gebhart/patrepeval huggingface dataset:
Myelin-Associated Glycoprotein Is a Myelin Signal that Modulates the Caliber of Myelinated Axons (1998)

Myelination increases neuronal conduction velocity through its insulating properties and an unidentified extrinsic effect that increases axonal caliber. Although it is well established that demyelination can cause axonal atrophy, the myelin molecule that regulates axonal caliber is not known. Loss of the structural proteins of compact peripheral nervous system (PNS) myelin, P0 protein, and myelin basic protein does not lead to axonal atrophy. This study demonstrates that mice with a null mutation of the myelin-associated glycoprotein (MAG) gene have a chronic atrophy of myelinated PNS axons that results in paranodal myelin tomaculi and axonal degeneration. Absence of MAG was correlated with reduced axonal calibers, decreased neurofilament spacing, and reduced neurofilament phosphorylation. Because axonal atrophy and degeneration in MAG-deficient mice occur in the absence of inflammation, hypomyelination, significant demyelination-remyelination, or gain of function mutations, these data support a functional role for MAG in modulating the maturation and viability of myelinated axons.
DNA polymerase I gene of Saccharomyces cerevisiae: nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases. (1988)

A 5600-base pair segment spanning the coding region of the Saccharomyces cerevisiae DNA polymerase I gene was sequenced and found to contain an open reading frame of 1468 codons, corresponding to a polypeptide of Mr 166,794. A pol1 temperature-sensitive mutation, encoding a DNA-polymerase-primase complex with altered stability, has a single base-pair substitution that changes the glycine at position 493 to a positively charged arginine. Protein sequence comparison with other prokaryotic and eukaryotic DNA polymerases reveals three major regions of homology. This observation suggests that certain DNA polymerases might require the conservation of critical amino acid residues for activity.
Increased C reactive protein and cardiac enzyme levels after coronary stent implantation. Is there protection by remote ischaemic preconditioning? (2006)

RIPC does not reduce, but exacerbates, the enzyme and TNI release from the heart after single-vessel angioplasty with stent. Furthermore, the increased circulating CRP remains raised. It seems that there is an enhanced inflammatory response after RIPC in the absence of statin treatment.
Seed encoding with LFSRs and cellular automata (2003)

Reseeding is used to improve fault coverage of pseudo-random testing. The seed corresponds to the initial state of the PRPG before filling the scan chain. In this paper, we present a technique for encoding a given seed by the number of clock cycles that the PRPG needs to run to reach it. This encoding requires many fewer bits than the bits of the seed itself. The cost is the time to reach the intended seed. We reduce this cost using the degrees of freedom (due to don't cares in test patterns) in solving the equations for the seeds. We show results for implementing our technique completely in on-chip hardware and for applying it from a tester. Simulations show that with low hardware overhead, the technique provides 100% single-stuck fault coverage. Also, when compared with conventional reseeding from an external tester or on-chip ROM, the technique reduces seed storage by up to 85%. We show how to apply the technique for both LFSRs and CA.
Mutations of Human Topoisomerase IIα Affecting Multidrug Resistance and Sensitivity (1999)

Two mutations, R450Q and P803S, in the coding region of the human topoisomerase II alpha gene have been identified in the atypical multidrug resistant (at-MDR) cell line, CEM/VM-1, which exhibits resistance to many structurally diverse topoisomerase II-targeting antitumor drugs such as VM-26, doxorubicin, m-AMSA, and mitoxantrone. The R450Q mutation mapped in the ATP utilization domain, while the P803S mutation mapped in the vicinity of the active site tyrosine of human topoisomerase II alpha. However, the roles of these two mutations in conferring multidrug resistance are unclear. To study the roles of these two mutations in conferring multidrug resistance, we have characterized the recombinant human DNA topoisomerase II alpha containing either single or double mutations. We show that both R450Q and P803S mutations confer resistance in the absence of ATP. However, in the presence of ATP, the R450Q, but not the P803S, mutation can confer multidrug resistance. The R450Q enzyme was shown to exhibit impaired ATP utilization both for enzyme catalysis and for its ability to form the circular protein clamp. Interestingly, an unrelated mutation, G437E, which is also located in the same domain as the R450Q mutation, exhibited multidrug hypersensitivity in the absence of ATP. However, in the presence of ATP, the G437E enzyme is only minimally hypersensitive to various topoisomerase II drugs. In contrast to the R450Q enzyme, the G437E enzyme exhibited enhanced ATP utilization for enzyme catalysis. In the aggregate, these results support the notion that the multidrug resistance and sensitivity of these mutant enzymes are due to a specific defect in ATP utilization during enzyme catalysis.
Human C′3: Evidence for the Liver as the Primary Site of Synthesis (1969)

The liver is the primary, if not sole, site of synthesis of the third component of human complement, as shown by a change in the recipient from C'3 FS(0.6) to C'3 SS, the donor type, following homotransplantation of the liver.
Regulation of mesangial cell function by vasodilatory signaling molecules (2001)

Proliferation of mesangial cells and expansion of mesangial matrix is a hallmark of glomerular disease leading to end-stage renal failure and requiring renal replacement therapy. Independently from the type of injury, e.g. in glomerulonephritis or diabetic nephropathy, the response to injury is remarkably uniform. Chronic glomerular disease is frequently associated with increases in systemic blood pressure and altered intraglomerular hemodynamics. Furthermore, reduction of systemic blood pressure and inhibition of the vasoconstrictor peptide angiotensin II have been shown to delay end-stage renal failure in various types of human kidney disease. Since vasoconstrictors of mesangial cells and efferent glomerular arterioli, such as angiotensin II, are thought to be detrimental for the progression of chronic glomerular disease, we propose that vasodilatory factors which antagonize the effects of angiotensin II, might have beneficial effects during the course of progressive kidney disease. To support this concept we will summarize currently available data on the role of vasodilatory signaling molecules such as natriuretic peptides (ANP, BNP and CNP), nitric oxide (NO), the prostaglandines PGE2 and prostacycline, and the purine mediator adenosine in the regulation of mesangial function.
Phenol red in tissue culture media is a weak estrogen: implications concerning the study of estrogen-responsive cells in culture. (1986)

Although much attention has been paid to the removal of hormones from sera and to the development of serum-free media for studies on hormone-responsive cells in culture, little consideration has been given to the possibility that the media components themselves may have hormonal activity. We have found that phenol red, which bears a structural resemblance to some nonsteroidal estrogens and which is used ubiquitously as a pH indicator in tissue culture media, has significant estrogenic activity at the concentrations (15-45 microM) at which it is found in tissue culture media. Phenol red binds to the estrogen receptor of MCF-7 human breast cancer cells with an affinity 0.001% that of estradiol (Kd = 2 X 10(-5) M). It stimulates the proliferation of estrogen receptor-positive MCF-7 breast cancer cells in a dose-dependent manner but has no effect on the growth of estrogen receptor-negative MDA-MB-231 breast cancer cells. At the concentrations present in tissue culture media, phenol red causes partial estrogenic stimulation, increasing cell number to 200% and progesterone receptor content to 300% of that found for cells grown in phenol red-free media, thereby reducing the degree to which exogenous estrogen is able to stimulate responses. The antiestrogens tamoxifen and hydroxytamoxifen inhibit cell proliferation below the control level only when cells are grown in the presence of phenol red; in the absence of phenol red, the antiestrogens do not suppress growth. The estrogenic activity of phenol red should be considered in any studies that utilize estrogen-responsive cells in culture.
Distinct roles of haptoglobin-related protein and apolipoprotein L-I in trypanolysis by human serum (2007)

Apolipoprotein L-I (apoL-I) is a human high-density lipoprotein (HDL) component able to kill Trypanosoma brucei brucei by forming anion-selective pores in the lysosomal membrane of the parasite. Another HDL component, haptoglobin-related protein (Hpr), has been suggested as an additional toxin required for full trypanolytic activity of normal human serum. We recently reported the case of a human lacking apoL-I (apoL-I(-/-)HS) as the result of frameshift mutations in both apoL-I alleles. Here, we show that this serum, devoid of any trypanolytic activity, exhibits normal concentrations of HDL-bound Hpr. Conversely, the serum of individuals with normal HDL-bound apoL-I but who lack Hpr and haptoglobin [Hp(r)(-/-)HS] as the result of gene deletion (anhaptoglobinemia) exhibited phenotypically normal but delayed trypanolytic activity. The trypanolytic properties of Hp(r)(-/-)HS were mimicked by free recombinant apoL-I, whereas recombinant Hpr did not affect trypanosomes. The lysis delay observed with either Hp(r)(-/-)HS or recombinant apoL-I could entirely be attributed to a defect in the uptake of the lytic components. Thus, apoL-I is responsible for the trypanolytic activity of normal human serum, whereas Hpr allows fast uptake of the carrier HDL particles, presumably through their binding to an Hp/Hpr surface receptor of the parasite.
Identification of highest-affinity ligands by affinity selection from equimolar peptide mixtures generated by robotic synthesis (1992)

A fully automated peptide synthesizer has been constructed that is capable of the simultaneous synthesis of up to 36 individual peptides and the synthesis of equimolar peptide mixtures. The instrument consists of an array of reaction vessels, a series of solenoid valves to control liquid flow, and a Zymark robot to deliver solvents and reagents; all components are computer controlled and coordinated. Equimolar peptide mixtures are obtained by algorithms that automate the mixing and distribution of peptide-resin particles. This technology was used to synthesize a library of 361 peptides, generated by randomizing two critical binding residues of a 10-mer epitope known to bind an anti-human immuno-deficiency virus gp120 monoclonal antibody. Each critical residue was substituted with 19 amino acids consisting of all the natural amino acids except cysteine. The library was synthesized as 19 pools, each containing 19 peptides. Each pool was screened in a solution-phase competition ELISA assay. The 12 most inhibitory peptides in the library were isolated by a rapid affinity-selection method and were identified by mass spectrometry and amino acid analysis. The binding properties of these 12 selected peptides were verified by synthesis and assay of the individual peptides. The two critical residues investigated were found to contribute independently to antibody binding.
The plasma lecithin:cholesterol acyltransferase reaction (1968)

Evidence for the existence of a plasma lecithin : cholesterol acyltransferase is reviewed with emphasis not only on the lipid reactants, but also on the lipoprotein "substrates" and "products." The cholesteryl esters of all major lipoprotein classes become labeled when plasma is incubated with cholesterol-(14)C. However, the smaller, lecithin-rich high density lipoproteins appear to be preferred substrates. Most studies of factors that influence the acyltransferase reaction have not adequately distinguished between effects on the enzyme and effects on the lipoprotein substrates. However, the fact that cholesterol esterification is diminished in plasma from eviscerated animals or from patients with reduced liver function suggests that the liver may regulate both the level of the enzyme and that of the substrates. Several indications exist that the acyltransferase reaction is the major source of plasma esterified cholesterol in man. Furthermore, the reaction may have a broader, extracellular function. One possibility is that it plays a role in the transport of cholesterol from peripheral tissues to the liver.
Viracept (Nelfinavir Mesylate, AG1343):  A Potent, Orally Bioavailable Inhibitor of HIV-1 Protease (1997)

Using a combination of iterative structure-based design and an analysis of oral pharmacokinetics and antiviral activity, AG1343 (Viracept, nelfinavir mesylate), a nonpeptidic inhibitor of HIV-1 protease, was identified. AG1343 is a potent enzyme inhibitor (Ki = 2 nM) and antiviral agent (HIV-1 ED50 = 14 nM). An X-ray cocrystal structure of the enzyme-AG1343 complex reveals how the novel thiophenyl ether and phenol-amide substituents of the inhibitor interact with the S1 and S2 subsites of HIV-1 protease, respectively. In vivo studies indicate that AG1343 is well absorbed orally in a variety of species and possesses favorable pharmacokinetic properties in humans. AG1343 (Viracept) has recently been approved for marketing for the treatment of AIDS.
Spatio-temporal and events based analysis of topic popularity in twitter (2013)

We present the first comprehensive characterization of the diffusion of ideas on Twitter, studying more than 5.96 million topics that include both popular and less popular topics. On a data set containing approximately 10 million users and a comprehensive scraping of 196 million tweets, we perform a rigorous temporal and spatial analysis, investigating the time-evolving properties of the subgraphs formed by the users discussing each topic. We focus on two different notions of the spatial: the network topology formed by follower-following links on Twitter, and the geospatial location of the users. We investigate the effect of initiators on the popularity of topics and find that users with a high number of followers have a strong impact on topic popularity. We deduce that topics become popular when disjoint clusters of users discussing them begin to merge and form one giant component that grows to cover a significant fraction of the network. Our geospatial analysis shows that highly popular topics are those that cross regional boundaries aggressively.
Cholera-Like Enterotoxins and Regulatory T cells (2010)

Cholera toxin (CT) and the heat-labile enterotoxin of E. coli (LT), as well as their non toxic mutants, are potent mucosal adjuvants of immunization eliciting mucosal and systemic responses against unrelated co-administered antigens in experimental models and in humans (non toxic mutants). These enterotoxins are composed of two subunits, the A subunit, responsible for an ADP-ribosyl transferase activity and the B subunit, responsible for cell binding. Paradoxically, whereas the whole toxins have adjuvant properties, the B subunits of CT (CTB) and of LT (LTB) have been shown to induce antigen specific tolerance when administered mucosally with antigens in experimental models as well as, recently, in humans, making them an attractive strategy to prevent or treat autoimmune or allergic disorders. Immunomodulation is a complex process involving many cell types notably antigen presenting cells and regulatory T cells (Tregs). In this review, we focus on Treg cells and cholera-like enterotoxins and their non toxic derivates, with regard to subtype, in vivo/in vitro effects and possible role in the modulation of immune responses to coadministered antigens.
Transformation of Schwanniomyces occidentalis with an ADE2 gene cloned from S. occidentalis (1988)

We have developed an efficient transformation system for the industrial yeast Schwanniomyces occidentalis (formerly Schwanniomyces castellii). The transformation system is based on ade2 mutants of S. occidentalis deficient for phosphoribosylaminoimidazole carboxylase that were generated by mutagenesis. As a selectable marker, we isolated and characterized the S. occidentalis ADE2 gene by complementation in an ade2 strain of Saccharomyces cerevisiae. S. occidentalis was transformed with the recombinant plasmid pADE, consisting of a 4.5-kilobase-pair (kbp) DNA fragment from S. occidentalis containing the ADE2 gene inserted into the S. cerevisiae expression vector pYcDE8 by a modification of the spheroplasting procedure of Beggs (J. D. Beggs, Nature [London] 275:104-108, 1978). Intact plasmids were recovered in Escherichia coli from whole-cell lysates of ADE+ transformants, indicating that plasmids were replicating autonomously. High-molecular-mass species of pADE2 were found by Southern hybridization analysis of intact genomic DNA preparations. The shift to higher molecular mass of these plasmids during electrophoresis in the presence ethidium bromide after exposure to shortwave UV suggests that they exist in a supercoiled form in the transformed host. Subclones of the 4.5-kbp insert indicated that ADE2-complementing activity and sequences conferring autonomous replication in S. occidentalis were located within a 2.7-kbp EcoRI-SphI fragment. Plasmids containing this region cloned into the bacterial vector pUC19 complemented ade2 mutants of S. occidentalis with efficiencies identical to those of the original plasmid pADE.
Expression of CD26 and its associated dipeptidyl peptidase IV enzyme activity enhances sensitivity to doxorubicin-induced cell cycle arrest at the G(2)/M checkpoint. (2001)

CD26, a M(r) 110,000 surface-bound ectopeptidase with dipeptidyl peptidase IV (DPPIV) activity, has an array of diverse functional properties, with a role in T-cell physiology and the development of certain human cancers. In this study, we report that surface expression of CD26, through its associated DPPIV enzyme activity, enhanced sensitivity of Jurkat T-cell transfectants to G(2)-M arrest induced by the chemotherapeutic drug, doxorubicin. This was associated with disruption of cell cycle-related events, including hyperphosphorylation and inhibition of p34(cdc2) kinase activity, phosphorylation of cdc25C, and alteration in cyclin B1 expression. In addition, we demonstrate that the addition of exogenous soluble DPPIV enhanced sensitivity of lymphoid tumor cell lines to doxorubicin, suggesting a potentially useful clinical role for CD26/DPPIV in the treatment of selected human hematological malignancies.
Triply periodic bicontinuous structures through interference lithography: a level-set approach (2003)

Interference lithography holds the promise of fabricating large-area, defect-free photonic structures on the sub-micrometer scale both rapidly and cheaply. There is a need for a procedure to establish a connection between the structures that are formed and the parameters of the interfering beams. There is also a need to produce self-supporting three-dimensional bicontinuous structures. A generic technique correlating parameters of the interfering beams with the symmetry elements present in the resultant structures by a level-set approach is developed. A particular space group is ensured by equating terms of the intensity equation to a representative level surface of the desired space group. Single- and multiple-exposure techniques are discussed. The beam parameters for certain cubic bicontinuous structures relevant to photonic crystals, viz.,the diamond(D), the simple cubic (P), and the chiral gyroid (G) are derived by utilizing either linear or elliptically polarized light.
Homogenized Magnetoelastic Behavior Model for the Computation of Strain Due to Magnetostriction in Transformers (2015)

This paper deals with the prediction of the deformation of a multilayer transformer core made of an assembly of anisotropic E-shaped and I-shaped sheets. This magnetomechanical coupled problem is solved by a stepping finite-element method sequential approach: magnetic resolution is followed by mechanical resolution. A 3-D simplified multiscale model describing both magnetic and magnetostrictive anisotropies is used as the constitutive law of the material. The transformer core structure is modeled in 2-D, and a homogenization technique is implemented to take the anisotropic behavior of each layer into consideration and define an average behavior at each element of the finite-element mesh. A three-layer transformer prototype is fabricated with Hi-B grain-oriented iron-silicon alloy. Experimental measurements are carried out and compared with the modeling results. Small discrepancies are observed and discussed.
Studies on the attachment of carbohydrate to ovalbumin nascent chains in hen oviduct. (1976)

We have examined the question, is the carbohydrate moiety of ovalbumin attached to nascent chains or to the completed protein after its release from polyribosomes. Ovalbumin nascent chains have been isolated from hen oviduct by immunoprecipitation of ovalbumin-synthesizing polysomes and subsequent isolation of peptidyl-tRNA by DEAE-cellulose chromatography. Our results indicate that both glucosamine and mannose are incorporated into ovalbumin nascent chains by hen oviduct fragments. Although the asparagine to which the carbohydrates are attached is 10 amino acid residues from the NH2 terminus, the majority of the carbohydrate, if not all, is attached only to those peptide chains that have been essentially completed.
Roentgen: radiation therapy and case-based reasoning (2002)

Roentgen is a case-based aid to radiation therapy planning. It relies on an archive of past therapy cases to suggest plans for new therapy patients. Roentgen supports therapy planning by: (1) retrieving the case which best matches the geometry and treatment constraints of the new patient; (2) tailoring the plan to the specific details of the patient; (3) evaluating the results of applying the plan; and (4) repairing the plan to avoid any discovered faults in treatment results. This final plan is the system's suggestion to the human planner. Roentgen breaks new ground in solving problems in a domain dominated by spatial reasoning and the satisfying of constraints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Opening Wedge Osteotomies for Correction of Hallux Valgus (2009)

Osteotomy of the proximal metatarsal for the correction of moderate to severe hallux valgus deformity is commonly performed. The purpose of this study is to review the early results of a technique for the correction of hallux valgus, an opening wedge osteotomy of the proximal first metatarsal with opening wedge plate fixation. A review was performed of the results of 47 patients (49 feet) who underwent correction of hallux valgus with proximal metatarsal opening wedge osteotomy. All osteotomies were secured with plate fixation on the medial side. Evaluation consisted of preoperative and postoperative radiographic as well as clinical evaluations. Mean corrections of 7 degrees were achieved for the 1-2 intermetatarsal angles. Fourteen complications occurred, 6 of which involved mild hardware irritation and did not affect outcome. Four nonunions or delayed unions were identified. The authors find the opening wedge osteotomy of the proximal first metatarsal to be a technically straightforward procedure for correcting moderate to severe hallux valgus. The correction obtained is comparable to other described techniques.