gebhart/patrepeval huggingface dataset:
On entropy-constrained trellis coded quantization (1994)

An entropy-constrained trellis coded quantization (TCQ) scheme is presented for encoding memoryless sources. A simple 8-state trellis is used to encode the memoryless Gaussian source with mean-squared-error (MSE) performance within about 0.5 dB of the rate-distortion function. This performance is achieved at all non-negative encoding rates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Non-contact optical measurement of lens capsule thickness during simulated accommodation (2005)

Purpose: To non-invasively measure the thickness of the anterior and posterior lens capsule, and to determine if it significantly changes during accommodation. Methods: Anterior and posterior capsule thickness was measured on post-mortem lenses using a non-contact optical system using a focus-detection technique. The optical system uses a 670nm laser beam delivered to a single-mode fiber coupler. The output of the fiber coupler is focused on the tissue surface using an aspheric lens (NA=0.68) mounted on a translation stage with a motorized actuator. Light reflected from the sample surface is collected by the fiber coupler and sent to a photoreceiver connected to a computer-controlled data acquisition system. Optical intensity peaks are detected when the aspheric lens is focused on the capsule boundaries. The capsule thickness is equal to the distance traveled between two peaks multiplied by the capsule refractive index. Anterior and posterior lens capsule thickness measurements were performed on 18 cynomolgus (age average: 6±1 years, range: 4-7 years) eyes, 1 rhesus (age: 2 years) eye, and 12 human (age average: 65±16, range: 47-92) eyes during simulated accommodation. The mounted sample was placed under the focusing objective of the optical system so that the light was incident on the center pole. Measurements were taken of the anterior lens capsule in the unstretched and the stretched 5mm states. The lens was flipped, and the same procedure was performed for the posterior lens capsule. Results: The precision of the optical system was determined to be ±0.5um. The resolution is 4um and the sensitivity is 52dB. The human anterior lens capsule thickness was 6.0±1.2um unstretched and 4.9±0.9um stretched (p=0.008). The human posterior lens capsule was 5.7±1.2um unstretched and 5.7±1.4um stretched (p=0.974). The monkey anterior lens capsule thickness was 5.9±1.9um unstretched and 4.8±1.0um stretched (p=0.002). The monkey posterior lens capsule was 5.9±2.0um unstretched and 5.1±1.3um stretched (p=0.128). Conclusions: The results indicate that the primate anterior lens capsule thickness changes during accommodation.
A Graphene-Enhanced Fiber-Optic Phase Modulator With Large Linear Dynamic Range (2014)

We propose a graphene-based modulator integrated into currently used communication fibers. The graphene is directly built into the core of the fiber to ensure the coupling efficiency. The fiber is deliberately side-polished to enhance the light-graphene interaction. The two-dimensional model analysis method and three-dimensional finite difference time domain method are used to rigorously disclose the light modulation mechanism under the anisotropic graphene modeling, which is merely conducted in previous studies. Based on such a structure, a phase modulator with an arm length of 127 μm is numerically demonstrated with enhanced modulation efficiency. A quasi-linear relation between the phase change and chemical potential of graphene is found theoretically for the first time, providing a large linear dynamic range to control the phase of optical modulation.
Combinatorial Immunotherapy (2012)

Cancer immunotherapy attempts to harness the immune system by breaking tolerance and generating a robust anticancer response. We have recently demonstrated a synergistic enhancement in tumor clearance following therapeutic, dual PD-1 and LAG-3 blockade. Here, we discuss the implications of these findings in the context of future combinatorial immunotherapeutic approaches.
A Universal Expression/Silencing Vector in Plants (2007)

A universal vector (IL-60 and auxiliary constructs), expressing or silencing genes in every plant tested to date, is described. Plants that have been successfully manipulated by the IL-60 system include hard-to-manipulate species such as wheat (Triticum duram), pepper (Capsicum annuum), grapevine (Vitis vinifera), citrus, and olive (Olea europaea). Expression or silencing develops within a few days in tomato (Solanum lycopersicum), wheat, and most herbaceous plants and in up to 3 weeks in woody trees. Expression, as tested in tomato, is durable and persists throughout the life span of the plant. The vector is, in fact, a disarmed form of Tomato yellow leaf curl virus, which is applied as a double-stranded DNA and replicates as such. However, the disarmed virus does not support rolling-circle replication, and therefore viral progeny single-stranded DNA is not produced. IL-60 does not integrate into the plant's genome, and the construct, including the expressed gene, is not heritable. IL-60 is not transmitted by the Tomato yellow leaf curl virus's natural insect vector. In addition, artificial satellites were constructed that require a helper virus for replication, movement, and expression. With IL-60 as the disarmed helper "virus," transactivation occurs, resulting in an inducible expressing/silencing system. The system's potential is demonstrated by IL-60-derived suppression of a viral-silencing suppressor of Grapevine virus A, resulting in Grapevine virus A-resistant/tolerant plants.
EAHP news for January issue (2014)

A new report on medicine shortages experienced in European healthcare systems reveals that over 86% of hospital pharmacists are experiencing difficulties in sourcing medicines with 66% reporting this as a daily or weekly problem. The top-affected areas are medicines to fight infection, cancer drugs and anaesthetics.

The report by the European Association of Hospital Pharmacists (EAHP) surveyed the experiences of over 600 hospital pharmacists in 36 European countries and presented a striking picture of how medicine shortages are affecting the treatment of patients across the continent.

A total of 75% of surveyed hospital pharmacists either agreed or strongly agreed with the statement ‘medicines shortages in my hospital are having a negative impact on patient care’. Consequences for patients included delayed or interrupted chemotherapy treatment, unnecessary experience by patients of side effects, heightened Clostridium difficile risk and …
Tissue‐specific regulatory elements in mammalian promoters (2007)

Transcription factor-binding sites and the cis-regulatory modules they compose are central determinants of gene expression. We previously showed that binding site motifs and modules in proximal promoters can be used to predict a significant portion of mammalian tissue-specific transcription. Here, we report on a systematic analysis of promoters controlling tissue-specific expression in heart, kidney, liver, pancreas, skeletal muscle, testis and CD4 T cells, for both human and mouse. We integrated multiple sources of expression data to compile sets of transcripts with strong evidence for tissue-specific regulation. The analysis of the promoters corresponding to these sets produced a catalog of predicted tissue-specific motifs and modules, and cis-regulatory elements. Predicted regulatory interactions are supported by statistical evidence, and provide a foundation for targeted experiments that will improve our understanding of tissue-specific regulatory networks. In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes.
Hybrid hydrogel sheets that undergo pre-programmed shape transformations (2014)

This communication describes a novel strategy to achieve programmable shape transformation of hybrid hydrogel sheets by modulating both the in-plane and out-of-plane mismatches in mechanical properties. Both our experimental and computational results demonstrate that the shape transformation of hybrid hydrogel sheets shows rich features (e.g., rolling direction, axis, chirality, etc.) and versatile tunability (e.g., via various external stimuli, material properties, pattern geometry, etc.). This work can provide guidance for designing soft materials that are able to undergo more precise and complex shape transformation.
Bryostatin, an activator of the calcium phospholipid-dependent protein kinase, blocks phorbol ester-induced differentiation of human promyelocytic leukemia cells HL-60. (1986)

Phorbol esters bind to and activate a calcium phospholipid-dependent protein kinase (C kinase). Some researchers believe that activation of C kinase is necessary for the induction of phorbol ester biologic effects. Our research indicates that bryostatin, a macrocyclic lactone that binds to the phorbol ester receptor in human polymorphonuclear leukocytes, also binds to this receptor in the human promyelocytic leukemia cell line, HL-60. Bryostatin activates partially purified C kinase from HL-60 cells in vitro, and when applied to HL-60 cells in vivo, it decreases measurable cytoplasmic C kinase activity. Unlike the phorbol esters, bryostatin is unable to induce a macrophage-like differentiation of HL-60 cells; however, bryostatin, in a dose-dependent fashion, blocks phorbol ester-induced differentiation of HL-60 cells and, if applied within 48 hr of phorbol esters, halts further differentiation. These results suggest that activation of the C kinase by some agents is not sufficient for induction of HL-60 cell differentiation and imply that some of the biologic effects of phorbol esters may occur through a more complex mechanism than previously thought.
Polypropylene fiber–matrix bonds in cementitious composites (2000)

Abstract It is known that for creating advanced polyolefin/cement-based composites the polymer surface should be converted into a layer which is compatible with the inorganic component. In this respect, plasma chemistry offers additional solutions to the wet chemistry approach. It has been demonstrated during the last decade that cold plasma-mediated reactions are suitable for etching and surface functionalizing even the most inert polymeric substrates, including Teflon, polypropylene (PP), and polyethylene (PE). In this paper composite preparations from SiCl4-cold plasma and chromic acid-treated fibrillated PP substrates and cement are described. The nature of plasma- and wet chemistry-induced surface functionalization and etching processes was monitored using survey and high-resolution X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), and dynamic water contact angle measurements. It has been demonstrated that the plasma-exposed surfaces result in increased adhesion between the fibers and the cementitious matrix in comparison with the chromic acid-modified fibers. It has been shown that the improved tensile strength values can be related to the treatment-generated polar surface functionalities as well as roughness. Keywords: POLYPROPYLENE FIBERSPLASMAWET-CHEMISTRY TREATMENTCEMENTITIOUS MATRIX
Versatile nitrilases: Nitrile-hydrolysing enzymes (1994)

Nitrilase, which catalyses the hydrolysis of nitriles to the corresponding acids and ammonia, was originally discovered as a plant hormone indoleacetic acid-synthesising enzyme. It is expected to be useful as a catalyst in organic chemical processing, and to have versatile functions in academic and applied fields.
New control scheme for AC-DC-AC converter without DC link electrolytic capacitor (2002)

A novel concept for a static three-phase to three-phase power converter for an AC motor drive with unity power factor and reduced harmonics on the utility line is presented. The power circuit consists of two back-to-back connected six-pulse bridges having only a 5-/spl mu/F ceramic capacitor in the DC link. By controlling the active power balance between two bridges, the DC link voltage can be maintained within a 20-V deviation from the nominal value with the small ceramic capacitor regardless of the load variation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tissue and Serum Mesothelin Are Potential Markers of Neoplastic Progression in Barrett's Associated Esophageal Adenocarcinoma (2012)

Current surveillance methods in Barrett's esophagus are invasive and neither cost-effective nor sensitive. This pilot study suggests that serum mesothelin is a marker of neoplastic transformation in BE and may provide a noninvasive method to improve identification of malignant transformation.
Prostate Cancer Cells Promote Osteoblastic Bone Metastases through Wnts (2005)

Prostate cancer produces painful osteoblastic bone metastases. Although prostate cancer cells produce numerous osteogenic factors, to date, none have been shown to mediate osteoblastic bone metastases in an in vivo model of prostate cancer. Wnts are a large family of proteins that promote bone growth. Wnt activity is antagonized by endogenous proteins including dickkopf-1 (DKK-1). We explored if prostate cancer cells mediate osteoblastic activity through Wnts using DKK-1 as a tool to modify Wnt activity. A variety of Wnt mRNAs were found to be expressed in prostate cancer cell lines and Wnt mRNA expression was increased in primary prostate cancer compared with nonneoplastic prostate tissue. In addition to expressing Wnts, PC-3 prostate cancer cells expressed the Wnt inhibitor DKK-1. To determine if DKK-1 masked Wnt-mediated osteoblastic activity in osteolytic PC-3 cells, the cells were stably transfected with DKK-1 short hairpin RNA. Decreasing DKK-1 enabled PC-3 cells to induce osteoblastic activity, including alkaline phosphatase production and mineralization, in murine bone marrow stromal cells indicating that DKK-1 blocked Wnt-mediated osteoblastic activity in PC-3 cells. Another prostate cancer cell line, C4-2B, induces mixed osteoblastic/osteolytic lesions. To determine if Wnts contribute to C4-2B's ability to induce mixed osteoblastic/osteolytic lesions, C4-2B cells were stably transfected with either empty vector or DKK-1 expression vector to block Wnt activity. The cells were then injected in the tibiae of mice and allowed to grow for 12 weeks. Blocking Wnt activity converted the C4-2B cells to a highly osteolytic tumor. Taken together, these data show that Wnts contribute to the mechanism through which prostate cancer induces osteoblastic activity.
Use of catalytic topoisomerase II inhibitors to probe mechanisms of chemical-induced clastogenicity in Chinese hamster V79 cells (2000)

Determination of the clastogenic potential of new chemical entities, particularly pharmaceuticals, is an important part of the overall safety assessment of such drugs. It is appreciated that clastogenicity can arise from perturbation of many different cellular processes distinct from direct DNA/drug interactions. One such alternative clastogenic process is inhibition of DNA topoisomerase II, during which process the topoisomerase/DNA/drug ternary complex forms stable DNA double-strand breaks (cleavable complex), which become templates for recombinational, mutagenic, and chromosomal fragmentation events. Without extensive experimentation, it is generally not possible to distinguish clastogenicity arising from direct drug/DNA interaction from that arising from inhibition of topoisomerase II. In the present investigation, we demonstrate that specific catalytic inhibitors of DNA topoisomerase II reduce the clastogenicity of topoisomerase poisons but not that arising via non-topoisomerase-dependent mechanisms. In particular, it is shown that catalytic topoisomerase II inhibitors such as chloroquine, sodium azide, and A-74932, as well as certain intercalating agents such as 9-aminoacridine and ethidium bromide, strongly antagonize the formation of micronuclei induced by the DNA gyrase inhibitor clinafloxacin and the antitumor topoisomerase II poison etoposide. These catalytic inhibitors are also shown to antagonize the clastogenicity of experimental compounds and novel pharmaceuticals presumed to be DNA intercalating agents by virtue of their response in a cell-based bleomycin amplification assay. We extend our previous hypothesis, suggesting that the clastogenicity of some nonstructurally alerting drugs may be due to an as yet unappreciated propensity for DNA intercalation. It is further proposed that intercalation-dependent inhibition of DNA topoisomerase II may be responsible for this clastogenicity and that this may be detected in intact mammalian cells with the use of catalytic topoisomerase inhibitors.
Mechanical stimulation prevents osteocyte apoptosis: requirement of integrins, Src kinases, and ERKs (2005)

Osteocytes, former osteoblasts entombed in the bone matrix, form an extensive cell communication network that is thought to detect microdamage and mechanical strains and to transmit signals leading to repair and compensatory bone augmentation or reduction. Bone active hormones and drugs control the integrity of this network by regulating osteocyte apoptosis, which might be a determinant of bone strength. Herein we demonstrate that mechanical stimulation by stretching activates the ERKs, which in turn are responsible for the attenuation of osteocyte apoptosis. The effect of osteocyte stretching is transmitted by integrins and cytoskeletal and catalytic molecules, such as Src kinases. Stretch-induced antiapoptosis also requires nuclear translocation of ERKs and new gene transcription. The evidence linking mechanical stimulation, activation of an integrin/cytoskeleton/Src/ERK signaling pathway, and osteocyte survival provides a mechanistic basis for the profound role of mechanical forces, or lack thereof, on skeletal health and disease.
The Shed Ectodomain of Nr-CAM Stimulates Cell Proliferation and Motility, and Confers Cell Transformation (2005)

Nr-CAM, a cell-cell adhesion molecule of the immunoglobulin-like cell adhesion molecule family, known for its function in neuronal outgrowth and guidance, was recently identified as a target gene of beta-catenin signaling in human melanoma and colon carcinoma cells and tissue. Retrovirally mediated transduction of Nr-CAM into fibroblasts induces cell motility and tumorigenesis. We investigated the mechanisms by which Nr-CAM can confer properties related to tumor cell behavior and found that Nr-CAM expression in NIH3T3 cells protects cells from apoptosis in the absence of serum by constitutively activating the extracellular signal-regulated kinase and AKT signaling pathways. We detected a metalloprotease-mediated shedding of Nr-CAM into the culture medium of cells transfected with Nr-CAM, and of endogenous Nr-CAM in B16 melanoma cells. Conditioned medium and purified Nr-CAM-Fc fusion protein both enhanced cell motility, proliferation, and extracellular signal-regulated kinase and AKT activation. Moreover, Nr-CAM was found in complex with alpha4beta1 integrins in melanoma cells, indicating that it can mediate, in addition to homophilic cell-cell adhesion, heterophilic adhesion with extracellular matrix receptors. Suppression of Nr-CAM levels by small interfering RNA in B16 melanoma inhibited the adhesive and tumorigenic capacities of these cells. Stable expression of the Nr-CAM ectodomain in NIH3T3 cells conferred cell transformation and tumorigenesis in mice, suggesting that the metalloprotease-mediated shedding of Nr-CAM is a principal route for promoting oncogenesis by Nr-CAM.
Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences (1988)

We have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.
The Dominant Epitope ofBorrelia gariniiOuter Surface Protein C Recognized by Sera from Patients with Neuroborreliosis Has a Surface-Exposed Conserved Structural Motif (1998)

Epitope mapping of outer surface protein C (OspC) by using sera from patients with neuroborreliosis led to the identification of one single major immunodominant epitope within the C-terminal 10 amino acid residues. Peptide binding studies and alanine replacement scanning of the C-terminal decapeptide, PVVAESPKKP, revealed a critical role for the PKKP sequence and its terminal carboxyl group for the binding of immunoglobulin M (IgM) antibodies from patients with Lyme borreliosis. Electron microscopy of antibody-labeled spirochetes indicated that the C-terminal region is exposed on the surface of the spirochete. Based on homology to proteins of known function, this region most probably adopts a polyproline II-like helix, which is found in surface-exposed structures involved in protein-protein interactions. This structural motif is highly conserved in Borrelia species causing Lyme borreliosis and subjected to purifying selection. We suggest that the abundance of the C-terminal region of OspC on the surface of B. burgdorferi allows a multimeric high-avidity interaction between the spirochete and surface Igs on B cells. The resulting cross-linking of surface Igs on B cells may induce a T-cell-independent B-cell activation without IgM-to-IgG switching, thus explaining the lack of IgG antibodies to OspC in neuroborreliosis.
On the Preparation of Carbohydrate−Protein Conjugates Using the Traceless Staudinger Ligation (2005)

[reaction: see text] The nature of a linker used for preparing glycoconjugate vaccines is of utmost importance as it may lead to immunogenic biomolecules. We report the conjugation of carbohydrate haptens to protein carriers leading to potential vaccines using the traceless Staudinger ligation. The ligation relies on the selective transfer of a phosphane substituent to an azide to form a native amide bond in the final product upon release of an oxidized phosphane byproduct. We designed new phosphino-functionalized cross-linkers suitable for protein carrier derivatization. We evaluated their utility in preparing conjugates using both synthetic and purified bacterial carbohydrates. The use of a borane-protected phosphane which is deprotected at the time of the ligation reaction led to the best results observed thus far in terms of stability toward oxidation and reactivity.