gebhart/patrepeval huggingface dataset:
<title>Morphology Dependent Contrast Measurements Of Microscopically Textured Germanium Films</title> (1983)

Optical recording characteristics of textured germanium show a systematic variation in the slope of contrast vs writing energy, as a function of sample production parameters. Textured surfaces have been studied for application to optical storage medial and represent an alternative mechanism to the usual ablative hole-opening process. The important advantage of the textured media is that the slope, S=dC/dE, in the contrast, C, vs writing power, E, curve can be easily altered by adopting various etching conditions in the texturing process.
An international, randomized, phase III trial of bacillus Calmette-Guerin (BCG) plus allogeneic melanoma vaccine (MCV) or placebo after complete resection of melanoma metastatic to regional or distant sites (2007)

8508 Background: Active specific immunotherapy with BCG and an allogeneic, melanoma cell vaccine can induce antibody and T-lymphocyte immune responses to numerous antigens expressed by melanoma cells. This study compared overall and disease-free survival in patients receiving BCG plus placebo versus BCG plus MCV. Methods: Between June 1998 and November 2005, 1,656 patients without evidence of residual disease after resection of stage III (n = 1,160) or stage IV (n = 496) melanoma were randomly assigned to the two treatment arms (1:1). BCG was given as an immunologic adjuvant for the first two injections of both MCV and placebo, which thereafter were administered by intradermal injection every two weeks for the next three injections, every month for the remainder of the first year, every two months for the second year and every three months for years three, four and five. Results: Based on the recommendation of the independent Data and Safety Monitoring Board (DSMB), both studies were terminated after the interim analysis. The recommendation was based on a low probability of demonstrating significant improvement in survival of the BCG plus MCV arm if the study had continued to completion of follow-up and final analysis. Conclusions: This is the largest multicenter clinical trial of postoperative adjuvant immunotherapy after resection of melanoma metastatic to regional lymph nodes or distant sites. It is a landmark study not only because it represents the first randomized multicenter trial to use surgical resection as initial therapy for stage IV melanoma patients with up to five metastatic sites, but also because its results demonstrate excellent survival for the entire study population with 42.3% of stage IV and 63.4% of stage III patients projected to be alive at five years. Updated data for survival and immunologic endpoints which show a significant correlation between immune responses and survival will be provided at the meeting. [Table: see text]
Free-space coherent optical communication with orbital angular, momentum multiplexing/demultiplexing using a hybrid 3D photonic integrated circuit (2013)

We demonstrate free-space space-division-multiplexing (SDM) with 15 orbital angular momentum (OAM) states using a three-dimensional (3D) photonic integrated circuit (PIC). The hybrid device consists of a silica planar lightwave circuit (PLC) coupled to a 3D waveguide circuit to multiplex/demultiplex OAM states. The low excess loss hybrid device is used in individual and two simultaneous OAM states multiplexing and demultiplexing link experiments with a 20 Gb/s, 1.67 b/s/Hz quadrature phase shift keyed (QPSK) signal, which shows error-free performance for 379,960 tested bits for all OAM states.
Using dependency order templates to improve generality in translation (2007)

Today's statistical machine translation systems generalize poorly to new domains. Even small shifts can cause precipitous drops in translation quality. Phrasal systems rely heavily, for both reordering and contextual translation, on long phrases that simply fail to match out-of-domain text. Hierarchical systems attempt to generalize these phrases but their learned rules are subject to severe constraints. Syntactic systems can learn lexicalized and unlexicalized rules, but the joint modeling of lexical choice and reordering can narrow the applicability of learned rules. The treelet approach models reordering separately from lexical choice, using a discriminatively trained order model, which allows treelets to apply broadly, and has shown better generalization to new domains, but suffers a factorially large search space. We introduce a new reordering model based on dependency order templates, and show that it outperforms both phrasal and treelet systems on in-domain and out-of-domain text, while limiting the search space.
CD19 is a major B cell receptor–independent activator of MYC-driven B-lymphomagenesis (2012)

PAX5, a B cell-specific transcription factor, is overexpressed through chromosomal translocations in a subset of B cell lymphomas. Previously, we had shown that activation of immunoreceptor tyrosine-based activation motif (ITAM) proteins and B cell receptor (BCR) signaling by PAX5 contributes to B-lymphomagenesis. However, the effect of PAX5 on other oncogenic transcription factor-controlled pathways is unknown. Using a MYC-induced murine lymphoma model as well as MYC-transformed human B cell lines, we found that PAX5 controls c-MYC protein stability and steady-state levels. This promoter-independent, posttranslational mechanism of c-MYC regulation was independent of ITAM/BCR activity. Instead it was controlled by another PAX5 target, CD19, through the PI3K-AKT-GSK3β axis. Consequently, MYC levels in B cells from CD19-deficient mice were sharply reduced. Conversely, reexpression of CD19 in murine lymphomas with spontaneous silencing of PAX5 boosted MYC levels, expression of its key target genes, cell proliferation in vitro, and overall tumor growth in vivo. In human B-lymphomas, CD19 mRNA levels were found to correlate with those of MYC-activated genes. They also negatively correlated with the overall survival of patients with lymphoma in the same way that MYC levels do. Thus, CD19 is a major BCR-independent regulator of MYC-driven neoplastic growth in B cell neoplasms.
Detection of Cytochrome P450 Substrates by Using a Small‐Molecule Droplet Array on an NADH‐Immobilized Solid Surface (2011)

Seeing below the surface: A small-molecule droplet array platform on an NADH-immobilized solid surface and a biotinylated acetophenone derivative were developed to identify the substrate candidates for soluble P450 enzymes of interest. This methodology is thought to be easily applicable to other class I P450 systems, including those that use NADPH as cofactor.
Anti-angiogenic activity of melatonin in advanced cancer patients. (2001)

This study, by showing that melatonin-induced control or the neoplastic growth is associated with a decline in VEGF secretion, would suggest that the pineal hormone may control tumor growth at least in part by acting as a natural anti-angiogenic molecule, with a following opposition or angiogenesis-dependent cancer proliferation.
The in vitro activity of ADAM‐10 is inhibited by TIMP‐1 and TIMP‐3 (2000)

A recombinant soluble form of the catalytic domain of human ADAM-10 was expressed as an Fc fusion protein from myeloma cells. The ADAM-10 was catalytically active, cleaving myelin basic protein and peptides based on the previously described 'metallosheddase' cleavage sites of tumour necrosis factor alpha, CD40 ligand and amyloid precursor protein. The myelin basic protein degradation assay was used to demonstrate that hydroxamate inhibitors of matrix metalloproteinases (MMPs) were also inhibitors of ADAM-10. The natural MMP inhibitors, TIMP-2 and TIMP-4 were unable to inhibit ADAM-10, but TIMP-1 and TIMP-3 were inhibitory. Using a quenched fluorescent substrate assay and ADAM-10 we obtained approximate apparent inhibition constants of 0.1 nM (TIMP-1) and 0.9 nM (TIMP-3). The TIMP-1 inhibition of ADAM-10 could therefore prove useful in distinguishing its activity from that of TACE, which is only inhibited by TIMP-3, in cell based assays.
Direct transfer of cloned genes from bacteria to mammalian cells. (1980)

Induction of a virus infection by cloned simian virus 40 DNA was chosen as a test system to detect transfer of genes from bacteria to cultured mammalian cells. Escherichia coli cells containing a recombinant plasmid with three tandem inserts of simian virus 40 DNA were able to infect CV-1 monkey cells under various conditions. The gene transfer was resistant to DNase I and therefore seems not to occur via free DNA but most likely via uptake of whole bacteria, followed by release of plasmid DNA and generation of infectious circular simian virus 40 DNA in a recombination-excision process. Spontaneous transfer was found to be infrequent, 4 x 10(9) bacteria yielding one infection per 10(7) monkey cells. The frequency was greatly increased by adding bacteria as a calcium phosphate coprecipitate or by fusion of lysozyme-treated bacteria (protoplasts) with monkey cells in the presence of polyethylene glycol. With the latter technique, 10(4) protoplasts gave rise to one infection per 15 monkey cells. Experiments with other cell lines of human, monkey, and mouse origin, and also with bacteria harboring another recombinant plasmid, indicate that DNA transfer from bacteria to mammalian cells is a general phenomenon.
A chip set core for image compression (1990)

Two components for image compression which provide almost all the computational power required by today's efficient codecs for full motion image compression are presented. The first component computes 8*8 discrete-cosine transform and zigzag conversion of coefficient scanning for a pixel rate up to 27 MHz. The second component computes full-search motion estimation for a pixel rate up to 18 MHz. System implementation for image compression is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning and characterization of human papillomavirus type 52 from cervical carcinoma in Indonesia (1991)

Human papillomavirus (HPV) type 52 from a cervical carcinoma in Indonesia was molecularly cloned and characterized. By hybridization with cervical carcinoma DNAs from Indonesian patients, HPV 52 was detected in 3 of 52 cases (6%), whereas HPV 16 and 18 were detected in 8 and 7 cases, respectively (15% and 13%). Sequence analysis revealed that the E6-E7 ORFs contained several DNA binding motifs (Cys-X-X-Cys) like previously sequenced HPVs. The E6 ORF also contained splice donor and acceptor signals, which may allow the expression of E6* protein. The E7 ORF encoded an amino acid sequence that is conserved in some DNA tumor viruses and is involved in binding to Rb protein and in cellular transformation. Transfection of a subgenomic fragment of HPV 52 under the control of a heterologous promoter showed that the E7 ORF alone induced anchorage-independent growth of established rodent cells and immortalized primary rat embryo fibroblasts (REF), and that in cooperation with activated ras, it induced malignant transformation of REF. The E6 ORF also induced, less efficiently, anchorage-independent growth. These results strongly suggest that HPV 52, like HPV 16 and 18, has oncogenic potential.
Realtime control of multiple-focus phased array heating patterns based on noninvasive ultrasound thermography (2010)

We present results from realtime feedback control of single- and multiple-focus phased array heating patterns based on ultrasound thermography. The results illustrate several important aspects of realtime control of phased array heating patterns as they are envisioned to be used in noninvasive, image guided thermal therapy applications. First, complex, multiple focus heating patterns require multi-point, noninvasive temperature feedback that may not be easily available using thermocouple or other invasive probes. Second, multiple-focus pattern synthesis must be optimized to maintain the highest efficiency of the phased array driver in order to achieve the control objectives. This has led to the development of a dynamic power reallocation algorithm for realtime management of the power share of each focus according to maximize its heating rate. Third, realtime integration between the feedback thermography and array driver control with high spatial and temporal resolution is necessary, especially for short exposures used in ablative treatments. These aspects are well illustrated by the results shown: 1) realtime thermography at frame rates up to 100 fps, 2) realtime multiple-focus pattern resynthesis with update rates up to 1000 patterns per second, and 3) an intelligent dynamic power reallocation scheme to distribute the available driving power according to the collective needs of the individual foci in the multiple-focus heating patterns. Without this dynamic power reallocation, the standard multiple-focus pattern synthesis may produce low-efficiency driving patterns that may fail to achieve the control objective at the some or all control points in the heating pattern.
Adherence of ovine and humanBordetella parapertussisto continuous cell lines and ovine tracheal organ culture (2001)

The adherence of ovine and human isolates of Bordetella parapertussis to ovine and human continuous culture cell lines and to ovine tracheal organ culture was compared. Adherence to non-ciliated respiratory continuous culture cells did not reveal any host-specificity of the isolates. In contrast, adherence of ovine B. parapertussis strains to ciliated ovine tracheal organ culture was significantly greater than that of human strains. These results indicate that tracheal organ culture is a useful tool for studying host-specific adherence of B. parapertussis and suggest that adherence of B. parapertussis to ciliated epithelia is species-specific making it unlikely that the transfer of B. parapertussis between humans and sheep will result in an infection.
Isolation and characterization of cDNAs coding for the beta subunit of the high-affinity receptor for immunoglobulin E. (1988)

Among receptors that bind the Fc region of immunoglobulins ("Fc receptors"), only the one with high affinity for immunoglobulin E (IgE) is known to consist of more than a single polypeptide. In addition to the IgE-binding alpha chain, the receptor contains a single beta chain and two, disulfide-linked, gamma chains. From a cDNA library of a rat mucosal mast cell tumor, from which we recently cloned cDNAs coding for the alpha chain, we have now isolated cDNAs coding for the beta subunit. In vitro transcription-translation of the cDNA directed the synthesis of a polypeptide reactive with two distinctive anti-beta monoclonal antibodies and whose molecular weight was identical to that of authentic beta chains. Polyclonal antibodies to beta peptides expressed in Escherichia coli reacted with intact receptors and isolated beta chains. The gene encodes a protein of 243 residues with no leader sequence. A hydropathicity plot suggests that the polypeptide crosses the plasma membrane four times. The epitope recognized by one of the monoclonal antibodies was localized to the NH2 terminus; that by the other was localized to the COOH terminus. Since those antibodies react with membranes and not with intact cells, we suggest that both ends of the beta subunit are cytoplasmic. RNA transfer blots at high stringency failed to reveal mRNA for beta chains in a variety of cells (in particular, monocytes) that do not contain the high-affinity receptor for IgE.
Post-synthetic modification of the metal–organic framework compound UiO-66 (2010)

Post-synthetic modification is a viable route for the introduction of surface sites with new chemical properties in metal–organic framework compounds. Herein we demonstrate that it is possible to perform covalent post-synthetic modifications of the UiO-66–NH2 MOF with four different acid anhydrides. FT-IR is employed to monitor the reactions and the extent of reaction depends on the bulkiness of the anhydrides. For the smallest one, acetic anhydride, 100% conversion to UiO-66–NHCOCH3 was observed.
A Structural and Mechanistic Study of Two Members of Cupin Family Protein (2022)

is a functionally diverse large group of proteins sharing a jelly roll ?-barrel fold. An enzymatic member 3-hydroxyanthranilate-3,4-dioxygenase (HAO) and a non-enzymatic member pirin, which is a human nuclear metalloprotein of unknown function present in all human tissues, were selected for structural and functional studies in this dissertation work. HAO is an important enzyme for tryptophan catabolism and for 2-nitrobenzoic acid biodegradation. In this work, seven catalytic intermediate were captured in HAO single crystals, enabling for the first time a nearly complete structural snapshot viewing of the entire molecular oxygen activation and insertion mechanism in an iron- and O2-depedent enzyme. The rapid catalytic turnover rate was found achieved in large part by protein dynamics that facilitates O2 binding to the catalytic iron, which is bound to the enzyme by a facile 2-His-1-carboxylate ligand motif. An iron storage and chaperon mechanism was also discovered in the bacterial source of this enzyme, which led to a proposed novel biological function of a mononuclear iron-sulfur center. Although human pirin protein shares the same structural fold with HAO, its iron ion is coordinated by a 3-His-1-carboxylate ligand motif. Pirin belongs to a subset of proteins whose members are playing regulatory functions in the superfamily. In this work, pirin is shown to act as a redox sensor for the NF-?B transcription factor, a critical mediator of intracellular signaling that has been linked to cellular responses to pro-inflammatory signals which controls the expression of a vast array of genes involved in immune and stress responses.
291: Novel approach for predicting GVHD reactive T cells using Vβ spectratype analysis of dividing CFSE-labeled T cells from a mixed lymphocyte reaction (2007)

The major complication associated with allogeneic hematopoietic stem cell transplantation (HSCT) is graft-versus-host disease (GVHD), which is mediated by mature T cells in the donor transplant inoculum. Since donor T cells are also important in preventing graft failure, opportunistic infections and leukemia relapses after transplant, it would be highly advantageous to identify and separate T cells with GVHD-reactivity from those capable of mediating graft-versus-leukemia (GVL) responses. In this regard, TCR Vβ repertoire analysis by CDR3-size spectratyping can be a powerful tool to characterize alloreactive T cell responses. As an initial test of this capability, we studied lethal GVHD in the B6 -> CXB-2 MHC-matched, minor histocompatibility antigen disparate murine model to determine the correlation between the in vitro detected alloreactive B6 CD8+ T cell responses and their actual involvement in the development of GVHD upon transfer to lethally irradiated CXB-2 recipients. Previous methods to obtain the Vβ repertoire from responding mixed lymphocyte reactions (MLR) required expansion of the alloreactive cells in secondary stimulation cultures, for a total of 20 days. To significantly shorten this incubation period, in order to eventually adapt this technique for clinical use, we used the fluorescent-based intracellular dye CFSE to label responding cells in a 4-day MLR and fluorescent cell sorting to isolate the divided alloreactive cells that could then be processed for Vβ spectratype analysis. In a comparative study of the predictive value of the Vβ repertoire detected in traditional MLR versus CFSE/MLR, the results indicated that the former approach correlated with 78% of the Vβ CDR3-size skewing patterns observed in mice with B6 -> CXB-2 GVHD, and the CFSE/MLR approach corresponded to 65% of those skewed Vβ families found in vivo. These results suggest that in vitro spectratyping analysis, and particularly the use of CFSE to predict in vivo reactivity, may be a useful technique in eventually guiding the manipulation of the donor T cell inoculum in order to improve the outcome of HSCT.
Use of an anti-pan T-lymphocyte ricin a chain immunotoxin in steroid- resistant acute graft-versus-host disease (1990)

Acute steroid-resistant graft-versus-host disease (AGVHD) after allogeneic bone marrow transplantation is frequently fatal. A new treatment for this T-lymphocyte-mediated condition uses an immunotoxin, H65-RTA, comprised of a monoclonal antibody that recognizes the CD5 lymphocyte differentiation antigen coupled to ricin A chain, a cytotoxic enzyme that inhibits protein synthesis. The safety and efficacy of this lymphocyte-targeted immunotoxin was evaluated in patients with severe AGVHD in a phase I-II dose escalation study with group expansion at the two middle doses. Thirty-four patients received up to 14 daily intravenous infusions of the immunotoxin. The principal side effects were constitutional symptoms such as fatigue and myalgias, and hypoalbuminemia with weight gain was seen at all doses. Thirty-two patients were evaluated for improvement or resolution of disease. Durable complete or partial responses were not dose-related and were seen in 16 patients. Skin GVHD had the highest incidence of response (73%), although improvement or resolution in gastrointestinal tract (45%) and liver (28%) GVHD was also noted. Survival in responding patients was significantly prolonged at all times as compared with those with no response (P = .03). Treatment was associated with a rapid decrease in peripheral blood T lymphocytes, which persisted for greater than 1 month after therapy. Anti-immunotoxin antibodies were seen in 6 of the 23 patients tested; these were of low titer and did not block immunotoxin binding to T cells. Results of this study indicate that anti-T-lymphocyte immunotoxins may form a new class of immunosuppressive agents useful in T-lymphocyte-mediated diseases.
N-acyl-dopamines: novel synthetic CB1 cannabinoid-receptor ligands and inhibitors of anandamide inactivation with cannabimimetic activity in vitro and in vivo (2000)

We reported previously that synthetic amides of polyunsaturated fatty acids with bioactive amines can result in substances that interact with proteins of the endogenous cannabinoid system (ECS). Here we synthesized a series of N-acyl-dopamines (NADAs) and studied their effects on the anandamide membrane transporter, the anandamide amidohydrolase (fatty acid amide hydrolase, FAAH) and the two cannabinoid receptor subtypes, CB(1) and CB(2). NADAs competitively inhibited FAAH from N18TG2 cells (IC(50)=19-100 microM), as well as the binding of the selective CB(1) receptor ligand, [(3)H]SR141716A, to rat brain membranes (K(i)=250-3900 nM). The arachidonoyl (20:4 omega 6), eicosapentaenoyl (20:5 omega 3), docosapentaenoyl (22:5 omega 3), alpha-linolenoyl (18:3 omega 3) and pinolenoyl (5c,9c,12c 18:3 omega 6) homologues were also found to inhibit the anandamide membrane transporter in RBL-2H3 basophilic leukaemia and C6 glioma cells (IC(50)=17.5-33 microM). NADAs did not inhibit the binding of the CB(1)/CB(2) receptor ligand, [(3)H]WIN55,212-2, to rat spleen membranes (K(i)>10 microM). N-arachidonyl-dopamine (AA-DA) exhibited 40-fold selectivity for CB(1) (K(i)=250 nM) over CB(2) receptors, and N-docosapentaenoyl-dopamine exhibited 4-fold selectivity for the anandamide transporter over FAAH. AA-DA (0.1-10 microM) did not displace D1 and D2 dopamine-receptor high-affinity ligands from rat brain membranes, thus suggesting that this compound has little affinity for these receptors. AA-DA was more potent and efficacious than anandamide as a CB(1) agonist, as assessed by measuring the stimulatory effect on intracellular Ca(2+) mobilization in undifferentiated N18TG2 neuroblastoma cells. This effect of AA-DA was counteracted by the CB(1) antagonist SR141716A. AA-DA behaved as a CB(1) agonist in vivo by inducing hypothermia, hypo-locomotion, catalepsy and analgesia in mice (1-10 mg/kg). Finally, AA-DA potently inhibited (IC(50)=0.25 microM) the proliferation of human breast MCF-7 cancer cells, thus behaving like other CB(1) agonists. Also this effect was counteracted by SR141716A but not by the D2 antagonist haloperidol. We conclude that NADAs, and AA-DA in particular, may be novel and useful probes for the study of the ECS.