gebhart/patrepeval huggingface dataset:
Pd-catalyzed synthesis of arylacetic acid derivatives from boronic acids (2001)

A palladium(0)-catalyzed cross-coupling reaction between arylboronic acids or esters and α-bromoacetic acid derivatives is described which allows the synthesis of various functionalized arylacetic acid derivatives under mild conditions.
Ryanodine receptor in different malignant hyperthermia-susceptible porcine muscles (1991)

The sarcoplasmic reticulum (SR) ryanodine receptor was studied in SR vesicles isolated from the vastus intermedius skeletal muscle and cardiac muscle of malignant hyperthermia-susceptible (MHS) and normal pigs. MHS and normal heavy SR preparations isolated from the vastus intermedius muscle had similar yields, polyacrylamide gel electrophoretic patterns, Ca2(+)-ATPase activities, mitochondrial enzyme activities, calsequestrin contents, and maximal [3H]ryanodine-binding activities. However, while half-maximal calcium concentrations (Ca0.5) for stimulation of MHS and normal vastus intermedius SR [3H]ryanodine binding were not significantly different, the Ca0.5 for inhibition of [3H]ryanodine binding to MHS vastus intermedius SR (76 +/- 17 microM) was significantly greater than to normal SR (16 +/- 9 microM). MHS vastus intermedius SR also exhibited a significantly lower Kd value (62 +/- 15 nM) for [3H]ryanodine binding compared with normal SR (Kd = 284 +/- 102 nM). These values for MHS and normal vastus intermedius SR are similar to those reported using SR isolated from a muscle composed of predominantly fast-twitch fibers, indicating the similarity of the ryanodine receptor in fast- and slow-twitch skeletal muscles. In contrast, there were no differences in the properties of the ryanodine receptor of porcine cardiac SR isolated from MHS and normal pigs. We therefore conclude that there is a defect in the SR ryanodine receptor of both slow- and fast-twitch skeletal muscle fiber types but not in cardiac muscle of MHS individuals.
Colour Constancy Using the Chromagenic Constraint (2005)

In this paper we propose that two images are captured of every scene: a normal image and an image captured where a coloured filter is placed in front of the camera. This additional information is then used in solving for colour constancy. The novelty of our approach is not that we add a colour filter (this is an old idea) but in how we use the additional information. In contradistinction to previous work we propose that the dimensionality of the 6 measurements per image pixel remains at 3 (not 6): we do not add a filter to increase the number of degrees of freedom but rather as a way of estimating the illuminant. We say that a filter is chromagenic if the relationship between filtered and unfiltered RGBs varies with and depends strongly on illumination. The canonical chromagenic algorithm works by testing the applicability of pre-computed relations in situ in an image. We extend the chromagenic approach to incorporate knowledge of the gamut of colours we expect to see under a given light and so in effect we make a hybrid gamut mapping + chromagenic algorithm. Experiments validate our approach with chromagenic gamut mapping shown to deliver significantly better constancy than all other algorithms tested.
Development of a fusion partner cell line for efficient production of human monoclonal antibodies from peripheral blood lymphocytes (2002)

We developed a unique fusion partner cell line that is capable of fusing with both human peripheral blood and lymph node lymphocytes at a high efficiency. The cell line was generated by fusing a murine myeloma cell line with a human myeloma cell line, producing a heteromyeloma (B6B11), which was subsequently fused with a human lymph node lymphocyte to produce a trioma (MFP-2). B6B11 and MFP-2 fuse well with human lymphocytes from both spleen and lymph nodes. Interestingly, MFP-2 also fuses with a high efficiency to peripheral blood lymphocytes. The resulting hybrids are stable for extended periods of time and produce human monoclonal antibodies at significant levels. The utility of MFP-2 as a fusion partner was demonstrated by the isolation of several hybridoma cell lines using lymph node and peripheral blood lymphocytes from patients with breast cancer. These hybridomas produce monoclonal antibodies displaying specificity to breast cancer tissue and cell lines.
Gibberellins Are Required for Seed Development and Pollen Tube Growth in Arabidopsis (2002)

Gibberellins (GAs) are tetracyclic diterpenoids that are essential endogenous regulators of plant growth and development. GA levels within the plant are regulated by a homeostatic mechanism that includes changes in the expression of a family of GA-inactivating enzymes known as GA 2-oxidases. Ectopic expression of a pea GA 2-oxidase2 cDNA caused seed abortion in Arabidopsis, extending and confirming previous observations obtained with GA-deficient mutants of pea, suggesting that GAs have an essential role in seed development. A new physiological role for GAs in pollen tube growth in vivo also has been identified. The growth of pollen tubes carrying the 35S:2ox2 transgene was reduced relative to that of nontransgenic pollen, and this phenotype could be reversed partially by GA application in vitro or by combining with spy-5, a mutation that increases GA response. Treatment of wild-type pollen tubes with an inhibitor of GA biosynthesis in vitro also suggested that GAs are required for normal pollen tube growth. These results extend the known physiological roles of GAs in Arabidopsis development and suggest that GAs are required for normal pollen tube growth, a physiological role for GAs that has not been established previously.
The Use of Internet-Based Learning in Biology (2002)

Previous research has suggested that Internet-based project learning might sustain both psychological and cognitive engagement of learners over an extended period of time. The study described here implemented an Internet-based project in a biology class and investigated its effect on the cognitive preferences held by students and on their performance. The data showed an effect on students'cognitive preferences, with a shift from disfavour to favour of questioning. It was also found that students who did the Internet-based project had higher scores for short-answer questions than those who had experienced more traditional teaching, while students who experienced the latter had higher scores in multiple-choice tests.
Amino acid sequence of the Fv region of a human monoclonal IgM (protein WEA) with antibody activity against 3,4-pyruvylated galactose in Klebsiella polysaccharides K30 and K33. (1983)

We have determined the amino acid sequence of the Fv [variable heavy (VH) and variable light (VL)] region of a human monoclonal IgM-kappa with antibody activity against 3,4-pyruvylated galactose, isolated from the plasma of patient WEA with Waldenström macroglobulinemia. The VH region has 114 residues, belongs to subgroup III, and has a very short third complementarity-determining region (CDR3), probably due to a small D segment/or an unusual D-J rearrangement (D, diversity; J, joining). The VL region has 108 residues and belongs to subgroup V kappa I. Compared to other members of the human VHIII and V kappa I families, WEA Fv does not appear to have significant differences within the framework residues but has unique CDRs that might be responsible for the particular antibody activity. Another IgM-kappa (GAL), which has an as-yet-undetermined antibody activity, shares a striking homology in V kappa with WEA, including an identical CDR1.
Methods and strategies of peptide ligation (2001)

This review focuses on the concept, methods, and strategies of orthogonal peptide ligation. It updates our previous review in 1999 on the same subject matter in Biopolymers (Peptide Science, 1999, Vol. 51, p. 311). Orthogonal peptide ligation is an amino terminal specific method to couple chemically unprotected peptides or proteins derived from synthetic or biosynthetic sources. Unlike conventional chemical methods, peptide ligation methods do not require coupling reagents or protection schemes, but are achieved through a variable chemoselective capture step and then an invariable intramolecular acyl transfer reaction. It is also a convergent method with the fewest steps. More than a dozen orthogonal ligation methods have been developed based on captures by either imine or thioester chemistries to afford native and unusual amino acids at ligation sites of linear, branched, or cyclic peptides. The ligation strategies for multiple segments including sequential and tandem ligations are also discussed. © 2001 John Wiley & Sons, Inc. Biopolymers (Pept Sci) 60: 194–205, 2001
Size Selective Supramolecular Cages from Aryl-Bisimidazolium Derivatives and Cucurbit[8]uril (2011)

A series of bisimidazolium salts were synthesized as novel guests for the macrocyclic host molecule cucurbit[8]uril (CB[8]). These bisimidazolium-CB[8] binary complexes exhibited a unique cage structure with the imidazolium rings acting as lids, leading to a size-dependent binding selectivity by altering the hydrophobic linker between the two imidazolium moieties. This new class of CB[8] complexes was also capable of binding small solvent molecules, including acetone, acetonitrile, diethyl ether, and tetrahydrofuran (THF) in an aqueous environment.
Generalized Assorted Pixel Camera: Postcapture Control of Resolution, Dynamic Range, and Spectrum (2010)

We propose the concept of a generalized assorted pixel (GAP) camera, which enables the user to capture a single image of a scene and, after the fact, control the tradeoff between spatial resolution, dynamic range and spectral detail. The GAP camera uses a complex array (or mosaic) of color filters. A major problem with using such an array is that the captured image is severely under-sampled for at least some of the filter types. This leads to reconstructed images with strong aliasing. We make four contributions in this paper: 1) we present a comprehensive optimization method to arrive at the spatial and spectral layout of the color filter array of a GAP camera. 2) We develop a novel algorithm for reconstructing the under-sampled channels of the image while minimizing aliasing artifacts. 3) We demonstrate how the user can capture a single image and then control the tradeoff of spatial resolution to generate a variety of images, including monochrome, high dynamic range (HDR) monochrome, RGB, HDR RGB, and multispectral images. 4) Finally, the performance of our GAP camera has been verified using extensive simulations that use multispectral images of real world scenes. A large database of these multispectral images has been made available at http://www1.cs.columbia.edu/CAVE/projects/gap_camera/ for use by the research community.
Metastable Impact Electron Spectroscopy (MIES) and Reflection Absorption Infrared Spectroscopy (RAIRS) Study of Acetic Acid Interacting with Amorphous Solid Water (2007)

The interaction of cyclic dimers of acetic acid with amorphous solid water (D2O) on polycrystalline silver was investigated. Metastable impact electron spectroscopy (MIES) was utilized to obtain information on the electronic structure of the outermost surface. Reflection absorption infrared spectroscopy (RAIRS) allowed for the identification of the acetic acid species and provided information on their hydration and the water-induced fragmentation. The interpretation of the results required also the study of the interaction of acetic acid with the neat silver substrate. On amorphous solid water (ASW), the acetic acid species quickly saturate the dangling OD groups present at the water surface at a coverage of less than 0.5 layers. In the first layer, the cyclic acid dimers break up under the influence of their interaction with the D2O molecules. For coverages >0.5 layers, strong lateral interaction between the acid molecules is responsible for the completion of the first adlayer. The second and following layers formed at 124 K consist of cyclic dimers. The splitting of the cyclic dimers by their interaction with the amorphous solid water, followed by their hydration, allows for a detailed characterization of the various acetic acid species resulting from the acetic acid−water interaction.
Direct detection of methylated cytosine in DNA by use of the restriction enzyme Mspl (1979)

The extent of methylation of the internal C in the sequence CCGG in DNA from various eukaryotic sources has been determined using the restriction enzyme MspI known to be specific for this sequence. The methylation of the CCGG sequence is reflected in the restriction pattern obtained by DNA treated with MspI and its isoschizomer HpaII and analyzed by gel electrophoresis. A direct method for detection 5-methylcytosine in the sequence CCGG has been deviced. DNA fragments obtained with MspI were radioactively labeled at their 5' ends and subsequently degraded to the corresponding 5'-deoxyribonucleoside monophosphates. 5 methylcytidylic acid has been found in most of the 5' ends of MspI fragments of calf thymus DNA (about 90%) indicating heavy methylation of the sequence CCGG in calf thymus DNA. The results also reveal a symmetric methylation of both strands at this sequence in calf thymus DNA. In contrast, the CCGG sequence in other eukaryotic DNAs from organisms like Neurospora, Drosophila and Herpes virus proved to be undermethylated at this sequence.
Fab-dsFv: A bispecific antibody format with extended serum half-life through albumin binding (2016)

An antibody format, termed Fab-dsFv, has been designed for clinical indications that require monovalent target binding in the absence of direct Fc receptor (FcR) binding while retaining substantial serum presence. The variable fragment (Fv) domain of a humanized albumin-binding antibody was fused to the C-termini of Fab constant domains, such that the VL and VH domains were individually connected to the Cκ and CH1 domains by peptide linkers, respectively. The anti-albumin Fv was selected for properties thought to be desirable to ensure a durable serum half-life mediated via FcRn. The Fv domain was further stabilized by an inter-domain disulfide bond. The bispecific format was shown to be thermodynamically and biophysically stable, and retained good affinity and efficacy to both antigens simultaneously. In in vivo studies, the serum half-life of Fab-dsFv, 2.6 d in mice and 7.9 d in cynomolgus monkeys, was equivalent to Fab'-PEG.
Control Genes and Variability: Absence of Ubiquitous Reference Transcripts in Diverse Mammalian Expression Studies (2002)

Control genes, commonly defined as genes that are ubiquitously expressed at stable levels in different biological contexts, have been used to standardize quantitative expression studies for more than 25 yr. We analyzed a group of large mammalian microarray datasets including the NCI60 cancer cell line panel, a leukemia tumor panel, and a phorbol ester induction time course as well as human and mouse tissue panels. Twelve housekeeping genes commonly used as controls in classical expression studies (including GAPD, ACTB, B2M, TUBA, G6PD, LDHA, and HPRT) show considerable variability of expression both within and across microarray datasets. Although we can identify genes with lower variability within individual datasets by heuristic filtering, such genes invariably show different expression levels when compared across other microarray datasets. We confirm these results with an analysis of variance in a controlled mouse dataset, showing the extent of variability in gene expression across tissues. The results show the problems inherent in the classical use of control genes in estimating gene expression levels in different mammalian cell contexts, and highlight the importance of controlled study design in the construction of microarray experiments.
Do hippocampal pyramidal cells signal non-spatial as well as spatial information? (1999)

It is generally agreed that the rat hippocampus is involved in spatial memory. Whether this is its sole or primary function, or merely one component of a broader function, is still debated. It has been suggested, for example, that the hippocampus stores information about flexible relations between stimuli, both spatial and non-spatial. In this paper, I reiterate the basic tenet of the cognitive map theory that the processing and storage of spatial information is the primary and perhaps the exclusive role of the hippocampus in the rat, and that data that appear to contradict this have been misinterpreted. These data are found in reports of non-spatial correlates of unit activity recorded in the awake animals and reports of deficits on non-spatial tasks following hippocampal lesions. In this paper, I examine both claims and suggest alternative explanations of the data. The first part of the paper contains a review of some of the properties of hippocampal place cells, which might be misinterpreted as non-spatial in "non-spatial" tasks. For example, if an animal is trained to carry out a sequence of stereotyped actions in different parts of an environment, there will be a strong correlation between the performance of each behaviour and the animal's location, and it is necessary to rule out the locational correlate as the cause of the firing pattern. The second part of the paper looks at the results of experiments on conditioning and non-spatial discrimination tasks and concludes that the results are less supportive of a more general relational theory of hippocampal function than has been suggested. Furthermore, there is often a discrepancy between the correlates of unit firing in non-spatial tasks and the absence of an effect of hippocampal damage on these same or similar tasks. It is concluded that, contrary to the claims of its detractors, the cognitive map theory is still the theory of hippocampal function that is most clearly specified, makes the most testable predictions, and for which there is the strongest experimental support.
Abnormalities in membrane phospholipid organization in sickled erythrocytes. (1981)

In contrast to the wealth of information concerning membrane phospholipid asymmetry in normal human erythrocytes, very little is known about membrane phospholipid organization in pathologic erythrocytes. Since the spectrin-actin lattice, which has been suggested to play an important role in stabilizing membrane phospholipid asymmetry, is abnormal in sickled erythrocytes, we determined the effects of sickling on membrane phospholipid organization. We used two enzymatic probes: been venom phospholipase A2 and Staphylococcus aureus sphingomyelinase C, which do not penetrate the membrane and react only with phospholipids located in the outer leaflet of the bilayer. Our results suggest that the distribution of glycerophospholipids within the membrane of sickled cells is different from that in nonsickled cells. Compared with the normal erythrocyte, the outer membrane leaflet of the deoxygenated, reversibly sickled cells (RSC) and irreversibly sickled cells (ISC) was enriched in phosphatidyl ethanolamine in addition to containing phosphatidyl serine. These changes were compensated for by a decrease in phosphatidyl choline in that layer. The distribution of sphingomyelin over the two halves of the bilayer was unaffected by sickling. In contrast to ICS, where the organization of phospholipids was abnormal under both oxy and deoxy conditions, reoxygenation of RSC almost completely restored the organization of membrane phospholipids to normal. These results indicate that the process of sickling induces an abnormality in the organization of membrane phospholipids to normal. These results indicate that the process of sickling induces an abnormality in the organization of membrane lipids in RSC which become permanent in ISC.
High-speed liquid lens with 2 ms response and 80.3 nm root-mean-square wavefront error (2009)

A liquid lens structure with a step response time of 2 ms, a refractive power range of 52 D, and a root-mean-square (rms) wavefront error of 80.3 nm is reported. This lens uses a liquid-liquid interface with a pinned contact line as a variable refractive surface, and its shape is controlled by a piezostack actuator via a built-in hydraulic amplifier. The measured wavefront error suggests that the method of pinning the contact line to a precise shape is an important factor in achieving higher optical performance.
Anti-epileptic Drugs For Pain Management (2001)

Antiepileptic drugs (AED's) depress abnormal neuronal discharges and raise the threshold for neural impulse propagation. They have been found to have therapeutic efficacy in neuropathic pain states. Carbamazepine(CZ) and phenytoin (PT) were the drugs of choice for treating trigeminal neuralgia for 40 plus years. These two agents have been largely replaced due to the introduction of many newer, better-tolerated, and safer antiepileptic drugs. CLINICAL USE/MECHANISM OF ACTION/SIDE EFFECTS: There has been an explosion in the number of available AEDs. Many studies are ongoing to evaluate their efficacy in neuropathic pain states. Only CZ, PT, gabapentin (GB), and lamotrigine (LT) have been evaluated in double blind trials. (4,5,6) Some tenets of use are common in all of these medications. Initial dosing should be done at a low dose administered at bedtime, increased slowly up to a therapeutic level over 4 to 8 weeks. These medications do not have a ceiling dose, but are usually more effective at higher doses. Clinically the dose should be titrated upwards until side effects are encountered, then back down a small amount. The pain relief obtained is gradual with most agreeing that an adequate trial of an AED for pain should last 4-8 weeks at therapeutic doses prior to calling a medication ineffective. A brief summary of clinical uses, mechanism of action, and side effects will be presented for the following AEDs.
Tumor selective reactivity of a monoclonal antibody prepared against a recombinant peptide derived from the DF3 human breast carcinoma-associated antigen. (1992)

The DF3 antigen is a member of a family of high molecular weight glycoproteins aberrantly expressed in malignant mammary epithelium. We have generated a monoclonal antibody (MAb), designated DF3-P, against a recombinant DF3/beta-galactosidase fusion protein. Characterization of this MAb has demonstrated reactivity with immature precursors of DF3 antigen and not with the secreted form. These findings are in contrast to those obtained with MAb DF3, a previously described antibody with predominant reactivity against the mature glycoprotein. The finding that deglycosylation of secreted DF3 antigen with neuraminidase and endo-alpha-N-acetylgalactosaminidase is associated with increased MAb DF3-P reactivity provided additional support for the selectivity of this antibody against the protein core. Epitope mapping studies demonstrate that both the DF3-P and DF3 epitopes are located at a TRPAPGS domain in the 20-amino acid tandem repeat. The results of competition studies with synthetic peptides indicate that the proline in this domain is involved in both epitopes, while the potential glycosylation sites at threonine and serine may contribute to the differential reactivity of MAbs DF3 and DF3-P. Taken together, these findings suggest that both antibodies react with a similar epitope that is modified by the presence of carbohydrate moieties. The results of immunoperoxidase staining studies further demonstrate that while MAb DF3-P reacts with formalin-fixed sections of breast carcinomas, this antibody exhibits little if any reactivity with normal mammary epithelium. Selective expression of the DF3-P epitope in malignant breast cells may be useful in identifying this transformed phenotype.
Eotaxin-3 in Churg-Strauss syndrome: a clinical and immunogenetic study (2011)

Objectives. To determine the potential of eotaxin-3 as a diagnostic marker for active disease and genetic susceptibility factor for ChurgStrauss syndrome (CSS).