gebhart/patrepeval huggingface dataset:
A critical role for p38MAPK signalling pathway during reprogramming of human fibroblasts to iPSCs (2017)

Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) holds enormous promise for regenerative medicine. Reprogramming is a stepwise process with well-defined stages of initiation, maturation and stabilisation which are critically dependent on interactions between key pluripotency transcription factors, epigenetic regulators and signalling pathways. In this manuscript we have investigated the role of p38 MAPK signalling pathway and have shown a subpopulation- and phase-specific pattern of activation occurring during the initiation and maturation stage of reprogramming in partially and fully reprogrammed cells respectively. Downregulation of p38 MAPK activity via RNA interference or small molecule inhibitor led to cell accumulation in G1 phase of the cell cycle and reduced expression of cell cycle regulators during the initiation stage of reprogramming. This was associated with a significant downregulation of key pluripotency marker expression, disruption of mesenchymal to epithelial transition (MET), increased expression of differentiation markers and presence of partially reprogrammed cells which retained a typical gene expression profile of mesendodermal cells and were unable to progress to fully reprogrammed phenotype. Together our data indicate an important role for p38 MAPK activity in proliferation, MET progression and establishment of pluripotent phenotype, which are necessary steps for the development of human iPSCs.
Growth Factor Delivery Approaches in Hydrogels (2008)

The controlled delivery of growth factors is a very challenging task because many different issues have to be addressed to develop the best suited system. A wide range of approaches have been employed for the controlled delivery of growth factors by hydrogels. Direct loading, electrostatic interaction, covalent binding, and the use of carriers are the main strategies presented in the literature. They are all detailed in the first part of this review. Recent work emphasizing biologically inspired strategies is also included. Also, both natural and synthetic materials are discussed. The second part comprises the methods to evaluate such delivery approaches. Both in vivo and in vitro techniques are presented. Improvements based on the discussed approaches may illustrate future paths toward the development of an ideal growth factor delivery system.
Registration errors in augmented reality systems (1996)

Augmented reality (AR) systems combine three-dimensional computer-generated imagery with the view of the real environment in order to make unseen objects visible or to present additional information. A critical problem is that the computer-generated objects do not currently remain correctly registered with the real environment---objects aligned from one viewpoint appear misaligned from another and appear to swim about as the viewer moves. This registration error is caused by a number of factors, such as system delay, optical distortion, and tracker measurement error, and is difficult to correct with existing technology. This dissertation presents a registration error model for AR systems and uses it to gain insight into the nature and severity of the registration error caused by the various error sources. My thesis is that a mathematical error model enables the system architect to determine . which error sources are the most significant, . the sensitivity of the net registration error to each error, . the nature of the distortions caused by each type of error, . the level of registration accuracy one can expect, and also provides insights on how best to calibrate the system. Analysis of a surgery planning application yielded the following main results: . Even for moderate head velocities, system delay causes more registration error than all other sources combined; . Using the eye&amp;apos;s center of rotation as the eyepoint in the computer graphics model reduces the error due to eye rotation to zero for points along the line of gaze. This should obviate the need for eye tracking; . Tracker error is a significant problem both in head tracking and in system calibration; . The World coordinate system should be omitted when possible; . Optical distortion is a significant err...
The TARC/sICAM5 Ratio in Patient Plasma is a Candidate Biomarker for Drug Resistant Epilepsy (2013)

Epilepsy is a common affliction that involves inflammatory processes. There are currently no definitive chemical diagnostic biomarkers in the blood, so diagnosis is based on a sometimes expensive synthesis of clinical observation, radiology, neuro-psychological testing, and interictal and ictal EEG studies. Soluble ICAM5 (sICAM5), also known as telencephalin, is an anti-inflammatory protein of strictly central nervous system tissue origin that is also found in blood. Here we have tested the hypothesis that plasma concentrations of select inflammatory cytokines, including sICAM5, might serve as biomarkers for epilepsy diagnosis. To test this hypothesis, we developed a highly sensitive and accurate electrochemiluminescent ELISA assay to measure sICAM5 levels, and measured levels of sICAM5 and 18 other inflammatory mediators in epilepsy patient plasma and controls. Patient samples were drawn from in-patients undergoing video-EEG monitoring, without regard to timing of seizures. Differences were defined by t-test, and Receiver Operating Condition (ROC) curves determined the ability of these tests to distinguish between the two populations. In epilepsy patient plasmas, we found that concentrations of anti-inflammatory sICAM5 are reduced (p = 0.002) and pro-inflammatory IL-1β, IL-2, and IL-8 are elevated. TARC (thymus and activation regulated chemokine, CCL17) concentrations trend high. In contrast, levels of BDNF and a variety of other pro-inflammatory mediators are not altered. Based on p-value and ROC analysis, we find that the ratio of TARC/sICAM5 discriminates accurately between patients and controls, with an ROC Area Under the Curve (AUC) of 1.0 (p = 0.034). In conclusion, we find that the ratio of TARC to sICAM5 accurately distinguishes between the two populations and provides a statistically and mechanistically compelling candidate blood biomarker for drug resistant epilepsy.
Advanced multistage turbine blade aerodynamics, performance, cooling, and heat transfer (1995)

The gas turbine has the potential for power production at the highest possible efficiency. The challenge is to ensure that gas turbines operate at the optimum efficiency so as to use the least fuel and produce minimum emissions. A key component to meeting this challenge is the turbine. Turbine performance, both aerodynamics and heat transfer, is one of the barrier advanced gas turbine development technologies. This is a result of the complex, highly three-dimensional and unsteady flow phenomena in the turbine. Improved turbine aerodynamic performance has been achieved with three-dimensional highly-loaded airfoil designs, accomplished utilizing Euler or Navier-Stokes Computational Fluid Dynamics (CFD) codes. These design codes consider steady flow through isolated blade rows. Thus they do not account for unsteady flow effects. However, unsteady flow effects have a significant impact on performance. Also, CFD codes predict the complete flow field. The experimental verification of these codes has traditionally been accomplished with point data - not corresponding plane field measurements. Thus, although advanced CFD predictions of the highly complex and three-dimensional turbine flow fields are available, corresponding data are not. To improve the design capability for high temperature turbines, a detailed understanding of the highly unsteady and three-dimensional flow through multi-stage turbines is necessary. Thus, unique data are required which quantify the unsteady three-dimensional flow through multi-stage turbine blade rows, including the effect of the film coolant flow. Also, as design CFD codes do not account for unsteady flow effects, the next logical challenge and the current thrust in CFD code development is multiple-stage analyses that account for the interactions between neighboring blade rows. Again, to verify and or direct the development of these advanced codes, complete three-dimensional unsteady flow field data are needed.
CTLA-4 Blockade with Ipilimumab: Long-term Follow-up of 177 Patients with Metastatic Melanoma (2012)

This report provides the longest follow-up of patients with melanoma treated with ipilimumab and shows that ipilimumab can induce durable, potentially curative tumor regression in a small percentage of patients with metastatic melanoma. The combination of ipilimumab and interleukin-2 seems to have an increased CR rate, but this needs to be tested in a randomized trial.
Rapid PCR for Identity Testing Using a Battery-Powered Miniature Thermal Cycler (1998)

Abstract A microfabricated, battery-powered thermal cycler was implemented in PCR-based DNA typing for human identification. HLA DQα and an STR triplex were PCR amplified using a device known as the Miniature Analytical Thermal Cycling Instrument (MATCI). The extremely efficient heating properties of the MATCI enabled thermal cycling to be completed in as little as 21 min. In addition, the feasibility of using the real-time fluorescent detection system of the MATCI was demonstrated. The successful application of this portable, prototype device to forensic identity testing is a significant milestone towards the eventual development of a completely integrated DNA testing instrument that would also incorporate sample preparation and allele detection.
Disturbed Osteoblastic Differentiation of Fibrous Hamartoma Cell from Congenital Pseudarthrosis of the Tibia Associated with Neurofibromatosis Type I (2011)

Congenital pseudarthrosis of the tibia appears to be caused by fibrous hamartoma originating from aberrant growth of Nf1 haploinsufficient periosteal cells, which failed in terminal osteoblastic differentiation and arrested at a certain stage of this process. This pathomechanism of CPT should be targeted in the development of novel therapeutic biologic intervention.
Dial-in virtual private networks using layer 3 tunneling (2002)

Corporate networks are making increasing use of the Internet to connect geographically diverse site networks rather than developing their own "leased line" WAN networks. Similarly, they are outsourcing their dial-in capability by replacing their banks of modems with a single connection to a service provider with geographically diverse Points Of Presence (POPs). In this way, users in a corporate network can dial local (or toll free) numbers which will be routed to the nearest POP; then, be connected to their corporate network using some form of tunneling. There are two common forms of tunneling in use in the Internet today: Layer 2 (using L2TP, for example) and Layer 3 (using Mobile IP, for example). The paper presents a design for a Layer 3 Dial-in Virtual Private Network Service (DVS), based on Mobile IP. This design has been implemented by Bay Networks.
Inducible expression of retrograde transynaptic genetic tracer in mice (2007)

A key step towards understanding the development and function of the central nervous system is by characterizing the connections between neurons. Tetanus toxin C fragment (TTC) is transynaptically and retrogradely transported without the toxin's pathogenic effect, and therefore, recently it has been used as a genetic tracer combined with beta-galactosidase or green fluorescent protein. Here, we introduce a new fusion construct, APTTC, consisting of the truncated human placental alkaline phosphatase with TTC, and generating the transgenic mouse line, (tetracycline operator) tetO-APTTC, for inducible expression of APTTC regulated by tetO. We demonstrate that APTTC is transported retrogradely and transynaptically, and allows us to robustly visualize the inputs of the expressing neurons when transgenetically expressed in mice, exemplified in the striatal neuronal circuit. Therefore, tetO-APTTC transgenic mouse line can be widely used for visualization of neuronal connectivity when combined with mice carrying tetracycline-controlled transactivator (tTA) in any specific neurons.
Silver-Zinc Redox-Coupled Electroceutical Wound Dressing Disrupts Bacterial Biofilm (2015)

Pseudomonas aeruginosa biofilm is commonly associated with chronic wound infection. A FDA approved wireless electroceutical dressing (WED), which in the presence of conductive wound exudate gets activated to generate electric field (0.3-0.9V), was investigated for its anti-biofilm properties. Growth of pathogenic P. aeruginosa strain PAO1 in LB media was markedly arrested in the presence of the WED. Scanning electron microscopy demonstrated that WED markedly disrupted biofilm integrity in a setting where silver dressing was ineffective. Biofilm thickness and number of live bacterial cells were decreased in the presence of WED. Quorum sensing genes lasR and rhlR and activity of electric field sensitive enzyme, glycerol-3-phosphate dehydrogenase was also repressed by WED. This work provides first electron paramagnetic resonance spectroscopy evidence demonstrating that WED serves as a spontaneous source of reactive oxygen species. Redox-sensitive multidrug efflux systems mexAB and mexEF were repressed by WED. Taken together, these observations provide first evidence supporting the anti-biofilm properties of WED.
Anemia in Liver Transplant Recipients Undergoing Antiviral Treatment for Recurrent Hepatitis C (2007)

Adherence to antiviral therapy is essential to achieve sustained virological responses in patients treated for hepatitis C. An important limitation to use of appropriate doses of ribavirin is development of anemia. The aim of this study is to identify risk factors associated with anemia in liver transplant recipients undergoing treatment for recurrent hepatitis C virus (HCV). Retrospective analysis was performed on 115 adult liver transplantation (LT) recipients who received antiviral treatment. Anemia was defined as hemoglobin of <10 gm/dL or the use of erythropoietin replacement therapy. Variables found to be significant in univariate analysis were further studied in multivariate analysis. The mean (+/- standard deviation [SD]) age of our cohort was 52.1 (+/- 8.8) yr. Anemia developed in 44 patients (38.3%). Mean (+/- SD) onset of anemia was 8.9 (+/- 6.8) weeks after initiation of antiviral therapy. A total of 30 patients (26%) required erythropoietin replacement, at a mean (+/- SD) of 7.9 (+/- 6.0) weeks after start of antiviral treatment. A total of 27 patients (24%) required ribavirin dose reduction, at a mean (+/- SD) time to dose reduction of 8.1 (+/- 6.3) weeks. In univariate analysis, body mass index (BMI) (P < 0.01), mycophenolate mofetil use (P = 0.05), trimethoprim-sulfamethoxazole (P = 0.02), and age (P = 0.02) were statistically significant. In conclusion, in multivariate analysis, BMI (P < 0.01) and age (P = 0.02) were found to be independent predictors of anemia. Anemia is common in liver transplant recipients treated for recurrent HCV. Special vigilance is required for older patients and patients with a low BMI.
Unrelated donor bone marrow transplantation without T cell depletion using a chemotherapy only condition regimen. Low incidence of failed engraftment and severe acute GVHD. (1996)

Twenty-five patients with hematologic malignancies were treated with busulfan (16 mg/kg) and cyclophosphamide (50 mg/kg x 3 days) as conditioning for bone marrow transplantation using marrow from serologically matched, DR locus genotypically identical unrelated donors. Previous studies of BuCy2 as conditioning for UD-BMT have reported a graft failure rate of up to 21% suggesting it may be insufficiently immunosuppressive in this setting. We elected not to use BuCy4 as it may have a higher incidence of extramedullary toxicity. In addition the patients received GM-CSF (500 mg/m2) from day 0, cyclosporine and short-course methotrexate (15 mg/m2 x 1, then 10 mg/m2 x 3) as GVHD prophylaxis and prophylactic ganciclovir at engraftment if either they or their donor were CMV antibody positive. The median age of the 25 patients was 41 years and the most common diagnosis was CML (76%). Seven patients were considered poor risk and eight males were recipients of marrow from female donors. Sixteen patients survive at a median of 435 days from transplant. The actuarial overall and disease-free survivals at 1 year in this group of older patients were 62 +/- 20% and 57 +/- 20% and 100-day survival was 70%. The engraftment rate was 100%; there have been no instances of secondary graft failure. Fifteen patients (60%) developed grade II-IV GVHD and 12 of 16 (75%) developed some chronic GVHD but only half of these were extensive. The performance status of survivors is good (median of 90); seven of 12 eligible patients are back at work. This study demonstrates that UD-BMT can be successfully performed in very closely HLA-matched older patients using a chemotherapy-only protocol and that low rates of severe acute GVHD can be achieved without T cell depletion.
Isolation, antimicrobial activities, and primary structures of hamster neutrophil defensins (1996)

Hamster (Mesocricetus auratus) neutrophil granules contain at least four microbicidal peptides belonging to the defensin family. These compounds were purified from granule acid extracts by reverse-phase chromatography and termed HaNP-1 to -4 (hamster neutrophil peptide). HaNP-1 and HaNP-3 revealed the most bactericidal activity, with a 50% inhibitory concentration of 0.3 to 0.8 microg/ml for Staphylococcus aureus and Streptococcus pyogenes strains. The HaNP-4 was always isolated in concentrations exceeding about 10 times the concentrations of other hamster peptides, but its antibacterial activity as well as that of HaNP-2 was relatively lower, probably as a result of conserved Arg residue substitutions. Other microorganisms were also tested, and generally, hamster defensins exhibited less potency against gram-negative bacteria. The amino acid sequence of hamster defensins showed a high percentage of identity to the sequence of mouse enteric defensins, reaching about 60% identical residues in the case of HaNP-3 and cryptdin 3.
Poly(4‐vinylimidazolium)s/Diazabicyclo[5.4.0]undec‐7‐ene/Zinc(II) Bromide‐Catalyzed Cycloaddition of Carbon Dioxide to Epoxides (2014)

Abstract Poly(4‐vinylimidazolium)s, derived from the self‐immobilization of 4‐vinylimidazoliums, with diazabicyclo[5.4.0]undec‐7‐ene (DBU) and zinc bromide (ZnBr 2 ) are used as a highly efficient catalyst for the chemical fixation of carbon dioxide. This catalytic system has been applied for the preparation of cyclic carbonates from terminal epoxides and carbon dioxide. Many functional groups, including chloro, vinyl, ether, and hydroxy groups are well tolerated in the reactions. Moreover, the catalytic system was found to catalyze the conversion of more sterically congested epoxides which are generally considered to be challenging substrates for fabricating the cyclic organic carbonates. In addition, the disubstituted epoxides are found to react with retention of configuration. The polymer precatalyst is easily recovered and reused. A plausible reaction mechanism is proposed. magnified image
New FATB thioesterases from a high‐laurate Cuphea species: Functional and complementation analyses (2006)

Abstract The New World genus Cuphea is a rich source of genes encoding enzymes specialized for seed‐specific synthesis of short‐ and medium‐chain fatty acids (FA). We isolated and characterized two new acyl‐acyl carrier protein (ACP) thioesterase (TE) cDNA, Cc FATB1 and Cc FATB2, from developing seeds of C. calophylla var. mesostemon . Cuphea calophylla is one of several species in the genus specializing in the synthesis of lauric acid (12:0). Phylogenetic clustering classified Cc FATB1 and Cc FATB2 as medium‐ and long‐chain FATB TE, respectively. Gene expression analysis indicated that Cc FATB1 was seed specific and Cc FATB2 was ubiquitous. Overexpression of Cc FATB1 in developing seeds of Arabidopsis partially redirected FA synthesis toward medium‐chain FA (12:0, 14:0, and 16:0). Laurate synthesis was preferentially increased by co‐expressing Cc FATB1 and Cw KAS A1, a medium‐chain‐specific ketoacyl‐ACP synthase (KAS) from another 12:0‐rich species, C. wrightii . Overexpression of Cc FATB1 cDNA complemented the low‐palmitate (16:0) but not the low‐stearate (18:0) phenotype in leaves and seeds of an Arabidopsis fatb‐2 mutant, whereas Cc FATB2 restored both long‐chain FA. The investigated Cuphea species provide a diverse source of seed‐specific FATB and KAS genes for combinatorial manipulation of medium‐chain FA content in oilseed plants.
On the Enhancement and Binarization of Mobile Captured Vehicle Identification Number for an Embedded Solution (2012)

An embedded solution for automatic detection of Vehicle Identification Numbers (VIN) captured by a mobile camera has a number of real world applications. But the performance of available open source Optical Character Recognition (OCR) systems on VIN images captured by mobile phones is extremely poor because of the image quality affected by various noises. In a recent study of such images, we have observed that the performance of existing open source OCR systems can be improved by applying several image enhancement techniques on these images before sending them to the OCR engine. In this article, we have presented such a method that improves the recognition accuracy from 5.89% up to 82.3%.
Distinctive patterns of microRNA expression in primary muscular disorders (2007)

The primary muscle disorders are a diverse group of diseases caused by various defective structural proteins, abnormal signaling molecules, enzymes and proteins involved in posttranslational modifications, and other mechanisms. Although there is increasing clarification of the primary aberrant cellular processes responsible for these conditions, the decisive factors involved in the secondary pathogenic cascades are still mainly obscure. Given the emerging roles of microRNAs (miRNAs) in modulation of cellular phenotypes, we searched for miRNAs regulated during the degenerative process of muscle to gain insight into the specific regulation of genes that are disrupted in pathological muscle conditions. We describe 185 miRNAs that are up- or down-regulated in 10 major muscular disorders in humans [Duchenne muscular dystrophy (DMD), Becker muscular dystrophy, facioscapulohumeral muscular dystrophy, limb-girdle muscular dystrophies types 2A and 2B, Miyoshi myopathy, nemaline myopathy, polymyositis, dermatomyositis, and inclusion body myositis]. Although five miRNAs were found to be consistently regulated in almost all samples analyzed, pointing to possible involvement of a common regulatory mechanism, others were dysregulated only in one disease and not at all in the other disorders. Functional correlation between the predicted targets of these miRNAs and mRNA expression demonstrated tight posttranscriptional regulation at the mRNA level in DMD and Miyoshi myopathy. Together with direct mRNA-miRNA predicted interactions demonstrated in DMD, some of which are involved in known secondary response functions and others that are involved in muscle regeneration, these findings suggest an important role of miRNAs in specific physiological pathways underlying the disease pathology.
Antibacterial testing of metal ions using a chemically defined medium (1990)

Data from in-vitro tests on potential germicides can be greatly influenced by the culture medium. The bioavailability and biochemical reactivity of the biocides can be influenced by chemical interference with media components (Spooner & Sykes 1972). Bird et al. (1985) showed that metal ions are particularly prone to chemical interferences. A chemically defined solid medium has been developed to monitor the antibacterial activity of metal ions. The minimum inhibitory concentrations of zinc and silver have been determined against a range of bacteria using this medium.