gebhart/patrepeval huggingface dataset:
Using word dependent transition models in HMM based word alignment for statistical machine translation (2007)

In this paper, we present a Bayesian Learning based method to train word dependent transition models for HMM based word alignment. We present word alignment results on the Canadian Hansards corpus as compared to the conventional HMM and IBM model 4. We show that this method gives consistent and significant alignment error rate (AER) reduction. We also conducted machine translation (MT) experiments on the Europarl corpus. MT results show that word alignment based on this method can be used in a phrase-based machine translation system to yield up to 1% absolute improvement in BLEU score, compared to a conventional HMM, and 0.8% compared to a IBM model 4 based word alignment.
Low Nonfasting Triglycerides and Reduced All-Cause Mortality: A Mendelian Randomization Study (2014)

Genetically reduced concentrations of nonfasting plasma triglycerides are associated with reduced all-cause mortality, likely through reduced amounts of cholesterol in remnant lipoproteins.
Isozyme-specific enzyme inhibitors. 13. S-[5'(R)-['N-triphosphoamino)methyl]adenosyl]-L-homocysteine, a potent inhibitor of rat methionine adenosyltransferases (1987)

A synthesis is described of the title compound and its 5'S epimer, which are two-substrate adducts of adenosine 5'-triphosphate (ATP) and L-methionine (Met) in which the C(5')H2OP system in ATP is replaced by CH(R)CH2NHP [R = L-S(CH2)2CH(NH2)CO2H]. The 5'R epimer was a potent nonselective competitive inhibitor [averaged Ki = 0.32 microM; KM(ATP)/Ki = 440] vs. ATP of the rat M-2 (normal tissue) and M-T (Novikoff ascitic hepatoma) variants of methionine adenosyltransferase. It produced simple noncompetitive inhibition (averaged Ki = 2.7 microM) vs. Met with both variants. The 5'S epimer inhibited M-T competitively vs. ATP, but was 74-fold less effective than the 5'R epimer. Replacement of the homocysteine moiety in the 5'R epimer by hydrogen markedly reduced inhibitory potency, as indicated by Ki values of 14 microM for competitive inhibition vs. ATP and 580 microM for noncompetitive inhibition vs. Met with M-2. The data suggest that the 5'R epimer can interact simultaneously with two enzymic sites. Information on the kinetic mechanism of a human counterpart of M-2 and inhibitor properties of a previously studied Met-ATP adduct are consistent with the view that the two sites might resemble those that interact with the initial products of the reaction, S-adenosylmethionine and triphosphate.
Efficient synthesis of nucleic acids heavily modified with non- canonical ribose 2'-groups using a mutantT7 RNA polymerase (RNAP) (1999)

A T7 RNAP mutant (Y639F) which eliminates discrimination of the chemical character of the NTP ribose 2'-group, facilitates incorporation of non-canonicalsubstrates into nucleic acids. However, transcripts containing a high percentage of non-canonical NMPs are poorly extended due to effects of the 2'-substituents on the transcript:template hybrid conformation. We tested the addition of compounds that stabilize A-type helix geometry to the reaction. High concentrations of polyamines, together with other changes in reaction conditions, greatly increased the synthesis of transcripts heavily substituted with non-canonical ribose 2'-groups. Template structures that facilitate promoter opening increased the efficiency of reactions where non-canonical substrates were incorporated during transcription of +1 to +6.
Studies of mammary carcinoma induced by 7,12-dimethylbenz(a)anthracene administration. (1972)

The experimental production of mammary tumors by administration of 7,12-dimethylbenz(a)anthracene was confirmed. Light microscopic examination of the multiple tumors thus produced showed different histological patterns in the same animal, although all tumors behaved similarly and none metastasized. Both epithelial and myoepithelial cells participated in tumor formation; the stroma also participated actively in tumor formation and growth. Unlike the case in human myoepithelial carcinoma of the breast, the enzyme alkaline phosphatase continued to be reactive on the plasma membrane of the proliferating myoepithelial cells. It is suggested that the lack of metastasis is related to several factors, all of which need further study. These factors include the simultaneous proliferation of myoepithelial and epithelial cells, the persistence of alkaline phosphatase on the plasma membrane of myoepithelial cells, and the infiltration of the tumor by mast cells.
An adaptive graph model for automatic image annotation (2006)

Automatic keyword annotation is a promising solution to enable more effective image search by using keywords. In this paper, we propose a novel automatic image annotation method based on manifold ranking learning, in which the visual and textual information are well integrated. Due to complex and unbalanced data distribution and limited prior information in practice, we design two new schemes to make manifold ranking efficient for image annotation. Firstly, we design a new scheme named the Nearest Spanning Chain (NSC) to generate an adaptive similarity graph, which is robust across data distribution and easy to implement. Secondly, the word-to-word correlations obtained from WordNet and the pairwise co-occurrence are taken into consideration to expand the annotations and prune irrelevant annotations for each image. Experiments conducted on standard Corel dataset and web image dataset demonstrate the effectiveness and efficiency of the proposed method for image annotation.
The Cytotoxic Activity of Ribosome-inactivating Protein Saporin-6 Is Attributed to Its rRNA N-Glycosidase and Internucleosomal DNA Fragmentation Activities (2003)

Saporin-6 produced by the plant Saponaria officinalis belongs to the family of single chain ribosome-inactivating proteins. It potently inhibits protein synthesis in eukaryotic cells, by cleaving the N-glycosidic bond of a specific adenine in 28 S rRNA, which results in the cell death. Saporin-6 has also been shown to be active on DNA and induces apoptosis. In the current study, we have investigated the roles of rRNA depurination and the activity of saporin-6 on genomic DNA in its cytotoxic activity. The role of putative active site residues, Tyr(72), Tyr(120), Glu(176), Arg(179), and Trp(208), and two invariant residues, Tyr(16) and Arg(24), proposed to be important for structural stability of saporin-6, has been investigated in its catalytic and cytotoxic activity. These residues were mutated to alanine to generate seven mutants, Y16A, R24A, Y72A, Y120A, E176A, R179A, and W208A. We show that for the RNA N-glycosidase activity of saporin-6, residues Tyr(16), Tyr(72), and Arg(179) are absolutely critical; Tyr(120) and Glu(176) can be partially dispensed with, whereas Trp(208) and Arg(24) do not appear to be involved in this activity. The residues Tyr(72), Tyr(120), Glu(176), Arg(179), and Trp(208) were found to be essential for the genomic DNA fragmentation activity, whereas residues Tyr(16) and Arg(24) do not appear to be required for the DNA fragmentation. The study shows that saporin-6 possesses two catalytic activities, namely RNA N-glycosidase and genomic DNA fragmentation activity, and for its complete cytotoxic activity both activities are required.
Calcitonin Gene-Related Peptide and Cerebral Blood Vessels: Distribution and Vasomotor Effects (1987)

The innervation of cerebral blood vessels by nerve fibers containing calcitonin gene-related peptide (CGRP) and the vasomotor effects of this peptide are described for a number of different mammalian species. CGRP-immunoreactive nerve fibers were present in the adventitia of cerebral arteries in all species examined (guinea pig, cat, rabbit, rat, and mouse). Numerous perikarya containing CGRP immunoreactivity are demonstrable in the trigeminal ganglion of all species. In the cerebral perivascular nerve fibers and in trigeminal perikarya, CGRP is often colocalized with substance P and neurokinin A. Marked interspecies differences exist both in the density of CGRP-immunoreactive nerve fibers and in the cerebrovascular levels measured with radioimmunoassay. The highest concentrations were observed in cerebral vessels from guinea pigs, the lowest concentration in rabbit vessels, and intermediate levels in the feline and human cerebral vasculature. CGRP is a potent dilator of cerebral arteries in all species examined (human pial, feline middle cerebral, rabbit, guinea pig and rat basilar arteries). The concentration of CGRP eliciting half-maximal responses ranged from 0.4 nM (human pial artery) to 3 nM (rat and rabbit basilar arteries). Pretreatment of cerebral arteries with low concentrations of either substance P (0.1 nM) or neurokinin A (3 nM) attenuated slightly the CGRP-induced relaxations of guinea pig basilar arteries. Calcitonin was found to be a very weak dilator of cerebral arteries from human and guinea pig. Thus, cardiovascular nerve fibers containing CGRP appear to be present in all mammalian species (although to varying degrees) and CGRP is invariably a potent dilator of the cerebral arteries for all species.
Role of the CD22 human B cell antigen in B cell triggering by anti-immunoglobulin. (1988)

As B cells mature during ontogeny the CD22 human differentiation Ag is exported from the cytoplasm onto the membrane. Surface expression is lost in terminal differentiation and after activation. In tonsils, CD22 is expressed on the surface of 60 to 80% of the dense B cells. Some IgM+ dense cells, however, and buoyant in vivo activated B cells are CD22-. This differential expression of CD22 and the finding that an anti-CD22 mAb augmented anti-Ig induced B cell proliferation suggested that CD22 may play a role in B cell activation. In this study we have found that CD22+ but not CD22- B cells could be triggered by anti-IgM or anti-IgD to have increased free intracellular calcium ([Ca2+]i). The presence of CD22 rather than of IgD seems to determine the ability of B cells to respond to anti-Ig with a [Ca2+]i flux. Also the proliferative response to anti-Ig or anti-Ig + B cell growth factor was restricted to the CD22+ population. Anti-CD22 mAb, although not inducing [Ca2+]i on their own after binding to B cells, did augment [Ca2+]i fluxes by anti-Ig when cross-linked. Together these results suggest that CD22 may regulate triggering of B cells through surface Ig perhaps by acting as a "bridge" to transmit an early signal into the cytoplasm.
Expression profiling: DNA arrays in many guises (1999)

DNA arrays have become the preferred method for large-scale expression measurement. Such data are needed in view of the large amounts of sequence data available: expression levels in a number of different tissues or situations provide a first step toward functional characterisation of new entities revealed by DNA sequencing. Although the basic principle of measurement is in all cases based on hybridisation of a mixed probe derived from tissue RNA to large sets of DNA fragments representing many genes, a number of different forms of implementation of this principle are at hand. They are briefly described and compared, emphasizing the important issue of sensitivity and sample requirements and the accessibility of the methods to academic scientists. When these factors are taken into account, it appears that, contrary to a largely prevalent impression, the "best" approach is not necessarily always provided by the widely advertised glass microarrays or oligonucleotide chips.
The MEK1/2 inhibitor, selumetinib (AZD6244; ARRY-142886), enhances anti-tumour efficacy when combined with conventional chemotherapeutic agents in human tumour xenograft models (2012)

The data presented suggests that MEK inhibition in combination with several standard chemotherapeutics or an Aurora B kinase inhibitor is a promising clinical strategy.
Chemical investigation of ceylonese plants. Part VIII. Trapezifolixanthone, a new di-isoprenylated xanthone from the bark of Calophyllum trapezifolium Thw. (Guttiferae) (1974)

From the bark extractives of Calophyllum trapezifolium Thw. calabaxanthone (I), taraxerol, β-simiarenol, β-sitosterol, and a new xanthone, trapezifolixanthone (III) have been isolated. The latter has been shown to be 5,10-dihydroxy-2,2-dimethyl-12-(3-methylbut-2-enyl)pyrano[3,2-b]xanthen-6(2H)-one.
Current Progress in Suicide Gene Therapy for Cancer (2002)

Standard chemotherapeutic agents and ionizing radiation destroy dividing cells. Because tumor cells divide more rapidly than normal cells, there is a therapeutic index in which damage to the cancer cells is maximized while keeping the toxicity to the normal host cells acceptable. Suicide gene therapy strives to deliver genes to the cancer cells, which convert nontoxic prodrugs into active chemotherapeutic agents. With this strategy, the systemically administered prodrug is converted to the active chemotherapeutic agent only in cancer cells, thereby allowing a maximal therapeutic effect while limiting systemic toxicity. A literature search was conducted using the MEDLINE database from 1990 to 2001 to identify articles related to suicide gene therapy for cancer. A number of suicide gene systems have been identified, including the herpes simplex virus thymidine kinase gene, the cytosine deaminase gene, the varicella-zoster virus thymidine kinase gene, the nitroreductase gene, the Escherichia coli gpt gene, and the E. coli Deo gene. Various vectors, including liposomes, retroviruses, and adenoviruses, have been used to transfer these suicide genes to tumor cells. These strategies have been effective in cell culture experiments, laboratory animals, and some early clinical trials. Advances in tissue- and cell-specific delivery of suicide genes using specific promoters will improve the clinical utility of suicide gene therapy.
Chemotherapy for Colorectal Cancer (1994)

Carcinoma of the large bowel, which will afflict over 150,000 Americans this year, is second only to lung cancer as a cause of death from cancer1. Although most patients present with surgically resectable disease, almost half die of the cancer. Radiation therapy has a largely palliative role. In the past, chemotherapy resulted in only infrequent and usually transient shrinkage of the tumor, scarcely justifying the discomforts and costs of the treatment. In recent years, however, there have been some advances. In the discussion that follows, credence is given only to therapeutic claims validated by controlled trials with sufficiently long . . .
Improving Semantic Segmentation via Video Propagation and Label Relaxation (2018)

Semantic segmentation requires large amounts of pixel-wise annotations to learn accurate models. In this paper, we present a video prediction-based methodology to scale up training sets by synthesizing new training samples in order to improve the accuracy of semantic segmentation networks. We exploit video prediction models' ability to predict future frames in order to also predict future labels. A joint propagation strategy is also proposed to alleviate mis-alignments in synthesized samples. We demonstrate that training segmentation models on datasets augmented by the synthesized samples leads to significant improvements in accuracy. Furthermore, we introduce a novel boundary label relaxation technique that makes training robust to annotation noise and propagation artifacts along object boundaries. Our proposed methods achieve state-of-the-art mIoUs of 83.5% on Cityscapes and 82.9% on CamVid. Our single model, without model ensembles, achieves 72.8% mIoU on the KITTI semantic segmentation test set, which surpasses the winning entry of the ROB challenge 2018. Our code and videos can be found at https://nv-adlr.github.io/publication/2018-Segmentation.
Three-dimensional imaging of skin melanoma in vivo by dual-wavelength photoacoustic microscopy (2006)

Dual-wavelength reflection-mode photoacoustic microscopy is used to noninvasively obtain three-dimensional (3-D) images of subcutaneous melanomas and their surrounding vasculature in nude mice in vivo. The absorption coefficients of blood and melanin-pigmented melanomas vary greatly relative to each other at these two optical wavelengths (764 and 584 nm). Using high-resolution and high-contrast photoacoustic imaging in vivo with a near-infrared (764-nm) light source, the 3-D melanin distribution inside the skin is imaged, and the maximum thickness of the melanoma (approximately 0.5 mm) is measured. The vascular system surrounding the melanoma is also imaged with visible light (584 nm) and the tumor-feeding vessels found. This technique can potentially be used for melanoma diagnosis, prognosis, and treatment planning.
Predictive factors of response and survival in myelodysplastic syndrome treated with erythropoietin and G-CSF: the GFM experience (2007)

We analyzed prognostic factors of response, response duration, and possible impact on survival of epoetin alpha, epoetin beta, or darbepoetin alpha (DAR) with or without granulocyte colony-stimulating factor in 403 myelodysplastic syndrome (MDS) patients. Sixty-two percent (40% major and 22% minor) and 50% erythroid responses were seen, and median response duration was 20 and 24 months according to IWG 2000 and 2006 criteria, respectively. Significantly higher response rates were observed with less than 10% blasts, low and int-1 International Prognostic Scoring System (IPSS), red blood cell transfusion independence, serum EPO level less than 200 IU/L, and, with IWG 2006 criteria only, shorter interval between diagnosis and treatment. Significantly longer response duration was associated with major response (IWG 2000 criteria), IPSS low to INT-1, blasts less than 5%, and absence of multilineage dysplasia. Minor responses according to IWG 2000 were reclassified as "nonresponders" or "responders" according to IWG 2006 criteria. However, among those IWG 2000 minor responders, response duration did not differ between IWG 2006 responders and nonresponders. Multivariate adjusted comparisons of survival between our cohort and the untreated MDS cohort used to design IPSS showed similar rate of progression to acute myeloid leukemia in both cohorts, but significantly better overall survival in our cohort, suggesting that epoetin or DAR treatment may have a favorable survival impact in MDS.
Biologically Active Decorin Is a Monomer in Solution (2004)

It has been reported that decorin and its protein core can have molecular masses nearly double the size of those previously published, suggesting a dimeric structure. In this study we tested whether biologically active decorin and its glycoprotein core would form dimers in solution. We used homo- and hetero-bifunctional chemical cross-linking reagents, BS3 and sulfo-SMPB, respectively, as well as glutaraldehyde and found no preferential dimer formation, whether chemical cross-linking was performed in the presence or absence of live cells. Under the same experimental conditions, we easily detected dimers of epidermal growth factor receptor and basic fibroblast growth factor, two glycoproteins known to dimerize. Only at very high cross-linker to decorin molar ratios (2000:1) were trimers and multimers observed, but performing the chemical cross-linking in the presence of a reducing agent abolished these. The elution of decorin protein core in Superose 6 gel chromatography gave masses compatible with monomeric proteins, both before and after denaturation with 2.5 M guanidine HCl. Matrix-assisted laser desorption ionization gave a mass of 44,077 Da for decorin protein core, without any evidence of dimers or oligomers. Extensive oligomerization of the decorin protein core was observed only after dialysis against water and freeze-drying. These oligomers were considered artifacts because they were independent of chemical cross-linking and were resistant to heat denaturation and disulfide-bond reduction. Oligomeric preparations showed markedly reduced biological activity in both phosphorylation and collagen fibrillogenesis assays. Thus, biologically active decorin is a monomer in solution and, as such, is a monovalent ligand for various extracellular matrix proteins, growth factors, and cell surface receptors.
Managing the Privacy and Security of eHealth Data (2015)

The large scale adoption of mobile medicine, supported by an increasing number of medical devices and remote access to health services, correlated with the continuous involvement of the patients in their own healthcare, led to the emergence of tremendous amounts of clinical data. They need to be securely transferred, archived and accessed. This paper refers to a new approach for protecting the privacy and security of clinical data through the use of a state of the art encryption scheme and attribute-based access control authorization framework. As personal medical records are often used by different entities (e.g. Doctors, pharmacists, nurses, etc.), there is a need for different degrees of authorization access for specific parts of the personal dossier. Appropriate cryptographic tools are presented for allowing partial visibility and valid protection on authorized parts for hierarchical privacy protection of eHealth data. The encryption process relies on ARCANA, a security platform developed at ERISCS research laboratory from University Aix-Marseille. It provides the appropriate cryptographic tools for secure hierarchical access to healthcare data. This ensures that the access of various entities to the healthcare data is accurately and hierarchically controlled. The access control framework used in this research is based on XACML, a standard access control decision model specified by OASIS. The applicability and feasibility of XACML-based policies to regulate the access to patient data are demonstrated through SAFAX. SAFAX is a new public authorization framework developed by the Eindhoven University of Technology tested among others on eHealth case studies, in cooperation with Munich University of Applied Sciences. It is envisioned that the usage of data encryption and public authorization solutions to regulate access control on patients clinical data will have a big impact on the patient's trust in electronic healthcare systems and will speed up their large scale adoption.
Dimerization, DNA Binding, and Transactivation Properties of Hypoxia-inducible Factor 1 (1996)

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric basic helix-loop-helix transcription factor that regulates hypoxia-inducible genes including the human erythropoietin (EPO) gene. In this study, we report structural features of the HIF-1alpha subunit that are required for heterodimerization, DNA binding, and transactivation. The HIF-1alpha and HIF-1beta (ARNT; aryl hydrocarbon receptor nuclear translocator) subunits were coimmunoprecipitated from nuclear extracts, indicating that these proteins heterodimerize in the absence of DNA. In vitro-translated HIF-1alpha and HIF-1beta generated a HIF-1/DNA complex with similar electrophoretic mobility and sequence specificity as HIF-1 present in nuclear extracts from hypoxic cells. Compared to 826-amino acid, full-length HIF-1alpha, amino acids 1-166 mediated heterodimerization with HIF-1beta (ARNT), but amino acids 1-390 were required for optimal DNA binding. A deletion involving the basic domain of HIF-1alpha eliminated DNA binding without affecting heterodimerization. In cotransfection assays, forced expression of recombinant HIF-1alpha and HIF-1beta (ARNT) activated transcription of reporter genes containing EPO enhancer sequences with intact, but not mutant, HIF-1 binding sites. Deletion of the carboxy terminus of HIF-1alpha (amino acids 391-826) markedly decreased the ability of recombinant HIF-1 to activate transcription. Overexpression of a HIF-1alpha construct with deletions of the basic domain and carboxy terminus blocked reporter gene activation by endogenous HIF-1 in hypoxic cells.