gebhart/patrepeval huggingface dataset:
Transgenic engineering of neuromuscular junctions in Xenopus laevis embryos transiently overexpressing key cholinergic proteins. (1994)

To examine the role of key cholinergic proteins in the formation of neuromuscular junctions (NMJs), we expressed DNAs encoding the mouse muscle nicotinic acetylcholine receptor (nAChR) or human brain and muscle acetylcholinesterase (hAChE) in developing Xenopus laevis embryos. Acetylthiocholine hydrolysis and alpha-bungarotoxin binding in homogenates of transgenic embryos revealed transient overexpression of the respective proteins for at least 4 days postfertilization. Moreover, hAChE injection induced an approximately 2-fold increase in endogenous Xenopus nAChR. Electron microscopy coupled with cytochemical staining for AChE activity revealed that AChE-stained areas, which reached 0.17 microns2 in NMJs of control embryos raised at 21 degrees C, increased up to 0.53 and 0.60 microns2 in nAChR and hAChE transgenics, respectively. These increases coincided with the appearance of a class of large NMJs with average postsynaptic lengths up to 1.8-fold greater than controls. As much as 57% and 34% of the NMJs in animals transgenic for nAChR and hAChE, respectively, displayed AChE activity in nerve terminals in addition to muscle labeling, as compared with 10% nerve-labeled NMJs in control animals. Moreover, area, but not length values, were > 2-fold larger in hAChE-expressing NMJs labeled in their nerve terminals than in those labeled in muscle alone, reflecting a hAChE-induced increase in synaptic cleft width. These findings indicate that modulation of cholinergic neurotransmission in NMJs modifies the features of nerve-muscle connections.
An Interpretable Model with Globally Consistent Explanations for Credit Risk (2018)

We propose a possible solution to a public challenge posed by the Fair Isaac Corporation (FICO), which is to provide an explainable model for credit risk assessment. Rather than present a black box model and explain it afterwards, we provide a globally interpretable model that is as accurate as other neural networks. Our "two-layer additive risk model" is decomposable into subscales, where each node in the second layer represents a meaningful subscale, and all of the nonlinearities are transparent. We provide three types of explanations that are simpler than, but consistent with, the global model. One of these explanation methods involves solving a minimum set cover problem to find high-support globally-consistent explanations. We present a new online visualization tool to allow users to explore the global model and its explanations.
Protein kinase C ε expression correlates with the aggressiveness of human prostate cancer (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

339 

Prostate cancer (PCa) is the most common type of cancer in men and ranks second to lung cancer in cancer-related deaths. PCa first manifests as an androgen-dependent (AD) disease and can be treated with androgen-deprivation therapy. Despite the initial success of androgen ablation therapy, PCa progresses from AD to androgen-independent (AI). The hormone refractory invasive PCa is the end stage and accounts for the majority of PCa patient deaths. Defining the molecular mechanisms linking the transition of AD PCa to a hormone refractory PCa is essential in planning strategies in the management of PCa. We determined that Protein kinase Ce (PKCe) may be linked in vivo to the progression of human AI PCa and should be explored as a molecular target for the prevention and therapy of hormone refractory PCa. PKCe is among the PKC isoforms expressed in human and mouse prostate tissue. PKCe levels were determined by immunohistochemistry of human prostate tissue microarrays prepared from paraffin-fixed benign, hyperplastic and carcimona (Grades I-IV) specimens ([Table][1]). Results showed that PKCe was located predominantly in the cytoplasm of both benign (non-neoplastic) and malignant (neoplastic) epithelial cells. PKCe was uniformly distributed in cancer cells. PKCe was more densely located in the apical (luminal) side of the cytoplasm in normal epithelial cells. In addition, some cancer cells showed slight dense staining for PKCe in the nuclear membrane. Stromal cells were also positive for PKCe, but the intensity was lower than that in epithelial cells. The results of the level of the expression of PKCe are shown in the [table][1]. The level of expression of PKCe appear to correlate with the aggressiveness of PCa. Also, evidence from in vitro studies have demonstrated that PKCe, as compared to AD prostate cancer cell lines, is overexporessed in AI cell lines DU145 and PC3. Also, PKCe has also shown to transform the AD human prostate cancer cell line LNCaP to an AI variant, which forms tumors in castrated male nude mice. PKCe may be a molecular marker of AI PCa. [Table][1]: PKCe expression in human prostate specimens. The level of expression is denoted by the sign +. One + is the lowest and four + is the highest.



![Figure][2] [1]: #F1
 [2]: pending:yes
A Prediction System for Web Requests using N-gram Sequence Models (2000)

As an increasing number of users access information on the web, there is a great opportunity to learn from the server logs to learn about the users’ probable actions in the future. In this paper, we present an n-gram based model to utilize path profiles of users from very large data sets to predict the users’ future requests. Since this is a prediction system, we cannot measure the recall in a traditional sense. We, therefore, present the notion of applicability to give a measure of the ability to predict the next document. Our model is based on a simple extension of existing point-based models for such predictions, but our results show for n-gram based prediction when n is greater than three, we can increase precision by 20% or more for two realistic web logs. Also we present an efficient method that can compress our model to 30% of its original size so that the model can be loaded in main memory. Our result can potentially be applied to a wide range of applications on the web, including pre-sending, pre-fetching, enhancement of recommendation systems as well as web caching policies. Our tests are based on three realistic web logs. Our algorithm is implemented in a prediction system called WhatNext, which shows a marked improvement in precision and applicability over previous approaches.
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications (2007)

Supplementary data are available at Bioinformatics online.
Emulation of Spasticity Symptoms in Upper Limb Part-Task Trainer for Physiotherapist Education (2013)

The aim of this study is to develop an adequate part-task trainer occupied with varying levels of severity in spasticity symptoms focusing on the upper limb disorder for occupational therapists. Using the developed part-task trainer, the occupational therapists will have opportunities to repetitively engage in training without patient involvement. The part-task trainer is developed following the structure of human arm articulations with the ability to reproduce the spasticity stiffness. The structured interface programming is built providing three levels of spasticity: mild, moderate and severe. The programming was based on the clinical assessment of spasticity, measuring elbow joint angles and forces exerted by the patients. The recreated spasticity stiffness was evaluated by experienced occupational therapists. Therapists provided positive feedback regarding the mild and moderate level of spasticity leaving further improvement needed in order to reproduce the spasticity at the severe level.
Susceptibility of Gram-Negative Anaerobic Bacilli to Gentamicin and Other Aminoglycosides (1971)

Journal Article Susceptibility of Gram-Negative Anaerobic Bacilli to Gentamicin and Other Aminoglycosides Get access Sydney M. Finegold, Sydney M. Finegold From the Medical and Research Services, Wadsworth General Hospital, Veterans Administration, and the Department of Medicine, University of California School of Medicine, Los Angeles, California Search for other works by this author on: Oxford Academic PubMed Google Scholar Vera L. Sutter Vera L. Sutter From the Medical and Research Services, Wadsworth General Hospital, Veterans Administration, and the Department of Medicine, University of California School of Medicine, Los Angeles, California Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 124, Issue Supplement_1, December 1971, Pages S56–S58, https://doi.org/10.1093/infdis/124.Supplement_1.S56 Published: 01 December 1971
Reactions over metal catalysts. Part II. Hydrogenolysis of 3,3-dimethylnortricyclene and nortricyclene-3-spirocyclopropane (1976)

Hydrogenolysis of 3,3-dimethylnortricyclene in solution or in the vapour phase over a series of palladium and platinum catalysts gives a mixture of 2,2- and 7,7-dimethylnorbornanes with the latter predominating. Hydrogenolysis over palladium on pumice catalyst gives a mixture of products including several which arise from carbon–carbon bond breaking and formation. The formation of this latter type of product is more prevalent in reactions of nortricyclene-3-spirocyclopropane (5).
Antioxidant Capacity As Influenced by Total Phenolic and Anthocyanin Content, Maturity, and Variety of<i>Vaccinium</i>Species (1998)

Different cultivars of four Vaccinium species [Vaccinium corymbosum L (Highbush), Vaccinium ashei Reade (Rabbiteye), Vaccinium angustifolium (Lowbush), and Vaccinium myrtillus L (Bilberry)] were analyzed for total phenolics, total anthocyanins, and antioxidant capacity (oxygen radical absorbance capacity, ORAC). The total antioxidant capacity of different berries studied ranged from a low of 13.9 to 45.9 μmol Trolox equivalents (TE)/g of fresh berry (63.2−282.3 μmol TE/g of dry matter) in different species and cultivars of Vaccinium. Brightwell and Tifblue cultivars of rabbiteye blueberries were harvested at 2 times, 49 days apart. Increased maturity at harvest increased the ORAC, the anthocyanin, and the total phenolic content. The growing location (Oregon vs Michigan vs New Jersey) did not affect ORAC, anthocyanin or total phenolic content of the cv. Jersey of highbush blueberries. A linear relationship existed between ORAC and anthocyanin (rxy = 0.77) or total phenolic (rxy = 0.92) content. In general, blueberries are one of the richest sources of antioxidant phytonutrients of the fresh fruits and vegetables we have studied. Keywords: Vitamin C; ascorbate; blueberry; bilberry; highbush; lowbush; rabbiteye; ORAC; HPLC
Relative Flow Volume, a Novel Blood Flow Index in the Human Retina Derived From Laser Speckle Flowgraphy (2014)

These results suggest that RFV values obtained with LSFG can be considered an accurate and reliable index of relative blood flow in the human retina. Thus, RFV, a novel LSFG-derived variable, has potential for assessing retinal blood flow alterations in ocular disease.
Formation and Properties of Sub-Image and Latent-Image Silver Specks. Part II: Properties of Silver Sub-Specks Produced by Chemical Reduction (1976)

Reduction sensitization of monodisperse cubic or octahedral AgBr emulsion leads at shorter digestion times and/or milder reduction conditions to emulsions of increased overall speed but without any preference of latent image formation at the site, where the reduction centres have been created. These centres—probably the smallest reduction specks—behave like hole traps during exposure. After longer and/or stronger reduction conditions specks are formed which determine latent image topography and hence act like electron traps.
Leptomycin B stabilizes and activates p53 in primary prostatic epithelial cells and induces apoptosis in the LNCaP cell line (2003)

p53 in primary cultures of normal and malignant prostate cells, although dysfunctional in that it is not responsive to DNA damage, is activated by LMB. The ability of LMB to stabilize p53 and induce expression of p53-responsive growth inhibitory genes may be a useful lead in the development of chemopreventive or therapeutic small molecules that can modulate p53 function in prostatic epithelial cells.
Purification and Characterization of an Aminopeptidase from Lactobacillus helveticus LHE-511 (1992)

the organoleptic and rheological properties of cheese have been published. In related studies, various exopeptidases have been isolated from Streptococcus diacetylactis (now named Lactococcus lactis ssp. diacetylactis) (5), Lactobacillus lactis (6), Lactobacillus acidophilus (12), and Lactococcus lactis ssp. cremoris Some researchers have been interested ill using Lactobacillus helveticus (1, 2, 3), which has potent proteolytic activity, to accelerate the ripening of Cheddar and Gouda cheeses in order to shorten the long manufacturing time. However, there have been fewer studies of proteolytic enzymes from L. helveticus than studies of enzymes from other lactic acid bacteria used in cheese manufacture. Zevaco and Gripon (15) and Khalid and Marth ( The aim of the present study was to purify and characterize the aminopeptidase from L. helveticus UIE-
Identification of Bakb, a new platelet-specific antigen associated with posttransfusion purpura (1988)

Baka is a platelet alloantigen whose putative allele, Bakb, has not been identified previously. By using a serum, "Har," obtained from a patient with posttransfusion purpura, we describe the platelet alloantigen Bakb. The Har serum reacted with an NP-40-extractable platelet membrane protein of 142 kd with mobility similar to platelet glycoprotein IIb alpha. We found that the antigen recognized by the Har serum is inherited in an autosomal dominant mode with an apparent gene frequency of .39. Chi-square analysis of observed and expected phenotype frequencies indicated that serum Har recognizes Bakb, the anticipated allele of Baka. Our findings provide new evidence for polymorphism of glycoprotein IIb and for the association of posttransfusion purpura with alloimmunization to determinants on this glycoprotein.
A potential role for Dkk-1 in the pathogenesis of osteosarcoma predicts novel diagnostic and treatment strategies (2007)

Canonical Wnt signalling is an osteoinductive signal that promotes bone repair through acceleration of osteogenic differentiation by progenitors. Dkk-1 is a secreted inhibitor of canonical Wnt signalling and thus inhibits osteogenesis. To examine a potential osteoinhibitory role of Dkk-1 in osteosarcoma (OS), we measured serum Dkk-1 in paediatric patients with OS (median age, 13.4 years) and found it to be significantly elevated. We also found that Dkk-1 was maximally expressed by the OS cells at the tumour periphery and in vitro, Dkk-1 and RANKL are coexpressed by rapidly proliferating OS cells. Both Dkk-1 and conditioned media from OS cells reduce osteogenesis by human mesenchymal cells and by immunodepletion of Dkk-1, or by adding a GSK3beta inhibitor, the effects of Dkk-1 were attenuated. In mice, we found that the expression of Dkk-1 from implanted tumours was similar to the human tumour biopsies in that human Dkk-1 was present in the serum of recipient animals. These data demonstrate that systemic levels of Dkk-1 are elevated in OS. Furthermore, the expression of Dkk-1 by the OS cells at the periphery of the tumour probably contributes to its expansion by inhibiting repair of the surrounding bone. These data demonstrate that Dkk-1 may serve as a prognostic or diagnostic marker for evaluation of OS and furthermore, immunodepletion of Dkk-1 or administration of GSK3beta inhibitors could represent an adjunct therapy for this disease.
Lack of SCN1A Mutations in Familial Febrile Seizures (2002)

Our study demonstrated that SCN1A is not frequently involved in common FSs and suggested the involvement of specific FS genes.
Enhanced Stability of LiCoO<sub>2</sub>Cathodes in Lithium-ion Batteries Using Surface Modification by Atomic Layer Deposition (2010)

Ultrathin atomic layer deposition (ALD) coatings were found to enhance the performance of lithium-ion batteries (LIBs). Previous studies have demonstrated that LiCoO 2 cathode powders coated with metal oxides with thicknesses of ~100-1000 grown using wet chemical techniques improved LIB performance. In this study, LiCoO 2 powders were coated with conformal Al 2 O 3 ALD films with thicknesses of only ~3-4 established using 2 ALD cycles. The coated LiCoO 2 powders exhibited a capacity retention of 89% after 120 charge-discharge cycles in the 3.3~4.5 V (vs. Li/Li + ) range. In contrast, the bare LiCoO 2 powders displayed only a 45% capacity retention. This dramatic improvement may result from the ultrathin Al 2 O 3 ALD film acting to minimize Co dissolution or to reduce surface electrolyte reactions.
Melphalan 200 mg/m2 versus melphalan 100 mg/m2 in newly diagnosed myeloma patients: a prospective, multicenter phase 3 study (2009)

High-dose (200 mg/m(2), MEL200) and intermediate-dose melphalan (100 mg/m(2), MEL100) showed significant activity in myeloma. In a phase 3 study, 298 patients were randomly assigned to receive 2 autologous transplantations after conditioning with MEL200 or MEL100. Ninety-six of 149 (64%) completed MEL200 and 103 of 149 (69%) MEL100. Best response to MEL200 was: complete remission 22 of 149 (15%); partial remission 95 of 149 (64%), for an overall response rate of 79%. Best response to MEL100 was: complete remission 12 of 149 (8%); partial remission 95 of 149 (64%), for an overall response rate of 72%. Overall survival did not differ (P = .13); median progression-free survival (31.4 vs 26.2 months, P = .01), median time to progression (34.4 vs 27.0 months, P = .014) were longer in the MEL200. Treatment-related mortality was 3.1% in the MEL200 and 2.9% in the MEL100 group. Severe neutropenia and infections were marginally superior, whereas severe thrombocytopenia, mucositis, gastrointestinal adverse events, and the overall occurrence of at least 1 nonhematologic grade 3 or 4 adverse event were significantly higher in the MEL200 cohort. We conclude that MEL200 leads to longer remission duration and should be considered the standard conditioning regimen for autologous transplantation. This study was registered at www.clinicaltrials.gov as #NCT00950768.
JOMR: Multi-join optimizer technique to enhance map-reduce job (2014)

Map-Reduce is a programming model and execution an environment developed by Google to process very large amounts of data. Query optimizer is needed to find more efficient plans for declarative SQL query. In classic database: join algorithms are optimized to execute the entire query result, but they ignore the importance of tables order especially in multi-join query. But we can see that the orders for tables are an important factor to get the best performance of a query plan and will be very effective in performance when join tables content huge number of rows in addition to more than one join operation. In this paper we proposed a new technique called JOMR (Join Order In Map-Reduce) that optimizes and enhances Map-Reduce job. This technique uses enhanced parallel Travel Salesman Problem (TSP) using Map-Reduce for improving the performance of query plans according to change the order for join tables. Also we build a cost model that supports our algorithm to find best join order. We will focus on Hive especially multi-join query and our experiments result for JOMR algorithm proving the effectiveness of our query optimizer and this performance is improved more when increasing the number of join and size of data.
Development and Experimental Evaluation of a Contrast Medium for Computed Tomographic Examination of the Liver and Spleen (1979)

A lipoid based contrast material containing 53% of ethiodized oil in emulsion form was developed for computed tomography (CT) of the liver and spleen and tested in rabbits and monkeys. An intravenous dose of 0.2 ml/kg selectively opacified the liver and spleen, resulting in an average increase of 23 EMI units (500 scales) in the attenuation of the liver and a higher increase in the attenuation of the spleen. When injected into rhesus monkeys with carcinogen induced hepatomas there was a significant improvement in the visualization of the tumor, and small lesions, undetectable on the preliminary CT scan, became visible. Toxicity studies are in progress.
Cellular Uptake of Nanoparticles by Membrane Penetration: A Study Combining Confocal Microscopy with FTIR Spectroelectrochemistry (2012)

It is well-known that nanomaterials are capable of entering living cells, often by utilizing the cells' endocytic mechanisms. Passive penetration of the lipid bilayer may, however, occur as an alternative process. Here we have focused on the passive transport of small nanoparticles across the plasma membranes of red blood cells, which are incapable of endocytosis. By using fluorescence microscopy, we have observed that zwitterionic quantum dots penetrate through the cell membranes so that they can be found inside the cells. The penetration-induced structural changes of the lipid bilayer were explored by surface-enhanced infrared absorption spectroscopy and electrochemistry studies of model membranes prepared on solid supports with lipid compositions identical to those of red blood cell membranes. A detailed analysis of the infrared spectra revealed a markedly enhanced flexibility of the lipid bilayers in the presence of nanoparticles. The electrochemistry data showed that the overall membrane structure remained intact; however, no persistent holes were formed in the bilayers.
4,5,6,7‐Tetrahydro‐1<i>H</i>‐imidazo[4,5‐<i>c</i>]pyridine‐6‐carboxylic acids (spinacines) (1991)

Abstract New derivatives of the naturally occurring amino acid 4,5,6,7‐tetrahydro‐1 H ‐imidazo[4,5‐ c ]pyridine‐6‐carboxylic acid (spinacine) are reported. These include amide, ester, 5‐alkyl and acyl, and regiospecific N im ‐alkyl and aralkyl derivatives. Synthesis via the Pictet‐Spengler reaction on N im ‐substituted histidines is described. Cyclic hydantoin derivatives of spinacines are included.
FRACTURE HEALING IN COMPRESSION OSTEOSYNTHESIS IN THE DOG (1968)

1. The healing of the radius and tibia in dogs after compression plating of osteotomies made by a Gigli saw was studied. 2. The methods used were indian ink microangiography and terramycin labelling. The Spalteholz technique and azane colouring were used. 3. Revascularisaton of the fracture region took place both from newly formed vessels in the Haversian systems and from periosteal and endosteal vessels. 4. The fracture gap was filled at an early stage by a vascular network. Under stable conditions direct angiogenic bone formation took place around this network. 5. Rebuilding of the cortical bone in the fracture region occurred by osteoclastic activity. Groups of osteoclasts made cavities in the necrotic bone and were immediately followed by loops of vessels; behind and around the loop new bone was formed. Another form of bone absorption consisted of bundles of vessels which eroded necrotic cortical bone without new bone formation. 6. The new bone was initially oriented along the fracture gap but, by conversion into secondary osteones, it became progressively oriented longitudinally in the direction of the original bone. 7. Under stable conditions some periosteal and endosteal callus formation occurred though it was of slight importance. It regressed very soon and was seldom seen in the radiographs.