gebhart/patrepeval huggingface dataset:
Reexpression of type IIA procollagen by adult articular chondrocytes in osteoarthritic cartilage (1999)

Type IIA procollagen is reexpressed by adult articular chondrocytes in OA cartilage degeneration, indicating the potential reversion of the cells to a chondroprogenitor cellular phenotype. The absence of type IIA mRNA and protein in normal adult articular cartilage and its onset in the diseased state suggests type IIA procollagen as a marker of OA.
Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis (2006)

We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.
<title>Nonrigid multimodality image registration</title> (2001)

We have designed, implemented, and validated an algorithm capable of 3D PET-CT registration in the chest, using mutual information as a similarity criterion. Inherent differences in the imaging protocols produce significant non-linear motion between the two acquisitions. To recover this motion, local deformations modeled with cubic B-splines are incorporated into the transformation. The deformation is defined on a regular grid and is parameterized by potentially several thousand coefficients. Together with a spline-based continuous representation of images and Parzen histogram estimates, the deformation model allows for closed-form expressions of the criterion and its gradient. A limited-memory quasi-Newton optimization package is used in a hierarchical multiresolution framework to automatically align the images. To characterize the performance of the algorithm, 27 scans from patients involved in routine lung cancer screening were used in a validation study. The registrations were assessed visually by two observers in specific anatomic locations using a split window validation technique. The visually reported errors are in the 0-6mm range and the average computation time is 100 minutes.
Management of Agitation in Huntington’s Disease: A Review of the Literature (2020)

Huntington's disease (HD) is a rare neurodegenerative disease of the central nervous system characterized by choreatic movements, behavioral disturbances, and neuropsychiatric sequelae. The disease is inherited in an autosomal dominant fashion by an increased number of CAG repeats on the short arm of chromosome 4p16.3 in the Huntingtin gene. Huntington's disease demonstrates the genetic principle of anticipation, where the larger the number of CAG repeats the earlier the signs and symptoms of the disease appear in subsequent generations. The symptoms often consist of behavioral disturbances and learning disturbances. The disease is suspected based on signs and symptoms and confirmed by genetic testing. There is no cure for the disease, and there is a high rate of neuropsychiatric symptoms including depression, and aggressive behavior. A significant risk of suicide in this population exists given the severity and unrelenting nature of the disease. Most patients will have multiple hospitalizations during the course of the illness. A consultant psychiatrist may be asked to evaluate and make recommendations for the treatment of acute agitation in HD patients. This can be a challenging task given the limited number of studies and the complex nature of agitation in the hospital setting. The aim of this review is to look at the currently available data for the treatment of acute agitation in patients with Huntington's disease.
Imaging of single molecule diffusion. (1996)

In recent years observations at the level of individual atoms and molecules became possible by microscopy and spectroscopy. Imaging of single fluorescence molecules has been achieved but has so far been restricted to molecules in the immobile state. Here we provide methodology for visualization of the motion of individual fluorescent molecules. It is applied to imaging of the diffusional path of single molecules in a phospholipid membrane by using phospholipids carrying one rhodamine dye molecule. For this methodology, fluorescence microscopy was carried to a sensitivity so that single fluorescent molecules illuminated for only 5 ms were resolvable at a signal/noise ratio of 28. Repeated illuminations permitted direct observation of the diffusional motion of individual molecules with a positional accuracy of 30 nm. Such capability has fascinating potentials in bioscience--for example, to correlate biological functions of cell membranes with movements, spatial organization, and stoichiometries of individual components.
Simple fast vector quantization of the line spectral frequencies (2002)

The authors propose a simple fast-search VQ of the LSFs to be used on top of the split VQ, that is, in each of the sub-vector domains. The main trait of the proposed method is that no suboptimal codebooks are used and there is no further reduction in performance. In each sub-vector domain, a full-size optimally trained codebook typically of size 1024, is searched using a fast-search algorithm. The result of this search is identical to that of a full-search, yet, only about 25% of a full-search complexity is needed.
Multiplex ligation-dependent probe amplification versus karyotyping in prenatal diagnosis: the M.A.K.E. study (2008)

The protocol is registered in the clinical trial register number ISRCTN47252164.
Nutrient solution growth of sorghum and corn in mineral nutrition studies (1982)

Abstract The growth of plants in nutrient solutions is an invaluable tool for mineral nutrition studies. Successful growth of plants in nutrient solutions require special attention and consideration. Details and helpful ideas for the growth of plants in nutrient solutions are often omitted in publications where techniques like these are used. The objective of this report is to focus on some of the concerns, successes, experiences, and problems noted for the growth of sorghum and corn in nutrient solutions. Topics discussed are nutrient solution composition, pH of nutrient solutions, phosphorus concentrations, sources of Fe in solutions, plus several suggestions and comments for successful growth of sorghum and corn in nutrient solutions. Key words: Sorghum bicolor (L.) Moench Zea mays LWater cultureSolution cultureHydroponicsNutrient solution pHNO3/NH4 in solutionsP toxicity
Native oxide stabilization of AlAs-GaAs heterostructures (1991)

Data are presented on the stabilization of AlAs-GaAs heterostructures against atmospheric (destructive) hydrolysis using the native oxide that can be formed (N2+H2O, 400 °C, 3 h) on the AlAs layer. The ∼0.1-μm-thick native oxide formed from the AlAs layer is shown to be stable with aging (∼100 days), while unoxidized samples degrade through the AlAs (0.1 μm) down into the GaAs as deep as ∼1 μm. Relative to oxides formed (∼25 °C) on AlAs (or AlxGa1−xAs, x ≳ 0.7) under atmospheric conditions (hydrolysis), oxides formed (via N2 +H2O) at higher temperatures (≳400 °C) are much more stable and seal the underlying crystal (e.g., GaAs).
Monoclonal anticolon carcinoma antibodies in complement‐dependent cytotoxicity (1981)

Hybridoma-derived monoclonal anticolon carcinoma (ACC) antibodies mediated specific complement-dependent cytotoxicity (CDC) against human colon carcinoma cells either grown in culture or obtained directly from patients. These ACC antibodies did not lyse normal colonic mucosa or other normal and malignant human cells. Absorption of these antibodies to cells of established colon carcinoma cell lines totally eliminated their specific lytic capacity. ACC antibodies were able to bind in vivo to colon carcinoma cells grown in nude mice but did not bind to lung or kidney cells from tumor-bearing animals. These monoclonal antibodies did not, however, inhibit the growth of colon carcinoma tumor cells in nude mice.
Semantic grep: regular expressions + relational abstraction (2003)

Searching source code is one of the most common activities of software engineers. Text editors and other support tools normally provide searching based on lexical expressions (regular expressions). Some more advanced editors provide a way to add semantic direction to some of the searches. Recent research has focused on advancing the semantic options available to text-based queries. Most of these results make use of heavy weight relational database management technology. In this paper we explore the extension of lexical pattern matching by means of light weight relational queries, implemented using a tool called grok. A "semantic grep" (sgrep) command was implemented, which translates queries in a mixed algebraic and lexical language into a combination of grok queries and grep commands. This paper presents the design decisions behind sgrep, and example queries that can be posed. The paper concludes with a case study in which sgrep was used to identify architectural anomalies in PostgreSQL, an open source Database Management System.
A Novel Class of DNA Analogs Bearing 5′- C -Phosphonothymidine Units: Synthesis and Physicochemical and Biochemical Properties (2006)

S(C) and R(C) diastereomers of 5'-C-(O,O-diethyl)-phosphonylthymidine ((R)T and (S)T) were used for the synthesis of the dimers T(R)T and T(S)T, respectively. These dimers were incorporated at selected sites in oligonucleotide constructs. Melting temperature (Tm) experiments demonstrated that relative to the unmodified oligodeoxyribonucleotide, the presence of the (R)T moiety reduced the thermal stability of the duplexes by approximately 5.0 degrees C per modification, whereas their (S)T counterparts only slightly destabilized the duplex structure (deltaTm < or = 1 degree C/modification). The stability of the triple-helical complexes containing one, two, or three modified thymidines is slightly higher than that of the parent complex. Nuclease resistance studies performed with snake venom phosphodiesterase, calf spleen phosphodiesterase, and 3'-exonuclease from human plasma showed that cleavage of the oligonucleotides at the site of the modification was completely suppressed regardless of the stereochemistry of the 5'-C-chiral center. The influence of the (R)T and (S)T modification in the recognition sequence of HindIII, EcoRI, and HpaI restriction endonucleases was also investigated. Although the catalytic activity of HindIII was not affected by the presence of the 5'-C-ethoxyphosphonyl modification, the activities of the two remaining restriction enzymes were partially suppressed depending on the site of modification or the stereochemistry of the modification or both ((R)T vs. (S)T).
Olivine LiCoPO[sub 4] as 4.8 V Electrode Material for Lithium Batteries (1999)

Reversible extraction and insertion of lithium from and into olivine at vs. lithium have shown that this material is a good candidate for a high‐voltage lithium‐ion battery. Electrochemical extraction was limited to 0.42 lithium per formula unit, with a charge capacity of and a discharge capacity of . In this case. the material retains its structural integrity with a slight contraction of the unit cell upon cycling. The crystallinity of the electrode during charge and discharge processes was not affected, as deduced from the sharpness of the X‐ray diffraction peaks of the cycled cathode material. ©2000 The Electrochemical Society
Intestinal Intraepithelial Lymphocytes Are Primed for Gamma Interferon and MIP-1β Expression and Display Antiviral Cytotoxic Activity despite Severe CD4+T-Cell Depletion in Primary Simian Immunodeficiency Virus Infection (1998)

Intraepithelial lymphocytes (IEL) are a critical effector component of the gut-associated lymphoid tissue (GALT) and play an important role in mucosal immunity as well as in the maintenance of the epithelial cell integrity and barrier function. The objective of this study was to determine whether simian immunodeficiency virus (SIV) infection of rhesus macaques would cause alterations in the immunophenotypic profiles of IEL and their mitogen-specific cytokine (gamma interferon [IFN-gamma] and MIP-1beta) responses (by flow cytometry) and virus-specific cytotoxic T-cell (CTL) activity (by the chromium release assay). Virally infected IEL were detected through the entire course of SIV infection by in situ hybridization. Severe depletion of CD4(+) single-positive and CD4(+)CD8(+) double-positive T cells occurred early in primary SIV infection, which was coincident with an increased prevalence of CD8(+) T cells. This was in contrast to a gradual depletion of CD4(+) T cells in peripheral blood. The CD8(+) IEL were the primary producers of IFN-gamma and MIP-1beta and were found to retain their potential to produce both IFN-gamma and MIP-1beta through the entire course of SIV infection. SIV-specific CTL activity was detected in primary IEL at 1, 2, and 4 weeks post-SIV infection. These results demonstrated that IEL may be involved in generating antiviral immune responses early in SIV infection and in suppressing viral infection thereafter. Alterations in homeostasis in epithelia due to severe CD4(+) T-cell depletion accompanied by changes in the cytokine and chemokine production by IEL may play a role in the enteropathogenesis of SIV infection.
Magnetic resonance imaging of the entorhinal cortex and hippocampus in mild cognitive impairment and Alzheimer's disease (2001)

Volume reductions in the ERC and hippocampus may be early signs of AD pathology that can be measured using MRI.
Contribution of NK cells to immunotherapy mediated by PD-1/PD-L1 blockade (2018)

Checkpoint blockade immunotherapy targeting the PD-1/PD-L1 inhibitory axis has produced remarkable results in the treatment of several types of cancer. Whereas cytotoxic T cells are known to provide important antitumor effects during checkpoint blockade, certain cancers with low MHC expression are responsive to therapy, suggesting that other immune cell types may also play a role. Here, we employed several mouse models of cancer to investigate the effect of PD-1/PD-L1 blockade on NK cells, a population of cytotoxic innate lymphocytes that also mediate antitumor immunity. We discovered that PD-1 and PD-L1 blockade elicited a strong NK cell response that was indispensable for the full therapeutic effect of immunotherapy. PD-1 was expressed on NK cells within transplantable, spontaneous, and genetically induced mouse tumor models, and PD-L1 expression in cancer cells resulted in reduced NK cell responses and generation of more aggressive tumors in vivo. PD-1 expression was more abundant on NK cells with an activated and more responsive phenotype and did not mark NK cells with an exhausted phenotype. These results demonstrate the importance of the PD-1/PD-L1 axis in inhibiting NK cell responses in vivo and reveal that NK cells, in addition to T cells, mediate the effect of PD-1/PD-L1 blockade immunotherapy.
Identification and intracellular location of MAGE-3 gene product. (1995)

The human MAGE-3 gene encodes a melanoma antigenic epitope recognized by specific cytotoxic T lymphocytes, but its gene product has not been identified thus far. We produced a recombinant MAGE-3 gene product by expression cloning of the entire reading frame in the context of a fusion protein characterized by a 10-histidine tail, allowing purification by metal chelation on a nickel Sepharose column. The semipurified product was used to generate MAGE-3-specific monoclonal antibodies. One reagent could identify by immunoblotting the native MAGE-3 gene product as a M(r) 48,000 protein in lysates of cell lines showing evidence of MAGE-3 gene expression. No apparent cross-reactivity with recombinant or native MAGE-1 gene product was observed. Immunohistochemistry shows that, closely resembling the MAGE-1 gene product, MAGE-3 is a cytoplasmic protein.
[Comparison of the acrylamide level in microwaved popcorn with that of ordinarily heated one]. (2007)

The microwaved popcorns tested are safer in general because the acrylamide level of them except that with high simple sugar content is obviously lower than that of ordinarily heated one.
Photocleavable Peptide-Conjugated Magnetic Beads for Protein Kinase Assays by MALDI-TOF MS (2010)

Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.
A transmit/receive active antenna with fast low-power optical switching (2000)

This paper presents an optically switched X-band active antenna element for half-duplex transmit/receive (T/R) applications. The antenna element is designed to be a unit cell of a quasioptical array with fast switching between T and R and with built-in phase-shifterless beamforming. The measured performance of the active element is 14 dB gain contributed by the power amplifier (PA) in transmission and 16 dB gain contributed by the low-noise amplifier in reception, with 30 dB isolation between T and R. The switching is accomplished with only 1 /spl mu/W of optical power for 1.7 /spl mu/s switching time (1.7 pJ of optical energy) and a rise time of 2 ns at 10 GHz with 7 mW of optical power (14 pJ of optical energy). The design, implementation, and measured performance of the optically controlled transmit/receive circuit are presented.
A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. (1991)

ABF2 (ARS-binding factor 2), a small, basic DNA-binding protein that binds specifically to the autonomously replicating sequence ARS1, is located primarily in the mitochondria of the yeast Saccharomyces cerevisiae. The abundance of ABF2 and the phenotype of abf2- null mutants argue that this protein plays a key role in the structure, maintenance, and expression of the yeast mitochondrial genome. The predicted amino acid sequence of ABF2 is closely related to the high-mobility group proteins HMG1 and HMG2 from vertebrate cell nuclei and to several other DNA-binding proteins. Additionally, ABF2 and the other HMG-related proteins are related to a globular domain from the heat shock protein hsp70 family. ABF2 interacts with DNA both nonspecifically and in a specific manner within regulatory regions, suggesting a mechanism whereby it may aid in compacting the mitochondrial genome without interfering with expression.
Design of precursors for the CVD of inorganic thin films (2006)

Applications of inorganic thin films in the electronics industry have spurred activity in the area of chemical vapor deposition (CVD). This article discusses the increasingly sophisticated design strategies for precursor complexes through a series of case studies on CVD of metal oxide and metal nitride films.
Origin of Stratification in Creaming Emulsions (1996)

Colloidal suspensions aging under gravity have long been known to spontaneously separate into layers. We demonstrate through flow visualization experiments that a lateral temperature gradient as small as $10\mathrm{mK}/\mathrm{cm}$ can be responsible for such stratification and that strata correspond to a stack of convection rolls. A linear stability analysis suggests that the onset of stratification results from a convective instability peculiar to fluids with inhomogeneous mass densities subjected to lateral thermal gradients.
Outcomes of clomiphene citrate treatment in young hypogonadal men (2011)

• Long-term follow-up of CC treatment for HG shows that it appears to be an effective and safe alternative to testosterone supplementation in men wishing to preserve their fertility.
Mother-to-infant transmission of TT virus: prevalence, extent and mechanism of vertical transmission (2000)

Our data prove that TT virus is efficiently transmitted transplacentally. The increase of its prevalence in the group of newborns older than 1 week suggests that it may be furthermore transmitted postnatally. Therefore in our Caucasian population, vertical transmission, particularly in utero transmission, of TTV is likely to account for a major part of TTV infection in early childhood. However, no disease activity could be established for the novel virus by this infection route.
Airways obstruction, chronic expectoration, and rapid decline of FEV1 in smokers are associated with increased levels of sputum neutrophils. (1996)

Airways obstruction and chronic expectoration, as well as accelerated decline in lung function, are associated with increased numbers of neutrophils in the sputum of smokers and ex-smokers which suggests that neutrophilic inflammation of the airways may be involved in the pathogenesis of chronic obstructive pulmonary disease.
Gene targeting: a practical approach. (1993)

Gene targeting vectors for mammalian cells, Paul Hasty and Allan Bradley production of targeted embryonic stem cell clones, Wolfgang Wurst and Alexandra L. Joyner analysis of gene transfer in bone marrow stem cells, Kateri A. Moore and John W. Belmont production of chimeras and genetically-defined offspring from targeted ES cells, Virginia Papiaoannou and Randall Johnson production of completely ES cell-derived foetuses, Andras Nagy and Janet Rossant gene and enhancer trap screens in ES cell chimeras, A. Gossler and J. Zachgo. Appendix: Suppliers of specialist items.
Infinite resolution textures (2016)

We propose a new texture sampling approach that preserves crisp silhouette edges when magnifying during close-up viewing, and benefits from image pre-filtering when minifying for viewing at farther distances. During a pre-processing step, we extract curved silhouette edges from the underlying images. These edges are used to adjust the texture coordinates of the requested samples during magnification. The original image is then sampled --- only once! --- with the modified coordinates. The new technique provides a resolution-independent image representation capable of billions of texels per second on a mid-range graphics card.