gebhart/patrepeval huggingface dataset:
Imaging of neuroinflammation in dementia: a review (2015)

We are still very limited in management strategies for dementia, and establishing effective disease modifying therapies based on amyloid or tau remains elusive. Neuroinflammation has been increasingly implicated as a pathological mechanism in dementia and demonstration that it is a key event accelerating cognitive or functional decline would inform novel therapeutic approaches, and may aid diagnosis. Much research has therefore been done to develop technology capable of imaging neuroinflammation in vivo. The authors performed a systematic search of the literature and found 28 studies that used in vivo neuroimaging of one or more markers of neuroinflammation on human patients with dementia. The majority of the studies used positron emission tomography (PET) imaging of the TSPO microglial marker and found increased neuroinflammation in at least one neuroanatomical region in dementia patients, most usually Alzheimer's disease, relative to controls, but the published evidence to date does not indicate whether the regional distribution of neuroinflammation differs between dementia types or even whether it is reproducible within a single dementia type between individuals. It is less clear that neuroinflammation is increased relative to controls in mild cognitive impairment than it is for dementia, and therefore it is unclear whether neuroinflammation is part of the pathogenesis in early stages of dementia. Despite its great potential, this review demonstrates that imaging of neuroinflammation has not thus far clearly established brain inflammation as an early pathological event. Further studies are required, including those of different dementia subtypes at early stages, and newer, more sensitive, PET imaging probes need to be developed.
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations (1983)

Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first‐ or second‐derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
Analysis and optimization of a deeply pipelined FPGA soft processor (2014)

FPGA soft processors have been shown to achieve high frequency when designed around the specific capabilities of heterogenous resources on modern FPGAs. However, such performance comes at a cost of deep pipelines, which can result in a larger number of idle cycles when executing programs with long dependency chains in the instruction sequence. We perform a full design-space exploration of a DSP block based soft processor to examine the effect of pipeline depth on frequency, area, and program runtime, noting the significant number of NOPs required to resolve dependencies. We then explore the potential of a restricted data forwarding approach in improving runtime by significantly reducing NOP padding. The result is a processor that runs close to the fabric limit of 500MHz with a case for simple data forwarding.
Expert System on a Chip: An Engine for Real-Time Approximate Reasoning (1986)

The role of inferencing with uncertainty is becoming more important in rule-based expert systems (ES), since knowledge given by a human expert is often uncertain or imprecise. We have succeeded in designing a VLSI chip which can perform an entire inference process based on fuzzy logic. The design of the VLSI fuzzy inference engine emphasizes simplicity, extensibility, and efficiency (operational speed and layout area). It is fabricated in 2.5 mm CMOS technology. The inference engine consists of three major components; a rule set memory, an inference processor, and a controller. In this implementation, a rule set memory is realized by a read only memory (ROM). The controller consists of two counters. In the inference processor, one data path is laid out for each rule. The number of the inference rule can be increased adding more data paths to the inference processor. All rules are executed in parallel, but each rule is processed serially. The logical structure of fuzzy inference proposed in the current paper maps nicely onto the VLSI structure.A two-phase nonoverlapping clocking scheme is used. Timing tests indicate that the inference engine can operate at approximately 20.8 MHz. This translates to an execution speed of approximately 80,000 Fuzzy Logical Inferences Per Second (FLIPS), and indicates that the inference engine is suitable for a demanding real-time application. The potential applications include decision-making in the area of command and control for intelligent robot systems, process control, missile and aircraft guidance, and other high performance machines.
Chromosome 10 deletion mapping in human gliomas: a common deletion region in 10q25. (1995)

The high incidence of loss of chromosome 10 alleles in glioblastoma multiforme suggests the presence on this chromosome of a tumor suppressor gene that is important in glioma tumorigenesis and progression. Our initial deletion mapping studies using restriction fragment length polymorphism markers indicated a common deletion region in 10q24-qter. In an attempt to localize the deleted region further, we screened a panel of 117 gliomas for loss of heterozygosity for chromosome 10 loci using 10 microsatellite markers. Seventeen tumors showed partial loss of a copy of chromosome 10 and were further analysed using 28 additional microsatellite markers. Of these, 10 had terminal deletion in the q arm, three had deletions in both p and q arms, two contained interstitial deletion in 10q and two carried deletions in 10p. In the 15 tumors with deletions in 10q, the minimal overlapping deletion region was in distal 10q between markers D10S587 and D10S216. Loci D10S587 and D10S216 are approximately mapped to a 5 cM region in 10q25.1.
Purification and partial characterization of a novel binding protein for retinoic acid from neonatal rat. (1988)

This report describes the purification and partial characterization of a novel retinoic acid-binding protein (CRABP-II) from neonatal rat pups. The isolation procedure included gel filtration on Sephadex G-75, ion exchange chromatography on DEAE-cellulose, and high performance liquid chromatography (HPLC) on a DEAE 5PW column. Two retinoic acid-binding peaks were resolved at the DEAE-cellulose step, with CRABP-I in the major peak and CRABP-II in the minor peak. Apparent homogeneity was achieved for both binding proteins after the HPLC step. CRABP-II consists of a single polypeptide, migrating with an apparent Mr of 15,000 in sodium dodecyl sulfate-polyacrylamide gel. It has an isoelectric point of 5.0. The dissociation constant for CRABP-II of retinoic acid was estimated to be 65 nM by fluorescence titration. Amino-terminal sequence analysis showed that CRABP-II has a distinct sequence, while the CRABP-I sequence is exactly identical to that of the rat testis CRABP. Despite the extensive sequence homology between CRABP-I and CRABP-II, antibodies directed against CRABP-I did not cross-react with CRABP-II.
Application of Reverse Transcription Polymerase Chain Reaction to Detect Porcine Epidemic Diarrhea Virus in Vero Cell Culture (1999)

Porcine epidemic diarrhea (PED) is a contagious diarrheal disease of swine. The disease is very similar to transmissible gastroenteritis (TGE), with high mortality in swine of all ages and high morbidity in neonates. 3,5 PED virus (PEDV), a coronavirus, was identified in 1978 as the etiologic agent of the disease. 4 PEDV is unable to grow in porcine cell cultures permissive to TGE virus. A method to propagate PEDV in Vero cells was described in 10 years after the first report of PED. 1 However, the high cost and prolonged time required to isolate and propagate PEDV in Vero cells have propelled the search for other diagnostic tests. Virus isolation has important implications in the diagnosis, epidemiology, and control of disease. The development of new techniques for the rapid identification of PEDV adaptation in Vero cells would greatly enhance PEDV detection. The objective of the present study was to describe the application of the reverse transcription polymerase chain reaction (RTPCR) technique to detect PEDV in Vero cell culture. Cell growth medium consisted of minimal essential medium (MEM) buffered with 20 mM HEPES and 0.2% (w/v) bicarbonate, supplemented with 5% (v/v) fetal bovine serum and antibiotics (10,000 IU/ml and penicillin, 10 mg/ml dihydrostreptomycin, 5 mg/ml neomycin, 10,000 IU/ml polymyxin). Virus infection medium consisted of MEM with 30 mM HEPES, a 1% (v/v) 0.3 M NaOH, 0.3% (w/v) tryptose phosphate broth, b 10 mg/ml trypsin (1:250), and antibiotics. Forty-one piglets from 35 farms were used to isolate PEDV. The presence of PEDV in the intestinal tissue of each of the pigs was confirmed by direct immunofluorescence antibody test using an anti-PEDV‐fluorescein isothiocyanate conjugate. c The mucosa and the content of the small intestine were collected and pooled, diluted 1:5 in phosphate-buffered saline (0.01 M, pH 7.2), ground by homogenization, and centrifuged for 20 minutes at 9,000 3 g. Before inoculation, the cell growth medium of monolayered Vero cells grown in 25-cm 2 flasks was removed, and the monolayers were washed twice with cell growth medium. The cells were inoculated with 1 ml of the homogenate per flask. After adsorption in the dark for 2 hours at room temperature, virus infection medium was added (5 ml/flask) without removing the virus inoculum. Because trypsin is thermolabile, 80% of virus infection medium was changed daily. Inoculated cell cultures were checked microscopically for cytopathic effects (CPE) daily. If the cell layer did not show CPE after 4 days of incubation, cells and supernatant fluids were frozen and thawed 3 times to release intracellular virus
MIMO relaying for multiaccess communication in cellular networks (2008)

We study an amplify and forward (AF) relaying scheme that uses a multiple-input-multiple-output (MIMO) relay to improve the performance of multi-point to point communication in cellular networks. With the assumption that perfect channel state information (CSI) is known, the MIMO relay and the base station (BS) receiver are jointly optimized. The objective is to minimize the sum mean-square error (MSE) while keeping the total transmit power of the relay constant. This problem is solved suboptimally using iterative as well as non-iterative methods. Computer simulations show the performance improvements of the proposed methods over conventional all-pass MIMO relay.
Safety and Efficacy of TG101348, a Selective JAK2 Inhibitor, in Myelofibrosis (2011)

TG101348 is well tolerated and produces significant reduction in disease burden and durable clinical benefit in patients with myelofibrosis.
Structure and chromosomal location of the human gene encoding cartilage matrix protein. (1990)

Cartilage matrix protein (CMP) is a major component of the extracellular matrix of nonarticular cartilage. The structure and chromosomal location of the human gene encoding CMP was determined by molecular cloning analysis. We used a partial chicken CMP cDNA probe to isolate three overlapping human genomic clones. From one of these clones, a probe containing 2 human CMP exons was isolated and used to map the gene to chromosome 1p35 and to screen a human retina cDNA library. Two overlapping cDNA clones were isolated. The predicted protein sequence of 496 amino acids includes a 22-residue signal peptide and a 474-residue mature protein of Mr 51,344. The human CMP gene and polypeptide are strikingly similar to the chicken CMP gene and polypeptide. Human CMP is 79% identical to chicken CMP and contains two homologous domains separated by an epidermal growth factor-like domain. One potential N-glycosylation site is conserved between the two species. The human CMP gene spans 12 kilobase pairs with 8 exons and 7 introns which are similar in size to those of the chicken CMP gene. Both RNA splice junctions of intron G in the human and chicken CMP genes are nonconforming to the consensus splice sequences. This suggests that the CMP gene utilizes a new RNA splicing mechanism.
INTELLIGENT BUILDINGS, A DESIGNER'S POINT OF VIEW (1999)

The building services installations in the new city library of The Hague are as part of the design of the building complex, responsible for the level of intelligence of this building. The integrated design and its flexible layout of the installations make the city library a very intelligent building. A summary of the installations as designed by Valstar Simonis and some of its aspects are discussed. In particular the environmental friendly thermal-heat storage system for the air-conditioning is explained.
Differences in Immunophenotyping of Mucosal Lymphocytes Between Ulcerative Colitis and Crohn`s Disease (1997)

From these results, there are increased T cell markers, IL-2R, TR, and CD3/HLA-DR in UC, but differently, decreased CD3, TCR alpha/beta and TCR gamma/delta in CD compared with control. In addition, definitive differences in lymphocytes markers, CD19, TR, TCR alpha/beta and TCR gamma/delta, which are higher in UC than in CD, may elucidate the different immunopathogenesis between UC and CD.
Flat spectral response arrayed-waveguide gratingmultiplexer with parabolic waveguide horns (1996)

An eight-channel flat spectral response arrayed-waveguide grating multiplexer with parabolic waveguide horns has been fabricated on a planar lightwave circuit (PLC). A double-peaked intensity distribution is formed at the slab interface by the parabolic waveguide horn. A 1 dB bandwidth of 98 GHz, 3 dB bandwidth of 124 GHz and 20 dB bandwidth of 196 GHz are obtained for 200 GHz channel spacing. The crosstalk to neighbouring channels is less than –27 dB and the on-chip insertion losses range from 6.1 to 6.4 dB, respectively.
CSF-1 Receptor/Insulin Receptor Chimera Permits CSF-1-dependent Differentiation of 3T3-L1 Preadipocytes (1997)

A chimeric growth factor receptor (CSF1R/IR) was constructed by splicing cDNA sequences encoding the extracellular ligand binding domain of the human colony stimulating factor-1 (CSF-1) receptor to sequences encoding the transmembrane and cytoplasmic domains of the human insulin receptor. The addition of CSF-1 to cells transfected with the CSF1R/IR chimera cDNA stimulated the tyrosine phosphorylation of a protein that was immunoprecipitated by an antibody directed against the carboxyl terminus of the insulin receptor. Phosphopeptide maps of the 32P-labeled CSF1R/IR protein revealed the same pattern of phosphorylation observed in 32P-labeled insulin receptor beta subunits. CSF-1 stimulated the tyrosine phosphorylation of insulin receptor substrate-1 (IRS-1) and Shc in cells expressing the CSF1R/IR chimera. Lipid accumulation and the expression of a differentiation-specific marker demonstrated that 3T3-L1 preadipocytes undergo CSF-1-dependent differentiation when transfected with the CSF1R/IR chimera cDNA but not when transfected with the expression vector alone. A 12-amino acid deletion within the juxtamembrane region of the CSF1R/IR (CSF1R/IRDelta960) blocked CSF-1-stimulated phosphorylation of IRS-1 and Shc but did not inhibit CSF-1-mediated differentiation of 3T3-L1 preadipocytes. These observations indicate that adipocyte differentiation can be initiated by intracellular pathways that do not require tyrosine phosphorylation of IRS-1 or Shc.
Genetics and biotechnology (2004)

In essence, all properties of organisms depend on the sum of their genes. There are two broad categories of genes: structural and regulatory. Structural genes encode for amino acid sequences of proteins which, as enzymes, determine the biochemical capabilities of the organism by catalysing particular synthetic or catabolic reactions or, alternatively, play more static roles as components of cellular structures. In contrast, the regulatory genes control the expression of the structural genes by determining the rate of production of their protein products in response to intra- or extracellular signals. The derivation of these principles has been achieved using well-known genetic techniques which will not be considered further here.
Effect of Gamma Irradiation on the Human Immunodeficiency Virus and Human Coagulation Proteins (1989)

The effect of gamma irradiation on HIV and plasma coagulation factors F VIII:C, F VIII:vWF and FIX was studied. Donor plasma was harvested from single donations, frozen and irradiated in the frozen state at target doses from 0 to 40 kGy (0-4 mRad). HIV was inoculated into human plasma and irradiated in a similar manner. A range of other viruses, not suspended in plasma, were also irradiated to establish viral inactivation. An inactivation rate of 0.164 TCID50 dose/ml/kGy was demonstrated for HIV compared to rates of 0.00173, 0.00526 and 0.00286 log10 units/ml/kGy for F VIII:C,F VIII:vWF and FIX respectively. The use of gamma irradiation to inactivate infectious agents present in human plasma may eliminate the need for any post-production viral inactivation methods and provide a means of assuring the safety of as yet untreated products such as cryoprecipitate and fresh frozen plasma.
Circular binary segmentation for the analysis of array-based DNA copy number data (2004)

DNA sequence copy number is the number of copies of DNA at a region of a genome. Cancer progression often involves alterations in DNA copy number. Newly developed microarray technologies enable simultaneous measurement of copy number at thousands of sites in a genome. We have developed a modification of binary segmentation, which we call circular binary segmentation, to translate noisy intensity measurements into regions of equal copy number. The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set.
Molecular characterization of two novel mutations causing factor X deficiency in a Chinese pedigree (2005)

Factor X (FX) deficiency is a rare bleeding disorder inherited as an autosomal recessive trait. In this study, we investigated the molecular basis of FX deficiency in a Chinese pedigree. The proposita showed a markedly prolonged activated partial thromboplastin time and a mild prolongation of prothrombin time. The levels of FX antigen and FX activity were 58.6% and 2.5%, respectively. Molecular analysis revealed that the proposita was compound heterozygous for two novel mutations: IVS1 + 1G > A and G1185A (Arg347His). The aberrant transcripts from the IVS1 + 1G > A mutant allele were not detected by analyzing the splicing pattern of ectopic transcripts in leukocytes of the patient with nested polymerase chain reaction after reverse transcription. We thus hypothesize that the mRNA molecules originating from the IVS1 + 1G > A mutation were rapidly destroyed in vivo. Site-directed mutagenesis of FX cDNA was used to introduce FXG1185A mutation, and wild-type as well as mutant FX proteins were expressed by transient transfection in HEK 293 cells. Normal FX antigen levels both in the conditioned media of cells expressing the mutant and in cell lysates were detected by an enzyme-linked immunoadsorbent assay. Evaluation of wild-type and mutant coagulant activity demonstrated that the FX molecules carrying the Arg347His mutation have dramatically decreased activity.
Nanoparticle DNA Carrier with Poly(l-lysine) Grafted Polysaccharide Copolymer and Poly(d,l-lactic acid) (1997)

Biodegradable nanoparticles, which contain the sites for both polynucleotide adsorption and targeting ligand on their surfaces, were prepared as a novel carrier for genetic materials. The nanoparticles were obtained from poly(D,L-lactic acid) and poly(L-lysine)-graft-polysaccharide copolymers by using either a solvent evaporation method or a diafiltration method. The size of the particles prepared by the diafiltration method was controlled by varying the initial concentration of the graft copolymer. Nanoparticles as small as 60 nm in diameter were successfully obtained from the graft copolymers with high polysaccharide contents but not from the poly(L-lysine) homopolymer. Polysaccharide moieties on the surface of the nanoparticles were found to interact specifically with a particular lectin as verified by the aggregation assay. The polynucleotide adsorption capacity of the nanoparticles was increased with increasing polysaccharide contents in the graft copolymers, suggesting that the adsorption conformation of poly(L-lysine) moiety in the graft copolymer on the nanoparticle surface is different from that in poly(L-lysine) homopolymer. Moreover, the nanoparticles from the graft copolymer exhibited resistance against self-aggregation and nonspecific adsorption of serum proteins, presumably due to the polymer brush effect and/or exclusion effect from the polysaccharide graft chains. These results suggest that the nanoparticles prepared from poly(L-lysine)-graft-polysaccharide copolymer and poly(D,L-lactic acid) can serve as a good DNA carrier in vivo.
Characterization and Application of Manure-Based Bio-binder in Asphalt Industry (2010)

This paper introduces an environmentally friendly material, bio-binder to be used as partial replacement and modifier for asphalt binder on highways and airport pavements. This new binder is produced from thermochemical conversion of swine manure. To maintain a sustainable development, the highway paving industry has long been actively searching for a renewable alternative for petroleum-based asphalt binder. Production and application of bio-binder can address this need in addition to finding a solution for manure and its waste management. Application of bio-binder will improve asphalt binder’s properties while reducing asphalt pavements construction cost. Production of bio-oil (including bio-fuel and bio-binder) will reduce the need for landfills and lagoons to store swine manure and reduce environmental pollution. Moreover, bio-oil production reduces U.S. dependence on petroleum resources by supplementing 9 million barrels of bio-oil per year. This becomes even more significant taking into account the relatively low cost of bio-binder production ($0.54/gallon) while asphalt binder costs $2/gallon. Furthermore, social and environmental benefits will be gained by adding value to the waste management system and reducing carbon emissions otherwise made by gasoline. Hence, the findings of this study can benefit the economy, the environment, and energy independence. This study showed that addition of bio-binder can improve low temperature properties of asphalt binder significantly. It will also enhance binder’s wetability and workability allowing asphalt producers to conduct mixing and compaction at relatively lower temperature.
Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS (2008)

In yeast, the macromolecular complex Set1/COMPASS is capable of methylating H3K4, a posttranslational modification associated with actively transcribed genes. There is only one Set1 in yeast; yet in mammalian cells there are multiple H3K4 methylases, including Set1A/B, forming human COMPASS complexes, and MLL1-4, forming human COMPASS-like complexes. We have shown that Wdr82, which associates with chromatin in a histone H2B ubiquitination-dependent manner, is a specific component of Set1 complexes but not that of MLL1-4 complexes. RNA interference-mediated knockdown of Wdr82 results in a reduction in the H3K4 trimethylation levels, although these cells still possess active MLL complexes. Comprehensive in vitro enzymatic studies with Set1 and MLL complexes demonstrated that the Set1 complex is a more robust H3K4 trimethylase in vitro than the MLL complexes. Given our in vivo and in vitro observations, it appears that the human Set1 complex plays a more widespread role in H3K4 trimethylation than do the MLL complexes in mammalian cells.