gebhart/patrepeval huggingface dataset:
Chemical modification allows phallotoxins and amatoxins to be used as tools in cell biology (2012)

Phallotoxins inhibit the dynamics of microfilaments in cells and lead to apoptosis. Due to poor cellular uptake these effects cannot be studied in live cells, even at millimolar toxin concentrations, nor can phalloidin be used for the elimination of tumor cells. Uptake is greatly enhanced by conjugation of phallotoxins to either lipophilic or polycationic moieties, such as oleic acid, polylysine, or Tat-peptide. These conjugates were lethally toxic for cells, e.g., mouse fibroblasts or Jurkat leukemia cells, in the micromolar range. Uptake into cells starts with the attachment of the toxin conjugates to the plasma membrane, followed by endocytosis and, in most cases, cleavage of the toxin from the carrier. Interestingly, the internalization rate of phalloidin into cells was also significantly increased by the fluorescent moiety tetramethylrhodaminyl, as well as by high molecular weight methoxy-polyethyleneglycol, two compounds unknown so far for their uptake-mediating activity. Conjugation to carriers as investigated in this work will allow the use of phallotoxins in experimental cell biology and possibly in tumor therapy. The findings obtained with phallotoxins could be applied also to the family of amatoxins, where α-amanitin, for example, when conjugated to oleic acid was more than 100-fold more toxic for cells than the native toxin. This suggests the possibility of a more general use of the moieties examined here to enhance the uptake of hydrophilic peptides, or drugs, into live cells.
Isotype, VH genes, and antigen-binding analysis of hybridomas from newborn normal BALB/c mice. (1988)

In this study we report on the characterization of a panel of 62 hybridomas generated by fusing unstimulated spleen cells from neonatal (less than 24 hr old) normal BALB/c mice with the non-secreting Sp 2/0 cell line. The vast majority (98%) of these hybridomas secreted Ig but only 20% produced IgM. The isotype of the remaining hybridomas was determined as being IgG2b. Interestingly, when splenocytes from 1-day-old mice were stimulated with LPS for 48 h prior to the fusion event, 84% of the hybridomas were secreting IgM. The hybridoma supernatants were screened either by ELISA or RIA for binding reactivity using a panel of 17 Ag, proportionally divided between self and non-self. A binding reactivity could be assigned in 44% of cases. Of these, 29% were monoreactive, i.e., reactivity occurred with one Ag only, while the remaining 15% were multireactive. The majority (21 of 27) of hybridomas with a defined reactivity were directed against self-Ag. These included autologous red blood cells, DNA, histone H1, thyroglobulin, and Ag of the cell surface of T cells. The frequency of utilization of VH genes was determined using DNA probes for eight VH gene families. While all VH gene families appeared to have been used, one, VH 7183, had a slight but significant (p less than 0.02) higher utilization than expected by random expression. The frequency of all the other VH gene families was not significantly different from random utilization. No correlation was found between Ag reactivity in the supernatants and the utilization of a particular VH gene family. These findings indicate that early in the ontogeny the predominant reactivity of B cells is for self-Ag and, unlike what it is commonly believed, the IgM isotype is not dominant within these endogenously activated B cells at this time of ontogeny when genes from all VH families are utilized.
Adaptation of Hybrid ANN/HMM Models Using Linear Hidden Transformations and Conservative Training (2006)

A technique is proposed for the adaptation of automatic speech recognition systems using hybrid models combining artificial neural networks with hidden Markov models. The application of linear transformations not only to the input features, but also to the outputs of the internal layers is investigated. The motivation is that the outputs of an internal layer represent a projection of the input pattern into a space where it should be easier to learn the classification or transformation expected at the output of the network. A new solution, called conservative training, is proposed that compensates for the lack of adaptation samples in certain classes. Supervised adaptation experiments with different corpora and for different adaptation types are described. The results show that the proposed approach always outperforms the use of transformations in the feature space and yields even better results when combined with linear input transformations
Long-Term Follow-Up Study of Fecal Microbiota Transplantation (FMT) for Ulcerative Colitis (UC) (2012)

Purpose: The etiology of UC is unknown, but likely multifactorial, with the pathogenic role of intestinal flora being increasingly appreciated. FMT restores the diversity of the fecal microbiome in patients with C. difficile infection (CDI), and has resulted in impressive cure rates. The purpose of this study was to determine if FMT in UC results in similar therapeutic benefit. Methods: A long-term follow-up study was performed on the use of FMT in patients with UC. All patients underwent colonoscopic FMT (CFMT) at Montefiore Medical Center in 2010-2012. Six of 6 eligible patients were contacted and completed a questionnaire soliciting pre- and post-FMT and donor data. Results: 33% of patients were men with a mean age of 44 yrs (range: 26-73 yrs). Follow-up was from 3 to 13 months (mean: 6.2 months). First-degree relatives accounted for 33% of donors; the remaining 67% were spouses or otherwise related. All patients underwent one CFMT. After CFMT, our current UC regimen includes self-administered fecal enemas (SAFE) in a tapered and maintenance schedule; only one of our study patients was unable to successfully infuse and retain the SAFE. Although all 6 of our patients reported improvement after CFMT, the degree of benefit varied. Maximal benefit was seen in the subgroup of patients with concomitant CDI (n=2) and newly diagnosed UC in the setting of antibiotic use (n=1). These three patients reported improvement in stool frequency post-CFMT (pre-CFMT: >8 stools/day; post-CFMT: at baseline); resolution of abdominal pain (pre-CFMT: mild-severe; post CFMT: none); abdominal distention (pre-CFMT: none-moderate; post-CFMT: none); and rectal bleeding after CFMT (pre-CFMT: 10%-50% blood; post-CFMT: none). Cessation of oral prednisone was possible in 2 of these 3 patients, however, 1 patient seems to require low-dose daily prednisone (3 mg) in addition to azathiaprine. CFMT was not as effective in the 3 remaining patients, whose UC onset or worsening was not associated with CDI or antibiotic use. When these 3 patients were successfully performing SAFE, they all noted some improvement in stool frequency (pre-CFMT: 12 stools/day; post-FMT: 5 stools/day) and rectal bleeding (pre-CFMT: >50% blood; post-CFMT: none - <10%) post-CFMT. However, symptoms worsened in 1 patient who became unable to successfully infuse and retain the SAFE and in another patient upon tapering of SAFE. Conclusion: In this small group of patients with UC, FMT treatment seemed to effect the best clinical response in patients whose onset of UC was associated with an alteration in the fecal microbiome from antibiotic use or concomitant CDI.
Desynchronizing electrical and sensory coordinated reset neuromodulation (2012)

Coordinated reset (CR) stimulation is a desynchronizing stimulation technique based on timely coordinated phase resets of sub-populations of a synchronized neuronal ensemble. It has initially been computationally developed for electrical deep brain stimulation (DBS), to enable an effective desynchronization and unlearning of pathological synchrony and connectivity (anti-kindling). Here we computationally show for ensembles of spiking and bursting model neurons interacting via excitatory and inhibitory adaptive synapses that a phase reset of neuronal populations as well as a desynchronization and an anti-kindling can robustly be achieved by direct electrical stimulation or indirect (synaptically-mediated) excitatory and inhibitory stimulation. Our findings are relevant for DBS as well as for sensory stimulation in neurological disorders characterized by pathological neuronal synchrony. Based on the obtained results, we may expect that the local effects in the vicinity of a depth electrode (realized by direct stimulation of the neurons' somata or stimulation of axon terminals) and the non-local CR effects (realized by stimulation of excitatory or inhibitory efferent fibers) of deep brain CR neuromodulation may be similar or even identical. Furthermore, our results indicate that an effective desynchronization and anti-kindling can even be achieved by non-invasive, sensory CR neuromodulation. We discuss the concept of sensory CR neuromodulation in the context of neurological disorders.
Securing the border gateway routing protocol (2002)

We analyze the security of the border gateway routing protocol and identify a number of vulnerabilities in its design and the corresponding threats. We then present a set of proposed modifications to the protocol which minimize or eliminate the most significant threats. The innovation we introduce is the protection of the second-to-last information contained in the autonomous path attributes by the digital signatures, and the use of techniques developed for detecting loops in path-finding protocols to verify the selected route's path information. With these techniques we are able to secure full path information in near constant space, and avoid the recursive protection mechanisms previously assumed necessary.
Reverse Transcriptase Template Switching: A SMART™ Approach for Full-Length cDNA Library Construction (2001)

Here, we describe a fast, simple method for constructing full-length cDNA libraries using SMART technology. This novel procedure uses the template-switching activity of Moloney murine leukemia virus (MMLV) reverse transcriptase to synthesize and anchor first-strand cDNA in one step. Following reverse transcription, three cycles of PCR are performed using a modified oligo(dT) primer and an anchor primer to enrich the cDNA population for full-length sequences. Starting with 1 microgram human skeletal muscle poly(A)+ RNA, a cDNA library was constructed that contained 3 x 10(6) independent clones with an average insert size of 2 kb. Sequence analysis of 172 randomly selected clones showed that 77% of cDNA clones corresponding to known genes contained intact open reading frames. The average length of complete open reading frames was 2.4 kb. Furthermore, 86% of the full-length clones retained longer 5' UTR sequences than the longest 5' end deposited in the GenBank database. cDNA libraries generated using this method will be useful for accelerating the collection of mRNA 5' end sequence information, which is currently very limited in GenBank.
Oligomerization is required for the activity of recombinant soluble LOX‐1 (2009)

LOX-1 is a scavenger receptor that functions as the primary receptor for oxidized low-density lipoprotein (OxLDL) in endothelial cells. The binding of OxLDL to LOX-1 is believed to lead to endothelial activation, dysfunction, and injury, which constitute early atherogenic events. Because of its potential pathological role in atherosclerosis, LOX-1 has been proposed as a therapeutic target for the treatment of this disease. In order to antagonize the ligand-binding function of cell surface LOX-1, we generated a series of recombinant human LOX-1-crystallizable fragment (Fc) fusion proteins and subsequently characterized their biochemical properties and ligand-binding activities in vitro. Consistent with the notion that oligomerization of cell surface LOX-1 is required for high-avidity binding of ligands, we found that LOX-1-Fc fusion protein containing four ligand-binding domains per Fc dimer, but not the one containing two ligand-binding domains, exhibited ligand-binding activity. Optimal ligand-binding activity could be achieved via crosslinking of LOX-1-Fc fusion proteins with a polyclonal antibody against Fc. The crosslinked LOX-1-Fc protein also effectively inhibited the binding and internalization of OxLDL by cell surface LOX-1. These findings demonstrate that functional oligomerization is required for recombinant LOX-1-Fc to function as an effective antagonist.
Diarylureas are small-molecule inhibitors of insulin-like growth factor I receptor signaling and breast cancer cell growth (2006)

In breast and certain other cancers, receptor tyrosine kinases, including the insulin-like growth factor I receptor (IGF-IR), play an important role in promoting the oncogenic process. The IGF-IR is therefore an important target for developing new anti-breast cancer therapies. An initial screening of a chemical library against the IGF-IR in breast cancer cells identified a diaryl urea compound as a potent inhibitor of IGF-IR signaling. This class of compounds has not been studied as inhibitors of the IGF-IR. We studied the effectiveness of one diaryl urea compound, PQ401, at antagonizing IGF-IR signaling and inhibiting breast cancer cell growth in culture and in vivo. PQ401 inhibited autophosphorylation of the IGF-IR in cultured human MCF-7 cells with an IC50 of 12 micromol/L and autophosphorylation of the isolated kinase domain of the IGF-IR with an IC50 <1 micromol/L. In addition, PQ401 inhibited the growth of cultured breast cancer cells in serum at 10 micromol/L. PQ401 was even more effective at inhibiting IGF-I-stimulated growth of MCF-7 cells (IC50, 6 micromol/L). Treatment of MCF-7 cells with PQ401 was associated with a decrease in IGF-I-mediated signaling through the Akt antiapoptotic pathway. Twenty-four hours of treatment with 15 micromol/L PQ401 induced caspase-mediated apoptosis. In vivo, treatment with PQ401 (i.p. injection thrice a week) reduced the growth rate of MCNeuA cells implanted into mice. These studies indicate that diaryl urea compounds are potential new agents to test in the treatment of breast and other IGF-I-sensitive cancers.
Immunomodulatory Therapy in Ophthalmology – Is There a Place for Topical Application? (2004)

Topical corticosteroids, although effective in the treatment of ocular immune-mediated diseases, are well known for their ocular side-effects. Not surprisingly, a variety of alternative immunomodulatory agents have been tested for topical use including cyclosporin A (CsA), mycophenolate mofetil (MMF), tacrolimus (FK506), rapamycin (sirolimus) and leflunomide. Local application bears the possibility to avoid the severe side-effects of systemic therapy. The effect of topical therapy is naturally restricted to local immune response mechanisms, such as antigen presentation by Langerhans and dendritic cells. Moreover, many immunomodulatory agents (e.g. CsA) are lipophilic and thus have low water solubility and penetrate insufficiently intra-ocularly, often being stored in the lipophilic corneal epithelial barrier. Therefore, the therapeutical success is limited for intra-ocular immune-mediated diseases like anterior uveitis. However, a multitude of strategies have been introduced to circumvent these problems including complexing substances such as cyclodextrins (CDs) and liposomes. In the prevention and treatment of transplant rejection after keratoplasty, many attempts to introduce topical immunomodulatory therapy have failed; on the other hand, further therapeutic options not primarily expected are being evaluated today such as treatment of severe keratoconjunctivitis sicca. In our own studies, we investigated the pharmacokinetics of topical treatment with different agents including MMF and evaluated the efficacy of topical treatment in animal models for uveitis and keratoplasty. Taken together, topical immunomodulatory therapy will not replace systemic therapy but further treatment options can be expected.
Diimide reduction of porphyrins (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiimide reduction of porphyrinsHoward W. Whitlock Jr., R. Hanauer, M. Y. Oester, and B. K. BowerCite this: J. Am. Chem. Soc. 1969, 91, 26, 7485–7489Publication Date (Print):December 1, 1969Publication History Published online1 May 2002Published inissue 1 December 1969https://doi.org/10.1021/ja01054a044Request reuse permissionsArticle Views1565Altmetric-Citations256LEARN 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 InReddit PDF (664 KB) Get e-Alertsclose Get e-Alerts
Human nevocellular nevus cells are surrounded by basement membrane components. Immunohistologic studies of human nevus cells and melanocytes in vivo and in vitro. (1988)

Dermal nevus cells in the skin are surrounded by electron-dense deposits resembling a basement membrane (BM), and epidermal melanocytes rest on the epidermal BM. Using antibodies directed against various BM components, we have determined that the BM-like structure surrounding nevus cells in vivo contains type IV collagen, laminin, and BM-1 proteoglycan, analogous to BM throughout the body, but not bullous pemphigoid antigen or epidermolysis bullosa acquisita antigen that are keratinocyte-associated proteins present in the epidermal BM. Moreover, in vitro, both nevus cells and melanocytes derived from adult donors display intracellular and extracellular fibronectin, BM-1 proteoglycan, type IV collagen, and laminin. In contrast, newborn melanocytes maintained under identical culture conditions display none of these BM components, emphasizing the influence of donor age on cell behavior. The data suggest that dermal nevus cells manufacture a BM in vivo, as do certain other neural crest-derived cells. The apparent shared ability of cultured nevus cells and melanocytes to synthesize BM components, coupled with other previously noted behavioral and morphologic similarities in vitro, suggests that these cell types are very closely related; and that morphologic or histochemical differences present in vivo are the result of environmental influences rather than intrinsic differences.
Hyper IgM syndrome associated with defective CD40-mediated B cell activation. (1994)

Recent studies show that most patients with X-linked hyper IgM syndrome have defects in the gene for CD40 ligand. We evaluated 17 unrelated males suspected of having X-linked hyper IgM syndrome. Activated T cells from 13 of the 17 patients failed to bind a soluble CD40 construct. In these patients, the sequence of CD40 ligand demonstrated mutations. By contrast, T cells from the remaining four patients exhibited normal binding to the CD40 construct. Sequencing of the cDNA for CD40 ligand from these patients did not show mutations. The possibility that hyper IgM syndrome in these four patients was due to abnormalities in the B cell response to CD40-mediated signals was examined. Peripheral blood lymphocytes were stimulated with anti-CD40 alone, IL4 alone or anti-CD40 plus IL4. In comparison with B cells from controls or patients with hyper IgM syndrome and mutant CD40 ligand, B cells from the patients with hyper IgM syndrome and normal CD40 ligand were defective in their ability to secrete IgE (P < 0.02) or express activation markers, CD25 and CD23 (P < 0.02) in response to stimulation with anti-CD40. The failure of these B cells to respond to CD40-mediated activation could not be attributed to a generalized deficiency in B cell activation because IL4 induced normal up-regulation of CD23 and CD25 expression. These findings indicate that hyper IgM syndrome may result from defects in expression of CD40 ligand by activated T cells or defects in CD40-mediated signal transduction in B cells.
Structural and energetic evidence for highly peptide-specific tumor antigen targeting via allo-MHC restriction (2011)

Immunotherapies targeting peptides presented by allogeneic MHC molecules offer the prospect of circumventing tolerance to key tumor-associated self-antigens. However, the degree of antigen specificity mediated by alloreactive T cells, and their ability to discriminate normal tissues from transformed cells presenting elevated antigen levels, is poorly understood. We examined allorecognition of an HLA-A2-restricted Hodgkin's lymphoma-associated antigen and were able to isolate functionally antigen-specific allo-HLA-A2-restricted T cells from multiple donors. Binding and structural studies, focused on a prototypic allo-HLA-A2-restricted T-cell receptor (TCR) termed NB20 derived from an HLA-A3 homozygote, suggested highly peptide-specific allorecognition that was energetically focused on antigen, involving direct recognition of a distinct allopeptide presented within a conserved MHC recognition surface. Although NB20/HLA-A2 affinity was unremarkable, TCR/MHC complexes were very short-lived, consistent with suboptimal TCR triggering and tolerance to low antigen levels. These data provide strong molecular evidence that within the functionally heterogeneous alloreactive repertoire, there is the potential for highly antigen-specific "allo-MHC-restricted" recognition and suggest a kinetic mechanism whereby allo-MHC-restricted T cells may discriminate normal from transformed tissue, thereby outlining a suitable basis for broad-based therapeutic targeting of tolerizing tumor antigens.
Trifluoroacetic acid-catalyzed 1,3-cycloaddition of the simplest iminium ylide leading to 3- or 3,4-substituted pyrrolidines and 2,5-dihydropyrroles. (1985)

The 1, 3-dipolar cycloaddition of an intermediary iminium ylide formed from N-benzyl-N-(methoxymethyl) trimethylsilylmethylamine to conjugated olefinic and acetylenic dipolarophiles in the presence of a catalytic amount of trifluoroacetic acid has been found to give 3-or 3, 4-substituted pyrrolidines and 2, 5-dihydropyrroles.
Hemophilia as a defect of the tissue factor pathway of blood coagulation: effect of factors VIII and IX on factor X activation in a continuous-flow reactor. (1990)

The effect of factors VIII and IX on the ability of the tissue factor-factor VIIa complex to activate factor X was studied in a continuous-flow tubular enzyme reactor. Tissue factor immobilized in a phospholipid bilayer on the inner surface of the tube was exposed to a perfusate containing factors VIIa, VIII, IX, and X flowing at a shear rate of 57, 300, or 1130 sec-1. Factor Xa in the effluent was determined by chromogenic assay. The flux of factor Xa (moles formed per unit surface area per unit time) was strongly dependent on wall shear rate, increasing about 3-fold as wall shear rate increased from 57 to 1130 sec-1. The addition of factors VIII and IX at their respective plasma concentrations resulted in a further 2- to 3-fold increase. The direct activation of factor X by tissue factor-factor VIIa could be virtually eliminated by the lipoprotein-associated coagulation inhibitor; however, when factors VIII and IX were present at their approximate plasma concentrations, factor Xa production rates were enhanced 15- to 20-fold. These results suggest that the tissue factor pathway, mediated through factors VIII and IX, produces significant levels of factor Xa even in the presence of an inhibitor of the tissue factor-factor VIIa complex; moreover, the activation is dependent on local shear conditions. These findings are consistent both with a model of blood coagulation in which initiation of the system results from tissue factor and with the bleeding observed in hemophilia.