gebhart/patrepeval huggingface dataset:
Identification of multiple proteins expressed in murine embryos as binding partners for the WW domains of the ubiquitin-protein ligase Nedd4 (2000)

Nedd4 is a member of a growing family of ubiquitin-protein ligases which consist of a lipid-binding domain, two to four WW domains and a C-terminal ubiquitin-protein ligase domain. The Nedd4 mRNA levels are developmentally regulated and Nedd4 protein is highly expressed in many mouse embryonic tissues. In this study we have used a far-Western screen to identify embryonic proteins that interact with the WW domains in mouse Nedd4. We report here identification of eight Nedd4 WW-domain-interacting proteins from mouse embryonic cDNA expression libraries. Two of the proteins are novel, while two have been identified previously as ligands for a WW domain. All of these proteins contain one or more PY motifs. In seven of the eight proteins, these PY motifs are necessary for their interaction with the WW domains of Nedd4. Using site-directed mutagenesis, and by using individual WW domains of Nedd4 as probes for far-Western analysis, we show that the three WW domains in Nedd4 interact with varying affinities with the PY motifs present in various Nedd4-binding proteins. These results provide evidence that Nedd4 can potentially interact with multiple proteins, possibly simultaneously, through its WW domains.
Design of a silicon Mach–Zehnder modulator with a U-type PN junction (2013)

We have developed a silicon depletion-mode modulator featuring a novel U-type PN junction that enables a substantial improvement in electro-optical modulation efficiency. Through electrical, optical, and manufacturing process simulations, an ultralow V<sub>π</sub>L of 0.63 V·cm is exhibited with 3 V reverse bias. The high modulation efficiency enables a high extinction ratio (ER) of >17 dB with only a 1 mm phase shifter when the excess loss at the "on" state is 2 dB. The ER can maintain >12 dB at ∼28 GHz operation with a 3 V peak-to-peak voltage due to the small voltage attenuation of the short phase shifter.
8-Hydroxydeoxyguanosine formation at the 5' site of 5'-GG-3' sequences in double-stranded DNA by UV radiation with riboflavin (1993)

DNA damage caused by UV radiation in the presence of riboflavin or hematoporphyrin was characterized by the DNA sequencing technique using 32P-labeled DNA fragments and the analysis of 8-hydroxydeoxyguanosine (8-OH-dG) formation in calf thymus DNA. Exposure of double-stranded DNA to 365 or 302 nm radiation in the presence of riboflavin induced the sequence-specific DNA cleavage which is different from that caused by 302 or 254 nm irradiation in the absence of a sensitizer. The specific cleavage sites were the guanine residues located 5' to guanine. On the other hand, when denatured single-stranded DNA was irradiated at 365 nm with riboflavin or hematoporphyrin, cleavages occurred at most guanine residues. With D2O, the sequence-specific damage of double-stranded DNA by riboflavin was not enhanced, whereas the damage to single-stranded DNA by hematoporphyrin was greatly enhanced. Photodynamic action of riboflavin caused the formation of 8-OH-dG in double-stranded DNA. The enhancing effect of D2O on 8-OH-dG formation was not observed with riboflavin. By contrast, hematoporphyrin plus 365-nm light induced the 8-OH-dG formation only in denatured single-stranded DNA and the 8-OH-dG yield was increased about 2-fold in D2O. ESR spin destruction experiments suggested that photoexcited riboflavin reacts with dGMP to produce riboflavin anion radical and guanine cation radical, but not with other mononucleotides. The estimated ratio of 8-OH-dG yield to total guanine loss indicates that the photoexcited riboflavin induces 8-OH-dG formation specifically at the guanine residue located 5' to guanine through electron transfer. The mechanism was discussed in relation to UV carcinogenesis.
Treatment of Metastatic Head and Neck Cancer: Chemotherapy and Novel Agents (2006)

For more than a decade, the de facto "standard of care" for palliative mangement of recurrent head/neck squamous carcinoma (HNSCC) has been the combination of cisplatin/5-flourouracil. With the advent of new cytotoxins, such as the taxanes, and of the molecularly targeted agents, eg., the EGFR inhibitors, the number of options for treatment in this setting has increased. However, none of these new approaches has yet been proven to be more effective than cisplatin/5-fluorouracil. Further, despite the pallitive intent of therapy in this setting, the palliative effects have been only infrequently assessed, with many studies relying on response as a surrogate for palliation. This chapter will focus on clinical and translational research efforts in the past decade focusing on the patient with incurable locoregionally recurrent or metastatic HNSCC. Ongoing and planned future trails will also be discussed.
On multiple description streaming with content delivery networks (2003)

We propose a system that improves the performance of streaming media CDN by exploiting the path diversity provided by existing CDN infrastructure. Path diversity is provided by the different network paths that exist between a client and its nearby edge servers; and multiple description (MD) coding is coupled with this path diversity to provide resilience to losses. In our system, MD coding is used to code a media stream into multiple complementary descriptions, which are distributed across the edge servers in the CDN. When a client requests a media stream, it is directed to multiple nearby servers which host complementary descriptions. These servers simultaneously stream these complementary descriptions to the client over different network paths. This paper provides distortion models for MDC video and conventional video. We use these models to select the optimal pair of servers with complementary descriptions for each client while accounting for path lengths and path jointness and disjointness. We also use these models to evaluate the performance of MD streaming over CDN in a number of real and generated network topologies. Our results show that distortion reduction by about 20 to 40% can be realized even when the underlying CDN is not designed with MDC streaming in mind. Also, for certain topologies, MDC requires about 50% fewer CDN servers than conventional streaming techniques to achieve the same distortion at the clients.
Peptidoglycan Recognition Proteins (2001)

The innate immune system recognizes microorganisms through a series of pattern recognition receptors that are highly conserved in evolution. Insects have a family of 12 peptidoglycan recognition proteins (PGRPs) that recognize peptidoglycan, a ubiquitous component of bacterial cell walls. We report cloning of three novel human PGRPs (PGRP-L, PGRP-Ialpha, and PGRP-Ibeta) that together with the previously cloned PGRP-S, define a new family of human pattern recognition molecules. PGRP-L, PGRP-Ialpha, and PGRP-Ibeta have 576, 341, and 373 amino acids coded by five, seven, and eight exons on chromosomes 19 and 1, and they all have two predicted transmembrane domains. All mammalian and insect PGRPs have at least three highly conserved C-terminal PGRP domains located either in the extracellular or in the cytoplasmic (or in both) portions of the molecules. PGRP-L is expressed in liver, PGRP-Ialpha and PGRP-Ibeta in esophagus (and to a lesser extent in tonsils and thymus), and PGRP-S in bone marrow (and to a lesser extent in neutrophils and fetal liver). All four human PGRPs bind peptidoglycan and Gram-positive bacteria. Thus, these PGRPs may play a role in recognition of bacteria in these organs.
Aberrant Silencing of the CpG Island-Containing Human O 6 -Methylguanine DNA Methyltransferase Gene Is Associated with the Loss of Nucleosome-Like Positioning (1997)

Tumor-associated aberrant silencing of CpG island-containing genes has been correlated with increased cytosine methylation, a "closed" chromatin structure, and exclusion of transcription factor binding in the CpG island/promoter regions of affected genes. Given the lack of understanding of what constitutes a closed chromatin structure in CpG islands, however, it has been difficult to assess the relationship among cytosine methylation, chromatin structure, and inappropriate gene silencing. In this study, nuclease accessibility analysis was used to more clearly define the chromatin structure in the CpG island of the human O6-methylguanine DNA methyltransferase (MGMT) gene. Chromatin structure was then related to in vivo DNA-protein interactions and cytosine methylation status of the MGMT CpG island in human glioma cells varying in MGMT expression. The results of these studies indicated that the "open" chromatin structure associated with the MGMT CpG island in MGMT+ cells consisted of an approximately 250-bp transcription factor-binding, nuclease-accessible, nucleosome-free region of DNA, whose formation was associated with at least four flanking, precisely positioned nucleosome-like structures. In MGMT- cells, this precise nucleosomal array was lost and was replaced by randomly positioned nucleosomes (i.e., the closed chromatin structure), regardless of whether methylation of the CpG island was spread over the entire island or limited to regions outside the transcription factor binding region. These results suggest that CpG islands facilitate the expression of housekeeping genes by facilitating nucleosomal positioning and that the conditions that alter the formation of this array (such as perhaps methylation) may indirectly affect CpG island-containing gene expression.
Evidence for complement activation by protamine-heparin interaction after cardiopulmonary bypass. (1985)

Complement activation by the alternate pathway has been implicated in the pathophysiology of cardiopulmonary bypass (CPB), and laboratory studies suggest that the complement cascade may be activated by the protamine-heparin complex. To determine if the administration of protamine to patients receiving heparin activates complement, we studied 100 patients undergoing CPB by assaying levels of C3a and C4a (classic pathway) at regular intervals before and after protamine administration. In group I (90 patients), protamine was given at the usual interval (median 5 minutes) after CPB. In group II (10 patients), protamine was withheld until skin closure (median 45 minutes) after CPB. Results demonstrated that C4a was not activated during CPB in either group. After CPB, the C4a level in group I was 459 ng/dl and increased to 1047 ng/dl 10 minutes after protamine administration (p less than 0.001). In group II, the C4a level was 484 ng/dl at the end of CPB and 354 ng/dl 15 minutes later, which corresponds to the value immediately after protamine administration in group I. The delayed administration of protamine in group II caused a significant increase in C4a at the time of skin closure (1090 ng/dl; p less than 0.001). Corresponding results from C3a analysis before and after protamine administration confirmed the activation of complement cascade. Our study provides the first clinical evidence that the protamine-heparin complex activates complement via the classic (C4a) pathway. The hemodynamic effects of protamine after CPB may be related to complement activation.
Characterization of Neurons in the CA2 Subfield of the Adult Rat Hippocampus (2007)

The hippocampal cornu ammonis 2 (CA2) region is unique in being the only CA region receiving inputs from the hypothalamic supramammillary nucleus, of importance in modulating hippocampal theta rhythm, and is seizure resistant in temporal lobe epilepsy. CA2 has, however, been little studied, possibly because of its small size and difficulty encountered in defining its borders. To investigate the properties of CA2 interneurons, intracellular recordings with biocytin filling were made in adult hippocampal slices. Two types of basket cells were identified. A minority resembled those in CA1, with fast spiking behavior, vertically oriented dendrites, and axons confined to the region of origin. In contrast, the majority of parvalbumin-immunopositive CA2 basket and bistratified cells had long, horizontally oriented, sparsely spiny dendrites extending into all CA subfields in stratum oriens, adapting firing patterns and a pronounced "sag" in voltage responses to hyperpolarizing current, indicative of I(h). Broad CA2 basket cells innervated all three CA subfields and could thus provide CA1 and CA2 with feedforward and CA3 with feedback inhibition. In contrast, CA2 bistratified cell axons displayed striking subfield preference, innervating stratum oriens and stratum radiatum of CA2 and CA1 but stopping abruptly at the CA2/CA3 border, implying feedforward inhibition of CA2 and CA1. These unique features suggest that CA2 is more than a transitional region between CA1 and CA3. The pronounced slow sag current of many CA2 interneurons may contribute to coordination of pyramidal cell firing during theta, whereas the fast spiking behavior of a smaller population of interneurons supports more localized gamma.
Methionine aminopeptidase gene of Escherichia coli is essential for cell growth (1989)

We localized the methionine aminopeptidase (map) gene on the Escherichia coli chromosome next to the rpsB gene at min 4. Genetically modified strains with the chromosomal map gene under lac promoter control grew only in the presence of the lac operon inducer isopropyl-beta-thiogalactoside. Thus, methionine aminopeptidase is essential for cell growth.
Cryopreservation of peripheral nerve grafts (2000)

The utilization of viable biological nerve graft substitutes and nerve allografts raises the problem of nerve storage. To clarify this, rat sciatic nerve segments were harvested and stored in Dulbecco's modified eagle medium. The segments were divided into three groups. In the first group, no cryoprotectant was added, whereas the second had 10% dimethyl sulfoxide (DMSO) added as cryoprotectant. These two groups of nerve segments were subjected to controlled freezing. In a third group, segments were frozen uncontrolled in liquid nitrogen (-196 degrees C). All nerves were replanted orthotopically. Fresh conventional autografts (fourth group) served as control group. Histologically, freezing did not affect the structural elements such as basal lamina tubes and perineurial tissue. Morphometrically, all cryopreserved grafts had significantly reduced axon counts and less myelinization than did controls. Cryoprotected nerves (group 2) showed no different morphometric parameters compared with the group without DMSO (group 1). Controlled freezing was superior to uncontrolled freezing (group 3). Impaired regeneration was attributed mainly to delayed Wallerian degeneration and slower revascularization. Moreover, decreased survival of resident Schwann cells in the graft may impair regeneration due to the lack of neurotrophic, neurotropic, and attachment factors in early regeneration. Grafts subjected to controlled freezing support axonal regeneration to a certain extent, but further studies are required to assess various cooling patterns, cryoprotectants, and graft revascularization.
Trabeculectomy With the Use of Amniotic Membrane for Uncontrollable Glaucoma (1998)

Although trabeculectomy is an established surgical technique for glaucoma, in some cases it does not achieve a good filtering effect despite the use of mitomycin-C (MMC). The authors have developed a new surgical technique for uncontrollable glaucoma that uses amniotic membrane to prevent postoperative adhesion of conjunctiva and sclera. They performed trabeculectomy with a limbal-based conjunctival flap using 0.4 mg/ml of MMC for 2 minutes. Amniotic membrane was then placed under the scleral flap and sutured using 10-0 nylon. Among 14 eyes of 13 patients who underwent this procedure, intraocular pressure was controlled to less than 20 mm Hg after surgery in 13 eyes, including 3 eyes that underwent a second surgery with the same technique and 2 eyes that underwent laser trabeculoplasty. The authors' results suggest that this technique is efficacious for the reduction of intraocular pressure in high-risk glaucoma patients.
Effects of Stain Etchant Composition on the Photoluminescence and Morphology of Porous Silicon (2005)

Stain etching of silicon provides a spontaneous, self-limiting chemical method to produce nanocrystalline silicon films (porous Si). Whereas the existence of etchants capable of producing porous Si has been known for some time, little has been known concerning how solution composition influences the efficacy of porous Si production and the properties of the resulting films. We demonstrate that the fluoride species may be derived from either HF or acidified . A range of oxidants may be used as long as their counterions do not lead to precipitation. However, a large positive electrochemical potential is not a sufficient condition for efficient porous Si production. Bubble production, which is deleterious to film homogeneity and long thought to be inherent to the process, can be avoided by the use of transition metal-containing oxidants. Properties of the film, such as morphology, growth rate, porosity, and the wavelength of the photoluminescence maximum, respond to the etchant composition. We observe a blue shift in photoluminescence, which correlates with an increasingly positive electrochemical potential of the oxidant. It is argued that plays a role much like wavelength in photoelectrochemical etching and that smaller nanocrystals are produced with more positive values of .
Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance (1994)

Hui Cao, Scott A. Bowling, A. Susan Gordon, Xinnian Dong, Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance, The Plant Cell, Vol. 6, No. 11 (Nov., 1994), pp. 1583-1592
Transforming of images information to the implant part of retinal prosthesis, by converting of images to bit formats (2010)

Much recent research attention has focused on providing a vision substitute to blind people through electrical stimulation of a component of the visual system. This approach is referred to as “visual prosthesis”. The device consists of an extra ocular and an intraocular unit. The implantable component receives power and a data signal via a telemetric inductive link between the two units. The extra ocular unit includes a video camera and video processing board and a telemetry protocol encoder chip. The intraocular unit consists of a retinal chip with a telemetry protocol decoder, a stimulus signal generator, and an electrode array. Yet little work on devices that encode visual images into electrical stimuli have been reported to date. In this paper we focus on the information that should be transformed to the stimulator of electrodes. The idea is to transfer image information to the implant unit, in a “bit by bit” fashion.
Set operations on polyhedra using binary space partitioning trees (1987)

We introduce a new representation for polyhedra by showing how Binary Space Partitioning Trees (BSP trees) can be used to represent regular sets. We then show how they may be used in evaluating set operations on polyhedra. The BSP tree is a binary tree representing a recursive partitioning of d-space by (sub-)hyperplanes, for any dimension d. Their previous application to computer graphics has been to organize an arbitrary set of polygons so that a fast solution to the visible surface problem could be obtained. We retain this property (in 3D) and show how BSP trees can also provide an exact representation of arbitrary polyhedra of any dimension. Conversion from a boundary representation (B-reps) of polyhedra to a BSP tree representation is described. This technique leads to a new method for evaluating arbitrary set theoretic (boolean) expressions on B-reps, represented as a CSG tree, producing a BSP tree as the result. Results from our language-driven implmentation of this CSG evaluator are discussed. Finally, we show how to modify a BSP tree to represent the result of a set operation between the BSP tree and a B-rep. We describe the embodiment of this approach in an interactive 3D object design program that allows incremental modification of an object with a tool. Placement of the tool, selection of views, and performance of the set operation are all performed at interactive speeds for modestly complex objects.
Tlx, an Orphan Nuclear Receptor, Regulates Cell Numbers and Astrocyte Development in the Developing Retina (2004)

Tlx belongs to a class of orphan nuclear receptors that underlies many aspects of neural development in the CNS. However, the fundamental roles played by Tlx in the control of eye developmental programs remain elusive. By using Tlx knock-out (KO) mice, we show here that Tlx is expressed by retinal progenitor cells in the neuroblastic layer during the period of retinal layer formation, and it is critical for controlling the generation of appropriate numbers of retinal progenies through the activities of cell cycle-related molecules, cyclin D1 and p27Kip1. Tlx expression is restricted to Müller cells in the mature retina and appears to control their proper development. Furthermore, we show that Tlx is expressed by immature astrocytes that migrate from the optic nerve onto the inner surface of the retina and is required for their generation and maturation, as assessed by honeycomb network formation and expression of R-cadherin, a critical component for vasculogenesis. The impaired astrocyte network formation on the inner retinal surface is accompanied by the loss of vasculogenesis in Tlx KO retinas. Our studies thus indicate that Tlx underlies a fundamental developmental program of retinal organization and controls the generation of the proper numbers of retinal progenies and development of glial cells during the protracted period of retinogenesis.
Posterior Screw Placement on the Lateral Mass of Atlas (2004)

The width and height of the atlas lateral mass were larger than that of the C2 pedicle, and there was enough space to insert a 3.5-mm diameter screw in the atlas lateral mass over the C2 nerve. The pullout force of the screw on the lateral mass of the atlas was the same as that of the C2 pedicle screw. It is possible toinsert a 3.5-mm screw in the lateral mass of the atlas. The direction of the screw should be about 20 degrees anterosuperior in the vertical plane and 15 degrees inward in the horizontal plane. The suitable length of the screw should be approximately 22 mm inside the lateral mass.
HLA-DR antigens on colonic epithelial cells in inflammatory bowel disease: I. Relation to the state of activation of lamina propria lymphocytes and to the epithelial expression of other surface markers. (1987)

The colonic epithelial expression of HLA-DR molecules and of other markers of cell membrane perturbation was investigated by immunofluorescence in biopsy specimens from patients with ulcerative colitis and Crohn's disease. It was found that in virtually all specimens from either groups showing active inflammation there was a diffuse epithelial expression of HLA-DR molecules. There was no relation between the grading of active inflammation and the epithelial expression of HLA-DR antigens. The epithelium of virtually all specimens from the macro and microscopically uninvolved areas of patients with active colitis and from patients with histologically quiescent colitis showed no detectable expression of HLA-DR molecules. The counts of isolated lamina propria lymphocytes expressing the transferrin receptor and the interleukin 2 receptor were higher in specimens with HLA-DR+ epithelium than in those with a HLA-DR- epithelium. Twenty-nine of the 35 (83%) HLA-DR positive specimens proved to express the 4F2 antigen on their epithelium and 19 (54%) were positive for the transferrin receptor. All sections positive for either the 4F2 antigen or the transferrin receptor were also HLA-DR positive while all HLA-DR negative sections were also negative for either of the two other markers. Data in this study suggest that in active IBD the epithelial participation in active inflammation is associated with a sequence of cell membrane rearrangements, and that the expression of HLA-DR molecules is a part of this sequence.