gebhart/patrepeval huggingface dataset:
Binding of proteins to the PDZ domain regulates proteolytic activity of HtrA1 serine protease (2004)

HtrA1, a member of the mammalian HtrA (high temperature requirement A) serine protease family, has a highly conserved protease domain followed by a PDZ domain. Accumulating evidence has indicated that PDZ domains regulate protease activity of HtrA proteins. We searched for binding partners of the PDZ domain of mouse HtrA1 by yeast two-hybrid screening, and isolated proteins that were recognized by the HtrA1 PDZ domain through their C-terminal ends with a core consensus Phi-X-Phi-[V/L/F/A]-COOH sequence (where Phi is a hydrophobic/non-polar amino acid). C-propeptides of fibrillar collagens were most frequently isolated. Type III procollagen alpha1 C-propeptide, which was used as a model protein, was digested by HtrA1. HtrA1 cleavage of the collagen C-propeptide was enhanced by reductive denaturation of the C-propeptide and partly inhibited by removal of the C-terminal four amino acids from the C-propeptide, suggesting that the substrate recognition was facilitated by the binding of the free C-terminal ends of substrates to the PDZ domain of HtrA1. The synthetic oligopeptide (GM130Pep) that fitted the consensus recognition sequence bound to HtrA1 with a high affinity (K(d)=6.0 nM). GM130Pep stimulated HtrA1 protease activity 3- to 4-fold, but did not efficiently stimulate the activity of an HtrA1 mutant lacking the PDZ domain, supporting the notion that the PDZ domain enhances protease activity upon ligand binding. The peptide derived from Type III collagen alpha1 C-propeptide specifically stimulated protease activity of HtrA1, but did not stimulate nor significantly bind to HtrA2, suggesting that the collagen C-propeptide is a specific physiological regulator of HtrA1.
Expression of ghrelin receptor mRNA in the rat and the mouse brain (2005)

Ghrelin is a hormone that stimulates growth hormone secretion and signals energy insufficiency via interaction with its receptor, the growth hormone secretagogue receptor (GHSR). The GHSR is located in both the central nervous system and the periphery. Its distribution in the CNS, as assessed by in situ hybridization histochemistry (ISHH), has been described previously in a few mammalian species, although these studies were limited by either the detail provided or the extent of the regions examined. In the present study, we systematically examined the distribution of GHSR mRNA in the adult rat and mouse brains and cervical spinal cords by using ISHH with novel cRNA probes specific for the mRNA encoding functional GHSR (the type 1a variant). We confirmed GHSR mRNA expression in several hypothalamic nuclei, many of which have long been recognized as playing roles in body weight and food intake. GHSR also was found in several other regions previously unknown to express GHSR mRNA, including many parasympathetic preganglionic neurons. Additionally, we found GHSR mRNA within all three components of the dorsal vagal complex, including the area postrema, the nucleus of the solitary tract, and the dorsal motor nucleus of the vagus. Finally, we examined the coexpression of GHSR with tyrosine hydroxylase and cholecystokinin and demonstrate a high degree of GHSR mRNA expression within dopaminergic, cholecystokinin-containing neurons of the substantia nigra and ventral tegmental area.
Sensitivity and Specificity of Cetuximab-IRDye800CW to Identify Regional Metastatic Disease in Head and Neck Cancer (2017)

<b>Purpose:</b> Comprehensive cervical lymphadenectomy can be associated with significant morbidity and poor quality of life. This study evaluated the sensitivity and specificity of cetuximab-IRDye800CW to identify metastatic disease in patients with head and neck cancer.<b>Experimental Design:</b> Consenting patients scheduled for curative resection were enrolled in a clinical trial to evaluate the safety and specificity of cetuximab-IRDye800CW. Patients (<i>n</i> = 12) received escalating doses of the study drug. Where indicated, cervical lymphadenectomy accompanied primary tumor resection, which occurred 3 to 7 days following intravenous infusion of cetuximab-IRDye800CW. All 471 dissected lymph nodes were imaged with a closed-field, near-infrared imaging device during gross processing of the fresh specimens. Intraoperative imaging of exposed neck levels was performed with an open-field fluorescence imaging device. Blinded assessments of the fluorescence data were compared to histopathology to calculate sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV).<b>Results:</b> Of the 35 nodes diagnosed pathologically positive, 34 were correctly identified with fluorescence imaging, yielding a sensitivity of 97.2%. Of the 435 pathologically negative nodes, 401 were correctly assessed using fluorescence imaging, yielding a specificity of 92.7%. The NPV was determined to be 99.7%, and the PPV was 50.7%. When 37 fluorescently false-positive nodes were sectioned deeper (1 mm) into their respective blocks, metastatic cancer was found in 8.1% of the recut nodal specimens, which altered staging in two of those cases.<b>Conclusions:</b> Fluorescence imaging of lymph nodes after systemic cetuximab-IRDye800CW administration demonstrated high sensitivity and was capable of identifying additional positive nodes on deep sectioning. <i>Clin Cancer Res; 23(16); 4744-52. ©2017 AACR</i>.
Human Immunodeficiency Virus Type 1 (HIV-1) Vpr Enhances Expression from Unintegrated HIV-1 DNA (2003)

Retroviral DNA synthesized prior to integration, termed unintegrated viral DNA, is classically believed to be transcriptionally inert and to serve only as a precursor to the transcriptionally active integrated proviral DNA form. However, it has recently been found to be expressed under some circumstances during human immunodeficiency virus type 1 (HIV-1) replication and may play a significant role in HIV-1 pathogenesis. HIV-1 Vpr is a virion-associated accessory protein that is critical for HIV-1 replication in nondividing cells and induces cell cycle arrest and apoptosis. We find that Vpr, either expressed de novo or released from virions following viral entry, is essential for unintegrated viral DNA expression. HIV-1 mutants defective for integration in either the integrase catalytic domain or the cis-acting att sites can express unintegrated viral DNA at levels similar to that of wild-type HIV-1, but only in the presence of Vpr. In the absence of Vpr, the expression of unintegrated viral DNA decreases 10- to 20-fold. Vpr does not affect the efficiency of integration from integrase-defective HIV-1. Vpr-mediated enhancement of expression from integrase-defective HIV-1 requires that the viral DNA be generated in cells through infection and is mediated via a template that declines over time. Vpr activation of expression does not require exclusive nuclear localization of Vpr nor does it correlate with Vpr-mediated cell cycle arrest. These results attribute a new function to HIV-1 Vpr and implicate Vpr as a critical component in expression from unintegrated HIV-1 DNA.
An animal model for Epstein–Barr virus (EBV)‐associated lymphomagenesis in the human: Malignant lymphoma induction of rabbits by EBV‐related herpesvirus from cynomolgus (2000)

It is very important to develop and analyze animal models of Epstein-Barr virus (EBV)-associated tumors in the human. However, only a few reports on the animal models of EBV infection have been reported. Here we review those previous models and describe the details on our newly developed rabbit model of malignant lymphoma induced by EBV-related virus from cynomolgus. In brief, Si-IIA-EBV or Cyno-EBV induced T-cell lymphomas in rabbits inoculated intravenously (77-90%), orally (82-89%), subcutaneously (3/3) and intraperitoneally (2/3) about 2-5 months later. EBV-DNA was detected in peripheral blood by polymerase chain reaction 2 days after oral inoculation of Cyno-EBV while antiviral capsid antigen immunoglobulin G (IgG) was raised 3 weeks after the inoculation. Rabbit lymphomas and their cell lines contained EBV-DNA and expressed EBV-encoded small RNA-1 and EBV-associated nuclear antigen. Rabbit lymphoma cell lines, some of which have specific chromosomal abnormality, showed tumorigenicity in nude mice. The significance and further research subjects of this animal model will be discussed. We believe that the present rabbit model of lymphoma with specific chromosomal abnormalities is very useful for clarifying the role of EBV in human EBV-associated lymphoma and provides a means for studying prophylactic and therapeutic regimens.
The primary structure of two polypeptide chains from preparations of homeostatic thymus hormone (HTHα and HTHβ) (1985)

The primary structures of the 2 polypeptide chains (HTH alpha and HTH beta) of the homeostatic thymus hormone (HTH) were determined. The entire structures were found to be identical to those of histones H2A and H2B, respectively, without evidence for sub-types, proteolytic processings, or other peptide fragments. The results show that suggestions for new extranuclear and hormone-like histone functions apply to HTH preparations with intact protein chains of the H2 histones.
Development of a Field Guide for Portable Changeable Message Sign Use in Work Zones (2005)

In this report, researchers document the development of a field guide for portable changeable message sign use in work zone. Included in the report is a summary and critique of available national and state-level standards and guidance on portable changeable message sign (PCMS) use, description of the components included in the field guide, and implementation considerations for field guide deployment. The field guide was developed as a stand-alone product, but is included for illustrative purposes as an appendix to this report.
Online smoothing of live, variable-bit-rate video (2002)

Bandwidth smoothing techniques are effective at reducing the burstiness of a compressed, pre-recorded video stream by prefetching frames into the client playback buffer in advance of each burst. In contrast to stored video, live applications typically have limited knowledge of frame sizes and often require bounds on the delay between the source and the client(s). This paper addresses bandwidth smoothing for a growing number of live video applications, such as videocasts of courses or television news, where many clients be willing to tolerate a playback delay of several seconds or minutes in exchange for a smaller throughput requirement. Extending techniques for smoothing pre-recorded video, we develop online, window-based smoothing algorithms for these delay-tolerant applications. Experiments with MPEG traces demonstrate that the new algorithms significantly reduce the peak rate, coefficient of variation, and effective bandwidth of variable-bit-rate video streams using fairly small window sizes (1-10 seconds), closely approximating the performance of the optimal offline algorithm.
Papillary thyroid carcinoma in a 9‐year‐old girl with ataxia‐telangiectasia (2006)

A 9-year-old female with ataxia-telangiectasia (AT) presenting with papillary thyroid carcinoma and lymph nodes involvement is reported. We discuss this novel association, the general risk of neoplasic complications in these patients, the natural history of thyroid carcinoma in the pediatric population and the potential link between thyroid carcinogenesis and ataxia-telangiectasia mutated gene (ATM) mutation. We also expose our therapeutic attitude, according to both clinical status and particular genetic background of our patient.
Atomic Layer Deposition of Insulating Hafnium and Zirconium Nitrides (2004)

Highly uniform, smooth, and conformal coatings of higher nitrides of hafnium and zirconium were produced by atomic layer deposition from homoleptic tetrakis(dialkylamido)metal(IV) complexes and ammonia at low substrate temperatures (150−250 °C). The precursor vapors were alternately pulsed into a heated reactor, yielding 1.15−1.20 Å of metal nitride film for every cycle. Successful depositions were carried out on silicon, glass, quartz, and glassy carbon. All of the films showed good adhesion to the substrates, were chemically resistant, and did not oxidize over time. The films were characterized by Rutherford backscattering spectrometry and ellipsometry. These films were amorphous as deposited, as shown by X-ray diffraction and transmission electron microscopy. Step coverage is 100% in vias with an aspect ratio of 40:1, as determined by scanning electron microscopy. Evidence is given for the existence of nitrogen-rich phases with compositions Hf3N4 and Zr3N4. These two materials are insulating, transparent, and colored, in contrast to the well-known mononitrides, which are shiny, gold-colored, and highly conducting.
A Formal Approach to Design-Rule Checking (1987)

This paper describes the development of a layout model and the theoretical basis for a relatively technology-independent, false-error free, hierarchical design-rule checker for VLSI circuit layouts which have Manhattan geometry and are subject to some design-rule simplifications. A flat model of the layout of a VLSI circuit using set theory notation is first defined. Two primitive operations and five primitive set functions are formally defined to process the layout and to form a complete set of primitives in the algebra of design-rule checking. The most widely used design rules can be defined as functions in terms of these primitives. Each design-rule function determines if a geometrical shape on a layer conforms with that rule. Provisions are also made to handle inconsistent design rules (e.g., butting contacts) at some extra cost. Finally, graph theory is employed to extend the flat model to define a hierarchical model for the layout of a VLSI circuit. The hierarchical model has been used as the basis for the development of a hierarchical design-rule checker.
Synthesis of 1-Chloroacetyl-1-dehydroxy-2,3,5-tri-O-benzoyl-β-D-ribofuranose. A Potentially Versatile Intermediate for the Synthesis of C-Nucleosides (1992)

Abstract New key carbohydrate intermediate, 1-chloroacetyl-1-dehydroxy-2,3,5-tri-O-benzoyl-β-D-ribofuranose (1a), has been synthesized. The application of this key intermediate would be very wide. We have very conveniently synthesized several C-nucleosides including monocyclic and 5,5-membered bicyclic compounds from this intermediate.
Novel, Rapid, and Inexpensive Cell-Based Quantification of Antimalarial Drug Efficacy (2004)

We report on the development of a new SYBR Green I-based plate assay for analyzing the activities of antimalarial drugs against intraerythrocytic Plasmodium falciparum. This assay is considerably faster, less labor-intensive, and less expensive than conventional radiotracer (e.g., [3H]hypoxanthine and [3H]ethanolamine)-based assays or P. falciparum lactate dehydrogenase activity-based assays. The assay significantly improves the pace at which antimalarial drug discovery efforts may proceed.
Singular Configurations of Parallel Manipulators and Grassmann Geometry (1989)

Parallel manipulators have a specific mechanical architecture where all the links are connected both at the base and at the gripper of the robot. By changing the lengths of these links we are able to control the position 1 of the gripper. In general, for a given set of links lengths there is only one position for the gripper. However, it may be suspected that in some cases more than one solution may be found for the position of the gripper: the robot is in a singular configuration. To determine these singular configurations the classical method is to find the roots of the determinant of the jacobian matrix. In our case the jacobian matrix is complex, and it seems not to be possible to find these roots. We propose here a new method based on Grassmann line geometry. The set of lines, P 3 , constitutes a linear variety of rank 6. We show that a singular configuration is obtained when the variety spanned by the lines associated to the robot links has a rank less than 6. An important feature of the varieties of this geometry is that they can be described by simple geometric rules. Thus to find the singular configurations of parallel manipulators we have to find the configuration in which the robot matches these rules. Such an analysis is performed on a special parallel manip ulator. We show that we find all the well-known singular configurations, and also some new ones.
Peak to Average Ratio Reduction in Wireless OFDM Communication Systems (2006)

Future mobile communications systems reaching for ever increasing data rates require higher bandwidths than those typical used in today’s cellular systems. By going to higher bandwidth the (for low bandwidth) flat fading radio channel becomes frequency selective and time dispersive. Due to its inherent robustness against time dispersion Orthogonal Frequency Division Multiplex (OFDM) is an attractive candidate for such future mobile communication systems. OFDM partitions the available bandwidth into many subchannels with much lower bandwidth. Such a narrowband subchannel experiences now due to its low bandwidth an almost flat fading leading in addition to above mentioned robustness also to simple implementations. However, one potential drawback with OFDM modulation is the high Peak to Average Ratio (PAR) of the transmitted signal: The signal transmitted by the OFDM system is the superposition of all signals transmitted in the narrowband subchannels. The transmit signal has then due to the central limit theorem a Gaussian distribution leading to high peak values compared to the average power. A system design not taking this into account will have a high clip rate: Each signal sample that is beyond the saturation limit of the power amplifier suffers either clipping to this limit value or other non-linear distortion, both creating additional bit errors in the receiver. One possibility to avoid clipping is to design the system for very high signal peaks. However, this approach leads to very high power consumption (since the power amplifier must have high supply rails) and also complex power amplifiers. The preferred solution is therefore to apply digital signal processing that reduces such high peak values in the transmitted signal thus avoiding clipping. These methods are commonly referred to as PAR reduction. PAR reduction methods can be categorized into transparent methods – here the receiver is not aware of the reduction scheme applied by the transmitter – and non-transparent methods where the receiver needs to know the PAR algorithm applied by the transmitter. This master thesis would focus on transparent PAR reduction algorithms. The performance of PAR reduction method will be analysed both with and without the PSD constrained. The effect of error power on data tones due to clipping will be investigated in this report.
Imprinting of the gene encoding a human cyclin-dependent kinase inhibitor, p57KIP2, on chromosome 11p15. (1996)

Parental origin-specific alterations of chromosome 11p15 in human cancer suggest the involvement of one or more maternally expressed imprinted genes involved in embryonal tumor suppression and the cancer-predisposing Beckwith-Wiedemann syndrome (BWS). The gene encoding cyclin-dependent kinase inhibitor p57KIP2, whose overexpression causes G1 phase arrest, was recently cloned and mapped to this band. We find that the p57KIP2 gene is imprinted, with preferential expression of the maternal allele. However, the imprint is not absolute, as the paternal allele is also expressed at low levels in most tissues, and at levels comparable to the maternal allele in fetal brain and some embryonal tumors. The biochemical function, chromosomal location, and imprinting of the p57KIP2 gene match the properties predicted for a tumor suppressor gene at 11p15.5. However, as the p57KIP2 gene is 500 kb centromeric to the gene encoding insulin-like growth factor 2, it is likely to be part of a large domain containing other imprinted genes. Thus, loss of heterozygosity or loss of imprinting might simultaneously affect several genes at this locus that together contribute to tumor and/or growth- suppressing functions that are disrupted in BWS and embryonal tumors.
Continuous whole blood UltraPheresis procedure in patients with metastatic cancer. (1989)

Sixteen patients with metastatic cancer, each with bidirectionally measurable disease, were treated with a total of 24 membrane UltraPheresis procedures each to remove a low molecular weight (less than 150,000 daltons) plasma fraction. No other oncologic treatment was applied during the 2 months of study. The procedure was generally well tolerated, and no clinically significant adverse effects were observed from the procedure. A consistent tumor-specific inflammatory response was observed following the UltraPheresis procedure and was associated with lymphocytic infiltration of tumor and tumor necrosis that was demonstrated in those patients evaluable by repeat biopsy. In some patients, anergy was reversed and Karnofsky status improved. Six of the 16 patients had reduction of the sum of mean cross-sectional diameters of measureable lesions by 50% or more.
Role of lateral phase separation in the modulation of phospholipase A2 activity (1993)

Phospholipase A2-catalyzed hydrolysis of phosphatidylcholine large unilamellar vesicles is characterized by a period of slow hydrolysis followed by a rapid increase in the rate of hydrolysis. The temporal relationship between the burst of PLA2 activity and the lateral distribution of substrate and product lipids was examined by simultaneously recording product accumulation and the fluorescence of 1-pyrenyldecanoate, a fatty acid derivative sensitive to lipid distribution and lateral diffusion. The excimer: monomer ratio of the probe changes slowly prior to the burst in activity and then abruptly at the time of the burst. A partial phase diagram for the ternary codispersion of substrate and products (dipalmitoylphosphatidylcholine and 1:1 monopalmitoylphosphatidylcholine/palmitic acid) was constructed by differential scanning calorimetry and suggests gel/gel immiscibility in this system. Thus, the changes in pyrene fluorescence during the time course of hydrolysis appear to be due to lateral phase separation. The critical mole fraction of product both for lateral phase separation in the gel state and for elimination of the lag phase is approximately 0.083. The simultaneous recordings of PLA2 activity and pyrene fluorescence show that the lateral rearrangement of lipids begins prior to and continues during the rapid activation process of PLA2. Two possible effects of lateral phase separation are that concentration of the protein in the product-rich regions promotes putative dimerization or that formation of phase interface regions promotes enzyme activation.
Fine-Tuning the Weak-Link Approach:  Effect of Ligand Electron Density on the Formation of Rhodium(I) and Iridium(I) Metallomacrocycles (2003)

A novel bis(phosphinoalkyl-thioether)arene ligand with a fluorinated aryl group (1,4-(Ph(2)PCH(2)CH(2)S)(2)C(6)F(4)) has been synthesized. This ligand has been used to prepare symmetric bimetallic structures with Rh(I) and Ir(I) metal centers in high yield. Unlike their nonfluorinated counterparts, these complexes can be opened into large macrocyclic structures through straightforward ligand (i.e., carbon monoxide, nitriles, and isocyanides) substitution reactions at the metal-thioether linkage. In addition, the symmetric bimetallic structures have been shown to react with appropriately sized bifunctional aromatic molecules to form three-tiered host-guest structures.