gebhart/patrepeval huggingface dataset:
Arabic Handwritten Word Recognition Using HMMs with Explicit State Duration (2007)

We describe an offline unconstrained Arabic handwritten word recognition system based on segmentation-free approach and discrete hidden Markov models (HMMs) with explicit state duration. Character durations play a significant part in the recognition of cursive handwriting. The duration information is still mostly disregarded in HMM-based automatic cursive handwriting recognizers due to the fact that HMMs are deficient in modeling character durations properly. We will show experimentally that explicit state duration modeling in the HMM framework can significantly improve the discriminating capacity of the HMMs to deal with very difficult pattern recognition tasks such as unconstrained Arabic handwriting recognition. In order to carry out the letter and word model training and recognition more efficiently, we propose a new version of the Viterbi algorithm taking into account explicit state duration modeling. Three distributions (Gamma, Gauss, and Poisson) for the explicit state duration modeling have been used, and a comparison between them has been reported. To perform word recognition, the described system uses an original sliding window approach based on vertical projection histogram analysis of the word and extracts a new pertinent set of statistical and structural features from the word image. Several experiments have been performed using the IFN/ENIT benchmark database and the best recognition performances achieved by our system outperform those reported recently on the same database.
Comparative study of intraoperative mitomycin C and beta irradiation in pterygium surgery (2000)

The intraoperative administration of 0.04% mitomycin C is more effective than beta irradiation as an adjunctive treatment for pterygium surgery in the patient population examined in this study.
RasGAP Shields Akt from Deactivating Phosphatases in Fibroblast Growth Factor Signaling but Loses This Ability Once Cleaved by Caspase-3 (2015)

Fibroblast growth factor receptors (FGFRs) are involved in proliferative and differentiation physiological responses. Deregulation of FGFR-mediated signaling involving the Ras/PI3K/Akt and the Ras/Raf/ERK MAPK pathways is causally involved in the development of several cancers. The caspase-3/p120 RasGAP module is a stress sensor switch. Under mild stress conditions, RasGAP is cleaved by caspase-3 at position 455. The resulting N-terminal fragment, called fragment N, stimulates anti-death signaling. When caspase-3 activity further increases, fragment N is cleaved at position 157. This generates a fragment, called N2, that no longer protects cells. Here, we investigated in Xenopus oocytes the impact of RasGAP and its fragments on FGF1-mediated signaling during G2/M cell cycle transition. RasGAP used its N-terminal Src homology 2 domain to bind FGFR once stimulated by FGF1, and this was necessary for the recruitment of Akt to the FGFR complex. Fragment N, which did not associate with the FGFR complex, favored FGF1-induced ERK stimulation, leading to accelerated G2/M transition. In contrast, fragment N2 bound the FGFR, and this inhibited mTORC2-dependent Akt Ser-473 phosphorylation and ERK2 phosphorylation but not phosphorylation of Akt on Thr-308. This also blocked cell cycle progression. Inhibition of Akt Ser-473 phosphorylation and entry into G2/M was relieved by PHLPP phosphatase inhibition. Hence, full-length RasGAP favors Akt activity by shielding it from deactivating phosphatases. This shielding was abrogated by fragment N2. These results highlight the role played by RasGAP in FGFR signaling and how graded stress intensities, by generating different RasGAP fragments, can positively or negatively impact this signaling.
Loss of Heterozygosity Analysis Using Whole Genome Amplification, Cell Sorting, and Fluorescence-Based PCR (1999)

Loss of heterozygosity (LOH) is a common genetic lesion found in many human neoplasms. Extending investigation of LOH to large-scale clinical and public health science studies has proven difficult because of the small size and cellular and genetic heterogeneity of human neoplasms, in addition to the challenges associated with increasing throughput. Our approach to LOH analysis was developed using clinical biopsy samples from patients with Barrett's esophagus (BE) and uses flow cytometric cell sorting to increase sample purity, whole genome amplification to increase sample amount, and automated fluorescent genotyping to increase sample throughput. This approach allows LOH assessment at 20 loci in DNA extracted from 1000 flow-purified cells while maintaining accurate and reproducible allele ratios compared with the standard method of using genomic DNA. This method of analysis should allow accurate, reproducible determination of allele ratios in a variety of human tumors and premalignant conditions.
Gels from surfactant solutions with densely packed multilamellar vesicles (1995)

Results on surfactant gels containing densely packed multilamellar vesicles are reported. The gels form spontaneously when the bilayers of L alpha or L3 phases of alkyldimethylaminoxide and cosurfactant are charged up by the addition of ionic surfactant or HCl. The rheological behaviour on addition of excess salt was studied by dynamic rheological measurements for systems with surfactants of different chainlengths. Both the storage modulus, G', and the yield stress, sigma y, decay with rising salinity. This effect is caused by the reduction of both the electrical contribution of the bending constants of the bilayers and the compression modulus of the vesicles. The influence of the charge density on the rheological properties was determined. G' and sigma y increase with charge density and reach a plateau that depends on the chainlength of the surfactant. Measurements on samples prepared with waterglycerol mixtures show that the moduli and the yield stress value are independent of the solvent viscosity. Photographs of the surfactant gels that were taken with the interference contrast microscopy technique are presented. They reveal that some of the vesicles are much bigger than expected on the basis of TEM micrographs. The mean size of the vesicles can be estimated on basis of conductivity data. This method yields an average number of 5-6 shells per vesicle and corresponds with the value taken from the electron micrograph. The rheological data are explained with a model that was recently introduced by van der Linden. In connection with a model due to Lekkerkerker for the electric contribution of the bending constant of the bilayers and our own calculations of the osmotic pressure the van der Linden formula yields good results for describing the experimental data.
PLK1, A Potential Target for Cancer Therapy (2016)

Polo-like kinase 1 (PLK1) plays an important role in the initiation, maintenance, and completion of mitosis. Dysfunction of PLK1 may promote cancerous transformation and drive its progression. PLK1 overexpression has been found in a variety of human cancers and was associated with poor prognoses in cancers. Many studies have showed that inhibition of PLK1 could lead to death of cancer cells by interfering with multiple stages of mitosis. Thus, PLK1 is expected to be a potential target for cancer therapy. In this article, we examined PLK1's structural characteristics, its regulatory roles in cell mitosis, PLK1 expression, and its association with survival prognoses of cancer patients in a wide variety of cancer types, PLK1 interaction networks, and PLK1 inhibitors under investigation. Finally, we discussed the key issues in the development of PLK1-targeted cancer therapy.
A 0.3-/spl mu/m CMOS 8-Gb/s 4-PAM serial link transceiver (2000)

An 8-Gb/s 0.3-/spl mu/m CMOS transceiver uses multilevel signaling (4-PAM) and transmit preshaping in combination with receive equalization to reduce intersymbol interference due to channel low-pass effects. High on-chip frequencies are avoided by multiplexing and demultiplexing the data directly at the pads. Timing recovery takes advantage of a novel frequency acquisition scheme and a linear phase-locked loop that achieves a loop bandwidth of 35 MHz, phase margin of 50/spl deg/, and capture range of 20 MHz without a frequency acquisition aid. The transmitted 8 Gb/s data are successfully detected by the receiver after a 10-m coaxial cable. The 2/spl times/2 mm/sup 2/ chip consumes 1.1 W at 8 Gb/s with a 3-V supply.
Association between density of tumor-infiltrating lymphocytes and prognoses of patients with gastric cancer (2018)

The present study revealed that high density of intratumoral CD8 and CD3 T cells were associated with better OS in patients with gastric cancer.
Significance of RGD Loop and C-Terminal Domain of Echistatin for Recognition of αIIbβ3 and αvβ3 Integrins and Expression of Ligand-Induced Binding Site (1997)

Echistatin is a viper venom disintegrin containing RGD loop maintained by disulfide bridges. It binds with a high affinity to αvβ3 and αIIbβ3 and it induces extensive conformational changes in these integrins resulting in expression of ligand-induced binding site (LIBS) epitopes. We investigated the activities of echistatin and its three analogues (R24A, D27W, echistatin 1-41). R24A echistatin did not react with αIIbβ3 and αvβ3 integrins and did not cause LIBS effect. D27W echistatin showed increased binding to αIIbβ3 and decreased binding to αvβ3. This substitution impaired the ability of echistatin to induce LIBS in αvβ3 integrin. Deletion of nine C-terminal amino acids of echistatin decreased its ability to bind αIIbβ3 and inhibit platelet aggregation. Truncated echistatin failed to induce LIBS epitopes on cells transfected with αIIbβ3 and αvβ3 genes. The ability of echistatin 1-41 to compete with binding of vitronectin to immobilized αvβ3 and monoclonal antibody 7E3 to platelets and to VNRC3 cells was decreased, although this analogue, after immobilization, retained its ability to bind purified αvβ3. We propose a hypothesis in which echistatin's RGD loop determines selective recognition of αIIbβ3 and αvβ3 integrin, whereas the C-terminal domain supports its binding to resting integrin and significantly contributes to the expression of LIBS epitope and to conformational changes of the receptor, leading to a further increase of the binding affinity of echistatin and of the inhibitory effect.
Engineering of composite media for shields at microwave frequencies (2006)

Analytical and numerical modeling of composites with an isotropic dielectric base and multiphase conducting inclusions for the development of wideband microwave shields is considered. The model uses Maxwell Garnett formalism for multiphase mixtures. Such composites are required in many engineering applications, including electromagnetic compatibility.
Innate Immune Responses to TREM-1 Activation: Overlap, Divergence, and Positive and Negative Cross-Talk with Bacterial Lipopolysaccharide (2008)

TREM-1 (triggering receptor expressed on myeloid cells-1) is an orphan immunoreceptor expressed on monocytes, macrophages, and neutrophils. TREM-1 associates with and signals via the adapter protein DAP12/TYROBP, which contains an ITAM. TREM-1 activation by receptor cross-linking has been shown to be proinflammatory and to amplify some cellular responses to TLR ligands such as bacterial LPS. To investigate the cellular consequences of TREM-1 activation, we have characterized global gene expression changes in human monocytes in response to TREM-1 cross-linking in comparison to and combined with LPS. Both TREM-1 activation and LPS up-regulate chemokines, cytokines, matrix metalloproteases, and PTGS/COX2, consistent with a core inflammatory response. However, other immunomodulatory factors are selectively induced, including SPP1 and CSF1 (i.e., M-CSF) by TREM-1 activation and IL-23 and CSF3 (i.e., G-CSF) by LPS. Additionally, cross-talk between TREM-1 activation and LPS occurs on multiple levels. Although synergy in GM-CSF protein production is reflected in commensurate mRNA abundance, comparable synergy in IL-1beta protein production is not. TREM-1 activation also attenuates the induction of some LPS target genes, including those that encode IL-12 cytokine family subunits. Where tested, positive TREM-1 outputs are greatly reduced by the PI3K inhibitor wortmannin, whereas this attenuation is largely PI3K independent. These experiments provide a detailed analysis of the cellular consequences of TREM-1 activation and highlight the complexity in signal integration between ITAM- and TLR-mediated signaling.
The chemical consequences of the gradual decrease of the ionic radius along the Ln-series (2019)

In this research, extracellular polymeric substances (EPS), such as EPS flocs and EPS granules , were successfully extracted from activated and aerobic granular sludge, respectively, and tested as bio-based flame retardant materials. Flax fabric was coated by the biopolymeric substances and its flammability was evaluated based on a vertical burning test defined in US Federal Aviation Regulation. Both EPS flocs and EPS granules coated flax fabrics achieved the self-extinguishment due to effective char formation. In particular, the result of the EPS granules coated sample met the aviation requirements for the aircraft interior. Moreover, the presence of carbonated hydroxyapatite was identified in EPS granules char residue by using FTIR and XRD analysis. It can contribute to the self-extinguishing property of the fabric by enhancing char formation. Thermogravimetric analysis also demonstrated that EPS granules coated flax was able to produce greater amount of char residue and its decomposition rate was significantly reduced. This research indicates that there is a great potential to use this biopolymer as a resource for developing high performance bio-inspired flame retardant materials and contribute to a circular economy.
Pyrolysis of the Calcium Salts of Fatty Acids (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrolysis of the Calcium Salts of Fatty AcidsHsien-Liang Hsu, J. O. Osburn, and C. S. GroveCite this: Ind. Eng. Chem. 1950, 42, 10, 2141–2145Publication Date (Print):October 1, 1950Publication History Published online1 May 2002Published inissue 1 October 1950https://pubs.acs.org/doi/10.1021/ie50490a037https://doi.org/10.1021/ie50490a037research-articleACS PublicationsRequest reuse permissionsArticle Views141Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Microfabricated saturated absorption laser spectrometer (2007)

We demonstrate a miniature microfabricated saturated absorption laser spectrometer. The system consists of miniature optics, a microfabricated Rb vapor cell, heaters, and a photodetector, all contained within a volume of 0.1 cm(3). Saturated absorption spectra were measured with a diode laser at 795 nm. They are comparable to signals obtained with standard table-top setups, although the rubidium vapor cell has an interior volume of only 1 mm(3). We discuss the performance and prospects for using such systems as a miniature optical wavelength reference, compatible with transportable instruments.
5‘-Tethered Stilbene Derivatives as Fidelity- and Affinity-Enhancing Modulators of DNA Duplex Stability (2004)

A series of 5'-linked stilbene-DNA conjugates with different substituents in the distal aromatic ring of the stilbene was prepared, and the effect of the modifications on duplex stability was determined via UV-melting curves. A trimethoxystilbene derivative as a 5'-substituent increases duplex melting points by up to 12.2 degrees C per modification. With this alkoxystilbene substituent, terminal mismatches in DNA duplexes lower the melting point by up to 23.4 degrees C over the perfectly matched control, whereas terminal mismatches in unmodified DNA cause melting point depressions of no more than 6.1 degrees C. An aminomethylstilbene substituent linked to an oligopyrrolamide minor groove binder increases the melting point of an all-A/T decamer by up to 32.7 degrees C, thus shifting the melting point into a range typical for duplexes with statistical G/C-content. An affinity- and selectivity-enhancing effect was also observed when the trimethoxystilbene cap was employed on a small DNA microarray. The phosphoramidite of the trimethoxystilbene can be readily employed in automatic DNA synthesis, facilitating the generation of DNA chips with improved fidelity.
Purification and Characterization of NafY (Apodinitrogenase γ Subunit) from Azotobacter vinelandii (2004)

The formation of an active dinitrogenase requires the synthesis and the insertion of the iron-molybdenum cofactor (FeMo-co) into a presynthesized apodinitrogenase. In Azotobacter vinelandii, NafY (also known as gamma protein) has been proposed to be a FeMo-co insertase because of its ability to bind FeMo-co and apodinitrogenase. Here we report the purification and biochemical characterization of NafY and reach the following conclusions. First, NafY is a 26-kDa monomeric protein that binds one molecule of FeMo-co with very high affinity (K(d) approximately equal to 60 nm); second, the NafY-FeMo-co complex exhibits a S = 3/2 EPR signal with features similar to the signals for extracted FeMo-co and the M center of dinitrogenase; third, site-directed mutagenesis of nafY indicates that the His(121) residue of NafY is involved in cofactor binding; and fourth, NafY binding to apodinitrogenase or to FeMo-co does not require the presence of any additional protein. In addition, we have obtained evidence that suggests the ability of NafY to bind NifB-co, an FeS cluster of unknown structure that is a biosynthetic precursor to FeMo-co.
Synthesis and pharmacological characterization in vitro of cyclic enkephalin analogs: effect of conformational constraints on opiate receptor selectivity (1982)

Using a combination of solid-phase and solution methods, we synthesized a series of cyclic [Leu5]enkephalin analogues by substitution of D-alpha, omega-diamino acids in position 2 of the enkephalin sequence and cyclization of the omega-amino group to the C-terminal carboxy group of leucine. Cyclic analogues containing D-alpha, beta-diaminopropionic acid (1), D-alpha, gamma-diaminobutyric acid (2), D-ornithine (3), or D-lysine (4) in position 2 and the [D-Leu5] and [des-Leu5] analogues of 4 (5 and 6) showed, in general, high potency in the guinea pig ileum (GPI) assay and low potency in the mouse vas deferens (MVD) assay. IC50 (MVD)/IC50 (GPI) ratios ranging from 3.1 to 29.4 were obtained, indicating the preference of the cyclic analogues for mu receptors over delta receptors. With two exceptions, preferential affinity for mu receptors is reflected in the Ki ratios determined in parallel binding assays using [3H]naloxone and [3H] [D-Ala2, D-Leu5]enkephalin as mu and delta receptor selective radioligands, respectively. Comparison of the pharmacological profiles of the cyclic analogues 1-4 with those of their corresponding open-chain analogues, [D-Ala2, Leu5]enkephalinamide (1a), [D-Abu2, Leu5]enkephalinamide (2a), [D-Nva2, Leu5]enkephalinamide (3a), and [D-Nle2, Leu5]enkephalinamide (4a), revealed that the pronounced mu character of compounds 1-4 is a direct consequence of the conformational constraints introduced by cyclization. This finding is in agreement with the concept of different conformational requirements of mu- and delta-opiate receptors and raises the possibility of manipulating opiate receptor selectivity by varying the type and degree of conformational restriction.
Effects of Surface Roughness on Self- and Transport Diffusion in Porous Media in the Knudsen Regime (2001)

The effect of surface roughness on Knudsen diffusion in nanoporous media is investigated by means of dynamic Monte Carlo simulations in three-dimensional rough fractal pores. These simulations yield new insight and explain a number of apparent inconsistencies by revealing a striking difference between the roughness dependence of transport diffusion and gradientless (self- or tracer) diffusion. Both analytical and simulation results show a significant roughness dependence of self-diffusion in the Knudsen regime. Transport diffusion, on the other hand, is roughness independent, as the fluxes do not depend on the detailed residence time and molecular trajectories.
DETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES (2014)

BACKGROUND: The development of minimally-invasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital PCR-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. In particular we studied the plasma of 14 medulloblastoma, 13 WHO grade 2-3 glioma and 14 WHO grade IV astrocytoma cases for levels of ctDNA. METHODS: The basis of our approach is to differentiate DNA shed by normal cells from DNA derived from tumor cells. In order to distinguish the two populations of cell-free DNA, we first identify a tumor-specific alteration. We then query for that exact mutation in matching plasma from the same patient to generate a personalized tumor biomarker. Only DNA derived from the tumor will harbor the genetic alteration. We initially use targeted, exomic, or whole genome sequencing to identify sequence or structural alterations in tumor tissues of 410 individuals. DNA was extracted from less than 5 ml of plasma in each case. The majority of plasma samples were queried for levels of ctDNA using a high fidelity next-generation sequencing approach coined Safe-SeqS. RESULTS: We found that at least one tumor-specific mutant molecule could be identified in <5 mL of plasma in >75% of patients with advanced ovarian, colorectal, bladder, gastroesophoageal, pancreatic, breast, melanoma, hepatocellular and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. Approximately 40% of medulloblastoma and 10% of low or high grade glioma cases had detectable levels of ctDNA. In patients with localized non-CNS tumors, ctDNA was detected in 73%, 57%, 48% and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor (EGFR) blockade in 24 colorectal cancer patients who objectively responded to therapy but who subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase (MAPK) pathway. CONCLUSIONS: Taken together, these data suggest that ctDNA is a sensitive, specific and robust biomarker that can be used for a variety of clinical and research purposes in patients with several multiple different types of cancer. For individuals with CNS neoplasms, alternate strategies may need to be developed in order to detect cell-free tumor derived DNA at levels that are clinically meaningful. ABSTRACT CATEGORY: Neuropathology & Tumor Biomarkers.