gebhart/patrepeval huggingface dataset:
Immunotherapy Targets in Pediatric Cancer (2012)

Immunotherapy for cancer has shown increasing success and there is ample evidence to expect that progress gleaned in immune targeting of adult cancers can be translated to pediatric oncology. This manuscript reviews principles that guide selection of targets for immunotherapy of cancer, emphasizing the similarities and distinctions between oncogene-inhibition targets and immune targets. It follows with a detailed review of molecules expressed by pediatric tumors that are already under study as immune targets or are good candidates for future studies of immune targeting. Distinctions are made between cell surface antigens that can be targeted in an MHC independent manner using antibodies, antibody derivatives, or chimeric antigen receptors versus intracellular antigens which must be targeted with MHC restricted T cell therapies. Among the most advanced immune targets for childhood cancer are CD19 and CD22 on hematologic malignancies, GD2 on solid tumors, and NY-ESO-1 expressed by a majority of synovial sarcomas, but several other molecules reviewed here also have properties which suggest that they too could serve as effective targets for immunotherapy of childhood cancer.
Small intestinal bacterial overgrowth in North Indian patients with celiac disease. (2008)

This study indicates that a large number of celiac patients from North India suffer from bacterial overgrowth which can be accordingly treated with antibiotics.
Salivary Soluble CD44: A Potential Molecular Marker for Head and Neck Cancer (2005)

In this preliminary analysis, the salivary solCD44 ELISA seems to effectively detect HNSCC at all stages. Further study is indicated because early detection is clearly important in this disease.
Fundamental relationship between bilateral filtering, adaptive smoothing, and the nonlinear diffusion equation (2002)

In this paper, the relationship between bilateral filtering and anisotropic diffusion is examined. The bilateral filtering approach represents a large class of nonlinear digital image filters. We first explore the connection between anisotropic diffusion and adaptive smoothing, and then the connection between adaptive smoothing and bilateral filtering. Previously, adaptive smoothing was considered to be an inconsistent approximation to the nonlinear diffusion equation. We extend adaptive smoothing to make it consistent, thus enabling a unified viewpoint that relates nonlinear digital image filters and the nonlinear diffusion equation.
The Jalapeño virtual machine (2000)

Jalapeño is a virtual machine for Java™ servers written in the Java language. To be able to address the requirements of servers (performance and scalability in particular), Jalapeño was designed “from scratch“ to be as self-sufficient as possible. Jalapeño's unique object model and memory layout allows a hardware null-pointer check as well as fast access to array elements, fields, and methods. Run-time services conventionally provided in native code are implemented primarily in Java. Java threads are multiplexed by virtual processors (implemented as operating system threads). A family of concurrent object allocators and parallel type-accurate garbage collectors is supported. Jalapeño's interoperable compilers enable quasi-preemptive thread switching and precise location of object references. Jalapeño's dynamic optimizing compiler is designed to obtain high quality code for methods that are observed to be frequently executed or computationally intensive.
Double-blind trial of pyridoxine (vitamin B6) in the treatment of steroid-dependent asthma. (1993)

Pyridoxine has been reported to largely correct an abnormality of tryptophan metabolism present in patients with bronchial asthma and to reduce the symptoms of asthma in long-term studies. We enrolled 31 patients requiring steroids (oral or inhaled) for the treatment of their asthma in a double-blind, placebo-controlled assessment of 9 weeks' treatment with pyridoxine 300 mg per day (13) or placebo (18). Outcome variables included PEFR, FEV1, asthma symptom scores, 24 hour urinary 5-HIAA, skin test reactivity to histamine and compound 48/80 and blood serotonin levels. Plasma pyridoxine levels indicated overall patient compliance with a mean change from baseline to the end of the study of 82.5 +/- 27.7 ng/mL in patients on pyridoxine and -2.9 +/- 10.3 for those on placebo (P = .0001). Furthermore, patients routinely treated with theophylline had lower (10 +/- 8 ng/mL) plasma pyridoxine levels at baseline than those not on it (19 +/- 6 ng/mL; P = .01), suggesting that theophylline may lower plasma pyridoxine levels. There was no significant difference between the pyridoxine and placebo groups in the change from baseline to the last 2 weeks of treatment phase in any of the outcome variables. We conclude that under the conditions of the study, treatment with oral pyridoxine failed to improve the outcome variables in patients requiring steroids for the treatment of their asthma. The results of this study suggest that prescription or usage of oral pyridoxine for the treatment of asthma cannot be justified in such patients.
Snoring-a simple surgical solution (1996)

In this paper a new palatal surgical technique for the treatment of snoring is described and evaluated. All 22 patients were severe snorers with no significant obstructive sleep apnoea, as confirmed by detailed sleep studies. The aim of the surgical technique was to eliminate the vibration of the soft palate and the posterior pillars which occurs during snoring. This was achieved under general anaesthetic by making a 1.5 cm vertical full thickness incision in the soft palate from the superior pole of the tonsil towards the pterygoid hamulus using monopolar cutting diathermy. Specifically designed daily pain questionnaires were completed by the patients during the first 2 post-operative weeks and the level of snoring was assessed by the patient's sleeping partner at 2, 6 and 12 weeks. The presence of any complications was also documented at these times. The results demonstrate that this surgical technique is effective, quick, simple and bloodless. The post-operative pain created is mild and quickly resolves. All patients experienced a dramatic diminution of their snoring and in 55% complete cessation was achieved.
Pancreaticoduodenectomy (2004)

Pancreaticoduodenectomy continues to be associated with considerable morbidity. With careful patient selection, PD can be performed safely. Long-term survival in patients with periampullary adenocarcinoma can be predicted by preoperative laboratory values, intraoperative factors, and pathologic findings.
Elimination of dark line defects in GaAs-on-Si by post-growth patterning and thermal annealing (1991)

Post-growth patterning to &amp;lt;15 μm×15 μm size patterns combined with thermal annealing at 850 °C for ≳15 min eliminates the dark line defects (DLDs) in GaAs-on-Si as shown by the spatially resolved photoluminescence technique. Patterning to small size islands of GaAs facilitates dislocation migration laterally out of the crystal, and thermal annealing provides the activation energy for the dislocations to migrate and interact. Patterning to small size features also significantly reduces the thermally induced biaxial tensile stress as reported earlier. On large size patterns, the density of DLDs is significantly reduced near the surface leaving larger volume of the material free from DLDs.
A randomised, double-masked comparison study of diquafosol versus sodium hyaluronate ophthalmic solutions in dry eye patients (2012)

Diquafosol (3%) and sodium hyaluronate (0.1%) exhibit similar efficacy in improving fluorescein staining scores of dry eye patients, whereas, diquafosol exhibits superior efficacy in improving rose bengal staining scores. Diquafosol has high clinical efficacy and is well tolerated with a good safety profile.
Disruption of Dendroctonus frontalis (Col., Scolytidae) infestations with an inhibitor (1992)

Use of the Dendroctonus frontalis inhibitor pheromone verbenone, as a treatment on trees within infestations, is effective in suppressing or halting infestation growth. It is hypothesized that the inhibitor disrupts the orientation of flying adult D. frontalis to host trees and, as a result, sufficient attacking adults are not available at any given time on a tree to successfully over take it. Seasonal changes in abundance, longevity, and dispersal of beetle populations may impact the effectiveness of the inhibitor-based treatment.
Effect of pH on metabolic and cardiorespiratory responses during progressive exercise (1984)

Six healthy male subjects performed three exercise tests in which the power output was increased by 100 kpm/min each minute until exhaustion. The studies were carried out after oral administration of CaCO3 (control), NH4Cl (metabolic acidosis), and NaHCO3 (metabolic alkalosis). Ventilation (VE), O2 intake (VO2), and CO2 output (VCO2) were monitored continuously. Arterialized-venous blood samples were drawn at specific times and analyzed for pH, PCO2, and lactate concentration. Resting pH (mean +/- SE) was lowest in acidosis (7.29 +/- 0.01) and highest in alkalosis (7.46 +/- 0.02). A lower peak power output (kpm/min) was achieved in acidosis (1,717 +/- 95) compared with control (1,867 +/- 120) alkalosis (1,867 +/- 125). Submaximal VO2 and VCO2 were similar, but peak VO2 and VCO2 were lower in acidosis. Plasma lactate concentration was lower at rest and during exercise in acidosis. Although lactate accumulation was reduced in acidosis, increases in hydrogen ion concentration were similar in the three conditions. We conclude that acid-base changes influence the maximum power output that may be sustained in incremental dynamic exercise and modify plasma lactate appearance, but have little effect on hydrogen ion appearance in plasma.
Individual heterojunctions of 3D germanium crystals on silicon CMOS for monolithically integrated X‐ray detector (2013)

Monolithic integration of absorber layer and readout electronics is expected to greatly improve spatial resolution and sensitivity of X‐ray imaging detectors. It requires, however, heteroepitaxial growth of thick, lattice, and thermally mismatched absorber layers on a Si substrate. Wafer bowing and layer cracks induced by temperature changes have so far appeared to be insurmountable obstacles in the way of realizing such a device. Here we present first results on a detector concept which does not suffer from such shortcomings. The absorber consists of closely spaced, tall Ge crystals, typically a few microns in width, each forming a heterojunction diode with the Si substrate. Electrical measurements on such diodes reveal reverse dark currents of the order of 1 mA/cm 2 , low enough for detector fabrication. We present a preliminary version of such a detector, where the pixel size is determined by the CMOS circuits rather than individual Ge crystals.
Simultaneous multiple-emitter fitting for single molecule super-resolution imaging (2011)

Single molecule localization based super-resolution imaging techniques require repeated localization of many single emitters. We describe a method that uses the maximum likelihood estimator to localize multiple emitters simultaneously within a single, two-dimensional fitting sub-region, yielding an order of magnitude improvement in the tolerance of the analysis routine with regards to the single-frame active emitter density. Multiple-emitter fitting enables the overall performance of single-molecule super-resolution to be improved in one or more of several metrics that result in higher single-frame density of localized active emitters. For speed, the algorithm is implemented on Graphics Processing Unit (GPU) architecture, resulting in analysis times on the order of minutes. We show the performance of multiple emitter fitting as a function of the single-frame active emitter density. We describe the details of the algorithm that allow robust fitting, the details of the GPU implementation, and the other imaging processing steps required for the analysis of data sets.
An Alternate Promoter in the Glucokinase Gene Is Active in the Pancreatic β Cell (1989)

An alternate promoter in the glucokinase gene is active in the beta cell and produces a glucokinase mRNA which is longer and that has a different leader sequence and translation start site than the hepatic glucokinase mRNA. The glucokinase beta cell promoter is located at least 12 kilobases upstream from the glucokinase hepatic promoter. Transcription from the glucokinase beta cell promoter initiates over a region of 62 bases. The absence of a TATA box homology in the proximal promoter region may account for the diffuse transcriptional initiation. Translation of the beta cell glucokinase mRNA predicts a glucokinase isozyme that is different from the hepatic isozyme by 15 amino acids at the N terminus. The use of alternative promoters apparently enables the glucokinase gene to be regulated by insulin in the liver and by glucose in the beta cell, thus possibly constituting an important feedback control loop for maintaining glucose homeostasis. Alternate RNA splicing of the beta cell glucokinase mRNA predicts at least two beta cell glucokinase isoforms. An alternate splice acceptor site in the 4th exon of the glucokinase gene was identified in two glucokinase cDNAs from rat insulinoma tissue. Use of the alternate splice acceptor site results in a 51-nucleotide in frame deletion in the beta cell glucokinase mRNA and removal of 17 amino acids from a region of the protein situated between the putative glucose and ATP binding domains. Analysis of the pattern of RNA splicing in tissues containing beta cells indicates that the splice acceptor site utilized in producing hepatic glucokinase mRNA is also utilized in the beta cell.
Gi-1/Gi-2-dependent signaling by single-transmembrane natriuretic peptide clearance receptor (2000)

Single-transmembrane natriuretic peptide clearance receptor (NPR-C), which is devoid of a cytoplasmic guanylyl cyclase domain, interacts with pertussis toxin (PTx)-sensitive G proteins to activate endothelial nitric oxide synthase (eNOS) expressed in gastrointestinal smooth muscle cells. We examined the ability of NPR-C to activate other effector enzymes in eNOS-deficient tenia coli smooth muscle cells; these cells expressed NPR-C and NPR-B but not NPR-A. Atrial natriuretic peptide (ANP), the selective NPR-C ligand cANP-(4-23), and vasoactive intestinal peptide (VIP) inhibited (125)I-ANP and (125)I-VIP binding to muscle membranes in a pattern indicating high-affinity binding to NPR-C. Interaction of VIP with NPR-C was confirmed by its ability to inhibit (125)I-ANP binding to membranes of NPR-C-transfected COS-1 cells. In tenia muscle cells, all ligands selectively activated G(i-1) and G(i-2); VIP also activated G(s) via VIP(2) receptors. All ligands stimulated phosphoinositide hydrolysis, which was inhibited by ANP-(1-11), PTx, and antibodies to phospholipase C-beta3 (PLC-beta3) and Gbeta. cANP-(4-23) contracted tenia muscle cells; contraction was blocked by U-73122 and PTx and by antibodies to PLC-beta3 and Gbeta in intact and permeabilized muscle cells, respectively. VIP and ANP contracted muscle cells only after inhibition of cAMP- and cGMP-dependent protein kinases. ANP and cANP-(4-23) inhibited forskolin-stimulated cAMP in a PTx-sensitive fashion. We conclude that NPR-C is coupled to activation of PLC-beta3 via betagamma-subunits of G(i-1) and G(i-2) and to inhibition of adenylyl cyclase via alpha-subunits.
Placental lesions associated with neurologic impairment and cerebral palsy in very low-birth-weight infants. (1998)

We found 2 types of fetal placental vascular lesions to be associated with neurologic impairment, namely, recent nonocclusive thrombi of chorionic plate vessels (P < .04) and severe villous edema (P < .01). Chorionic plate thrombi were seen only with chorioamnionitis and accounted for the increased risk of neurologic impairment seen with chorioamnionitis. Maternal vascular lesions showed a biphasic relation to neurologic impairment in the subgroup of patients without chorioamnionitis. Mild lesions were increased in controls (inadequate vascular remodeling, P=.03, and accelerated maturation, P=.004). A more severe lesion, multiple villous infarcts, although not reaching significance, was increased in the neurologically impaired cases. Finally, in a test of 9 selected placental lesions, cases with cerebral palsy were more likely to have 2 or more lesions (P < .0001) and were less likely to have no lesions (P < .04) than control infants.
Human amniotic membrane transplantation: Different modalities of its use in ophthalmology (2014)

The amniotic membrane (AM) is the inner layer of the fetal membranes and consist of 3 different layers: the epithelium, basement membrane and stroma which further consists of three contiguous but distinct layers: the inner compact layer, middle fibroblast layer and the outermost spongy layer. The AM has been shown to have anti-inflammatory, anti-fibrotic, anti-angiogenic as well as anti-microbial properties. Also because of its transparent structure, lack of immunogenicity and the ability to provide an excellent substrate for growth, migration and adhesion of epithelial corneal and conjunctival cells, it is being used increasingly for ocular surface reconstruction in a variety of ocular pathologies including corneal disorders associated with limbal stem cell deficiency, surgeries for conjunctival reconstruction, as a carrier for ex vivo expansion of limbal epithelial cells, glaucoma surgeries and sceral melts and perforations. However indiscriminate use of human AM needs to be discouraged as complications though infrequent can occur. These include risk of transmission of bacterial, viral or fungal infections to the recipient if the donors are not adequately screened for communicable diseases, if the membrane is not processed under sterile conditions or if storage is improper. Optimal outcomes can be achieved only with meticulous case selection. This review explores the ever expanding ophthalmological indications for the use of human AM.
Evaluation of PCR-based methods for the diagnosis of tuberculosis by identification of mycobacterial DNA in urine samples. (2002)

Neither the Githui method nor the Sechi method was sensitive enough to be recommended for routine use in clinical practice. PCR-based assays for the detection of M. tuberculosis DNA in urine will require further refinement before they can be recommended for use in clinical practice in Africa. The presence of mycobacterial DNA in urine samples of patients with pulmonary tuberculosis also requires further study.
Self-Normalizing Neural Networks (2017)

Deep Learning has revolutionized vision via convolutional neural networks (CNNs) and natural language processing via recurrent neural networks (RNNs). However, success stories of Deep Learning with standard feed-forward neural networks (FNNs) are rare. FNNs that perform well are typically shallow and, therefore cannot exploit many levels of abstract representations. We introduce self-normalizing neural networks (SNNs) to enable high-level abstract representations. While batch normalization requires explicit normalization, neuron activations of SNNs automatically converge towards zero mean and unit variance. The activation function of SNNs are "scaled exponential linear units" (SELUs), which induce self-normalizing properties. Using the Banach fixed-point theorem, we prove that activations close to zero mean and unit variance that are propagated through many network layers will converge towards zero mean and unit variance -- even under the presence of noise and perturbations. This convergence property of SNNs allows to (1) train deep networks with many layers, (2) employ strong regularization, and (3) to make learning highly robust. Furthermore, for activations not close to unit variance, we prove an upper and lower bound on the variance, thus, vanishing and exploding gradients are impossible. We compared SNNs on (a) 121 tasks from the UCI machine learning repository, on (b) drug discovery benchmarks, and on (c) astronomy tasks with standard FNNs and other machine learning methods such as random forests and support vector machines. SNNs significantly outperformed all competing FNN methods at 121 UCI tasks, outperformed all competing methods at the Tox21 dataset, and set a new record at an astronomy data set. The winning SNN architectures are often very deep. Implementations are available at: github.com/bioinf-jku/SNNs.
Peripheral pulse palpation: an unreliable physical sign. (1992)

Fifty observers, including two fully trained vascular surgeons, were asked to determine the presence or absence of the femoral and distal pulses of four patients with peripheral vascular disease and one asymptomatic subject (50 pulses assessed). Pulses felt by both vascular surgeons were deemed to be palpable. Among the other observers, the sensitivity of palpation was 95% or over for the femoral pulse, but 33% to 60% for observers of varying experience feeling for the posterior tibial pulse. Up to 20% false-positive observations were reported. Disease was diagnosed in over 10% of examinations of healthy limbs and was missed in over 10% of symptomatic limbs. The accuracy of pulse palpation was strongly correlated with the systolic blood pressure in the underlying artery. Accuracy was greater among more experienced observers, suggesting that careful teaching of this skill is likely to be beneficial. Even so, pulse palpation alone is an unreliable physical sign and should only be used in combination with objective measurements as a guide to clinical management.
Evaluation of the soft tissue biocompatibility of MgCa0.8 and surgical steel 316L in vivo: a comparative study in rabbits (2010)

Recent studies have shown the potential suitability of magnesium alloys as biodegradable implants. The aim of the present study was to compare the soft tissue biocompatibility of MgCa0.8 and commonly used surgical steel in vivo. A biodegradable magnesium calcium alloy (MgCa0.8) and surgical steel (S316L), as a control, were investigated. Screws of identical geometrical conformation were implanted into the tibiae of 40 rabbits for a postoperative follow up of two, four, six and eight weeks. The tibialis cranialis muscle was in direct vicinity of the screw head and thus embedded in paraffin and histologically and immunohistochemically assessed. Haematoxylin and eosin staining was performed to identify macrophages, giant cells and heterophil granulocytes as well as the extent of tissue fibrosis and necrosis. Mouse anti-CD79α and rat anti-CD3 monoclonal primary antibodies were used for B- and T-lymphocyte detection. Evaluation of all sections was performed by applying a semi-quantitative score. Clinically, both implant materials were tolerated well. Histology revealed that a layer of fibrous tissue had formed between implant and overlying muscle in MgCa0.8 and S316L, which was demarcated by a layer of synoviocyte-like cells at its interface to the implant. In MgCa0.8 implants cavities were detected within the fibrous tissue, which were surrounded by the same kind of cell type. The thickness of the fibrous layer and the amount of tissue necrosis and cellular infiltrations gradually decreased in S316L. In contrast, a decrease could only be noted in the first weeks of implantation in MgCa0.8, whereas parameters were increasing again at the end of the observation period. B-lymphocytes were found more often in MgCa0.8 indicating humoral immunity and the presence of soluble antigens. Conversely, S316L displayed a higher quantity of T-lymphocytes. Moderate inflammation was detected in both implant materials and resolved to a minimum during the first weeks indicating comparable biocompatibility for MgCa0.8 and S316L. Thus, the application of MgCa0.8 as biodegradable implant material seems conceivable. Since the inflammatory parameters were re-increasing at the end of the observation period in MgCa0.8 it is important to observe the development of inflammation over a longer time period in addition to the present study.