glutamic acid decarboxylase 67 (gad67) promoter. In the transgenic line Tg(gad67:mCherry), mCherry-positive gad67 cell bodies were predominantly localized to the olfactory bulb, pallial zones, subpallium zones, parvocellular preoptic nucleus, periventricular gray zone of optic tectum, torus semicircularis, posterior tuberculum, medial longitudinal fascicle, caudal zone of periventricular hypothalamus, and oculomotor nucleus. mCherry-positive fibers were widely distributed in the olfactory bulbs, subpallium, thalamus, ventral hypothalamic zone, tectum opticum, mesencephalon, and rhombencephalon. mCherry-positive neurons were also observed in the retina and the spinal cord. The anatomical relationships between GABAergic and gonadotrophin-releasing hormone 3 (GnRH3) neurons were investigated by crossing Tg(gad67:mCherry) fish with the previously established Tg(gnrh3:EGFP) transgenic line. GnRH3 cell bodies and fibers were contacted by GABAergic fibers directly in the ventral telencephalon and anterior tuberal nucleus. A subpopulation of GnRH3 neurons in the ventral telencephalic area was also labeled with mCherry, so some GnRH3 neurons are also GABAergic. GABAB receptor agonist (baclofen) and antagonist (CGP55845) treatments indicated that GABAB receptor signaling inhibited gnrh3 expression in larval fish but was stimulatory in adult fish. The expression of pituitary lhβ and fshβ was stimulated by intraperitoneal injection of baclofen in adult fish. We conclude that GABA via GABAB receptors regulates GnRH3 neurons in a developmentally dependent manner in zebrafish.
Fluvastatin treatment is not associated with an increased incidence of cancer

Concerns regarding a potential link between statin treatment and increased risk of cancer were raised following the increased cancer incidence observed in patients treated with pravastatin in the Cholesterol and Recurrent Events and Pravastatin in Elderly Individuals at Risk of Vascular Disease studies. The aim of the present study was to investigate the risk of cancer associated with fluvastatin treatment in clinical trials. A pooled analysis of all available, randomised, placebo‐controlled trials with fluvastatin with a minimum treatment period of 24 weeks was performed. The cancer incidences were compared in 3512 patients receiving fluvastatin, 20–80 mg/day, and 3289 patients receiving placebo. Overall, fewer patients were diagnosed with cancer in the fluvastatin group compared with the placebo group [220/3512 (6.3%) vs. 263/3289 (8.0%) respectively; p = 0.0309]. Cox regression analysis, adjusted for baseline covariates and stratified by study, revealed a hazard ratio for first cancer diagnosis of 0.812 [95% confidence interval (CI) 0.667–0.989; p = 0.037] for fluvastatin compared with placebo. No significant differences were observed in the incidence of cancers by site, with the exception of non‐melanoma skin cancer (103 vs. 125 cases in the fluvastatin and placebo groups respectively; p = 0.047). Cox regression analysis showed that there was no association between baseline low‐density lipoprotein cholesterol levels and the risk of developing cancer (hazard ratio 0.998, 95% CI 0.995–1.000; p = 0.107). In conclusion, fluvastatin treatment is not associated with an increased risk of cancer compared with placebo in clinical trials, independent of patient age, treatment duration and baseline cholesterol levels.
Dental Clinics as Potent Sources for Screening Undiagnosed Diabetes and Prediabetes

Introduction:This pilot study investigated the efficacy of dental clinics as potent sources for screening diabetes and prediabetes in undiagnosed individuals. Methods:Data were randomly collected from 385 patients (aged 40 years and older) visiting dental clinics. Patients already having a diagnosis of diabetes and/or prediabetes were excluded. Demographic data, body mass index and family and dental histories were recorded. Signs and symptoms of diabetes were investigated. Random blood glucose levels (RBGLs) were recorded. Individuals with RBGL ≥110 mg/dL underwent the oral glucose tolerance test and the glycosylated hemoglobin test (HbA1c). Results:Of the 385 patients, 60% (232) had RBGL <110 mg/dL, whereas 40% (153) had RBGL ≥110 mg/dL. Prevalence of confirmed diabetes and prediabetes among the study participants was 16.4% and 15.8%, respectively. Body mass index was significantly higher among patients with diabetes and prediabetes as compared with healthy controls. HbA1c level was statistically significantly higher among patients with diabetes than among patients with prediabetes. Symptoms of polyuria and polydipsia were significantly higher among patients with diabetes than in those without diabetes. Conclusions:A high percentage of undiagnosed type 2 diabetes and prediabetes among patients visiting dental clinics was found compared with that reported in the medical literature. Further studies with a lager sample size are needed to confirm these results.
The Early Interaction of Coxsackievirus B3 with HeLa Cells

Summary Purified coxsackievirus B3 labeled with 32P- or 14C-valine interacted with HeLa cells in a manner resembling that found by others for poliovirus. Radioactivity eluted from cells at 37°, pH 7, as noninfectious virus, but contained infectious RNA. Both elution and “eclipse” of virus were inhibited irreversibly at low pH to provide further evidence that these processes may be related properties of the cell surface.
Advances in mass spectrometry for the identification of pathogens

Abstract Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle‐based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix‐assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high‐throughput measurements. The MS detection of polymerase chain reaction (PCR)‐amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:1203–1224, 2011
Celiac Disease: A Multisystem Autoimmune Disorder

Just a few years ago, celiac disease was thought to be relatively rare in the United States, but recent data suggest celiac disease may affect 3 million Americans of all ages, many of whom have no diagnosis of the disease. With increased awareness of this disease among adult and pediatric primary care providers, there undoubtedly will be an increase in the number of persons being evaluated for celiac disease in outpatient diagnostic centers and gastroenterology practices. Gastroenterology nurses, therefore, need to have a thorough understanding of celiac disease to fully participate as members of the multidisciplinary team required to manage this challenging disease. This article discusses the pathogenesis, prevalence, diagnosis, clinical manifestations, management, and complications of celiac disease.
Three‐dimensional capillary geometry in gut tissue

Accurate characterization of capillary geometry is of the utmost importance for physiological tissue studies such as oxygen transport. We show that 3D microscopy can be used to measure tissue capillary geometry both in normal and disease states. We imaged fluorescently labeled gut mucosa capillary beds of three control rats and three rats 4 hours after i.p. injection of 9 mg/kg endotoxin. We used serial optical sectioning microscopy coupled with deconvolution to reconstruct 3D capillary geometry. Theoretical point spread functions accounting for depth into the specimen resulted in better reconstructions than experimentally measured point spread functions. We next derived the distribution of the shortest distances to the nearest capillary from all extravascular tissue voxels. In normal rats the shortest‐distance distributions were remarkably constant despite widely varying capillary geometry. Furthermore, the mean of the shortest‐distance distributions increased significantly for endotoxemic rats (4.8 ± 0.4 μm) compared to controls (4.3 ± 0.3 μm, P < 0.05). Hence, serial sectioning microscopy provides an accurate venue for measuring physiologically relevant 3D capillary structure. Microsc. Res. Tech. 61:428–437, 2003. © 2003 Wiley‐Liss, Inc.
Toward a General Model of the Learning Experience

In this paper we extend our previous bi-dimensional model of the experience - integrating experience styles and process characteristics - to account also for the peculiarities of the place. To each voxel of the resulting 3D space of representation can be associated a time dependent density that accounts for the relevance of such voxel at any time one takes a snapshot of the 3D space. Extrinsic and intrinsic forces (density gradients) are needed to make the system evolve from the initial state to a given final state (i.e. to origin the dynamics of educational processes).
Assessing the Rebound Hammer Test for Rammed Earth Material

Rammed-earth (RE) is a construction material manufactured from the soil. The soil is compacted at its optimum water content, inside a formwork to build a monolithic wall. RE material is attracting renewed interest throughout the world thanks to its sustainable characteristics: low embodied energy, substantial thermal inertia, and natural regulator of moisture; on the other hand, the existing historic RE buildings is still numerous. This is why several research studies have been carried out recently to study different aspects of this material. However, few investigations have been carried out to explore the possibility of applying the nondestructive techniques on RE walls. This paper presents an assessment of the well-known rebound hammer test on RE walls. The calibration curves of the rebound hammer test have been established for conventional concrete where the rebound number is more than 20. For RE material with lower compressive strengths, a new calibration curve must be established. In the present study, two soils were used and different homogenized specimens with different dry densities were manufactured and tested, to plot a general calibration curve. Then, this calibration curve was applied to RE specimens; different results at different positions in an earthen layer were observed, due to the inhomogeneity of the material. The final results showed an acceptable accuracy of the calibration curve in the prediction of the compressive strength of RE material.
Regional brain axial and radial diffusivity changes during development

The developing human brain shows rapid myelination and axonal changes during childhood, adolescence, and early adulthood, requiring successive evaluations to determine normative values for potential pathological assessment. Fiber characteristics can be examined by axial and radial diffusivity procedures, which measure water diffusion parallel and perpendicular to axons and show primarily axonal status and myelin changes, respectively. Such measures are lacking from widespread sites for the developing brain. Diffusion tensor imaging data were acquired from 30 healthy subjects (age 17.7 ± 4.6 years, range 8–24 years, body mass index 21.5 ± 4.5 kg/m2, 18 males) using a 3.0‐Tesla MRI scanner. Diffusion tensors were calculated, principal eigenvalues determined, and axial and radial diffusivity maps calculated and normalized to a common space. A set of regions of interest was outlined from widespread brain areas within rostral, thalamic, hypothalamic, cerebellar, and pontine regions, and average diffusivity values were calculated using normalized diffusivity maps and these regions of interest masks. Age‐related changes were assessed with Pearson's correlations, and gender differences evaluated with Student's t‐tests. Axial and radial diffusivity values declined with age in the majority of brain areas, except for midhippocampus, where axial diffusivity values correlated positively with age. Gender differences emerged within putamen, thalamic, hypothalamic, cerebellar, limbic, temporal, and other cortical sites. Documentation of normal axial and radial diffusivity values will help assess disease‐related tissue changes. Axial and radial diffusivities change with age,with fiber structure and organization differing between sexes in several brain areas. The findings may underlie gender‐based functional characteristics, and mandate partitioning age‐ and gender‐related changes during developmental brain pathology evaluation. © 2011 Wiley Periodicals, Inc.
Hepatic lipase activity is increased in non‐alcoholic fatty liver disease beyond insulin resistance

Hepatic lipase is a lipolytic enzyme mostly synthesized and localized at the surface of liver sinusoidal capillaries, which hydrolyses triglycerides and phospholipids of intermediate density, large low density (LDL) and high density lipoproteins. Hepatic lipase activity is increased in insulin resistant states. Non‐alcoholic fatty liver disease (NAFLD) is characterized by insulin resistance. However, at present, no data are available regarding the behaviour of hepatic lipase with regard to the degree of hepatic steatosis. Our aim was to evaluate hepatic lipase activity in NAFLD patients and its relationship to the severity of hepatic steatosis.