gebhart/patrepeval huggingface dataset:
Modeling Patent Quality: A System for Large-scale Patentability Analysis using Text Mining (2012)

Current patent systems face a serious problem of declining quality of patents as the larger number of applications make it difficult for patent officers to spend enough time for evaluating each application. For building a better patent system, it is necessary to define a public consensus on the quality of patent applications in a quantitative way. In this article, we tackle the problem of assessing the quality of patent applications based on machine learning and text mining techniques. For each patent application, our tool automatically computes a score called patentability, which indicates how likely it is that the application will be approved by the patent office. We employ a new statistical prediction model to estimate examination results (approval or rejection) based on a large data set including 0.3 million patent applications. The model computes the patentability score based on a set of feature variables including the text contents of the specification documents. Experimental results showed that our model outperforms a conventional method which uses only the structural properties of the documents. Since users can access the estimated result through a Web-browser-based GUI, this system allows both patent examiners and applicants to quickly detect weak applications and to find their specific flaws.
Expanding applications of SERS through versatile nanomaterials engineering (2017)

Surface-enhanced Raman scattering (SERS) spectroscopy has evolved into a cross-disciplinary analytical technique by unveiling relevant chemical, biological, material, and structural information. The focus of this review is on two critical properties for successfully expanding applications of SERS spectroscopy: quality of the plasmonic substrate and molecule localization to the substrate. In this review, we discuss recent work on quantifying SERS distance dependence, key factors for substrate characterization and performance evaluation, expansion of SERS applications through substrate development for UV plasmonics and short-distance capture strategies for optimizing analyte-surface structures. After surveying the recent developments of these seemingly disparate fields, we suggest new research directions that may originate from a synergistic blend of all the herein discussed topics. Finally, we discuss major challenges and open questions related to the application of SERS for understanding of chemical processes at the nanoscale, with special interest on in situ catalysts and biosensing.
Atomic Force Microscopy of Phase Separation on Ruptured, Giant Unilamellar Vesicles, and a Mechanical Pathway for the Co-Existence of Lipid Gel Phases (2019)

Giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs) are synthetic model systems widely used in biophysical studies of lipid membranes. Although SLBs are advantageous for biophysical analysis, phase separation behaviors of lipid species in these two model systems can differ due to the lipid-substrate interactions that are present only for SLBs. In the present study, we report that in binary systems, certain phase domains on GUVs retain their original shapes and patterns after the GUVs rupture on glass surfaces. This enabled atomic force microscopy (AFM) experiments on phase domains, a procedure difficult to perform and interpret when applied to GUVs. Unusual phase behavior was evident in binary GUVs containing DLPC and either DPPC or DSPC. These DLPC/DSPC and DLPC/DPPC GUVs both presented the thermodynamic anomaly of having two co-existing gel phases. One phase (a bright phase) included a relatively high concentration of DiI-C20 but excluded Bodipy-HPC, and the other (dark phase) excluded both probes. The bright phases are of interest because they seem to stabilize dark phases against coalescence. Results suggested that the gel phases labeled by DiIC20 in the DLPC/DSPC membrane, which surround the dark gel phase, is an extra layer of membrane, indicating a highly curved structure that might stabilize the interior dark domains, thereby enabling the co-existence of two different gel phases. Results show the utility of AFM on collapsed GUVs, and suggest a possible mechanism for stabilization of lipid domains.
Flap endonuclease of bacteriophage T7 (2014)

Gene 6 protein of bacteriophage T7 has 5′-3′-exonuclease activity specific for duplex DNA. We have found that gene 6 protein also has flap endonuclease activity. The flap endonuclease activity is considerably weaker than the exonuclease activity. Unlike the human homolog of gene 6 protein, the flap endonuclease activity of gene 6 protein is dependent on the length of the 5′-flap. This dependency of activity on the length of the 5′-flap may result from the structured helical gateway region of gene 6 protein which differs from that of human flap endonuclease 1. The flap endonuclease activity provides a mechanism by which RNA-terminated Okazaki fragments, displaced by the lagging strand DNA polymerase, are processed. 3′-extensions generated during degradation of duplex DNA by the exonuclease activity of gene 6 protein are inhibitory to further degradation of the 5′-terminus by the exonuclease activity of gene 6 protein. The single-stranded DNA binding protein of T7 overcomes this inhibition.
Isolation, Structure, and Electronic Calculations of the Heterofullerene Salt K 6 C 59 N (1996)

An intercalation compound of azafullerene, K 6 C 59 N, was prepared and structurally characterized. It is isostructural with the fullerene compound K 6 C 60 , adopts a body-centered-cubic structure (lattice constant a = 11.31 angstroms), and consists of quasi-spherical monomeric (C 59 N) 6− ions. Density functional calculations of the structural and electronic properties confirm the similarity to K 6 C 60 but also suggest a sizable deformation, principally confined in the vicinity of the nitrogen atom, of both the molecular structure and the electron states. These results show that study of the intercalation chemistry of azafullerene promises to reveal a rich family of both n - and p -doped systems with novel conducting and magnetic properties, like their fullerene antecedents.
Accelerated Blood Clearance of Antibodies by Nanosized Click Antidotes (2018)

Long blood half-life is one of the advantages of antibodies over small molecule drugs. At the same time, prolonged half-life is a problem for imaging applications or in the case of antibody-induced toxicities. There is a substantial need for antidotes that can quickly clear antibodies from systemic circulation and peripheral tissues. Engineered nanoparticles exhibit intrinsic affinity for clearance organs (mainly liver and spleen). trans-Cyclooctene (TCO) and methyltetrazine (MTZ) are versatile copper-free click chemistry components that are extensively being used for in vivo bioorthogonal couplings. To test the ability of nanoparticles to eliminate antibodies, we prepared a set of click-modified, clinically relevant antidotes based on several classes of drug carriers: phospholipid-PEG micelles, bovine serum albumin (BSA), and cross-linked dextran iron oxide (CLIO) nanoparticles. Mice were injected with IRDye 800CW-labeled, click-modified IgG followed by a click-modified antidote or PBS (control), and the levels of the IgG were monitored up to 72 h postinjection. Long-circulating lipid micelles produced a spike in IgG levels at 1 h, decreased IgG levels at 24 h, and did not decrease the area under the curve (AUC) and IgG accumulation in main organs. Long-circulating BSA decreased IgG levels at 1 and 24 h, decreased the AUC, but did not significantly decrease organ accumulation. Long-circulating CLIO nanoworms increased IgG levels at 1 h, decreased IgG levels at 24 h, did not decrease the AUC, and did not decrease the organ accumulation. On the other hand, short-circulating CLIO nanoparticles decreased IgG levels at 1 and 24 h, significantly decreasing the AUC and accumulation in the main organs. Multiple doses of CLIO and BSA were not able to completely eliminate the antibody from blood, despite the click reactivity of the residual IgG, likely due to exchange of IgG between blood and tissue compartments. Pharmacokinetic modeling suggests that short antidote half-life and fast click reaction rate should result in higher IgG depletion efficiency. Short-circulating click-modified nanocarriers are the most effective antidotes for elimination of antibodies from blood. This study sets a stage for future development of antidotes based on nanomedicine.
Structures and functions of proteins and nucleic acids in protein biosynthesis (1989)

Abstract Infrared and Raman spectroscopy is useful for studying helical conformations of polypeptides, which are determined by molecular structure parameters. Nuclear magnetic resonance spectroscopy, as well as X-ray analysis, is now established to be important for conformation studies of proteins and nucleic acids in solution. This article is mainly concerned with the conformational aspect and function regulation in protein biosynthesis. The strict recognition of transfer ribonucleic acid (tRNA) by aminoacyl-tRNA synthetase (ARS) is achieved by multi-step mutual adaptation. The conformations of ARS-bound amino acids have been elucidated by transferred nuclear Overhauser effect analysis. Aminoacyl-tRNA takes the 3′-isomeric form in the polypeptide chain elongation cycle. The regulation of codon recognition by post-transcriptional modification is achieved by conversion of the conformational characteristic of the anticodon of tRNA. The cytidine → lysidine modification of the anticodon of minor isoleucine tRNA concurrently converts the amino acid specificity and the codon specificity. As novel protein engineering, a basic strategy has been established for in vivo biosynthesis of proteins that are substituted with unnatural amino acids (alloproteins).
In vitroandin vivocharacterization of the bifunctional μ and δ opioid receptor ligand UFP‐505 (2018)

This article is part of a themed section on Emerging Areas of Opioid Pharmacology. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.14/issuetoc.
Overexpression of epidermal growth factor receptor in urothelium elicits urothelial hyperplasia and promotes bladder tumor growth. (2002)

Although urothelium is constantly bathed in high concentrations of epidermal growth factor (EGF) and most urothelial carcinomas overexpress EGF receptor (EGFr), relatively little is known about the role of EGFr signaling pathway in urothelial growth and transformation. In the present study, we used the uroplakin II gene promoter to drive the urothelial overexpression of EGFr in transgenic mice. Three transgenic lines were established, all expressing a higher level of the EGFr mRNA and protein in the urothelium than the nontransgenic controls. The overexpressed EGFr was functionally active because it was autophosphorylated, and its downstream mitogen-activated protein kinases were highly activated. Phenotypically, the urinary bladders of all transgenic lines developed simple urothelial hyperplasia that was strongly positive for proliferative cell nuclear antigen and weakly positive for bromodeoxyuridine incorporation. When coexpressed with the activated Ha-ras oncogene in double transgenic mice, EGFr had no apparent tumor-enhancing effects over the urothelial hyperplastic phenotype induced by Ha-ras oncogene. However, when coexpressed with the SV40 large T antigen, EGFr accelerated tumor growth and converted the carcinoma in situ of the SV40T mice into high-grade bladder carcinomas, without triggering tumor invasion. Our studies indicate that urothelial overexpression of EGFr can induce urothelial proliferation but not frank carcinoma formation. Our results also suggest that, whereas EGFr and Ha-ras, both of which act in the same signal transduction cascade, stimulated urothelial hyperplasia, they were not synergistic in urothelial tumorigenesis, and EGFr overexpression can cooperate with p53 and pRB dysfunction (as occurring in SV40T transgenic mice) to promote bladder tumor growth.
LXRβ is required for glucocorticoid-induced hyperglycemia and hepatosteatosis in mice (2010)

Although widely prescribed for their potent antiinflammatory actions, glucocorticoid drugs (e.g., dexamethasone) cause undesirable side effects that are features of the metabolic syndrome, including hyperglycemia, fatty liver, insulin resistance, and type II diabetes. Liver x receptors (LXRs) are nuclear receptors that respond to cholesterol metabolites and regulate the expression of a subset of glucocorticoid target genes. Here, we show LXRβ is required to mediate many of the negative side effects of glucocorticoids. Mice lacking LXRβ (but not LXRα) were resistant to dexamethasone-induced hyperglycemia, hyperinsulinemia, and hepatic steatosis, but remained sensitive to dexamethasone-dependent repression of the immune system. In vivo, LXRα/β knockout mice demonstrated reduced dexamethasone-induced expression of the key hepatic gluconeogenic gene, phosphoenolpyruvate carboxykinase (PEPCK). In perfused liver and primary mouse hepatocytes, LXRβ was required for glucocorticoid-induced recruitment of the glucocorticoid receptor to the PEPCK promoter. These findings suggest a new avenue for the design of safer glucocorticoid drugs through a mechanism of selective glucocorticoid receptor transactivation.
Molecular Detection of Biomarkers and Cells Using Magnetic Nanoparticles and Diagnostic Magnetic Resonance (2011)

The rapid and sensitive detection of molecular targets such as proteins, cells, and pathogens in biological specimens is a major focus of ongoing medical research, as it could promote early disease diagnoses and the development of tailored therapeutic strategies. Magnetic nanoparticles (MNP) are attractive candidates for molecular biosensing applications because most biological samples exhibit negligible magnetic susceptibility, and thus the background against which measurements are made is extremely low. Numerous magnetic detection methods exist, but sensing based on magnetic resonance effects has successfully been developed into a general detection platform termed diagnostic magnetic resonance (DMR). DMR technology encompasses numerous assay configurations and sensing principles, and to date magnetic nanoparticle biosensors have been designed to detect a wide range of targets including DNA/mRNA, proteins, enzymes, drugs, pathogens, and tumor cells with exquisite sensitivity. The core principle behind DMR is the use of MNP as proximity sensors that modulate the transverse relaxation time of neighboring water molecules. This signal can be quantified using MR imagers or NMR relaxometers, including miniaturized NMR detector chips that are capable of performing highly sensitive measurements on microliter sample volumes and in a multiplexed format. The speed, sensitivity, and simplicity of the DMR principle, coupled with further advances in NMR biosensor technology should provide a high-throughput, low-cost, and portable platform for large-scale parallel sensing in clinical and point-of-care settings.
Antimicrobial Peptide Mimetics Based on a Diphenylacetylene Scaffold: Synthesis, Conformational Analysis, and Activity (2020)

Mimics of natural antimicrobial peptides are promising compounds to fight the rising threat of multi-drug resistant bacteria. Here we report the design, synthesis and conformational analysis of a new class of antimicrobial peptide mimetics incorporating a diphenylacetylene scaffold. Within a small set of compounds, we observe a correlation between amphiphilicity, the efficiency of partitioning into negatively charged membranes and antibacterial activity. The most amphiphilic compound, which contains four isoleucine residues and four lysine residues, displays species-selective antibacterial activity (most active against Bacillus subtills) and low haemolytic activity. Solution-phase conformational analysis of this compound indicates that a defined structure is adopted in the presence of negatively charged phospholipid membranes and aqueous 2,2,2-trifluoroethanol but not in water. A conformation model indicates that the cationic and hydrophobic functional groups are segregated. These results may inform the development of highly selective antimicrobial peptide mimetics for therapeutic applications.
Thioredoxin-thioredoxin reductase system of Streptomyces clavuligerus: sequences, expression, and organization of the genes (1993)

The genes that encode thioredoxin and thioredoxin reductase of Streptomyces clavuligerus were cloned, and their DNA sequences were determined. Previously, we showed that S. clavuligerus possesses a disulfide reductase with broad substrate specificity that biochemically resembles the thioredoxin oxidoreductase system and may play a role in the biosynthesis of beta-lactam antibiotics. It consists consists of two components, a 70-kDa NADPH-dependent flavoprotein disulfide reductase with two identical subunits and a 12-kDa heat-stable protein general disulfide reductant. In this study, we found, by comparative analysis of their predicted amino acid sequences, that the 35-kDa protein is in fact thioredoxin reductase; it shares 48.7% amino acid sequence identity with Escherichia coli thioredoxin reductase, the 12-kDa protein is thioredoxin, and it shares 28 to 56% amino acid sequence identity with other thioredoxins. The streptomycete thioredoxin reductase has the identical cysteine redox-active region--Cys-Ala-Thr-Cys--and essentially the same flavin adenine dinucleotide- and NADPH dinucleotide-binding sites as E. coli thioredoxin reductase and is partially able to accept E. coli thioredoxin as a substrate. The streptomycete thioredoxin has the same cysteine redox-active segment--Trp-Cys-Gly-Pro-Cys--that is present in virtually all eucaryotic and procaryotic thioredoxins. However, in vivo it is unable to donate electrons to E. coli methionine sulfoxide reductase and does not serve as a substrate in vitro for E. coli thioredoxin reductase. The S. clavuligerus thioredoxin (trxA) and thioredoxin reductase (trxB) genes are organized in a cluster. They are transcribed in the same direction and separated by 33 nucleotides. In contrast, the trxA and trxB genes of E. coli, the only other organism in which both genes have been characterized, are physically widely separated.
Frequency response of atmospheric pressure gas breakdown in micro/nanogaps (2013)

In this paper, we study gas breakdown in micro/nanogaps at atmospheric pressure from low RF to high millimeter band. For gaps larger than about 10 μm, the breakdown voltage agrees with macroscale vacuum experiments, exhibiting a sharp decrease at a critical frequency, due to transition between the boundary- and diffusion-controlled regimes, and a gradual increase at very high frequencies as a result of inefficient energy transfer by field. For sub-micron gaps, a much lower breakdown is obtained almost independent of frequency because of the dominance of field emission.
Effect of Molecular Weight on Processing and Adhesive Properties of the Phenylethynyl-Terminated Polyimide LARC™-PETI-5 (1997)

Abstract Three different molecular weight versions of the phenylethynyl-terminated polyimide LARC™-PETI-5 were synthesized. The materials synthesized had theoretical number average molecular weights of 2500, 5000, and 10000 g mol. Differential Scanning Calorimetry (DSC) was performed on the dry powder form of these materials to establish cure conditions which result in high glass transition temperatures. Lap shear specimens were prepared from adhesive tape made from each material and with the thermal cure conditions determined from the DSC data. The tensile shear data established which processing conditions provided the best adhesive strengths. Titanium tensile shear strengths as high as 52.6 MPa (7630 psi) at RT and 35.2 MPa (5100 psi) at 177°C were determined. Processing temperatures as low as 316°C and pressures as low as 0.17 MPa (25 psi) resulted in good adhesive properties. The tensile shear properties of these materials were unaffected by hydraulic fluid. The molecular weight of LARC™-PETI-5 has an important effect on the bonding pressures required to obtain good tensile shear strengths. The effect of molecular weight on the utility of PETI-5 to be used as a primer to maintain surface quality for bonding was also investigated. Key Words: Adhesivespolyimidesphenylethynylprocessingmolecular weight.
Function of Cytoplasmic Fibers in Syncytia (1982)

Giant syncytia containing hundreds to thousands of nuclei are commonly observed in monolayer cultures of baby hamster kidney cells (BHK-21) after infection with a paramyxovirus, simian virus 5 (SV5) (Compans et al. 1966; Holmes and Choppin 1966, 1968). Large syncytia can also be induced by brief treatment of cells with concentrated solutions of polyethylene glycol (PEG) followed by a period of incubation (Pontecorvo 1975; Davidson and Gerald 1977). In both virus-infected and PEG-treated cultures, the formation of giant syncytia starts with the fusion of adjacent cells to form a binucleate cell. Such binucleate cells grow in size both by fusion with other multinucleate cells and by recruitment of single cells. After fusion of some cell lines, nuclei and most of the phase-dense granules move rapidly to the center of the syncytium. Such movements of nuclei and organelles become more extensive as the syncytia increase in size. In the case of...
The Proximal Biceps as a Pain Generator and Results of Tenotomy (2008)

Many palliative interventions have been proposed for patients in whom rotator cuff repair is not feasible as a result of advanced fatty infiltration, definitive loss of tendons, and proximal humeral migration. The long head of the biceps tendon has been proposed as a source of pain in patients with rotator cuff tears. This article presents a review of current concepts on the rationale for arthroscopic biceps tenotomy or tenodesis, and evaluates the objective, subjective, and radiographic results of these palliative procedures. On the basis of different studies, it seems that isolated arthroscopic biceps tenotomy or tenodesis is a valuable option for the treatment of rotator cuff tears in selected patients. Although it does not improve shoulder strength, tenotomy or tenodesis reduces pain and improves the functional range of motion with a high degree of patient satisfaction. However, the progressive radiographic changes that occur with long standing rotator cuff tears are not altered.
The Effect of Triple Pelvic Osteotomy on Hip Force in Dysplastic Dogs: A Theoretical Analysis (1996)

The effect of a triple pelvic osteotomy (TPO) procedure on the forces acting about the hip joint was examined in five dysplastic canine hips using a previously described theoretical analysis. Hip reaction force (Fh) and its angle of application (theta h) were calculated from radiographic measurements made before and after TPO procedures which sequentially increased acetabular ventroversion from 0 degree to 20 degrees, 30 degrees, and 40 degrees. The results of the in vitro study showed that Fh decreased with increasing acetabular ventroversion reaching an asymptotic value between 30 degrees and 40 degrees. The decrease in Fh corresponded to an increase in theta h toward the vertical, with statistical significance found in both Fh and theta h between 0 degree and 20 degrees. The changes observed in Fh and theta h after TPO were attributed to the medialization of the femoral head resulting from the reduction of the subluxated head. The results of this study suggest that the noted reduction in the magnitude of the forces acting on the hip joint may act in concert with increased coverage of the femoral head to effect the beneficial clinical results observed with the TPO procedure.