gebhart/patrepeval huggingface dataset:
Redundant logarithmic number systems (2003)

A new number system that offers advantages over conventional floating-point and sign/logarithm number systems is described. Called redundant logarithmic arithmetic, it relies, like conventional logarithmic arithmetic, on table lookups to make the arithmetic unit simpler than an equivalent floating-point unit. The cost of 32-b subtraction in a redundant logarithmic number system is lower than that of previously published logarithmic subtraction methods. Another advantage of a redundant logarithmic number system is that a single arithmetic unit can use the same hardware to add, subtract, or multiply in similar times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of ligand in antibody-directed endocytosis of liposomes by human T-leukemia cells. (1989)

The rate of uptake and intracellular processing of ligand-directed drug carriers may depend heavily on the endocytic pathway of the target antigen. We examined the role of the target antigen and type of antibody-liposome linkage in determining endocytosis of liposomes by three human T-cell leukemias, Jurkat, CEM, and Molt-4. Liposome-cell binding and internalization over time were studied using two independent assays for intracellular delivery of liposome contents: a new fluorescence assay using a pH-sensitive fluorescent dye; and a growth inhibition assay for delivery of cytotoxic drug, methotrexate-gamma-aspartate. Liposomes targeted against the transferrin receptor showed greater surface binding, internalization, and growth inhibition than liposomes targeted against the T-cell surface antigens, CD2, CD3, or CD5. Furthermore, liposomes made by conjugating the targeting antibody directly to the liposome surface were more efficiently internalized and retained than were liposomes linked to antibody-coated cells via Protein A. Selection of the type of antibody-liposome conjugate as well as the appropriate surface receptor to facilitate endocytosis is essential in antibody-directed drug treatment of cancer.
A microfluidic model for single-cell capillary obstruction by Plasmodium falciparum -infected erythrocytes (2003)

Severe malaria by Plasmodium falciparum is a potentially fatal disease, frequently unresponsive to even the most aggressive treatments. Host organ failure is associated with acquired rigidity of infected red blood cells and capillary blockage. In vitro techniques have played an important role in modeling cell deformability. Although, historically they have either been applied to bulk cell populations or to measure single physical parameters of individual cells. In this article, we demonstrate the unique abilities and benefits of elastomeric microchannels to characterize complex behaviors of single cells, under flow, in multicellular capillary blockages. Channels of 8-, 6-, 4-, and 2-microm widths were readily traversed by the 8 microm-wide, highly elastic, uninfected red blood cells, as well as by infected cells in the early ring stages. Trophozoite stages failed to freely traverse 2- to 4-microm channels; some that passed through the 4-microm channels emerged from constricted space with deformations whose shape-recovery could be observed in real time. In 2-microm channels, trophozoites mimicked "pitting," a normal process in the body where spleen beds remove parasites without destroying the red cell. Schizont forms failed to traverse even 6-microm channels and rapidly formed a capillary blockage. Interestingly, individual uninfected red blood cells readily squeezed through the blockages formed by immobile schizonts in a 6-microm capillary. The last observation can explain the high parasitemia in a growing capillary blockage and the well known benefits of early blood transfusion in severe malaria.
Path slicing (2005)

We present a new technique, path slicing , that takes as input a possibly infeasible path to a target location, and eliminates all the operations that are irrelevant towards the reachability of the target location. A path slice is a subsequence of the original path whose infeasibility guarantees the infeasibility of the original path, and whose feasibility guarantees the existence of some feasible variant of the given path that reaches the target location even though the given path may itself be infeasible. Our method combines the ability of program slicing to look at several program paths, with the precision that dynamic slicing enjoys by focusing on a single path. We have implemented Path Slicing to analyze possible counterexamples returned by the software model checker Blast . We show its effectiveness in drastically reducing the size of the counterexamples to less than 1% of their original size. This enables the precise verification of application programs (upto 100KLOC), by allowing the analysis to focus on the part of the counterexample that is relevant to the property being checked.
Orientation of respiratory tract cilia in patients with primary ciliary dyskinesia, bronchiectasis, and in normal subjects. (1989)

A reproducible technique, utilising a graphics tablet and a personal computer for measuring ciliary orientation from electron micrographs of ciliated epithelium, was assessed. Ciliary deviation was measured in 47 normal subjects (mean ciliary deviation +/- 1 SD was 14.6 (3.3 degrees)), in eight patients with bronchiectasis and normal ciliary function (15.1 (6.5 degrees], and in seven patients with primary ciliary dyskinesia (38.7 (7.8 degrees); significantly greater than the first two groups). Measurements of ciliary deviation at the tip, base, and basal feet showed very little variation along the ciliary shaft in all three groups, suggesting that valid measurements of ciliary deviation can be made at any level of the cilium. Mean ciliary deviation in normal subjects was always less than 30 degrees; all patients with a mean ciliary deviation of greater than 30 degrees had recurrent respiratory tract disease. Four of seven patients with primary ciliary dyskinesia had ciliary disorientation; in one this was the only defect. Measurements of inter- and intraobserver variability using this method showed a maximum difference between observations of 4.1 degrees. It is suggested that ciliary orientation should be measured in patients suspected of having defective ciliary function or structure, or both.
Review: Potential Uses of Cloning in Breeding Schemes: Dairy Cattle (2004)

Cloning by nuclear transfer has many potential applications in a dairy cattle breeding program. It can be used to increase the accuracy of selection and therefore the rate of genetic progress, to speed up the dissemination of the genes from animals of exceptionally high genetic merit to the commercial population, and to reproduce transgenic animals. Today, however, the main limitation of the use of cloning besides governmental regulations is its low success rate and consequently the high cost to produce an animal ready for reproduction. As a result cloning is mostly limited to the reproduction of animals of very high genetic merit or that carry genes of specific interest. Examples of this are top-ranked bulls which do not produce enough semen for the demand due to various reasons. A strategy that could be used by artificial insemination (AI) centers would be to create a bank of somatic cells for every bull entering AI facilities long before they are placed on the young sire proving program. The other use of cloning is to assist in the selection and reproduction of bull dams. Marker assisted selection (MAS) can substantially enhance the accuracy of selection for embryos or young animals without comprehensive performance records, and therefore can greatly increase the value of cloning such embryos or young animals.
Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s. (1985)

Four homologous oligopeptide-EDTA molecules, tri-, tetra, penta-, and hexa(N-methylpyrrolecarboxamide)-EDTA, in the presence of Fe(II), O2, and dithiothreitol, cleave 32P-end-labeled restriction fragments from plasmid pBR322 DNA at common locations rich in A X T base pairs that differ in the size of the binding site. From analysis of the cleavage patterns visualized by high-resolution denaturing gel electrophoresis, the oligopeptides with three, four, five, and six N-methylpyrrolecarboxamide units, containing four, five, six, and seven amide NHs, bind sites of A X T-rich DNA consisting of five, six, seven, and eight contiguous base pairs, respectively. The general rule of n amides affording binding site sizes of n + 1 base pairs is consistent with the oligopeptides binding in the minor groove of right-handed DNA, with the amide NH groups forming bridges between the adjacent N-3 and O-2 atoms of adenine or thymine on opposite strands of the DNA helix.
Evidence for a primary association of celiac disease to a particular HLA-DQ alpha/beta heterodimer. (1989)

Typing of DNA from 94 unrelated children with celiac disease (CD) with HLA-DQA1 and -DQB1 allele-specific oligonucleotide probes revealed that all but one (i.e., 98.9%) may share a particular combination of a DQA1 and a DQB1 gene. These genes are arranged in cis position on the DR3DQw2 haplotype and in trans position in DR5DQw7/DR7DQw2 heterozygous individuals. Thus, most CD patients may share the same cis- or trans-encoded HLA-DQ alpha/beta heterodimer.
Combined Local Application of Tetracycline and Bisphosphonate Reduces Alveolar Bone Resorption in Rats (2003)

In the present study, we found that tetracyclines can be most effective in reducing alveolar bone loss when applied locally. The combined local treatment of alendronate and tetracycline may have a synergistic effect.
The Importance of Nicotinic Acetylcholine Receptors in Schizophrenia, Bipolar Disorder and Tourettes Syndrome (2002)

As the prevalence of tobacco use has decreased, it has become clear that individuals with mental illness comprise a substantial portion of the remaining smokers. Seventy to eighty percent of patients with schizophrenia smoke and their smoking is established before their first psychotic episodes or the initiation of treatment. Many patients with schizophrenia, and approximately 50% of their first degree relatives have abnormalities in auditory sensory gating and/or smooth pursuit eye movements. These abnormalities are corrected by nicotine, and they appear to be transmitted as autosomal dominant traits. Evidence is accumulating that these abnormalities reflect genetic variations in nicotine receptor number and function, that may increase susceptibility for schizophrenia. Recent studies suggest that bupropion, added to treatment with an atypical antipsychotic, can enhance the likelihood of smoking cessation or reduction in patients with schizophrenia. The prevalence of smoking is also substantially increased among patients with bipolar disorder, perhaps especially so among those with psychotic features. Nicotine delivered by gum or transdermal patch can provide short term relief for exacerbations of Tourette's Syndrome, but its use is limited by frequent toxicity, primarily nausea.
Prospective Multicentric Randomized Phase III Study of Imatinib in Patients With Advanced Gastrointestinal Stromal Tumors Comparing Interruption Versus Continuation of Treatment Beyond 1 Year: The French Sarcoma Group (2007)

Imatinib interruption results in rapid progression in most patients with advanced GIST, and cannot be recommended in routine practice unless patient experience significant toxicity
Single-mode-fiber ring dye laser (1985)

Pulsed dye-laser operation in a single-mode fiber is demonstrated by incorporating an evanescent field amplifier into an all-fiber ring resonator. Laser threshold is obtained with 60 mW of pump power. Characteristics of the vanescent fiber amplifier are investigated as functions of pump power and dye solution index.
Selection of Escherichia coli Mutants Lacking Glucose-6-Phosphate Dehydrogenase or Gluconate-6-Phosphate Dehydrogenase (1968)

Glucose is metabolized in Escherichia coli chiefly via the phosphoglucose isomerase reaction; mutants lacking that enzyme grow slowly on glucose by using the hexose monophosphate shunt. When such a strain is further mutated so as to yield strains unable to grow at all on glucose or on glucose-6-phosphate, the secondary strains are found to lack also activity of glucose-6-phosphate dehydrogenase. The double mutants can be transduced back to glucose positivity; one class of transductants has normal phosphoglucose isomerase activity but no glucose-6-phosphate dehydrogenase. An analogous scheme has been used to select mutants lacking gluconate-6-phosphate dehydrogenase. Here the primary mutant lacks gluconate-6-phosphate dehydrase (an enzyme of the Enter-Doudoroff pathway) and grows slowly on gluconate; gluconate-negative mutants are selected from it. These mutants, lacking the nicotinamide dinucleotide phosphate-linked glucose-6-phosphate dehydrogenase or gluconate-6-phosphate dehydrogenase, grow on glucose at rates similar to the wild type. Thus, these enzymes are not essential for glucose metabolism in E. coli.
Crystal Structure of the Curcumin Derivative, Acetic Acid 4-[7-(4-Acetoxy-3-methoxyphenyl)-3,5-dioxoheptyl]-2-methoxyphenyl ester (2004)

C25H28O8 is monoclinic, P21. The unit-cell dimensions at 293 K are a = 8.054(1), b = 9.438(2), c = 15.701(1)Å, β = 98.875 (2)°, V = 1179.1(2)Å3, Dx = 1.286 g/cm3, and Z = 2. The R value is R = 0.046 for 4152 reflections. There is an intramolecular hydrogen bond with an O2…O1 distance of 2.496(1)Å. The molecules in the crystal are packed at the normal van der Waals distances.
Case Report: Hand-Foot Syndrome Induced by the Oral Fluoropyrimidine S-1 (2001)

Hand-foot syndrome (HFS) is a relatively common side effect of fluorouracil (5-FU) chemotherapy that has also been associated with the oral fluoropyrimidine capecitabine. Interestingly, HFS is virtually unknown to result from treatment with UFT, a combination of tegafur and uracil. Tegafur is a prodrug of 5-FU and is a component of S-1, another oral fluoropyrimidine active in a variety of solid tumors. We know of only one previously described case of S-1-induced HFS and the case reported here is the first to provide full documentation of this occurrence. The pathophysiology of chemotherapy-induced HFS remains unknown and very little pathological information is available. Treatment consists of topical emollient therapy, although pyridoxine has occasionally been beneficial. The study of HFS may provide an important insight into the pharmacology of fluoropyrimidines and allow for effective preventive strategies for this side effect of chemotherapy.
Curved Glide-Reflection Symmetry Detection (2011)

We generalize the concept of bilateral reflection symmetry to curved glide-reflection symmetry in 2D euclidean space, such that classic reflection symmetry becomes one of its six special cases. We propose a local feature-based approach for curved glidereflection symmetry detection from real, unsegmented 2D images. Furthermore, we apply curved glide-reflection axis detection for curved reflection surface detection in 3D images. Our method discovers, groups, and connects statistically dominant local glidereflection axes in an Axis-Parameter-Space (APS) without preassumptions on the types of reflection symmetries. Quantitative evaluations and comparisons against state-of-the-art algorithms on a diverse 64-test-image set and 1,125 Swedish leaf-data images show a promising average detection rate of the proposed algorithm at 80 and 40 percent, respectively, and superior performance over existing reflection symmetry detection algorithms. Potential applications in computer vision, particularly biomedical imaging, include saliency detection from unsegmented images and quantification of deviations from normality. We make our 64-test-image set publicly available.
AutoDimer: a screening tool for primer-dimer and hairpin structures (2004)

The ability to select short DNA oligonucleotide sequences capable of binding solely to their intended target is of great importance in developing nucleic acid based detection technologies. Applications such as multiplex PCR rely on primers binding to unique regions in a genome. Competing side reactions with other primer pairs or template DNA decrease PCR efficiency: Freely available primer design software such as Primer3 screens for potential hairpin and primer-dimer interactions while selecting a single primer pair. The development of multiplex PCR assays (in the range of 5 to 20 loci) requires the screening of all primer pairs for potential cross-reactivity. However, a logistical problem results due to the number of total number of comparisons required. Comparing the primer set for a 10-plex assay (20 total primer sequences) results in 210 primer-primer combinations that must be screened. The ability to screen sets of candidate oligomers rapidly for potential cross-reactivity reduces overall assay devlelopment time. Here we report the application of a familiar sliding algorithm for comparing two strands of DNA in an overlapping fashion. The algorithm has been employed in a software package wherein the user can compare multiple sequences in a single computational run. After the screening is completed, a score is assigned to potential duplex interactions exceeding a user-defined threshold. Additional criteria of predicted melting temperature (Tm) and free energy of melting (deltaG) are included for further ranking. Sodium counterion and total stand concentrations can be adjusted for the Tm and deltaG calculations. The predicted interactions are saved in a text file for further evaluation.
Rationally designed mutations convert complexes of human recombinant T cell receptor ligands into monomers that retain biological activity (2004)

Single-chain human recombinant T cell receptor ligands derived from the peptide binding/TCR recognition domain of human HLA-DR2b (DRA*0101/DRB1*1501) produced in Escherichia coli with and without amino-terminal extensions containing antigenic peptides have been described previously. While molecules with the native sequence retained biological activity, they formed higher order aggregates in solution. In this study, we used site-directed mutagenesis to modify the β-sheet platform of the DR2-derived RTLs, obtaining two variants that were monomeric in solution by replacing hydrophobic residues with polar (serine) or charged (aspartic acid) residues. Size exclusion chromatography and dynamic light scattering demonstrated that the modified RTLs were monomeric in solution, and structural characterization using circular dichroism demonstrated the highly ordered secondary structure of the RTLs. Peptide binding to the `empty' RTLs was quantified using biotinylated peptides, and functional studies showed that the modified RTLs containing covalently tethered peptides were able to inhibit antigen-specific T cell proliferation in vitro, as well as suppress experimental autoimmune encephalomyelitis in vivo. These studies demonstrated that RTLs encoding the Ag-binding/TCR recognition domain of MHC class II molecules are innately very robust structures, capable of retaining potent biological activity separate from the Ig-fold domains of the progenitor class II structure, with prevention of aggregation accomplished by modification of an exposed surface that was buried in the progenitor structure.
Hepatic and extrahepatic HCV RNA strands in chronic hepatitis C: Different patterns of response to interferon treatment (1993)

We investigated the presence of positive (genomic) and negative (replicative intermediate) hepatitis C virus RNA strands in liver, peripheral mononuclear cells and serum from patients with chronic hepatitis C using a selective and semiquantitative polymerase chain reaction procedure. Negative and positive hepatitis C virus RNA strands were present in liver, serum and lymphoid cells in all untreated patients and in all those who did not respond to interferon therapy. In the latter group of patients, the titers of RNA strands in the liver and peripheral mononuclear cells at the end of the treatment were similar to those encountered in untreated patients, but the serum titers were about 100 times lower than pretreatment values. In patients who responded to interferon with normalization of serum aminotransferase levels (n = 10), the rate of detection and the titer of the two viral strands in liver, serum and mononuclear cells were markedly decreased at the end of the therapy. In the six responders who did not relapse after interferon withdrawal, both hepatitis C virus RNA strands were absent from the liver, serum and lymphoid cells. By contrast, the positive RNA strand was present in liver cells, mononuclear cells or both at the end of therapy in all patients who experienced posttherapy relapse. In conclusion, our results indicate that interferon can clear hepatitis C virus from hepatic and extrahepatic sites only in responder patients. Disappearance of genomic hepatitis C virus RNA from the liver and from mononuclear cells may predict complete response without posttherapy relapse.
Metallothionein 1 h tumour suppressor activity in prostate cancer is mediated by euchromatin methyltransferase 1 (2013)

Metallothioneins (MTs) are a group of metal binding proteins thought to play a role in the detoxification of heavy metals. Here we showed by microarray and validation analyses that MT1h, a member of MT, is down-regulated in many human malignancies. Low expression of MT1h was associated with poor clinical outcomes in both prostate and liver cancer. We found that the promoter region of MT1h was hypermethylated in cancer and that demethylation of the MT1h promoter reversed the suppression of MT1h expression. Forced expression of MT1h induced cell growth arrest, suppressed colony formation, retarded migration, and reduced invasion. SCID mice with tumour xenografts with inducible MT1h expression had lower tumour volumes as well as fewer metastases and deaths than uninduced controls. MT1h was found to interact with euchromatin histone methyltransferase 1 (EHMT1) and enhanced its methyltransferase activity on histone 3. Knocking down of EHMT1 or a mutation in MT1h that abrogates its interaction with EHMT1 abrogated MT1h tumour suppressor activity. This demonstrates tumour suppressor activity in a heavy metal binding protein that is dependent on activation of histone methylation.