gebhart/patrepeval huggingface dataset:
Rationally Designed Influenza Virus Vaccines That Are Antigenically Stable during Growth in Eggs (2017)

Influenza virus vaccine production is currently limited by the ability to grow circulating human strains in chicken eggs or in cell culture. To facilitate cost-effective growth, vaccine strains are serially passaged under production conditions, which frequently results in mutations of the major antigenic protein, the viral hemagglutinin (HA). Human vaccination with an antigenically drifted strain is known to contribute to poor vaccine efficacy. To address this problem, we developed a replication-competent influenza A virus (IAV) with an artificial genomic organization that allowed the incorporation of two independent and functional HA proteins with different growth requirements onto the same virion. Vaccination with these viruses induced protective immunity against both strains from which the HA proteins were derived, and the magnitude of the response was as high as or higher than vaccination with either of the monovalent parental strains alone. Dual-HA viruses also displayed remarkable antigenic stability; even when using an HA protein known to be highly unstable during growth in eggs, we observed high-titer virus amplification without a single adaptive mutation. Thus, the viral genomic design described in this work can be used to grow influenza virus vaccines to high titers without introducing antigenic mutations.<b>IMPORTANCE</b> Influenza A virus (IAV) is a major public health threat, and vaccination is currently the best available strategy to prevent infection. While there have been many advances in influenza vaccine production, the fact that we cannot predict the growth characteristics of a given strain under vaccine production conditions <i>a priori</i> introduces fundamental uncertainty into the process. Clinically relevant IAV strains frequently grow poorly under vaccine conditions, and this poor growth can result in the delay of vaccine production or the exchange of the recommended strain for one with favorable growth properties. Even in strains that grow to high titers, adaptive mutations in the antigenic protein hemagglutinin (HA) that make it antigenically dissimilar to the circulating strain are common. The genomic restructuring of the influenza virus described in this work offers a solution to the problem of uncertain or unstable growth of IAV during vaccine production.
Laser Desorption/Ionization Mass Spectrometry of Proteins of Mass 100 000 to 250 000 Dalton (1989)

Irradiation of proteins in a nicotinic acid matrix with the 266‐nm light of a Nd‐YAG laser allowed the first determination of molecular masses up to 250 000 daltons. Since the peaks of multiply charged molecular ions and of oligomer ions can also be used in determination of molecular mass, this method attains a precision of ca. 0.1%. Its potential is demonstrated for β‐ D ‐galactosidase, glucose isomerase, and catalase.
Trisulfide Modification Impacts the Reduction Step in Antibody–Drug Conjugation Process (2013)

Antibody-drug conjugates (ADCs) utilizing cysteine-directed linker chemistry have cytotoxic drugs covalently bound to native heavy-heavy and heavy-light interchain disulfide bonds. The manufacture of these ADCs involves a reduction step followed by a conjugation step. When tris(2-carboxyethyl)phosphine (TCEP) is used as the reductant, the reaction stoichiometry predicts that for each molecule of TCEP added, one interchain disulfide should be reduced, generating two free thiols for drug linkage. In practice, the amount of TCEP required to achieve the desired drug-to-antibody ratio often exceeds the predicted, and is variable for different lots of monoclonal antibody starting material. We have identified the cause of this variability to be inconsistent levels of interchain trisulfide bonds in the monoclonal antibody. We propose that TCEP reacts with each trisulfide bond to form a thiophosphine and a disulfide bond, yielding no net antibody free thiols for conjugation. Antibodies with higher levels of trisulfide bonds require a greater TCEP:antibody molar ratio to achieve the targeted drug-to-antibody ratio.
Angiotensin II type 1 receptor expression in ovarian cancer and its correlation with tumour angiogenesis and patient survival (2006)

Angiotensin II, a main effector peptide in the renin-angiotensin system, acts as a growth-promoting and angiogenic factor via type 1 angiotensin II receptors (AT(1)R). We have recently demonstrated that angiotensin II enhanced tumour cell invasion and vascular endothelial growth factor (VEGF) secretion via AT1R in ovarian cancer cell lines in vitro. The aim of the present study was to determine whether AT1R expression in ovarian cancer is correlated with clinicopathological parameters, angiogenic factors and patient survival. Immunohistochemical staining for AT1R, VEGF, CD34 and proliferating cell nuclear antigen (PCNA) were analysed in ovarian cancer tissues (n = 67). Intratumour microvessel density (MVD) was analysed by counting the CD34-positive endothelial cells. Type 1 angiotensin II receptors were expressed in 85% of the cases examined, of which 55% were strongly positive. Type 1 angiotensin II receptors expression was positively correlated with VEGF expression intensity and MVD, but not with histological subtype, grade, FIGO stage or PCNA labelling index. In patients who had positive staining for AT1R, the overall survival and progression-free survival were significantly poor (P = 0.041 and 0.017, respectively) as compared to those in patients who had negative staining for AT1R, although VEGF, but not AT1R, was an independent prognostic factor on multivariate analysis. These results demonstrated that AT1R correlated with tumour angiogenesis and poor patient outcome in ovarian cancer, suggesting its clinical potential for a novel molecular target in strategies for ovarian cancer treatment.
U1 snRNP-Dependent Function of TIAR in the Regulation of Alternative RNA Processing of the Human Calcitonin/CGRP Pre-mRNA (2003)

Alternative RNA processing of human calcitonin/CGRP pre-mRNA is regulated by an intronic enhancer element. Previous studies have demonstrated that multiple sequence motifs within the enhancer and a number of trans-acting factors play critical roles in the regulation. Here, we report the identification of TIAR as a novel player in the regulation of human calcitonin/CGRP alternative RNA processing. TIAR binds to the U tract sequence motif downstream of a pseudo 5' splice site within the previously characterized intron enhancer element. Binding of TIAR promotes inclusion of the alternative 3'-terminal exon located more than 200 nucleotides upstream from the U tract. In cells that preferentially include this exon, overexpression of a mutant TIAR that lacks the RNA binding domains suppressed inclusion of this exon. In this report, we also demonstrate an unusual novel interaction between U6 snRNA and the pseudo 5' splice site, which was shown previously to bind U1 snRNA. Interestingly, TIAR binding to the U tract sequence depends on the interaction of not only U1 but also U6 snRNA with the pseudo 5' splice site. Conversely, TIAR binding promotes U6 snRNA binding to its target. The synergistic relationship between TIAR and U6 snRNA strongly suggests a novel role of U6 snRNP in regulated alternative RNA processing.
Mining Feature-Opinion in Online Customer Reviews for Opinion Summarization (2020)

Online customer reviews is considered as a significant informative resource which is useful for both potential customers and product manufacturers. In web pages, the reviews are written in natural language and are unstructured-free-texts scheme. The task of manually scanning through large amounts of review one by one is computational burden and is not practically implemented with respect to businesses and customer perspectives. Therefore it is more efficient to automatically process the various reviews and provide the necessary information in a suitable form. The high-level problem of opinion summarization addresses how to determine the sentiment, attitude or opinion that an author expressed in natural language text with respect to a certain feature. In this paper, we dedicate our work to the main subtask of opinion summarization. The task of product feature and opinion extraction is critical to opinion summarization, because its effectiveness significantly affects the performance of opinion orientation identification. It is important to properly identify the semantic relationships between product features and opinions. We proposed an approach for mining product feature and opinion based on the consideration of syntactic information and semantic information. By applying dependency relations and ontological knowledge with probabilistic based model, the result of our experiments shows that our approach is more flexible and effective.
Design and Validation of a Novel MR-Compatible Sensor for Respiratory Motion Modeling and Correction (2016)

It provides an alternative sensor solution for the respiratory motion problem during MR imaging and may improve the convenience of patient setup.
An Automatic Detection Scheme of Acute Stanford Type A Aortic Dissection Based on DCNNs in CTA Images (2019)

As a severely life-threatening disease, acute Stanford type A aortic dissection brings patients with high potential of death. Computed Tomography Angiography (CTA) images become the effective diagnostic basis of aortic dissection. In this paper, we propose a scheme for automatic patient-level and site-level detection of aortic dissection based on Deep Convolutional Neural Networks (DCNNs) in order to relieve the burden on doctors and diagnose accurately and timely. Firstly, Mask R-CNN is adopted to precisely detect and segment the aorta from the original CTA images. Taking advantage of spatial continuity among CTA images, we put forward an area-wise screening method to remove a handful of unsatisfactory segmentation results. Then we process the segmented aorta images to extract the edges by Canny edge detector. Finally, two ResNets are employed in processed aorta images for aortic dissection detection. Specially, we can detect not only the ascending and descending aorta, but also the aortic arch, which may be the site of onset. We tested on over 3500 images, achieving an accuracy of 98.66% in slice-level detection, 96.51% in patient-level detection and 91.47% in site-level detection.
Definition of Functionally Important Mechanistic Differences among Selective Estrogen Receptor Down-regulators (2007)

One subclass of antiestrogens, the selective estrogen receptor down-regulators (SERDs), have received considerable attention of late as they competitively inhibit estrogen binding and induce a rapid, proteasome-dependent degradation of the receptor. Contained within this class of molecules is the steroidal antiestrogen ICI182,780 (faslodex), recently approved for the treatment of metastatic cancer, and GW5638/DPC974, a SERD that is currently being evaluated in the clinic. Given that mechanistic differences between different selective estrogen receptor modulators have been translated into important clinical profiles, it was of interest to determine if the SERD subclass of ligands were likewise functionally or mechanistically distinguishable. In this study, we show that although the steroidal and nonsteroidal SERDs target ERalpha for degradation, the underlying mechanism(s) are different. Of note was the identification of a specific protein-protein interaction surface presented on ERalpha in the presence of the ICI182,780-activated receptor which is required for degradation. Interestingly, this surface is also presented on ERalpha in the presence of RU58,668, a SERD that is chemically distinct from ICI182,780. This surface is not required for GW5638-mediated degradation, and thus, this SERD seems to affect ERalpha down-regulation by a different mechanism. These data suggest that sequencing of therapies using drugs of this class is likely to be possible. Finally, because of the unmet need for orally active SERDS that function similarly to ICI182,780, we have used the insights from these mechanistic studies to develop and validate a high-throughput screen for compounds of this class with improved pharmaceutical properties.
Yap1 Protein Regulates Vascular Smooth Muscle Cell Phenotypic Switch by Interaction with Myocardin (2012)

The Hippo-Yap (Yes-associated protein) signaling pathway has emerged as one of the critical pathways regulating cell proliferation, differentiation, and apoptosis in response to environmental and developmental cues. However, Yap1 roles in vascular smooth muscle cell (VSMC) biology have not been investigated. VSMCs undergo phenotypic switch, a process characterized by decreased gene expression of VSMC contractile markers and increased proliferation, migration, and matrix synthesis. The goals of the present studies were to investigate the relationship between Yap1 and VSMC phenotypic switch and to determine the molecular mechanisms by which Yap1 affects this essential process in VSMC biology. Results demonstrated that the expression of Yap1 was rapidly up-regulated by stimulation with PDGF-BB (a known inducer of phenotypic switch in VSMCs) and in the injured vessel wall. Knockdown of Yap1 impaired VSMC proliferation in vitro and enhanced the expression of VSMC contractile genes as well by increasing serum response factor binding to CArG-containing regions of VSMC-specific contractile genes within intact chromatin. Conversely, the interaction between serum response factor and its co-activator myocardin was reduced by overexpression of Yap1 in a dose-dependent manner. Taken together, these results indicate that down-regulation of Yap1 promotes VSMC contractile phenotype by both up-regulating myocardin expression and promoting the association of the serum response factor-myocardin complex with VSMC contractile gene promoters and suggest that the Yap1 signaling pathway is a central regulator of phenotypic switch of VSMCs.
The Drosophila Heterogeneous Nuclear Ribonucleoprotein M Protein, HRP59, Regulates Alternative Splicing and Controls the Production of Its Own mRNA (2006)

The Drosophila heterogeneous nuclear ribonucleoprotein M, HRP59, is a nuclear protein that associates co-transcriptionally with pre-mRNA and is necessary for the correct expression of a subset of mRNAs. We show here that the hrp59 pre-mRNA is alternatively spliced to generate two different mRNAs that differ in the presence of exon 3. Exon 3-containing transcripts make up the majority of hrp59 transcripts and encode for the functional protein, HRP59-1. Transcripts that lack exon 3 contain a premature translation termination codon and are targeted to the nonsense mediated decay pathway. We show that exon 3 inclusion is itself inhibited by HRP59 and that changes in the HRP59 protein levels affect the splicing activity of the cell. We propose that the ability of HRP59 to regulate the alternative splicing of its own pre-mRNA serves in a negative feedback loop that controls the levels of the HRP59 protein and maintains the homeostasis of the splicing environment.
Effects of Dipyridamole and Inhaled Nitric Oxide in Pediatric Patients with Pulmonary Hypertension (1998)

Inhaled nitric oxide (iNO) causes selective pulmonary vasodilation by increasing pulmonary vascular levels of cyclic guanosine monophosphate (cGMP). Dipyridamole, a drug with several putative vasodilator mechanisms, is an inhibitor of cGMP-specific phosphodiesterases (PDE5); it therefore has the potential to increase pulmonary vascular cGMP levels, lower pulmonary vascular resistance, augment iNO-induced pulmonary vasodilation, and attenuate excessive pulmonary vasoreactivity. To test dipyridamole in the pulmonary circulation, we studied pediatric patients undergoing cardiac catheterization who had severe resting pulmonary hypertension (Group 1; n = 11) or exaggerated acute hypoxia-induced pulmonary vasoconstriction (Group 2; n = 4). In Group 1, we compared the effects of iNO (20 ppm), dipyridamole (0.6 mg/kg), and combined treatments (iNO + dipyridamole) on pulmonary and systemic hemodynamics. In Group 2 we measured the pulmonary and systemic effects of dipyridamole while the patients were breathing room air and hypoxic gas mixtures (FIO2 = 0.16). One patient in Group 1 had a hypotensive response to dipyridamole and was exluded from study. In the remaining 12 studies done on 10 patients, iNO caused a selective decrease in mean pulmonary artery pressure (Ppa) and indexed pulmonary vascular resistance (PVRI) without affecting mean aortic pressure (Pao) or indexed systemic vascular resistance (SVRI). Dipyridamole decreased PVRI to similar values as did iNO, but this effect was primarily due to an increase in cardiac index (CI), and was not associated with any change in Ppa, and was associated with a decrease in Pao and SVRI. In comparison with individual treatments, combined therapy (iNO + dipyridamole) did not augment pulmonary vasodilation in the group as a whole; however, in 50% of patients, combined therapy decreased PVRI by 20% more than did iNO or dipyridamole alone. In Group 2, Ppa and the pulmonary-to-systemic resistance ratio (Rp/Rs) increased to suprasystemic levels during acute hypoxia. Pretreatment with dipyridamole blunted the increase in Ppa and Rp/Rs during repeat hypoxia, keeping Ppa at a subsystemic level and Rp/Rs < 1. We conclude that: (1) dipyridamole nonselectively reduces PVRI, primarily through an increase in CI; (2) in combination with iNO, dipyridamole augments the decrease in PVRI in some patients; and (3) dipyridamole blunts the severity of acute hypoxic pulmonary vasoconstriction in children with exaggerated hypoxic pressor responses.
BK Virus-Plasmid Expression Vector That Persists Episomally in Human Cells and Shuttles into Escherichia coli (1984)

We describe a novel expression vector, pBK TK-1, that persists episomally in human cells that can be shuttled into bacteria. This vector includes sequences from BK virus (BKV), the thymidine kinase (TK) gene of herpes simplex virus type 1, and plasmid pML-1. TK+-transformed HeLa and 143 B cells contained predominantly full-length episomes. There were typically 20 to 40 (HeLa) and 75 to 120 143 B vector copies per cell, although some 143 B transformants contained hundreds. Low-molecular-weight DNA from TK+-transformed cells introduced into Escherichia coli were recovered as plasmids that were indistinguishable from the input vector. Removal of selective pressure had no apparent effect upon the episomal status of pBK TK-1 molecules in TK+-transformed cells. BKV T antigen may play a role in episomal replication of pBK TK-1 since this viral protein was expressed in TK+ transformants and since a plasmid that contained only the BKV origin of replication was highly amplified in BKV-transformed human cells that synthesize BKV T antigen.
Efficient Selective Mapping PAPR Reduction Technique (2015)

OFDM is a form of multicarrier modulation technique with high spectral efficiency and immunity to interference. One major drawback of OFDM systems is the high peak to average power ratio (PAPR) which leads to power inefficiency and signal distortion with practical power amplifiers used at the transmitter. Selective Mapping (SLM) is a distortion less technique that can reduce PAPR efficiently without increase in power requirement and incurring data rate loss. The simulation result shows that proposed SLM technique has better PAPR reduction performance.
Speech bandwidth extension (2001)

A common narrow-band speech signal is expanded into a wide-band speech signal. The expanded signal gives the impression of a wide-band speech signal regardless of what type of vocoder is used in a receiver. The robust techniques suggested herein are based on speech acoustics and fundamentals of human hearing. That is the techniques extend the harmonic structure of the speech signal during voiced speech segments and introduce a linearly estimated amount of speech energy in the wide frequency-band. During unvoiced speech segments, a fricated noise may be introduced in the upper frequency-band.
Synthesis of Electronically Diverse Tetraarylimidazolylidene Carbenes via Catalytic Aldimine Coupling (2008)

A new method for synthesizing symmetrical N-heterocyclic imidazolium salts is described. Catalytic coupling of aldimines with cyanide followed by oxidation gives alpha-diketimines, which can then be cyclized with formaldehyde in acidic media. This two-step procedure requires no chromatography and allows the synthesis of electronically diverse 1,3,4,5-tetraarylimidazolylidene carbenes.
Electromagnetic interference shielding properties of carbon nanotube buckypaper composites (2009)

Preformed carbon nanotube thin films (10-20 microm), or buckypapers (BPs), consist of dense and entangled nanotube networks, which demonstrate high electrical conductivity and provide potential lightweight electromagnetic interference (EMI) solutions for composite structures. Nanocomposite laminates consisting of various proportions of single-walled and multi-walled carbon nanotubes, having different conductivity, and with different stacking structures, were studied. Single-layer BP composites showed shielding effectiveness (SE) of 20-60 dB, depending on the BP conductivity within a 2-18 GHz frequency range. The effects on EMI SE performance of composite laminate structures made with BPs of different conductivity values and epoxy or polyethylene insulating layer stacking sequences were studied. The results were also compared against the predictions from a modified EMI SE model. The predicted trends of SE value and frequency dependence were consistent with the experimental results, revealing that adjusting the number of BP layers and appropriate arrangement of the BP conducting layers and insulators can increase the EMI SE from 45 dB to close to 100 dB owing to the utilization of the double-shielding effect.
Phytoestrogen intake and prostate cancer: A case‐control study using a new database (1999)

In the last several years, attention has been focused on comparing the Western diet, which is rich in fat, protein, and refined carbohydrates, with the Asian diet, which is rich in phytoestrogens, as a possible explanation for the contrasting rates of clinically relevant prostate cancer. Phytoestrogens, plant-derived nutrients, include several isoflavones, flavonoids, lignans, phytosterols, and coumestans, some of which have been postulated as having anticarcinogenic properties. Using a new database, we examined the role of phytoestrogen intake and prostate cancer risk in 83 Caucasian cases and 107 controls. Controls reported consuming higher amounts of foods containing genistein, daidzein, and coumestrol and lower amounts of foods containing campesterol and stigmasterol. Multivariate analysis, after adjustment for age, family history of prostate cancer, alcohol consumption, and total calorie intake, showed an inverse association between coumestrol (p = 0.03) and daidzein (p = 0.07) and prostate cancer risk. Genistein, the most studied phytoestrogen, showed a slight protective effect (p = 0.26). However, a positive association was found between campesterol (p = 0.08) and stigmasterol (p = 0.03) and risk of prostate cancer. These results are suggestive of a possible relationship between phytoestrogen intake and prostate cancer risk. Larger comprehensive studies are needed to further refine the role of phytoestrogen intake in prostate cancer risk.