gebhart/patrepeval huggingface dataset:
Functional humanization of an anti-CD30 Fab fragment for the immunotherapy of Hodgkin's lymphoma using an in vitro evolution approach (2005)

CD30, the so-called Reed-Sternberg antigen, constitutes a promising cell-specific target for the treatment of Hodgkin's lymphoma. Starting from the previously characterized cognate HRS3 mouse monoclonal antibody, the bacterially produced functional Fab fragment was humanized by grafting the CDRs from the mouse antibody framework on to human immunoglobulin consensus sequences. This procedure led to a 10-fold decreased antigen affinity, which surprisingly was found to be mainly due to the VH domain. To improve the antigen-binding activity, an in vitro evolution strategy was employed, wherein random mutations were introduced into the humanized VH domain by means of error-prone PCR, followed by a filter sandwich Escherichia coli colony screening assay for functional Fab fragments using a recombinant extracellular domain of the CD30 antigen. After three cycles of in vitro affinity maturation, the optimized Fab fragment huHRS3-VH-EP3/1 was identified, which carried four exchanged residues within or close to the VH CDRs and had an affinity that was almost identical with that of the murine HRS3 Fab fragment. The resulting humanized Fab fragment was fully functional with respect to CD30 binding both in ELISA with the recombinant antigen and in FACS experiments with CD30-positive L540CY cells. In the light of the previously successful clinical application of an alphaCD30 x alphaCD16 bispecific mouse quadroma antibody derived from HRS3, the humanized Fab fragment comprises an important step towards the construction of a fully recombinant therapeutic agent. The combination of random mutagenesis and colony filter screening assay that was successfully applied here should be generally useful as a method for the rapid functional optimization of humanized antibody fragments.
Caspase-2 Acts Upstream of Mitochondria to Promote Cytochromec Release during Etoposide-induced Apoptosis (2002)

DNA damage induced by the cancer chemotherapeutic drug etoposide triggers the onset of a series of intracellular events characteristic of apoptosis. Among the early changes observed is the release of cytochrome c from mitochondria, although the mechanism responsible for this effect is unclear. We demonstrate here a role for caspase-2 in etoposide-induced cytochrome c release. In particular, Jurkat T-lymphocytes treated with an irreversible caspase-2 inhibitor, benzyloxycarbonyl-Val-Asp-Val-Ala-Asp-fluoromethyl ketone (z-VDVAD-fmk), or stably transfected with pro-caspase-2 antisense (Casp-2/AS) are refractory to cytochrome c release stimulated by etoposide. Experiments performed using a reconstituted cell-free system indicate that etoposide-induced cytochrome c release by way of caspase-2 occurs independently of cytosolic factors, suggesting that the nuclear pool of pro-caspase-2 is critical to this process. Apart from inhibiting cytochrome c release, undermining caspase-2 activity results in an attenuation of downstream events, such as pro-caspase-9 and -3 activation, phosphatidylserine exposure on the plasma membrane, and DNA fragmentation. Taken together, our data indicate that caspase-2 provides an important link between etoposide-induced DNA damage and the engagement of the mitochondrial apoptotic pathway.
Palladium‐Catalyzed Borylation of Aryl Chlorides: Scope, Applications, and Computational Studies (2007)

From chloride to boronate: Catalysts comprising palladium and biaryl monophosphine ligands provide highly active systems for the borylation of aryl and heteroaryl chlorides (see scheme). Symmetrical and unsymmetrical biaryl products can also be prepared directly from two aryl chlorides without isolation of the intermediate boronate esters. Computational studies provide insight into the roles of the biaryl phosphine ligand and the KOAc base in the catalytic cycle. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701551_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Efficacy of a canarypox virus‐vectored vaccine against feline leukaemia (2003)

Canarypox virus recombinant vaccines have a unique efficacy and safety profile for the vaccinated host because the canarypox virus is non-replicative in mammalian hosts. After the vaccination of a mammalian species, recombinant canarypox viruses express the inserted genes but cannot multiply in the host. They stimulate a strong immune response in the absence of any virus amplification in the host or any viral spread into the environment. A new canarypox-based recombinant vaccine is the canarypox-feline leukaemia virus (FeLV) vaccine (EURIFEL FeLV; Merial) that expresses the FeLV env and gag protective genes. This paper describes experiments which demonstrate that it is effective against any oronasal FeLV challenge. The protection was shown to be solid against an oronasal challenge one year after the initial vaccination, and was effective against a very severe 'in-contact' challenge. Furthermore, the canarypox virus-FeLV vaccine was effective without an adjuvant.
The crystal structure of the amino-terminal pentapeptide of suzukacillin. Occurrence of a four-fold peptide helix (1982)

The monohydrate of the protected amino-terminal pentapeptide of suzukacillin, t-butoxycarbonyl-α-aminoisobutyryl-L-prolyl-L-valyl-α-aminoisobutyryl-L-valine methyl ester, C29H51N5O8, crystallizes in the orthorhombic space group P212121 with a= 10.192, b= 10.440, c= 32.959 Å, and Z= 4. The structure has been solved by direct methods and refined to an R value of 0.101 for 1 827 observed reflections. The molecule exists as a four-fold helix with a pitch of 5.58 Å. The helix is stabilised by N–H ⋯ O hydrogen bonds, two of the 5→1 type (corresponding to the α-helix) and the third of the 4→1 type (310 helix). The carbonyl oxygen of the amino-protecting group accepts two hydrogen bonds, one each from the amide NH groups of the third (4→1) and fourth (5→1) residues. The remaining 5→1 hydrogen bond is between the two terminal residues. The lone water molecule in the structure is hydrogen bonded to carbonyl oxygens of the prolyl residue in one molecule and the non-terminal valyl residue in a symmetry-related molecule.
Stress, Inflammation and the Irritable Bowel Syndrome (1999)

Studies in animals have shown that inflammation of the mucosa of the gastrointestinal tract is accompanied by changes in enteric nerve and smooth muscle function, and in gut motility and sensation. In some instances, these changes persist long after resolution of the mucosal inflammation. Some of these observations have been made in human studies of irritable bowel syndrome (IBS) in patients after an enteric infection or in patients in remission from ulcerative colitis. Stress has also been implicated as a modulator of gastrointestinal inflammation in both animal and human studies. In animals, stress causes a reactivation of previous enteric inflammation and induces the attendant physiological changes. Prior stress also enhances the response to subsequent inflammatory stimuli. In humans, postinfectious IBS tends to occur in patients with psychological profiles similar to those observed in IBS patients and in whom there is a higher incidence of stressful life events just before exposure to the infection. Taken together, these observations link stress and inflammation as a putative pathogenetic mechanism in at least a subset of IBS patients.
Gettering in high resistive float zone silicon wafers for silicon detector applications (1989)

An intrinsic gettering technique for float-zone highly resistive silicon using TCA+O/sub 2/ has been described. The capacitance-voltage technique was used to determine the flat-band voltage and stretch-out of MOS (metal oxide semiconductor) structures made on various oxides. It has found that this intrinsic getting process improves minority-carrier-generation lifetime and SiO/sub 2//Si interface properties, leading to the reduction of leakage current in the p-i-n detector configuration. Direct comparisons of intrinsic gettering and extrinsic gettering using As ion-implantation have been made. Intrinsic gettering has been found to be the dominant process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Maternal immunization to Gov system alloantigens on human platelets (1997)

This report of three cases of maternal alloimmunization to antigens in the Gov system indicates that immunization can occur via placental transfer of antigen and that Gov system alloantibodies may be associated with neonatal alloimmune thrombocytopenia.
Recent advances in the isolation of liver cells (1994)

The development of new and refined separation techniques--including FACS, FFE, CFE and isopyknic gradients--has had a profound impact on the ability of investigators to isolate specific cell types from the liver. Although some of these techniques, such as FFE, may be of limited preparative value, they are nonetheless important analytical tools that detect subtle differences among cell subpopulations. The isolation of highly purified preparations of liver cells in large yields requires the use of more conventional purification methods such as CFE and isopyknic centrifugation. Immunological approaches represent a key development for the isolation of specific liver cell types, especially when they are used in combination with other techniques. Excellent, reliable and relatively simple techniques now exist to isolate highly purified preparations of hepatocytes, cholangiocytes, KCs, SCs, FSC, myofibroblasts and pit cells. Additional work is necessary to refine techniques for the isolation of dendritic cells and lymphocytes.
[Kaposi's sarcoma in a female patient taking corticosteroids for a long time]. (1989)

A 65-year-old female patient has been orally taking corticosteroids (8 pills of prednisolone) for a severe form of bronchial asthma. In 1979 Kaposi's sarcoma was diagnosed for the first time; the diagnosis has been histologically confirmed. Several times the patient has been effectively treated with prospidin. The disease course got worse from 1984 on: the eruptions disseminated and the condition recurred every 2-3 months. This case is remarkable because Kaposi's sarcoma has developed in a patient treated with corticosteroids for asthma for a long time.
Regulation of calcium release by interdomain interaction within ryanodine receptors (2002)

In excitation-contraction (E-C) coupling, various types of activation signals, which are received presumably at the bulky cytoplasmic domain of the ryanodine receptor (RyR), are translated (or transduced) into the opening of the Ca2+ release channel located in the trans-membrane domain of the RyR. In order to elucidate the detailed mechanism of the signal transduction process, it is essential (i) to identify various sub-domains of the RyR that are involved in the Ca2+ channel regulation, (ii) to characterize the events occurring in these sub-domains during the activation process, and (iii) to characterize the modes of active interactions among these sub-domains. Recent developments in the E-C coupling research have provided us with new insight into each of these aspects, as outlined in this review. Of many putative regulatory sub-domains of the RyR, two domains (designated as N-terminal domain and central domain) are particularly interesting, because disease-linked mutations that have occurred in these domains (malignant hyperthermia and central core disease in skeletal muscle, and inheritable cardiac disease) induce abnormal modes of Ca2+ channel regulation. Pieces of evidence accumulated to this date suggest the following hypothesis. The N-terminal and central domains form, at least partly, the interacting domain pair, and unzipping and zipping actions of such domain-pair are involved in the opening and closing actions of the Ca2+ channel, respectively. We also propose that there are local conformational changes in the signal reception domains (e.g. the II-III loop-binding core), and such conformational changes are coupled with the aforementioned actions of the interacting domain pair. It seems that by virtue of such a coordination of the events occurring in various regions of the RyR, the Ca2+ channel can recognize the activation signal received at the cytoplasmic region of the RyR.
Syntheses of isoretronecanol and lupinine (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of isoretronecanol and lupinineTakashi Iwashita, Takenori Kusumi, and Hiroshi KakisawaCite this: J. Org. Chem. 1982, 47, 2, 230–233Publication Date (Print):January 1, 1982Publication History Published online1 May 2002Published inissue 1 January 1982https://pubs.acs.org/doi/10.1021/jo00341a010https://doi.org/10.1021/jo00341a010research-articleACS PublicationsRequest reuse permissionsArticle Views327Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Embajadas. Empleo en precario (2001)

Los empleados laborales de las embajadas espanolas se movilizan para que el Gobierno les reconozca los derechos recogidos en el Estatuto de los Trabajadores
Integrated system identification and PID controller tuning by frequency loop-shaping (2001)

A systematic design methodology for proportional-integral-derivative (PID) controllers is presented. Starting from data sets, a model of the system and its uncertainty bounds are obtained. The parameters of the controller are tuned by a convex optimization algorithm, minimizing a weighted difference between the actual loop transfer function and a target in an /spl Lscr//sub 2///spl Lscr//sub /spl infin// sense. The target selection is guided by the identified model and its uncertainty. The problem of disjoint data sets and/or different models for the same system is also addressed. The method has proved successful in numerous practical cases showing both expediency in controller design and implementation and improved performance over existing controllers.
A phase II study of recombinant human alpha-interferon in advanced hormone-refractory prostate cancer (1992)

To determine the efficacy of recombinant human leukocyte alpha-interferon (IFL-RA) in advanced hormone-refractory prostate cancer, the authors treated 40 patients with IFL-RA administered intramuscularly at a dose of 10 x 10(6) U/m2 three times weekly. Toxicity was substantial and necessitated at least a 50% dose reduction in all but five patients during the first 1-2 months of therapy. No responses were observed in patients with bone metastases, but complete and partial regression of nodal disease were observed in two patients with extraosseous disease (overall response rate, 5%; 95% confidence interval, 0.64-17.75%). The authors conclude that IFL-RA cannot be recommended at this dose and schedule in patients with advanced prostate cancer, but additional study of its use in patients with nodal disease may be warranted.
Heterologous expression of an insecticidal gene from the armed spider (Phoneutria nigriventer) (2008)

Insect-pests are global problems that cause severe damage to crop plants, and their control is commonly based on chemical insecticides. However, negative effects of pesticides on the environment and human health emphasize the necessity to develop alternative methods for insect-pest control. In the present study, a gene coding for the insecticidal peptide TX4(6-1) of the Brazilian armed spider (Phoneutria nigriventer) was cloned in fusion with maltose binding protein (MBP) and expressed in Escherichia coli. The affinity purified protein MBP-GlyTX4 was cleaved with the Xa factor and used for a bioassay against Spodoptera frugiperda and rabbit immunization. Five micrograms GlyTX4 protein injected into the hemocoel of larvae and abdominal cavity of adults produced trembling and uncoordinated movements immediately after injection and all adult insects died after 12h. After two days, larvae became paralyzed and the epidermal color changed to dark brown. Furthermore, the development stage was prolonged for two weeks. Alternatively, slices of maize leaves were imbibed with 15 micrograms of the recombinant protein cleaved with the Xa factor and used as diet for larvae. In this experiment, all larvae died in about 30 minutes. Polyclonal antibodies anti-MBP-GlyTX4 were effective for recognizing MBP and GlyTX4 in whole cell extract from E. coli expressing the recombinant protein.
The interaction of methylene blue, azure B, and thionine with DNA: Formation of complexes with polynucleotides and mononucleotides as model systems (1995)

Abstract The interactions of methylene blue, azure B, and thionine with calf thymus DNA, [poly (dG‐dC)] 2 , [poly(dA‐dT)] 2 , and the constituent mononucleotides 2′‐deoxyguanosine‐5′‐monophosphate(dGMP), 2′‐deoxyadenosine‐5′‐monophosphate(dAMP), 2′‐deoxycytidine‐5′‐monophosphate(dCMP), and thymidine‐5′‐monophosphate(dTMP) have been studied by steady‐state absorption spectroscopy and with equilibrium dialysis. Scatchard plots for binding of the dyes to the nucleic acid polymers were convex downward at low binding ratios, characteristic of intercalation, and binding constants for this mode were calculated under conditions of varying ionic strength. For each of the dyes, binding constants with [poly(dG‐dC)] 2 and [poly(dA‐dT)] 2 were of the same order of magnitude, so that previously reported (G‐C) preferentially is not very marked. At high binding ratios, the Scatchard plots did not return to the abscissa but curved upward, indicative of a weaker cooperative binding mode, occurring under conditions where the dye is in excess, which is suggested to be external stacking of the dye molecules promoted by the polyanion. The dependence of the absorption spectra on added salt demonstrated a shift in the strong binding mode for the three dyes with [poly(dA‐dT)] 2 with increasing ionic strength, while with [poly(dG‐dC)] 2 this does not occur. The dyes were found to bind to purine but not pyrimidine mononucleotides with dGMP and dAMP, 1:1 complexes were formed initially and also 1:2 dye/nucleotide complexes with increasing nucleotide concentrations. Under low salt conditions, binding to dAMP was slightly stronger than to dGMP for the three dyes studied, while at high ionic strength, when the binding constants are significantly lower, all binding constants become very similar. Binding to mononucleotides is suggested to be primarily stabilised by π‐π stacking interactions between the planar dyes and the nucleobases: for thionine and azure B there also appears to be H‐bonds between the exocyclic amines and the sugar–phosphates conferring extra stability. Neither increasing the number of phosphate groups on the nucleotides nor changing from deoxyribose to ribose sugars had any significant effect on the binding constants. © 1995 John Wiley &amp; Sons, Inc.
The central exons of the human MUC2 and MUC6 mucins are highly repetitive and variable in sequence between individuals (2018)

The DNA sequence of the two human mucin genes MUC2 and MUC6 have not been completely resolved due to the repetitive nature of their central exon coding for Proline, Threonine and Serine rich sequences. The exact nucleotide sequence of these exons has remained unknown for a long time due to limitations in traditional sequencing techniques. These are still very poorly covered in new whole genome sequencing projects with the corresponding protein sequences partly missing. We used a BAC clone containing both these genes and third generation sequencing technology, SMRT sequencing, to obtain the full-length contiguous MUC2 and MUC6 tandem repeat sequences. The new sequences span the entire repeat regions with good coverage revealing their length, variation in repeat sequences and their internal organization. The sequences obtained were used to compare with available sequences from whole genome sequencing projects indicating variation in number of repeats and their internal organization between individuals. The lack of these sequences has limited the association of genetic alterations with disease. The full sequences of these mucins will now allow such studies, which could be of importance for inflammatory bowel diseases for MUC2 and gastric ulcer diseases for MUC6 where deficient mucus protection is assumed to play an important role.
A Strain of Enterococcus faecium (18C23) Inhibits Adhesion of Enterotoxigenic Escherichia coli K88 to Porcine Small Intestine Mucus (2000)

Few studies, if any, have addressed the adhesion of enterococci to the intestinal mucosa and their interference with the adhesion of pathogens, although more than 60% of probiotic preparations in the market contain strains of enterococci. The objective of this study was to investigate if Enterococcus faecium 18C23 has the ability to inhibit the adhesion of Escherichia coli K88ac and K88MB to the small intestine mucus of piglets. Approximately 9% of E. faecium 18C23 organisms adhered to the small intestine mucus, and the adhesion was found to be specific. Living E. faecium 18C23 culture efficiently inhibited the adhesion of E. coli K88ac and K88MB to the piglet intestine mucus. Inhibition of the adhesion of E. coli K88ac to the small intestine mucus was found to be dose dependent. Inhibition of >90% was observed when 10(9) CFU or more of living E. faecium 18C23 culture per ml was added simultaneously with E. coli to immobilized mucus. The substances from both the 18C23 cells and the spent culture supernatant contributed to the inhibition of adhesion of E. coli K88 to the small intestine mucus receptors. The inhibiting effect was not solely a pH effect since considerable inhibitory action was demonstrated after neutralizing the mixture or spent culture supernatant to pH 7.0. Part of the inhibition of adhesion of E. coli K88ac by E. faecium 18C23 or its supernatant might occur through steric hindrance.
Mechanism of Lipid Bilayer Disruption by the Human Antimicrobial Peptide, LL-37 (2003)

LL-37 is an amphipathic, alpha-helical, antimicrobial peptide. (15)N chemical shift and (15)N dipolar-shift spectroscopy of site-specifically labeled LL-37 in oriented lipid bilayers indicate that the amphipathic helix is oriented parallel to the surface of the bilayer. This surface orientation is maintained in both anionic and zwitterionic bilayers and at different temperatures and peptide concentrations, ruling out a barrel-stave mechanism for bilayer disruption by LL-37. In contrast, electrostatic factors, the type of lipid, and the presence of cholesterol do affect the extent to which LL-37 perturbs the lipids in the bilayer as observed with (31)P NMR. The (31)P spectra also show that micelles or other small, rapidly tumbling membrane fragments are not formed in the presence of LL-37, excluding a detergent-like mechanism. LL-37 does increase the lamellar to inverted hexagonal phase transition temperature of both PE model lipid systems and Escherichia coli lipids, demonstrating that it induces positive curvature strain in these environments. These results support a toroidal pore mechanism of lipid bilayer disruption by LL-37.