gebhart/patrepeval huggingface dataset:
Crystal Structure of NC1 Domains (2002)

Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. The network underlies all epithelia as a component of basement membranes, which play important roles in cell adhesion, growth, differentiation, tissue repair and molecular ultrafiltration. The specificity of both protomer and network assembly is governed by amino acid sequences of the C-terminal noncollagenous (NC1) domain of each chain. In this study, the structural basis for protomer and network assembly was investigated by determining the crystal structure of the ubiquitous [(alpha1)(2).alpha2](2) NC1 hexamer of bovine lens capsule basement membrane at 2.0 A resolution. The NC1 monomer folds into a novel tertiary structure. The (alpha1)(2).alpha2 trimer is organized through the unique three-dimensional domain swapping interactions. The differences in the primary sequences of the hypervariable region manifest in different secondary structures, which determine the chain specificity at the monomer-monomer interfaces. The trimer-trimer interface is stabilized by the extensive hydrophobic and hydrophilic interactions without a need for disulfide cross-linking.
Preclinical and Clinical Assessment of Cannabinoids as Anti-Cancer Agents (2016)

Cancer is the second leading cause of death in the United States with 1.7 million new cases estimated to be diagnosed in 2016. This disease remains a formidable clinical challenge and represents a substantial financial burden to the US health care system. Therefore, research and development of novel therapeutics for the treatment of cancer is of high priority. Cannabinoids and their derivatives have been utilized for their medicinal and therapeutic properties throughout history. Cannabinoid activity is regulated by the endocannabinoid system (ECS), which is comprised of cannabinoid receptors, transporters, and enzymes involved in cannabinoid synthesis and breakdown. More recently, cannabinoids have gained special attention for their role in cancer cell proliferation and death. However, many studies investigated these effects using <i>in vitro</i> models which may not adequately mimic tumor growth and metastasis. As such, this article aims to review study results which evaluated effects of cannabinoids from plant, synthetic and endogenous origins on cancer development in preclinical animal models and to examine the current standing of cannabinoids that are being tested in human cancer patients.
Resistance to Streptococcus pneumoniae is induced by a phosphocholine-protein conjugate. (1983)

Abstract Previous studies demonstrated that naturally occurring antibodies to the pneumococcal cell wall hapten phosphocholine (PC) are important for the survival of mice against infection with Streptococcus pneumoniae, and that passively administered hybridoma antibody to PC results in added resistance. To determine if a PC-protein conjugate could elicit protective levels of anti-PC antibody, mice were immunized with PC-keyhole limpet hemocyanin (KLH) and tested for their ability to resist challenge with virulent S. pneumoniae. PC-KLH-immunized mice were observed to be resistant to 10- to 1000-fold more organisms than unimmunized control animals. The levels of protection were comparable to those induced with capsular polysaccharide antigens, but had the advantage of not being type-specific; immunization with PC-KLH protected mice against both type 1 and type 3 organisms. The induced immunity appeared to be antibody-mediated; it could be passively transferred with immune serum, and absorption of the immune serum with PC-Sepharose removed its protective capacity. Anti-PC antibodies in the serum of immunized mice were primarily IgM and IgG3 and possessed predominantly the T15 idiotype. Antibodies with these particular isotypes and this idiotype also arise after immunization with heat-killed rough pneumococci and recently were shown to be important in the resistance of mice to pneumococcal infection.
PRINS and In Situ PCR Protocols (1996)

Cutting edge researchers demonstrate step-by-step how oligonucleotide primers may be successfully used to detect and amplify or extend complimentary sequences in situ. Through these procedures-often invented by the authors-the door is opened to rapid identification and characterization of chromosomal DNA sequences, viral genomes, and rare messenger RNAs in cells-at hitherto unmatched degrees of sensitivity and specificity. Their innovative techniques-suitable for both novice and experienced researchers-have rapidly become indispensable for many clinical diagnostic procedures, whether in quantification of chromosomes in the identification of aneuploidy for prenatal diagnosis, or in the identification of viral infection in the early stages, or of rare messenger RNAs present in cells
Cell adhesion molecule Nr-CAM is over-expressed in human brain tumors (1998)

Using the technique of differential display-polymerase chain reaction (DD-PCR), we isolated a cDNA fragment that is over-expressed in glioblastoma multiforme tissue as compared to normal brain tissue. Sequence analysis indicated that this sequence is identical to the previously isolated human neuron-glia-related cell adhesion molecule hNr-CAM. Gene-specific RT-PCR analysis indicated that hNr-CAM is over-expressed in high-grade astrocytomas, gliomas and glioblastoma tumor tissues as compared to normal brain tissue. High levels of hNr-CAM expression also were observed in cell lines derived from astrocytomas, gliomas and glioblastoma multiforme tumors. Low levels of hNr-CAM expression were observed in neuroblastoma, meningiomas, melanoma, normal breast and prostate tumor tissues. Northern blot analysis showed an alternatively spliced mRNA of 1.4 kb in several tumors as compared to the 7.5 kb transcript found in normal brain tissue. Genomic Southern blot analysis of DNA from 3 brain tumor cell lines showed that over-expression of hNr-CAM in brain tumors was not due to gene amplification. In situ hybridization analysis indicated that 11 of the 20 human brain tumor samples studied showed hNr-CAM over-expression. Our results suggest that hNr-CAM is over-expressed in malignant brain tumors and can serve as a novel marker for brain tumor detection and perhaps therapy.
PTPRO promoter methylation is predictive of poorer outcome for HER2-positive breast cancer: indication for personalized therapy (2013)

PTPRO methylation is a common event in the primary breast cancer and can be reliably detected in peripheral blood samples. PTPRO methylation is associated with poor survival only in HER2-positive patients, suggesting use of PTPRO methylation as a prognostic factor for breast cancer and for optimizing individualized therapy for HER2-positive patients.
High-performance computer architecture (1987)

From the Publisher:
design ideas embodied in many high-performance machines and stresses techniques for evaluating them. Stone develops a proper understanding of the design process by treating the various trade-offs that exist in designing choices, and shows how good designs make efficient use of technology.
Features
Teaches techniques for the design and analysis of high-performance machines
Develops students' intuition for design by treating various tradeoffs that exist in design choices
Discusses many important topics: RISC architectures, interconnection meshes, Cache coherent and multiprocessors, and Cache Memory.
Includes enhanced descriptions of RISC Processors
Expands material on Cache Memory Analysis
Current technology in RISC with a focused look on super scalar
Additional memory models and techniques for doing Cache design
New porposals for coherent memory systems in System C parallel processors
Both design and thought problems and problems with limiting parameters are provided
Modeling vapor deposition of low-K polymers: Parylene and polynaphthalene (1999)

By using different mechanisms of deposition and growth, new models of Parylene deposition rates have been developed and compared with experimental data over a wide range of conditions. It is shown that the surface adsorption (boundary) condition is a crucial factor in determining how the results of these models behave. Minimal differences in the behavior of the overall rates of deposition are obtained among the Parylene models using the same adsorption condition with either surface or bulk film reactions. However, their basic structures are considerably different. Although both diffusion/reaction and surface reaction models with either Langmuir-type or Flory-type monomer adsorption have attractive features, they fail to represent the data on rates of deposition over the wide range of conditions reported in the literature. In contrast, the models based on Brunauer, Emmett, and Teller multilayer adsorption seem to include the benefits of both Langmuir and Flory adsorption and simulate the data well over a much broader range of temperature. This suggests that multilayer adsorption is an important phenomenon in the low temperature vapor deposition of these polymers. Here we try to clarify the important physical/chemical mechanisms involved as well as the similarities and differences among various approaches to formulation of deposition models. A polynaphthalene deposition model is developed on the basis of both gas phase reactions followed by adsorption on the surface with subsequent reaction to form the film. The model is capable of simulating the data very accurately. However, the data available are limited in range and more experimental data are required to establish the uniqueness of the rate equations proposed.
A greedy tree growing algorithm for the design of variable rate vector quantizers (image compression) (1991)

A technique for directly designing a variable-rate tree-structured vector quantizer by growing the tree one node at a time rather than one layer at time is presented. The technique is a natural extension of a tree growing method for decision trees. When the tree is pruned with a generalized algorithm for optimally pruning trees, improvement is measured in the signal-to-noise ratio at high rates over pruning a fixed-rate tree-structured vector quantizer of the same initial rate. The growing algorithm can be interpreted as a constrained inverse of the pruning algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation (2012)

One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.
Pathology services in developing countries-the West African experience. (2011)

The existing facilities and infrastructure can be augmented with provision of material and professional assistance from other pathology associations in more developed countries and should, among other things, focus on supplementing residency education. Virtual residency programs, short-visit observerships, development of simple but practical laboratory information systems, and closer ties with pathologists in these countries are some of the suggested steps in achieving this goal.
Lossless coding of floating point data with JPEG 2000 Part 10 (2004)

JPEG 2000 Part 10 is a new work part of the ISO/IEC JPEG Committee dealing with the extension of JPEG 2000 technologies to three-dimensional data. One of the issues in Part 10 is the ability to encode floating point datasets. Many Part 10 use cases come from the scientific and engineering communities, where floating point data is often produced either from numerical simulations or from remote sensing instruments. This paper presents the technologies that are currently being developed to accommodate this Part 10 requirement. The coding of floating point datasets with JPEG 2000 requires two changes to the coding pipeline. Firstly, the wavelet transformation stage is optimized to correctly decorrelate data represented with the IEEE 754 floating point standard. Special IEEE 754 floating point values like Infinities and NaN's are signaled beforehand as they do not correlate well with other floating point values. Secondly, computation of distortion measures on the encoder side is performed in floating point space, rather than in integer space, in order to correctly perform rate allocation. Results will show that these enhancements to the JPEG 2000 coding pipeline lead to better compression results than Part 1 encoding where the floating point data had been retyped as integers.
Fiber-optic evanescent field modulator using a magnetic fluid as the cladding (2006)

A kind of fiber-optic modulation-depth-tunable modulator is developed in this paper. In this modulator, a magnetic fluid is used as the cladding of the drawn fiber, which attenuates the evanescent field when the light is guided in the fiber. Because the attenuation depends on the strength of the applied external magnetic field, the emergent light intensity from the fiber is modulated with the change of the magnetic field strength. The response times, i.e., the span for the light intensity to reach the final steady value from the time when the magnetic field is turned on or off, are evaluated quantitatively.
Automated Grading of Gliomas using Deep Learning in Digital Pathology Images: A modular approach with ensemble of convolutional neural networks. (2015)

Brain glioma is the most common primary malignant brain tumors in adults with different pathologic subtypes: Lower Grade Glioma (LGG) Grade II, Lower Grade Glioma (LGG) Grade III, and Glioblastoma Multiforme (GBM) Grade IV. The survival and treatment options are highly dependent of this glioma grade. We propose a deep learning-based, modular classification pipeline for automated grading of gliomas using digital pathology images. Whole tissue digitized images of pathology slides obtained from The Cancer Genome Atlas (TCGA) were used to train our deep learning modules. Our modular pipeline provides diagnostic quality statistics, such as precision, sensitivity and specificity, of the individual deep learning modules, and (1) facilitates training given the limited data in this domain, (2) enables exploration of different deep learning structures for each module, (3) leads to developing less complex modules that are simpler to analyze, and (4) provides flexibility, permitting use of single modules within the framework or use of other modeling or machine learning applications, such as probabilistic graphical models or support vector machines. Our modular approach helps us meet the requirements of minimum accuracy levels that are demanded by the context of different decision points within a multi-class classification scheme. Convolutional Neural Networks are trained for each module for each sub-task with more than 90% classification accuracies on validation data set, and achieved classification accuracy of 96% for the task of GBM vs LGG classification, 71% for further identifying the grade of LGG into Grade II or Grade III on independent data set coming from new patients from the multi-institutional repository.
Genes coding for RNA polymerase β subunit in bacteria (1988)

The plasma half-life of recombinant human interleukin-6 (rhIL-6) was determined in rats by measuring the disappearance of the biological activity as well as of the radioactivity of 125I-rhIL-6 from the circulation. The kinetics of clearance were biphasic. It consisted of a rapid initial disappearance corresponding to a half-life of 3 min, and of a second slow one corresponding to a half-life of about 55 min. By cellulose-acetate electrophoresis it was shown that rhIL-6 binds to a plasma protein resulting in a complex migrating in the beta-gamma region; 20 min after intravenous injection, about 80% of the 125I-rhIL-6 that had disappeared from the circulation was found in the liver. 125I-rhIL-6 was exclusively localized on the surface of parenchymal cells suggesting the existence of an interleukin-6 receptor on the hepatocytes.
Fatty acid nitroalkenes ameliorate glucose intolerance and pulmonary hypertension in high-fat diet-induced obesity (2014)

These observations support that the pleiotropic signalling actions of electrophilic fatty acids represent a therapeutic strategy for limiting the complex pathogenic responses instigated by obesity.
Phosphorylation of 25-kDa Synaptosome-associated Protein (1996)

Protein kinase C-mediated phosphorylation of a 25-kDa synaptosome-associated protein (SNAP-25) was examined in living PC12 cells. Phorbol 12-myristate 13-acetate treatment enhanced high potassium-induced [3H]-norepinephrine release, and a 28-kDa protein recognized by an anti-SNAP-25 antibody was phosphorylated on Ser residues. The molecular size of the phosphorylated band decreased slightly following treatment with Clostridium botulinum type A neurotoxin, whereas the band disappeared after treatment with botulinum type E neurotoxin, indicating that the 28-kDa protein was SNAP-25. A phosphorylation is likely to occur at Ser187, as this is the only Ser residue located between the cleavage sites of botulinum type A and E neurotoxins. SNAP-25 of PC12 cells was phosphorylated by purified protein kinase C in vitro, and the amount of syntaxin co-immunoprecipitated with SNAP-25 was decreased by phosphorylation. These results suggest that the phosphorylation of SNAP-25 may be involved in protein kinase C-mediated regulation of catecholamine release from PC12 cells.
Defective interfering particles of Sindbis virus do not interfere with the homologous virus obtained from persistently infected BHK cells but do interfere with Semliki Forest virus (1981)

Defective interfering particles derived from wild-type Sindbis virus no longer interfere with the infectious virus cloned from BHK cells persistently infected with Sindbis virus for 16 months. These particles do interfere with the replication of Semliki Forest virus.
The Cell Surface Glycosphingolipids SSEA-3 and SSEA-4 Are Not Essential for Human ESC Pluripotency (2006)

Pluripotent cells can be isolated from the human blastocyst and maintained in culture as self-renewing, undifferentiated, human ESCs (hESCs). These cells are a valuable model of human development in vitro and are the focus of substantial research aimed at generating differentiated populations for cellular therapies. The extracellular markers that have been used to characterize hESCs are primarily carbohydrate epitopes on proteoglycans or sphingolipids, such as stage-specific embryonic antigen (SSEA)-3 and -4. The expression of SSEA-3 and -4 is tightly regulated during preimplantation development and on hESCs. Although this might imply a molecular function in undifferentiated cells, it has not yet been tested experimentally. We used inhibitors of sphingolipid and glycosphingolipid (GSL) biosynthesis to block the generation of SSEA-3 and -4 in hESCs. Depletion of these antigens and their precursors was confirmed using immunostaining, flow cytometry, and tandem mass spectroscopy. Transcriptional analysis, immunostaining, and differentiation in vitro and in teratomas indicated that other properties of pluripotency were not noticeably affected by GSL depletion. These experiments demonstrated that the GSLs recognized as SSEA-3 and -4 do not play critical functional roles in maintaining the pluripotency of hESCs, but instead suggested roles for this class of molecules during cellular differentiation.
Genetic Correction of Human Induced Pluripotent Stem Cells from Patients with Spinal Muscular Atrophy (2012)

Spinal muscular atrophy (SMA) is among the most common genetic neurological diseases that cause infant mortality. Induced pluripotent stem cells (iPSCs) generated from skin fibroblasts from SMA patients and genetically corrected have been proposed to be useful for autologous cell therapy. We generated iPSCs from SMA patients (SMA-iPSCs) using nonviral, nonintegrating episomal vectors and used a targeted gene correction approach based on single-stranded oligonucleotides to convert the survival motor neuron 2 (SMN2) gene into an SMN1-like gene. Corrected iPSC lines contained no exogenous sequences. Motor neurons formed by differentiation of uncorrected SMA-iPSCs reproduced disease-specific features. These features were ameliorated in motor neurons derived from genetically corrected SMA-iPSCs. The different gene splicing profile in SMA-iPSC motor neurons was rescued after genetic correction. The transplantation of corrected motor neurons derived from SMA-iPSCs into an SMA mouse model extended the life span of the animals and improved the disease phenotype. These results suggest that generating genetically corrected SMA-iPSCs and differentiating them into motor neurons may provide a source of motor neurons for therapeutic transplantation for SMA.
A limited sampling method for the estimation of AUC and Cmax of carbamazepine and carbamazepine epoxide following a single and multiple dose of a sustained‐release product (1998)

The method described here may be used to estimate AUC and Cmax for CBZ and CBZE without detailed pharmacokinetic studies following single or multiple dose of CBZ.
Computation of Molecular Spectra on a Quantum Processor with an Error-Resilient Algorithm (2018)

Harnessing the full power of nascent quantum processors requires the efficient management of a limited number of quantum bits with finite coherent lifetimes. Hybrid algorithms, such as the variational quantum eigensolver (VQE), leverage classical resources to reduce the required number of quantum gates. Experimental demonstrations of VQE have resulted in calculation of Hamiltonian ground states, and a new theoretical approach based on a quantum subspace expansion (QSE) has outlined a procedure for determining excited states that are central to dynamical processes. We use a superconducting-qubit-based processor to apply the QSE approach to the H 2 molecule, extracting both ground and excited states without the need for auxiliary qubits or additional minimization. Further, we show that this extended protocol can mitigate the effects of incoherent errors, potentially enabling larger-scale quantum simulations without the need for complex error-correction techniques.
Studies on Medicinal Plants of Sri Lanka (1980)

The major alkaloid of Sida acuta was shown to be cryptolepine which has antimicrobial activity against Proteus vulgaris. Thirty one samples of leaf, stem, root and seed of six Sida species collected from different localities in Sri Lanka were screened for the pharmacologically important alkaloids, cryptolepine, ephedrine, and vasicine. Medicinal applications of S. acuta and S. cordifolia have been related to dieir constituent alkaloids.