Miracle-dz/UniFAR-FTUs huggingface dataset:
Ischemic acute renal failure: long-term histology of cell and matrix changes in the rat.

BACKGROUND The cellular infiltration and matrix accumulation accompanying acute renal ischemia and reperfusion have been frequently noted but poorly defined. The long-term consequences of ischemia may irreversibly damage the kidney. METHODS Female Sprague-Dawley rats (200 g) underwent unilateral nephrectomy. After five days, the left renal pedicle was occluded for 45 minutes. Animals were sacrificed at 0, 1, 2, 4, 8, 16, 32, 64, and 180 days postischemia (N = 6). Immunohistochemistry for monocytes/macrophages (Mo/Mphi, ED-1), myofibroblasts [alpha-smooth muscle actin (alpha-SMA)], collagen III and IV, matrix metalloproteinase-2 (MMP-2) and proliferating cell nuclear antigen (PCNA) and terminal dUTP nick end labeling (TUNEL) were performed. RESULTS Kidney weights of postischemic animals were increased at all time points (postischemic to controls, 1.47 +/- 0.21 to 0.94 +/- 0.12 g at day 8; 1.49 +/- 0.20 to 1.27 +/- 0.13 g at day 64; and 1.86 +/- 0.1 to 1. 24 +/- 0.2 g at day 180). Serum creatinine values increased to 0.42 +/- 0.10 mmol/L at day 2 but returned to control levels by day 8 (0. 05 mmol/L). Glomerular collagen IV was decreased from 2 to 16 days postischemia, which was accompanied by an increase in MMP-2. The fractional area of the interstitium was greatest at day 8 (19.55 +/- 0.91% compared with day 0 at 8.08 +/- 0.27%), with a second increase observed at day 180 (16.61 +/- 0.70%). Interstitial Mo/Mphi increased postischemia from days 2 through 8 (8.84 +/- 2.12 to 133. 32 +/- 14.04 per 0.91 mm2) and then decreased. Myofibroblasts proliferated locally (PCNA double labeling was demonstrated), and increased numbers were found from days 2 through 16 (maximal at day 8, 26.96 +/- 3.04%, compared with day 0, 0.88 +/- 0.11%). In the postischemic groups, collagen IV increased to day 8 (20.84 +/- 1. 30%), but then decreased to below control values at day 64 (2.22 +/- 0.15%) before returning to normal by day 180. Interstitial collagen III increased to 8 days (0.45 +/- 0.07% to 2.55 +/- 0.36%) and then decreased to control levels by day 32, but showed a marked increase to approximately 6% at days 64 and 180. Cellular proliferation (PCNA) was maximal at days 2 and 4 (affecting tubule cells and myofibroblasts but not macrophages). Apoptosis was maximal at day 8 (in both interstitial and tubule cells) in the postischemic groups. CONCLUSION Marked changes in the accumulation of Mo/Mphi, MF, and collagen IV were found in this model of ischemic acute renal failure. The reversibility of functional and structural changes is in marked contrast to that found in progressive disease. The increases observed for collagen III at 64 and 180 days postischemia suggest that in the long term, however, further chronic structural changes may be observed.
Dietary supplementation with docosahexaenoic acid (DHA) improves seminal antioxidant status and decreases sperm DNA fragmentation

ABSTRACT The purpose of this study was to evaluate the effect of docosahexaenoic acid (DHA) dietary supplementation on semen quality, fatty acid composition, antioxidant capacity, and DNA fragmentation. In this randomized, double blind, placebo-controlled, parallel-group study, 74 subjects were recruited and randomly assigned to either the placebo group (n=32) or to the DHA group (n=42) to consume three 500-mg capsules of oil per day over 10 weeks. The placebo group received 1,500 mg/day of sunflower oil and the DHA group 1,500 mg/day of DHA-enriched oil. Seminal parameters (semen volume, sperm concentration, motility, morphology, and vitality), total antioxidant capacity, deoxyribonucleic acid fragmentation, and lipid composition were evaluated prior to the treatment and after 10 weeks. Finally, 57 subjects were included in the study with 25 in the placebo group and 32 in the DHA group. No differences were found in traditional sperm parameters or lipid composition of the sperm membrane after treatment. However, an increase in DHA and Omega-3 fatty acid content in seminal plasma, an improvement in antioxidant status, and a reduction in the percentage of spermatozoa with deoxyribonucleic acid damage were observed in the DHA group after 10 weeks of treatment.
Synaptic contact between melanopsin-containing retinal ganglion cells and rod bipolar cells.

PURPOSE Evidence indicates that the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) receive input from rods and cones, which are thought to modulate the irradiance detecting system driving entrainment of the circadian system and pupillomotor control. This study was performed to identify retinal cells that have synaptic contact with ipRGCs. METHODS Immunohistochemistry and high-power confocal microscopy were used to generate stacks of digital images of sections stained with antibodies against melanopsin, protein kinase C (PKCalpha), tyrosine hydroxylase (TH), presynaptic terminal markers (C-terminal binding protein 2 [CtBP2], vesicular monoamine transporter 2 [VMAT2] and postsynaptic marker (glutamate receptor subunit 4 [GluR4]). Results were analyzed in a computer-based three-dimensional reconstruction program for cellular contacts. RESULTS Markers and melanopsin rod bipolar processes were found to have axosomatic and axodendritic contact with melanopsin-containing RGCs. Typically, three to four contacts were found on the soma of the melanopsin-containing RGCs, together with contacts on proximal dendrites. Contacts visualized by only CtBP2 immunoreactivity could also be demonstrated on melanopsin cell bodies and processes representing contacts with other types of bipolar cells. At the border of the inner plexiform layer (IPL) and inner nuclear layer (INL), where melanopsin processes stratify, contacts between melanopsin and TH or VMAT2 immunoreactivity processes were observed. CONCLUSIONS Through confocal microscopy and computer-based three-dimensional analyses, this study demonstrates that melanopsin-containing RGCs have synaptic contact with PKC/CtBP2-containing rod bipolar cells and TH/VMAT2-immunoreactive amacrine cells through axodendritic and axosomatic contact, supporting electrophysiological observations that rods and cones signal to the melanopsin-containing intrinsically photosensitive RGCs.
Therapeutic neuroscience education via e-mail: a case report

Abstract Therapeutic neuroscience education (TNE) aims to alter a patient's thoughts and beliefs about pain and has shown efficacy in treating chronic pain. To date, TNE sessions mainly consist of one-on-one verbal communication. This approach limits availability of TNE to pain patients in remote areas. A 32-year-old patient with chronic low back pain (CLBP) who underwent surgery for thoracic outlet syndrome (TOS) attended a single clinic one-on-one TNE session followed by TNE via electronic mail (e-mail), pacing and graded exposure over a 4-month period. A physical examination, Numeric Rating Scale (NRS), Oswestry Disability Index (ODI), the Disabilities of Arm, Shoulder and Hand (DASH), and Fear-Avoidance Beliefs Questionnaire (FABQ) were assessed during her initial physical therapy visit as well as 1 and 4 months later. Pre-TNE, the patient reported: NPRS (arm) = 7/10; NPRS (leg) = 4/10; ODI = 10.0%; DASH = 36.7%; FABQ-W = 24; and FABQ-PA = 17. After 5 e-mail sessions all outcome measures improved, most noticeably NRS (arm) = 2/10; NRS (leg) = 0/10; DASH = 16.7%; FABQ-W = 8; and FABQ-PA = 7. TNE can potentially be delivered to suffering pain patients in remote areas or to individuals who have time and financial constraints, and likely at a significant reduced cost via e-mail.
SPARC Overexpression Inhibits Cell Proliferation in Neuroblastoma and Is Partly Mediated by Tumor Suppressor Protein PTEN and AKT

Secreted protein acidic and rich in cysteine (SPARC) is also known as BM-40 or Osteonectin, a multi-functional protein modulating cell–cell and cell–matrix interactions. In cancer, SPARC is not only linked with a highly aggressive phenotype, but it also acts as a tumor suppressor. In the present study, we sought to characterize the function of SPARC and its role in sensitizing neuroblastoma cells to radio-therapy. SPARC overexpression in neuroblastoma cells inhibited cell proliferation in vitro. Additionally, SPARC overexpression significantly suppressed the activity of AKT and this suppression was accompanied by an increase in the tumor suppressor protein PTEN both in vitro and in vivo. Restoration of neuroblastoma cell radio-sensitivity was achieved by overexpression of SPARC in neuroblastoma cells in vitro and in vivo. To confirm the role of the AKT in proliferation inhibited by SPARC overexpression, we transfected neuroblastoma cells with a plasmid vector carrying myr-AKT. Myr-AKT overexpression reversed SPARC-mediated PTEN and increased proliferation of neuroblastoma cells in vitro. PTEN overexpression in parallel with SPARC siRNA resulted in decreased AKT phosphorylation and proliferation in vitro. Taken together, these results establish SPARC as an effector of AKT-PTEN-mediated inhibition of proliferation in neuroblastoma in vitro and in vivo.
Encoding Bi-manual Coordination Patterns From Human Demonstrations

Humans perform tasks such as bowl mixing bi-manually, but programming them on a robot can be challenging specially in tasks that require force control or on-line stiffness modulation. In this paper we first propose a user-friendly setup for demonstrating bi-manual tasks, while collecting complementary information on motion and forces sensed on a robotic arm, as well as the human hand configuration and grasp information. Secondly for learning the task we propose a method for extracting task constraints for each arm and coordination patterns between the arms. We use a statistical encoding of the data based on the extracted constraints and reproduce the task using a cartesian impedance controller.
Optimized strategy for rapid cytochrome P450 2D6 genotyping by real-time long PCR.

BACKGROUND Because of genetic polymorphisms, cytochrome P450 2D6 (Cyp2D6) activity in humans varies widely and alters the metabolism of commonly used drugs such as antidepressants, neuroleptics, and cardioactive agents. Severe adverse effects or resistance to therapy may result. METHODS We performed long PCR on the LightCycler(TM) and used the product as a template for a previously validated multiplex PCR that examines the *3, *4, *6, *7, and *8 alleles of Cyp2D6. We used real-time PCR to identify the *5 null allele and duplication of Cyp2D6 with detection by either hybridization probes or SYBR Green((R)). The *2 -1584 C/G polymorphism and the *35 allele were identified by PCR with detection by hybridization probes. Products of all PCRs were visualized with gel electrophoresis using a 0.7-1.5% agarose gel and ethidium bromide. Samples containing the *35 allele were analyzed in parallel by digestion with NlaIII, MslI, and BstXI and SmaI. We analyzed samples from volunteers and patients (105 samples for deletion and duplication and 116 samples for preamplification). Of those samples, 59 were from depressive inpatients taking part in a trial not yet published. RESULTS Identical genotyping results for both real-time and conventional PCR were obtained and verified by gel electrophoresis. Use of long-PCR methods on the LightCycler enabled comprehensive analysis of all relevant polymorphisms of the Cyp2D6 gene in 1 working day with a hands-on time of approximately 3-4 h. CONCLUSIONS This is the first description of a successful long-PCR application on the LightCycler and the fastest technique for amplification and specific detection of a PCR product of comparable length. The method appears suitable for large clinical and epidemiologic studies.
Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions

Although the identification of inherent structure in chronic lymphocytic leukemia (CLL) gene expression data using class discovery approaches has not been extensively explored, the natural clustering of patient samples can reveal molecular subdivisions that have biological and clinical implications. To explore this, we preprocessed raw gene expression data from two published studies, combined the data to increase the statistical power, and performed unsupervised clustering analysis. The clustering analysis was replicated in 4 independent cohorts. To assess the biological significance of the resultant clusters, we evaluated their prognostic value and identified cluster-specific markers. The clustering analysis revealed two robust and stable subgroups of CLL patients in the pooled dataset. The subgroups were confirmed by different methodological approaches (non-negative matrix factorization NMF clustering and hierarchical clustering) and validated in different cohorts. The subdivisions were related with differential clinical outcomes and markers associated with the microenvironment and the MAPK and BCR signaling pathways. It was also found that the cluster markers were independent of the immunoglobulin heavy chain variable (IGVH) genes mutational status. These findings suggest that the microenvironment can influence the clinical behavior of CLL, contributing to prognostic differences. The workflow followed here provides a new perspective on differences in prognosis and highlights new markers that should be explored in this context.
Functional Analysis in Mouse Embryonic Stem Cells Reveals Wild-Type Activity for Three Msh6 Variants Found in Suspected Lynch Syndrome Patients

Lynch syndrome confers an increased risk to various types of cancer, in particular early onset colorectal and endometrial cancer. Mutations in mismatch repair (MMR) genes underlie Lynch syndrome, with the majority of mutations found in MLH1 and MSH2. Mutations in MSH6 have also been found but these do not always cause a clear cancer predisposition phenotype and MSH6-defective tumors often do not show the standard characteristics of MMR deficiency, such as microsatellite instability. In particular, the consequences of MSH6 missense mutations are challenging to predict, which further complicates genetic counseling. We have previously developed a method for functional characterization of MSH2 missense mutations of unknown significance. This method is based on endogenous gene modification in mouse embryonic stem cells using oligonucleotide-directed gene targeting, followed by a series of functional assays addressing the MMR functions. Here we have adapted this method for the characterization of MSH6 missense mutations. We recreated three MSH6 variants found in suspected Lynch syndrome families, MSH6-P1087R, MSH6-R1095H and MSH6-L1354Q, and found all three to behave like wild type MSH6. Thus, despite suspicion for pathogenicity from clinical observations, our approach indicates these variants are not disease causing. This has important implications for counseling of mutation carriers.
Elicitation and Grading of Subjective Attributes of 2-Channel Phantom Images

The subjective attributes of 2-channel phantom images of transient piano, continuous trumpet and male speech sources were elicited using pair-wise comparison between reference mono images and their phantom images. The attributes elicited included ‘image focus’, ‘image width’, ‘image distance’, ‘brightness’, ‘hardness’ and ‘fullness’. The effect of interchannel time and intensity differences on the perceived difference between the real image and its phantom image was investigated for each sound source in respect of the elicited subjective attributes. Results show that the type of panning method (pure time, pure intensity and combination of the two) had a statistically significant effect on image focus and image width attributes. It was also found that the type of sound source had a significant effect on all the attributes.
Metastasis: Recent Discoveries and Novel Perioperative Treatment Strategies with Particular Interest in the Hemostatic Compound Desmopressin

Metastatic disease is responsible for most of cancer lethality. A main obstacle for therapy of advanced cancers is that the outcome of metastasis depends on a complex interplay between malignant and host cells. The perioperative period represents an underutilized window of opportunity for cancer treatment where tumor-host interactions can be modulated, reducing the risk of local recurrences and distant metastases. Blood-saving agents are attractive compounds to be administered during tumor surgery. Desmopressin (DDAVP) is a safe and convenient hemostatic peptide with proved antimetastastic properties in experimental models and veterinary clinical trials. The compound seems to induce a dual angiostatic and antimetastatic effect, breaking the cooperative function of cancer cells and endothelial cells during residual tumor progression. DDAVP is therefore an interesting lead compound to develop novel synthetic peptide analogs with enhanced antitumor properties.
Understanding the sources of variation in software inspections

In a previous experiment, we determined how various changes in three structural elements of the software inspection process (team size and the number and sequencing of sessions) altered effectiveness and interval. Our results showed that such changes did not significantly influence the defect detection rate, but that certain combinations of changes dramatically increased the inspection interval. We also observed a large amount of unexplained variance in the data, indicating that other factors must be affecting inspection performance. The nature and extent of these other factors now have to be determined to ensure that they had not biased our earlier results. Also, identifying these other factors might suggest additional ways to improve the efficiency of inspections. Acting on the hypothesis that the “inputs” into the inspection process (reviewers, authors, and code units) were significant sources of variation, we modeled their effects on inspection performance. We found that they were responsible for much more variation in detect detection than was process structure. This leads us to conclude that better defect detection techniques, not better process structures, are the key to improving inspection effectiveness. The combined effects of process inputs and process structure on the inspection interval accounted for only a small percentage of the variance in inspection interval. Therefore, there must be other factors which need to be identified.
Search for a New Description of Protein Topology and Local Structure

A novel description of protein structure in terms of the generalized secondary structure elements (GSSE) is proposed. GSSE's are defined as fragments of the protein structure where the chain doesn't radically change its direction. In this new language, global protein topology becomes a particular arrangement of the relatively small number of large, rod like GSSE's. Protein topology can be described by an adjacency matrix giving information, which GSSE's are close in space to each other and defining a graph, where GSSE's are equivalent to vertices and interactions between them to edges. The information about the local structure is translated into the local density of pseudo-Calpha atoms along the chain and the curvature of the chain. This new description has a number of interesting and useful features. For instance, enumeration theorems of graph theory can be used to estimate a number of possible topologies for a protein built from a given number of elements. Different topologies, including novel ones, can be generated from the known by various permutations of elements. Many new regularities in protein structures become suddenly visible in a new description. A new local structure description is more amenable to predictions and easier to use in fold predictions.
Ethanol‐induced oxidative stress precedes mitochondrially mediated apoptotic death of cultured fetal cortical neurons

In utero ethanol exposure elicits apoptotic cell death in the fetal brain, and this may be mediated by oxidative stress. Our studies utilize cultured fetal rat cortical neurons and illustrate that ethanol elicits a rapid onset of oxidative stress, which culminates in mitochondrially mediated apoptotic cell death. Cells exposed to ethanol (2.5 mg/ml) remained attached to their polylysine matrix during a 24‐hr exposure, but they exhibited distinct signs of oxidative stress, decreased viability, and apoptosis. Confocal microscopy of live cortical neurons pretreated with dichlorodihydrofluorescein diacetate demonstrated an increase in reactive oxygen species (ROS) within 5 min of ethanol exposure. The levels of ROS further increased by 58% within 1 hr (P < .05) and by 82% within 2 hr (P < .05), accompanied by increases of mitochondrial 4‐hydroxynonenal (HNE). These early events were followed by decreased trypan blue exclusion of 10% to 32% (P < .05) at the 6‐ to 24‐hr time points, respectively. This culminates in apoptotic death, with increases of Annexin V binding of 43%, 89%, 123%, and 238%, at 2, 6, 12, and 24 hr of ethanol treatment, respectively, as well as DNA fragmentation increases of 50% and 65% by 12 and 24 hr, respectively. Release of cytochrome c by mitochondria increased by 53% at 6 hr of exposure (P < .05), concomitant with activation of caspase 3 (52% at 12 hr, P < .05). Pretreatment with N‐acetylcysteine increased cellular glutathione and prevented apoptosis. These studies provide a time line illustrating that oxidative stress and formation of a proapoptotic lipid peroxidation product, HNE, precede a cascade of mitochondrially mediated events in cultured fetal cortical neurons, culminating in apoptotic death. The prevention of apoptosis by augmentation of glutathione stores also strongly supports a role for oxidative stress in ethanol‐mediated apoptotic death of fetal cortical neurons. © 2003 Wiley‐Liss, Inc.
Personality and Persuasion : Need for Cognition Moderates the Persistence and Resistance of Attitude Changes

Hypotheses about the persistence and resistance of attitudes and beliefs formed by individuals scoring high or low in Need for Cognition (NC; Cacioppo & Petty, 1982) were derived from the Elaboration Likelihood Model of persuasion (Petty & Cacioppo, 1986). In Study 1, both high-NC and low-NC individuals formed evaluatively similar attitudes toward an unfamiliar attitude object (a new product) after exposure to a persuasive message (an advertisement). The newly formed attitudes of high-NC individuals decayed less than the newly formed attitudes of low-NC individuals over a 2-day period. In Study 2, both high-NC and low-NC individuals were persuaded by an initial message that a food additive was unsafe. However, when immediately exposed to a second countermessage arguing that the product was safe, the initial experimentally created beliefs of high-NC individuals were shown to be more resistant to change than the experimentally created beliefs of low-NC individuals.