gebhart/patrepeval huggingface dataset:
Supramolecular synthons in phenol–isonicotinamide adducts (2003)

Molecular complexes of four phenols (hydroquinone, resorcinol, phloroglucinol and 4-hydroxybenzoic acid) with isonicotinamide are characterized by X-ray diffraction. (Hydroquinone)0.5·(isonicotinamide) 1 and (resorcinol)·(isonicotinamide)22 have tapes of O–H⋯N and amide N–H⋯O dimer synthons. In (phloroglucinol)·(isonicotinamide)2·(H2O)23, six component self-assembly results in stacked dimers with four O–H⋯N and four amide N–H⋯O hydrogen bonds and the third phenol OH aggregates with two water molecules in a supramolecular chair cyclohexane array. Phenol⋯pyridine and amide N–H⋯O dimers are robust synthons in 1–3 for the self-assembly of 0D discrete aggregates and infinite 1D chains. Hydrogen bonding of amide dimers via N–H⋯Ophenol/water is ascribed to cooperative effects. The crystal structure of (4-hydroxybenzoic acid)·(isonicotinamide) 4 establishes the robustness of phenol⋯pyridine hydrogen bonding in the presence of carboxylic acid groups. Molecular components in 4 are arranged as zigzag tapes of O–H⋯N hydrogen bonds and acid⋯amide heterodimers. Supramolecular synthesis with phenol–isonicotinamide adducts expands the versatility of isonicotinamide as a co-crystallizing agent in crystal engineering.
Effect Of Normal Moveout On A Seismic Pulse (1973)

Abstract Using a synthetic seismogram as input, normal moveout correction stretches a reflection pulse in such a way that the spectrum of the pulse is a linearly compressed version of the uncorrected pulse spectrum. The amount of compression depends on t0, the source-detector separation, velocity, and the rate at which velocity varies with t0. The amplitude of the spectrum is increased by the same factor that expresses the spectral compression. As a result, the summed pulse from a CDP stack is richer in low frequencies than one might anticipate and has a smaller signal-to-noise ratio than the square root of the number of traces in the stack.
Retinoic acid metabolism and inhibition of cell proliferation: an unexpected liaison. (1996)

The rationale for the use of all-trans-retinoic acid (RA) as an anticancer agent is based on its ability to inhibit growth and promote differentiation of some neoplastic cells. However, RA is not effective in all conditions of cell culture, and in some cases, it may stimulate cell growth. We used a serum-free culture system to study the effect of RA on cell proliferation. Following 2 days of RA exposure, 9 of a total of 15 cell lines showed an inhibition of cell growth (RA-sensitive), while 6 of 15 cell lines showed resistance to RA (RA-resistant cells). Metabolic studies and high-performance liquid chromatography analysis of the cell-associated and medium extracts from cells incubated with [3H]RA revealed that all nine RA-sensitive cells showed a very high activity to metabolize RA to polar metabolites found in the medium. In sharp contrast, RA-resistant cells retained about 60% of the original RA at 76 h. However, conditioned medium from the sensitive cells was without activity on the growth of sensitive and resistant cells. We conclude that a relationship exists between RA inhibition of cell growth and intracellular RA metabolism. These data may help design useful strategies in cancer therapy by retinoids and dispel the notion that RA itself is responsible for the inhibition of cell growth.
Nuclear protein that binds sterol regulatory element of low density lipoprotein receptor promoter. II. Purification and characterization (1993)

This paper describes the purification and characterization of a sterol regulatory element binding protein (SREBP) that recognizes the SRE-1 sequence in the 5' flanking region of the gene for the low density lipoprotein (LDL) receptor. The protein was purified more than 38,000-fold from nuclear extracts of human HeLa cells by ion exchange, gel filtration, and DNA-affinity chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified preparation revealed a cluster of bands at 59-68 kDa, each of which bound to the SRE-1 element as revealed by cross-linking experiments. Binding of SREBP correlated perfectly with transcriptional activity in a series of 16 sterol regulatory elements with point mutations. In the LDL receptor promoter, the 10-base pair SRE-1 is embedded in a 16-base pair sequence designated Repeat 2, which is adjacent to Repeat 3, a binding site for nuclear factor Sp1. Oligonucleotides containing Repeat 2 + 3 bound SREBP and Sp1 as revealed by mobility shift assays. SREBP produced a DNase I footprint over the SRE-1 sequence, which was immediately adjacent to the footprint produced by Sp1. The current data are consistent with the concept that SREBP acts in concert with Sp1 to achieve high level, sterol-suppressible transcription of the gene for the LDL receptor.
ASTEC: an automated system for sitting-drop protein crystallization (1993)

An automated system for protein crystallization that is based on the vapor diffusion method has been developed using novel sitting-drop supports for standard Linbro plates. Laboratory robotics have been designed for liquid handling of stock solutions, silicone-grease dispensing and coverslip transfer. The system can handle up to four crystallization plates (96 wells) and ten stock solutions, without any user attendance. The software allows specification of several experimental parameters and records experiments, which may be accessed by the use of a bar-code label. Experiments may be conducted according to a user's specific design, a screening test or an incomplete factorial design. The system is capable of pipetting viscous solutions such as polyethylene glycol with good reproducibility. Automatic well-sealing techniques are discussed and preliminary protein-crystallization results are presented.
Red blood cell changes during the evolution of the sickle cell painful crisis (1992)

A longitudinal study of the red blood cell (RBC) deformability, percent of dense erythrocytes, and hematologic parameters has been conducted during 117 painful crises affecting 36 patients with sickle cell anemia between January, 1985 and December, 1990. RBC deformability was determined by osmotic gradient ektacytometry and the percentage of dense cells was quantitated by centrifugation on a discontinuous Stractan density gradient. The data indicate that the painful crisis is a process that follows a bimodal form of evolution. The first phase of the painful crisis is characterized by increase in the severity of pain, increase in the number of dense cells, and a decrease in RBC deformability. In some patients the changes in dense cells and RBC deformability are evident 1 to 3 days before the onset of pain. In addition, the hemoglobin level decreases and the reticulocyte count increases during this initial phase. The second phase of the crisis is characterized by reduction in pain intensity, decrease in the number of dense cells, and increase in RBC deformability to values higher than those seen in the steady state. Moreover, the improvement in RBC deformability and the decrease in the number of dense cells at the end of a crisis seem to constitute new risk factors that may incite a recurrence of the crisis within 1 month in about 50% of painful episodes. The pathophysiologic events responsible for this bimodal behavior of RBCs during painful episodes may represent the appearance of factors that induce (1) preferential trapping of deformable cells in the microcirculation during the first phase of the crisis, followed by a decrease of dense cells and the appearance of new deformable RBCs released from the bone marrow during the second phase of the crisis; or (2) variable sickling of all circulating RBCs during the first phase followed by disappearance of dense RBCs and their replenishment by deformable cells during the second phase.
Sequence-specific recognition of double helical RNA and RNA.DNA by triple helix formation. (1993)

The stabilities of eight triple helical pyrimidine.purine.pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine.pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25 degrees C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA.DNA hybrids.
Sex difference in the bed nucleus of the stria terminalis of the human brain (1990)

A quantitative analysis of the volume of the darkly staining region of the posteromedial bed nucleus of the stria terminalis was performed on the brains of 26 age-matched male and female human subjects. We suggest the term "darkly staining posteromedial" component of the bed nucleus of the stria terminalis (BNST-dspm) to describe this sexually dimorphic region of the human brain. The volume of the BNST-dspm was 2.47 times greater in males than in females. This region in humans appears to correspond to an area of the bed nucleus of the stria terminalis in laboratory animals that exhibits volumetric and neurochemical sexual dimorphisms, concentrates gonadal steroids, and is anatomically connected to several other sexually dimorphic nuclei. Furthermore, the bed nucleus of the stria terminalis is involved in sexually dimorphic functions, including aggressive behavior, sexual behavior, and gonadotropin secretion, which are also influenced by gonadal steroids. Therefore, it is possible that in human beings as well, gonadal hormones influence the sexual dimorphism in the BNST-dspm and that this morphological difference, in part, underlies sexually dimorphic function.
An introduction to wavelets (1995)

Wavelets were developed independently by mathematicians, quantum physicists, electrical engineers and geologists, but collaborations among these fields during the last decade have led to new and varied applications. What are wavelets, and why might they be useful to you? The fundamental idea behind wavelets is to analyze according to scale. Indeed, some researchers feel that using wavelets means adopting a whole new mind-set or perspective in processing data. Wavelets are functions that satisfy certain mathematical requirements and are used in representing data or other functions. Most of the basic wavelet theory has now been done. The mathematics have been worked out in excruciating detail, and wavelet theory is now in the refinement stage. This involves generalizing and extending wavelets, such as in extending wavelet packet techniques. The future of wavelets lies in the as-yet uncharted territory of applications. Wavelet techniques have not been thoroughly worked out in such applications as practical data analysis, where, for example, discretely sampled time-series data might need to be analyzed. Such applications offer exciting avenues for exploration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Western blot (immunoblot) based on recombinant-derived p41 with conventional tests for serodiagnosis of human immunodeficiency virus infections (1988)

To evaluate the performance of a serological test for human immunodeficiency virus type 1 (HIV-1) infections based on the use of a recombinant envelope gene-derived protein as the antigen, we caused expression of a 1.4-kilobase fragment of HIV.DNA that codes for the complete gp41 transmembrane protein in an Escherichia coli expression vector and used Western blots (WB; immunoblots) prepared with recombinant material (pEX-41) to detect antibodies to HIV-1. This test detected all 339 sera which were positive by a combination of conventional serodiagnostic assays and produced no false-positive results with 311 negative samples. Also no false-positive results were obtained with 20 sera from systemic lupus erythematosus patients which had high titers of cross-reactive autoantibodies. In six cases, the pEX-41 WB proved to be more sensitive than individual assays applied on their own, and in five cases it was even more sensitive than a combination of conventional assays. We tested 221 sera in both our pEX-41 WB and a commercially available recombinant enzyme immunoassay (EIA [Abbott]). The results were identical in 188 cases. A total of 27 sera containing antibodies to gp41 as demonstrated in the pEX-41 WB, as well as the Abbott recombinant EIA, had no antibodies to the recombinant core antigen as measured in the Abbott EIA. However, 25 of these sera did stain the 24-kilodalton band on a WB with purified virus. Six sera that were positive in all of the conventional confirmatory assays and reacted strongly with the pEX-41 WB did not recognize the surface antigen used in the Abbott recombinant EIA. We conclude that the use of WB prepared with recombinant-derived p41 offers a very sensitive and specific method to detect antibodies to HIV.
Use of polyclonal and monoclonal antibodies and analysis of viral RNA in the detection of unusual group A human rotaviruses (1988)

Immuno-enzymatic assay employing monoclonal antibodies and viral RNA analysis by gel electrophoresis were used to classify human group A rotaviruses (HRV) into subgroups I and II. Of 249 fecal samples positive for group A rotaviruses, 29 (11%) belonged to subgroup I and 215 (85%) were identified as subgroup II. Two samples (Ro-302 and Ro-500) contained mixed infections of the two subgroups. Three isolates belonged to neither one of the two subgroups, but they did not yield enough viral RNA to allow their classification. One subgroup I isolate (Ro-1845) contained components typical of subgroup II viruses in that it was identical to serotype 3 and yielded RNA with fast-moving 10th and 11th segments. After growth in culture, the two mixed infections yielded subgroup II viruses, which were identified as serotype 1. The three unclassified isolates grew poorly in culture and could not be further analyzed. The subgroup I isolate (Ro-1845) grew well in culture and yielded virus similar to the original one.
Accessing picture archiving and communication system text and image information through personal computers. (1994)

Recent advances in storage technology have made possible the archiving of tremendous amounts of text and image information within a picture archiving and communication system (PACS). However, a radiologist's access to this information typically has been limited to viewing workstations designed primarily to support clinical activities. Unfortunately, these workstations often overlook the benefits of PACS in teaching and research applications, which are of significant importance in an academic institution. To support such activities at our own institution, we have included two major objectives in our second-generation PACS development: (1) to provide access to text and image information archived within our PACS in an environment that is easily accessible to and comfortable for our radiologists, namely, their own Macintosh (Apple Computer, Cupertino, CA) personal computers; and (2) to provide this information in standard Macintosh formats, so that tools with which radiologists are already familiar can be used in frequently performed teaching activities--the production of slides and prints, the maintenance of personal teaching and research files, and specialized image analysis and processing.
Accuracy and predictability of intraocular lens power calculation after laser in situ keratomileusis (2001)

Hyperopic error after cataract surgery in post-LASIK eyes was significantly reduced by using refraction-derived keratometric values for IOL power calculation. Persistent hyperopic error was corrected by hyperopic LASIK.
A 700-Mb/s/pin CMOS signaling interface using current integrating receivers (1997)

A high speed CMOS signaling interface for application in multiprocessor interconnection networks has been developed. The interface utilizes I-V push-pull drivers, a delay line phase-locked loop (PLL), and sampling of the data on both edges of the clock. In order to increase the noise immunity of the reception, a current-integrating input pin sampler is used to receive the incoming data. Chips fabricated in a 0.8 /spl mu/m CMOS technology achieve transfer rates of 740 Mb/s/pin operating from a 3.3 V supply with a bit error rate of less than 10/sup -14/.
Lysostaphin Treatment of Experimental Methicillin-Resistant Staphylococcus aureus Aortic Valve Endocarditis (1998)

The emergence of clinical isolates of methicillin-resistant Staphylococcus aureus with reduced susceptibility to vancomycin has prompted a search for new and novel therapeutic agents active against S. aureus. Lysostaphin, a peptidase produced by Staphylococcus simulans, specifically cleaves the glycine-glycine bonds unique to the interpeptide cross-bridge of the S. aureus cell wall. The effectiveness of various regimens of dosing with intravenous lysostaphin was compared to that of vancomycin in the rabbit model of aortic valve endocarditis caused by a clinical methicillin-resistant S. aureus isolate. All animals were treated for a total of 3 days. The most active regimen, lysostaphin given three times daily, produced sterile vegetations in 10 of 11 treated rabbits, with a mean reduction in vegetation bacterial counts of 8.5 log10 CFU/g compared to the counts in the untreated controls. In contrast, vancomycin given twice daily sterilized no vegetations and reduced vegetation bacterial counts by only 4.8 log10 CFU/g. Lysostaphin given once daily was less effective, reducing mean vegetation bacterial counts by only 3.6 log10 CFU/g, but the combination of lysostaphin once daily and vancomycin twice daily reduced the mean vegetation bacterial density by 7.5 log10 CFU/g, a result that was significantly better than that for either regimen alone (P < 0.05). Lysostaphin was well tolerated by the rabbits, with no evidence of immunological reactions following up to 9 weeks of intravenous administration. We conclude that lysostaphin given alone or in combination with vancomycin is more effective in the treatment of experimental methicillin-resistant S. aureus aortic valve endocarditis than vancomycin alone.
Immunobiological barriers to xenotransplantation (2015)

Binding of natural anti-pig antibodies in humans and nonhuman primates to carbohydrate antigens expressed on the transplanted pig organ, the most important of which is galactose-α1,3-galactose (Gal), activate the complement cascade, which results in destruction of the graft within minutes or hours, known as hyperacute rejection. Even if antibody is removed from the recipient's blood by plasmapheresis, recovery of antibody is associated with acute humoral xenograft rejection. If immunosuppressive therapy is inadequate, the development of high levels of T cell-dependent elicited anti-pig IgG similarly results in graft destruction, though classical acute cellular rejection is rarely seen. Vascular endothelial activation by low levels of anti-nonGal antibody, coupled with dysregulation of the coagulation-anticoagulation systems between pigs and primates, leads to a thrombotic microangiopathy in the graft that may be associated with a consumptive coagulopathy in the recipient. The most successful approach to overcoming these barriers is by genetically-engineering the pig to provide it with resistance to the human humoral and cellular immune responses and to correct the coagulation discrepancies between the two species. Organs and cells from pigs that (i) do not express the important Gal antigen, (ii) express a human complement-regulatory protein, and (iii) express a human coagulation-regulatory protein, when combined with an effective immunosuppressive regimen, have been associated with prolonged pig graft survival in nonhuman primates.
A General Framework for Development and Data Analysis of Competitive High-Throughput Screens for Small-Molecule Inhibitors of Protein−Protein Interactions by Fluorescence Polarization (2004)

Equilibrium binding experiments are widely used for the accurate characterization of binding and competitive binding behavior in biological systems. Modern high-throughput discovery efforts in chemical biology rely heavily upon this principle. Here, we derive exact analytical expressions for general competitive binding models which can also explain a commonly encountered phenomenon in these types of experiments, anticooperative incomplete displacement. We explore the effects of nonspecific binding behavior and parameter misestimation. All expressions are derived in terms of total concentrations determined a priori. We discuss a general framework for high-throughput screening assays based on fluorescence polarization and strategies for assay development, sensitivity regimes, data quality control, analysis, and ranking. Theoretical findings are visualized by simulations using realistic parameter sets. Our results are the basis for the discovery of small-molecule inhibitors of the protein-protein interaction between human calcineurin and NFAT transcription factors, as discussed in the subsequent paper (31).
An Avian Influenza H5N1 Virus That Binds to a Human-Type Receptor (2007)

Avian influenza viruses preferentially recognize sialosugar chains terminating in sialic acid-alpha2,3-galactose (SAalpha2,3Gal), whereas human influenza viruses preferentially recognize SAalpha2,6Gal. A conversion to SAalpha2,6Gal specificity is believed to be one of the changes required for the introduction of new hemagglutinin (HA) subtypes to the human population, which can lead to pandemics. Avian influenza H5N1 virus is a major threat for the emergence of a pandemic virus. As of 12 June 2007, the virus has been reported in 45 countries, and 312 human cases with 190 deaths have been confirmed. We describe here substitutions at position 129 and 134 identified in a virus isolated from a fatal human case that could change the receptor-binding preference of HA of H5N1 virus from SAalpha2,3Gal to both SAalpha2,3Gal and SAalpha2,6Gal. Molecular modeling demonstrated that the mutation may stabilize SAalpha2,6Gal in its optimal cis conformation in the binding pocket. The mutation was found in approximately half of the viral sequences directly amplified from a respiratory specimen of the patient. Our data confirm the presence of H5N1 virus with the ability to bind to a human-type receptor in this patient and suggest the selection and expansion of the mutant with human-type receptor specificity in the human host environment.