gebhart/patrepeval huggingface dataset:
Noise-Robust Semi-Supervised Learning by Large-Scale Sparse Coding (2015)

This paper presents a large-scale sparse coding algorithm to deal with the challenging problem of noise-robust semi-supervised learning over very large data with only few noisy initial labels. By giving an L1-norm formulation of Laplacian regularization directly based upon the manifold structure of the data, we transform noise-robust semi-supervised learning into a generalized sparse coding problem so that noise reduction can be imposed upon the noisy initial labels. Furthermore, to keep the scalability of noise-robust semi-supervised learning over very large data, we make use of both nonlinear approximation and dimension reduction techniques to solve this generalized sparse coding problem in linear time and space complexity. Finally, we evaluate the proposed algorithm in the challenging task of large-scale semi-supervised image classification with only few noisy initial labels. The experimental results on several benchmark image datasets show the promising performance of the proposed algorithm.
Measurement of Myeloid Cell Immune Suppressive Activity (2010)

This unit presents simple methods to assess the immunosuppressive properties of immunoregulatory cells of myeloid origin, such as myeloid-derived suppressor cells (MDSCs), both in vitro and in vivo. These methods are general and could be adapted to test the impact of different suppressive populations on T cell activation, proliferation, and cytotoxic activity; moreover they could be useful to assess the influence exerted on immune suppressive pathways by genetic modifications, chemical inhibitors, and drugs.
The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence (1998)

Recently, the DinR protein was established as the cellular repressor of the SOS response in the bacterium Bacillus subtilis. It is believed that DinR functions as the repressor by binding to a consensus sequence located in the promoter region of each SOS gene. The binding site for DinR is believed to be synonymous with the formerly identified Cheo box, a region of 12 bp displaying dyad symmetry (GAAC-N4-GTTC). Electrophoretic mobility shift assays revealed that highly purified DinR does bind to such sites located upstream of the dinA, dinB, dinC, and dinR genes. Furthermore, detailed mutational analysis of the B. subtilis recA operator indicates that some nucleotides are more important than others for maintaining efficient DinR binding. For example, nucleotide substitutions immediately 5' and 3' of the Cheo box as well as those in the N4 region appear to affect DinR binding. This data, combined with computational analyses of potential binding sites in other gram-positive organisms, yields a new consensus (DinR box) of 5'-CGAACRNRYGTTYC-3'. DNA footprint analysis of the B. subtilis dinR and recA DinR boxes revealed that the DinR box is centrally located within a DNA region of 31 bp that is protected from hydroxyl radical cleavage in the presence of DinR. Furthermore, while DinR is predominantly monomeric in solution, it apparently binds to the DinR box in a dimeric state.
Recombinant human erythropoietin in the treatment of cancer-related or chemotherapy-induced anaemia in patients with solid tumours. (1998)

Patients with cancer frequently develop anaemia, due either to the malignant disease itself or to its treatment. Various factors, including the type of malignancy and the type and intensity of chemotherapy, influence the prevalence of anaemia and the need for transfusions. Among patients with solid tumours, those with lung cancer and ovarian cancer are reported to have the highest frequency of anaemia (52% and 51%, respectively) and the highest rate of transfusion requirements (28% and 25%, respectively). Patients with a low level of haemoglobin (Hb) (10-12 g/dl) at the start of chemotherapy are particularly at risk of developing anaemia and requiring transfusions. Similarly, patients treated with platinum-based regimens more often develop anaemia and need transfusions. The frequency of transfusion requirements in these patients can amount to 47%-100%, depending on the cumulative dose of platinum and other risk factors, such as advanced age, loss of body weight before treatment, advanced disease stage, and particularly a low primary level of Hb (11 g/dl) and a decrease in Hb level (1-2 g/dl) after the first cycle of treatment. The causative mechanism of platinum-induced anaemia is reported to be, beside myelosuppression, a deficient production of erythropoietin (EPO) resulting from drug-induced renal tubular damage. In a number of randomised and nonrandomised studies, recombinant human (rh) EPO has been shown to be effective in the treatment of cancer-related anaemia (CRA) and in the prevention and treatment of chemotherapy-induced anaemia. An appropriate dose of rhEPO for the start of treatment is 150 U/kg given subcutaneously three times per week (t.i.w.). The response rate of anaemia ranges from 40% to 85%. rhEPO is well tolerated, but the cost of treatment requires patient selection and parameters predicting response as early as possible after the start of treatment. Appropriate groups of patients for treatment with rhEPO are those with an Hb level of < 10 g/dl and those with a higher Hb level, but symptomatic anaemia. Other groups are patients who are going to receive chemotherapy and have a low primary level of Hb (10-12 g/dl) and patients who receive platinum-based chemotherapy and have experienced a marked decrease in their Hb level (1-2 g/dl) from baseline to the second cycle of treatment. These patients have a high risk of becoming anaemic and requiring transfusions during chemotherapy. In anaemic cancer patients treated with rhEPO, an early indicator of response is an increase in Hb level of at least 0.5 g/dl in patients not receiving chemotherapy and 1 g/dl in those receiving chemotherapy, combined with an increase in reticulocyte count of at least 40,000 cells/microliter after 2 weeks of treatment in the first group of patients and after 4 weeks in the second.
Lysosomal {beta}-mannosidase: cDNA cloning and characterization (1994)

Lysosomal {beta}-mannosidase is an exoglycosidase that cleaves the single {beta}-linked mannose residue from the non-reducing end of all N-linked glycoprotein oligosaccharides. Deficiency of this enzyme results in {beta}-mannosidosis, a severe neurodegenerative disease in goats and cattle. The human cases described have a milder, highly variable presentation. Study of the molecular pathology of this disease in ruminants and humans and development of the animal model for gene therapy studies required cloning of the gene for {beta}-mannosidase has been cloned. {beta}-Mannosidase cDNA were obtained from a bovine thyroid cDNA library by screening with mixed oligonucleotides derived from peptide sequences resulting from microsequencing of bovine {beta}-mannosidase peptides. A total of six independent positive clones were identified from 5 x 10{sup 5} plaques, covering about 80% of the C-terminal region. The missing 5{prime} region was obtained using 5{prime} RACE. The full-length construct contains 3852-bp nucleotides, encoding 879 amino acids. The initiation codon is followed by 17 amino acids containing the characteristics of a typical signal peptide sequence. The deduced amino acid sequence is colinear with all peptide sequences determined by protein microsequencing. Northern blot analysis demonstrated a 4.2 kb single transcript in various tissues from both normal and affected goats and calves. The mRNAmore » level was decreased in affected {beta}-mannosidosis animals. The gene encoding {beta}-mannosidase was localized on human chromosome 4 by Southern analysis of rodent/human somatic cell hybrids. The mutation in bovine {beta}-mannosidosis has been identified. This is the first report of cloning of the {beta}-mannosidase gene.« less
The Triterpenoid RTA 408 is a Robust Mitigator of Hematopoietic Acute Radiation Syndrome in Mice (2015)

Bone marrow suppression due to exposure to ionizing radiation is a significant clinical problem associated with radiation therapy as well as with nonmedical radiation exposure. Currently, there are no small molecule agents available that can enhance hematopoietic regeneration after radiation exposure. Here, we report on the effective mitigation of acute hematopoietic radiation syndrome in mice by the synthetic triterpenoid, RTA 408. The administration of a brief course of RTA 408 treatment, beginning 24 h after lethal doses of radiation to bone marrow, significantly increased overall survival. Importantly, treatment with RTA 408 led to the full recovery of steady state hematopoiesis with normalization of the frequency of hematopoietic stem and progenitor cells. Moreover, hematopoietic stem cells from RTA 408-mitigated mice showed lineage-balanced, long-term, multilineage potential in serial transplantation assays, indicative of their normal self-renewal activity. The potency of RTA 408 in mitigating radiation-induced bone marrow suppression makes it an attractive candidate for potential clinical use in treating both therapy-related and unanticipated radiation exposure.
Drug resistance in multiple myeloma: latest findings and new concepts on molecular mechanisms (2013)

In the era of new and mostly effective therapeutic protocols, multiple myeloma still tends to be a hard-to-treat hematologic cancer. This hallmark of the disease is in fact a sequel to drug resistant phenotypes persisting initially or emerging in the course of treatment. Furthermore, the heterogeneous nature of multiple myeloma makes treating patients with the same drug challenging because finding a drugable oncogenic process common to all patients is not yet feasible, while our current knowledge of genetic/epigenetic basis of multiple myeloma pathogenesis is outstanding. Nonetheless, bone marrow microenvironment components are well known as playing critical roles in myeloma tumor cell survival and environment-mediated drug resistance happening most possibly in all myeloma patients. Generally speaking, however; real mechanisms underlying drug resistance in multiple myeloma are not completely understood. The present review will discuss the latest findings and concepts in this regard. It reviews the association of important chromosomal translocations, oncogenes (e.g. TP53) mutations and deranged signaling pathways (e.g. NFκB) with drug response in clinical and experimental investigations. It will also highlight how bone marrow microenvironment signals (Wnt, Notch) and myeloma cancer stem cells could contribute to drug resistance in multiple myeloma.
General concepts for PCR primer design. (1993)

PCR is a technology born of the modern molecular biology era. The enzyme
Preclinical profile of docetaxel (taxotere): efficacy as a single agent and in combination. (1995)

Docetaxel (Taxotere; Rhône-Poulenc Rorer, Antony, France) is a new taxoid currently being studied in phase II and III clinical trials worldwide, with promising activity in breast cancer. Docetaxel was evaluated as a single agent against against seven mammary tumors, five from mice and two of human origin. Six of the seven models were found to be sensitive to docetaxel, exhibiting regressions of advanced-stage disease in murine models (MA16/C, MA13/C), and long tumor growth delays (Calc18) and cures (MX-1) in human tumor xenografts. In combination studies in tumor-bearing mice, synergism with docetaxel was observed with cyclophosphamide, 5-fluorouracil, etoposide, vinorelbine (Navelbine; Pierre Fabre Oncologie, Boulogne, France), and methotrexate. A similar level of efficacy was obtained in the cases of docetaxel/vincristine and docetaxel/mitomycin C, compared with the activity of the best single agent. Good activity was obtained with the docetaxel/doxorubicin, docetaxel/vinblastine, and docetaxel/cisplatin combinations; however, the activity of these combinations was lower than that of the best agent in the combination when tested in monotherapy. In terms of tolerance, 60% to 70% of the highest nontoxic dose of each agent could be administered in combination, except for vinca alkaloids, in which 80% to 100% of the maximum tolerated dose did not cause additional toxicity. Although docetaxel is a very potent agent when used in monotherapy, the above results suggest that it also will have a key role in clinical combination chemotherapy.
Endothelial–Mesenchymal Transition in Bleomycin-Induced Pulmonary Fibrosis (2009)

The pathological hallmark lesions in idiopathic pulmonary fibrosis are the fibroblastic foci, in which fibroblasts are thought to be involved in the tissue remodeling, matrix deposition, and cross-talk with alveolar epithelium. Recent evidence indicates that some fibroblasts in fibrosis may be derived from bone marrow progenitors as well as from epithelial cells through epithelial-mesenchymal transition. To evaluate whether endothelial cells could represent an additional source for fibroblasts, bleomycin-induced lung fibrosis was established in Tie2-Cre/CAG-CAT-LacZ double-transgenic mice, in which LacZ was stably expressed in pan-endothelial cells. Combined X-gal staining and immunocytochemical staining for type I collagen and alpha-smooth muscle actin revealed the presence of X-gal-positive cells in lung fibroblast cultures from bleomycin-treated mice. To explore the underlying mechanisms, by which loss of endothelial-specific markers and gain of mesenchymal phenotypes could be involved in microvascular endothelial cells, the effects of activated Ras and TGF-beta on the microvascular endothelial cell line MS1 were analyzed. Combined treatment with activated Ras and TGF-beta caused a significant loss of endothelial-specific markers, while inducing de novo mesenchymal phenotypes. The altered expression of these markers in MS1 cells with activated Ras persisted after withdrawal of TGF-beta in vitro and in vivo. These findings are the first to show that lung capillary endothelial cells could give rise to significant numbers of fibroblasts through an endothelial-mesenchymal transition in bleomycin-induced lung fibrosis model.
Capacity of the Gaussian Channel With Memory: The Multivariate Case (1974)

A formula is derived for the capacity of a multi-input, multi-output linear channel with memory, and with additive Gaussian noise. The formula is justified by a coding theorem and converse. The channel model under consideration can represent multipair telephone cable including the effect of far-end crosstalk. For such cable under large signal-to-noise conditions, we show that channel capacity and cable length are linearly related; for small signal-to-noise ratio, capacity and length are logarithmically related. Crosstalk tends to reduce the dependence of capacity on cable length. Moreover, for any channel to which our capacity formula applies, and for large signal-to-noise ratio, there is an asymptotic linear relation between capacity and signal-to-noise ratio with slope independent of the channel transfer function. For small signal-to-noise ratio, capacity and signal-to-noise ratio are logarithmically related. Also provided is a numerical evaluation of the channel capacity formula, using measured parameters obtained from an experimental cable.
Intratumoral echo-guided injection of interleukin-2 and lymphokine-activated killer cells in hepatocellular carcinoma. (1989)

Interleukin-2 has proved to be effective for the intralesional treatment of tumors of the bladder. There are examples in literature of hepatocellular carcinoma (HCC) treatment with lymphokine-activated killer (LAK) cells infused in the hepatic artery. We decided to check the effects of echo-guided intralesional injection of these cells in this disease. We treated 5 patients with inoperable hepatocellular carcinoma, following cirrhosis; in 4 cases the mass had a diameter less than 3 cm (small HCC) while in the remaining case it measured 7 cm. Tumor size remained unchanged in 3 of the 4 small HCC, and increased only slightly in the other (over a period of 10 months). This would appear to indicate that treatment halted neoplasm growth or at least slowed it down. The echo pattern of the lesions changed, with a constant reduction in echogenicity. Finally, in multiple control biopsies, fibrosis, present in only one case before treatment, was found fairly constantly after treatment. There were no significant side effects, apart from slight water retention in one patient. On the basis of our preliminary results, we consider it worthwhile continuing this study to establish the most suitable IL-2 doses and analyze in more detail the modifications induced in the neoplasm.
Coregulator Function: A Key to Understanding Tissue Specificity of Selective Receptor Modulators (2004)

Ligands for the nuclear receptor superfamily control many aspects of biology, including development, reproduction, and homeostasis, through regulation of the transcriptional activity of their cognate receptors. Selective receptor modulators (SRMs) are receptor ligands that exhibit agonistic or antagonistic biocharacter in a cell- and tissue context-dependent manner. The prototypical SRM is tamoxifen, which as a selective estrogen receptor modulator, can activate or inhibit estrogen receptor action. SRM-induced alterations in the conformation of the ligand-binding domains of nuclear receptors influence their abilities to interact with other proteins, such as coactivators and corepressors. It has been postulated, therefore, that the relative balance of coactivator and corepressor expression within a given target cell determines the relative agonist vs. antagonist activity of SRMs. However, recent evidence reveals that the cellular environment also plays a critical role in determining SRM biocharacter. Cellular signaling influences the activity and subcellular localization of coactivators and corepressors as well as nuclear receptors, and this contributes to gene-, cell-, and tissue-specific responses to SRM ligands. Increased understanding of the effect of cellular environment on nuclear receptors and their coregulators has the potential to open the field of SRM discovery and research to many members of the nuclear receptor superfamily.
Experimental demonstration of a hybrid plasmonic transverse electric pass polarizer for a silicon-on-insulator platform (2012)

We experimentally demonstrate a transverse electric (TE)-pass polarizer using the recently proposed hybrid plasmonic waveguide. The device consists of a silicon film separated from a chromium layer by a silica spacer. The device was characterized using a tunable laser in the 1.52-1.58 μm wavelength range. For a 30 μm long polarizer, the extinction ratio in this wavelength range varies from 23 to 28 dB and the insertion loss for the TE mode is 2-3 dB. The device is compact; its fabrication is completely compatible with silicon-on-insulator technology, and its performance compares favorably against previously reported silicon-based integrated optic TE-pass polarizers.
Effects of Structure of β-Cyclodextrin-Containing Polymers on Gene Delivery (2001)

Linear cationic beta-cyclodextrin-based polymers (betaCDPs) are capable of forming polyplexes with nucleic acids and transfecting cultured cells. The betaCDPs are synthesized by the condensation of a diamino-cyclodextrin monomer A with a diimidate comonomer B. In this paper, the effects of polymer structure on polyplex formation, in vitro transfection efficiency and toxicity are elucidated. By comparison of the betaCDPs to polyamidines lacking cyclodextrins, the inclusion of a cyclodextrin moiety in the comonomer A units reduces the IC50s of the polymer by up to 3 orders of magnitude. The spacing between the cationic amidine groups is also important. Different polymers with 4, 5, 6, 7, 8, and 10 methylene units (betaCDP4, 5, 6, 7, 8, and 10) in the comonomer B molecule are synthesized. Transfection efficiency is dependent on comonomer B length with up to 20-fold difference between polymers. Optimum transfection is achieved with the betaCDP6 polymer. In vitro toxicity varied by 1 order of magnitude and the lowest toxicity is observed with betaCDP8. The LD40 of the betaCDP6 to mice is 200 mg/kg, making this polymer a promising agent for in vivo gene delivery applications.
Elliptic Curves for Security (2016)

This memo specifies two elliptic curves over prime fields that offer a high level of practical security in cryptographic applications, including Transport Layer Security (TLS). These curves are intended to operate at the 128-bit and 224-bit security level, respectively, and are generated deterministically based on a list of required properties.
NMR studies of defensin antimicrobial peptides. 1. Resonance assignment and secondary structure determination of rabbit NP-2 and human HNP-1 (1992)

Two-dimensional nuclear magnetic resonance spectroscopy has been used to make resonance assignments of the proton spectra of two defensin antimicrobial peptides, human neutrophil peptide HNP-1 and rabbit neutrophil peptide NP-2. The secondary structures of these peptides were determined from analysis of the proton-proton NOEs and from the positions of slowly exchanging amide protons. Both peptides contain a long stretch of a double-stranded antiparallel beta-sheet in a hairpin conformation that contains a beta-bulge, a short region of triple-stranded beta-sheet, and several tight turns. The NMR results clearly show that HNP-1 forms a dimer or higher order aggregate in solution and that Pro8 exists as a cis peptide bond. The NMR data on these peptides are compared with NMR data for a homologous peptide NP-5 [Bach, A. C., Selsted, M. E., & Pardi, A. (1987) Biochemistry 26, 4389-4397]. Analysis of the conformation-dependent proton chemical shifts shows that it is not possible to confidently judge the structural similarity of the three defensins from chemical shift data alone. However, comparison of the 3JHN alpha coupling constants in NP-2 and NP-5 indicates that the backbone conformations for these peptides are very similar. A more detailed comparison of the solution conformations of the defensins peptides is made in the following paper in this issue where the NMR data are used as input for distance geometry and molecular dynamics calculations to determine the three-dimensional structures of HNP-1 and NP-2.
Collection statistics for fast duplicate document detection (2002)

We present a new algorithm for duplicate document detection that uses collection statistics. We compare our approach with the state-of-the-art approach using multiple collections. These collections include a 30 MB 18,577 web document collection developed by Excite@Home and three NIST collections. The first NIST collection consists of 100 MB 18,232 LA-Times documents, which is roughly similar in the number of documents to the Excite&amp;at;Home collection. The other two collections are both 2 GB and are the 247,491-web document collection and the TREC disks 4 and 5---528,023 document collection. We show that our approach called I-Match, scales in terms of the number of documents and works well for documents of all sizes. We compared our solution to the state of the art and found that in addition to improved accuracy of detection, our approach executed in roughly one-fifth the time.
Very Low Temperature Deposition of Polycrystalline Si Films Fabricated by Hydrogen Dilution with Electron Cyclotron Resonance Chemical Vapor Deposition (1995)

Characteristics of polycrystalline silicon films deposited both on SiO 2 and Corning 7059 glass substrates are presented in this paper. The silicon films were deposited by a hydrogen dilution method using electron cyclotron resonance chemical vapor deposition at 250° C without any thermal or laser annealing. The hydrogen dilution ratio was between 90% and 99%. The geometric configuration and surface morphology of polycrystalline silicon films were studied by atomic force microscopy. The largest grain size of the deposited silicon films, identified by plan-view transmission electron microscopy dark-field imaging, was about 1 µ m. From Raman spectrum, the crystalline fraction of polycrystalline silicon films was identified to be nearly 100%. The polycrystalline silicon was found to be preferentially &lt;111&gt;- and &lt;110&gt;-oriented, from the X-ray diffraction pattern.