gebhart/patrepeval huggingface dataset:
Extending the Cytoplasmic Tail of the Influenza A Virus M2 Protein Leads to Reduced Virus Replication In Vivo but Not In Vitro (2007)

A carboxy-terminal epitope tag introduced into the coding region of the A/WSN/33 M2 protein resulted in a recombinant virus (rWSN M2myc) which replicated to titers similar to those of the parental virus (rWSN) in MDCK cells. The rWSN M2myc virus was attenuated in its ability to induce mortality and weight loss after the intranasal inoculation of BALB/c mice, indicating that the M2 cytoplasmic tail plays a role in virus virulence. Mice infected with rWSN M2myc were completely protected from subsequent challenge with rWSN, suggesting that epitope tagging of the M2 protein may be a useful way of attenuating influenza A virus strains.
Polycystin-2, the protein mutated in autosomal dominant polycystic kidney disease (ADPKD), is a Ca <sup>2+</sup> -permeable nonselective cation channel (2000)

Defects in polycystin-2, a ubiquitous transmembrane glycoprotein of unknown function, is a major cause of autosomal dominant polycystic kidney disease (ADPKD), whose manifestation entails the development of fluid-filled cysts in target organs. Here, we demonstrate that polycystin-2 is present in term human syncytiotrophoblast, where it behaves as a nonselective cation channel. Lipid bilayer reconstitution of polycystin-2-positive human syncytiotrophoblast apical membranes displayed a nonselective cation channel with multiple subconductance states, and a high perm-selectivity to Ca2+. This channel was inhibited by anti-polycystin-2 antibody, Ca2+, La3+, Gd3+, and the diuretic amiloride. Channel function by polycystin-2 was confirmed by patch-clamping experiments of polycystin-2 heterologously infected Sf9 insect cells. Further, purified insect cell-derived recombinant polycystin-2 and in vitro translated human polycystin-2 had similar ion channel activity. The polycystin-2 channel may be associated with fluid accumulation and/or ion transport regulation in target epithelia, including placenta. Dysregulation of this channel provides a mechanism for the onset and progression of ADPKD.
ChemInform Abstract: Synthesis of 2‐exo‐Methylenepenam (II) and 3‐Chloro‐δ3‐cephem ( III) Through a Sequential Reductive 1,2‐Elimination/S‐S Bond Fission or Chloride Ion‐Addition/Cyclization of 3,4‐Disubstituted 2‐Butenoates (I) in Metal Salt/Metal Combinations. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Antiapoptotic Signaling Generated by Caspase-Induced Cleavage of RasGAP (2001)

Activation of caspases 3 and 9 is thought to commit a cell irreversibly to apoptosis. There are, however, several documented situations (e.g., during erythroblast differentiation) in which caspases are activated and caspase substrates are cleaved with no associated apoptotic response. Why the cleavage of caspase substrates leads to cell death in certain cases but not in others is unclear. One possibility is that some caspase substrates generate antiapoptotic signals when cleaved. Here we show that RasGAP is one such protein. Caspases cleave RasGAP into a C-terminal fragment (fragment C) and an N-terminal fragment (fragment N). Fragment C expressed alone induces apoptosis, but this effect could be totally blocked by fragment N. Fragment N could also block apoptosis induced by low levels of caspase 9. As caspase activity increases, fragment N is further cleaved into fragments N1 and N2. Apoptosis induced by high levels of caspase 9 or by cisplatin was strongly potentiated by fragment N1 or N2 but not by fragment N. The present study supports a model in which RasGAP functions as a sensor of caspase activity to determine whether or not a cell should survive. When caspases are mildly activated, the partial cleavage of RasGAP protects cells from apoptosis. When caspase activity reaches levels that allow completion of RasGAP cleavage, the resulting RasGAP fragments turn into potent proapoptotic molecules.
<title>Nanosensors: design and application to site-specific cellular analyses</title> (2002)

We report the development and application of an antibody-based nanoprobe for in situ measurements within a single cell. The nanoprobe has an antibody-based probe targeted to benzopyrene tetrol (BPT), a metabolite of the carcinogen benzo[a]pyrene (BaP) and the BaP-DNA adduct. Detection of BPT is of biomedical interest since this species can potentially serve as a biomarker for the monitoring of DNA damage due to BaP exposure and for possible pre-cancer diagnoses. The measurements were performed on the rat liver epithelial Clone 9 cell line, which was used as the model cell system. Nanoprobes were inserted into individual cells, incubated five minutes to allow antigen-antibody binding, and then removed for fluorescence detection. Prior to measurements, the cells had been treated with BPT. A concentration of 9.6 +/- 0.2 x 10<SUP>-11</SUP> M has been determined for BPT in the individual cells investigated. The results demonstrate the possibility of in situ measurements inside a single cell using an antibody-based nanoprobe.
Diet Quality Influences the δ13C and δ15N of Locusts and Their Biochemical Components (1998)

To determine whether relative enrichments of 15N and 13C in locusts are influenced by diet, locust nymphs were raised from hatchlings to adults on either seedling wheat or maize. Maize provided less hexose sugars and protein per gram than did wheat. Maize also depends on the C4 form of photosynthesis, while wheat uses the C3 form; this difference in photosynthetic pathways produces two distinguishable ranges of 13C values.The lower-quality maize diet corresponded to a 5.1 increase in animal 15N, relative to diet, whereas the wheat diet corresponded to an increase of only 2.3 . The maize-fed animals were more 13C-depleted in lipid, trehalose and chitin than those fed wheat. The results for 15N and 13C suggest that substrate recycling occurred on the low-quality maize diet. Consequently, we examined the variations in the isotopic differences between locusts and their diet at the biochemical level.
Visualization of 3D sound field using see-through head mounted display (2017)

We propose a visualization system of three-dimensional (3D) sound information using video and optical see-through head mounted displays (ST-HMDs). The Mixed Reality (MR) displays enable intuitive understanding of 3D information of a sound field which is quite difficult to project onto an ordinary two-dimensional (2D) display in an easily understandable way. As examples of the visualization, the sound intensity (a stationary vector field representing the energy flow of sound) around a speaker and a motor engine is shown.
[Research advance of brain natriuretic peptide and N-terminal brain natriuretic peptide in the diagnosis and treatment of pediatric cardiovascular diseases]. (2012)

Brain natriuretic peptide (BNP) and N-terminal brain natriuretic peptide (NT-proBNP) are important biomarkers for pediatric cardiovascular diseases. Peptide levels are associated with age and gender. Current studies have shown that BNP and NT-proBNP are valuable in the diagnosis of heart failure, with a high specificity and sensitivity. They also contribute to differentiating heart failure from acute respiratory distress induced by simple pulmonary factors. In addition, BNP and NT-proBNP are useful in the evaluation of disease severity and treatment guidance in children with pulmonary hypertension, cardiomyopathy and Kawasaki disease. Current limitations include the relatively small sample size of the study, the detection method and a range of normal values that are not completely uniform.
Surveillance for waterborne disease and outbreaks associated with recreational water use and other aquatic facility-associated health events--United States, 2005-2006. (2008)

CDC uses WBDO surveillance data to 1) identify the etiologic agents, types of aquatic venues, water-treatment systems, and deficiencies associated with outbreaks and case reports; 2) evaluate the adequacy of efforts (i.e., regulations and public awareness activities) to provide safe recreational water; 3) expand the scope of understanding about waterborne disease and health events associated with swimming and aquatics facilities; and 4) establish public health prevention priorities, data, and messaging that might lead to improved regulations, guidelines, and prevention measures at the local, state, and federal levels.
Effects of focused ion beam irradiation on MOS transistors (2002)

The effects of irradiation from a focused ion beam (FIB) system on MOS transistors are reported systematically for the first time. Three MOS transistor technologies, with 0.5, 1, and 3 /spl mu/m minimum feature sizes and with gate oxide thicknesses ranging from 11 to 50 nm, were analyzed. Significant shifts in transistor parameters (such as threshold voltage, transconductance, and mobility) were observed following irradiation with a 30 keV Ga/sup +/ focused ion beam with ion doses varying by over 5 orders of magnitude. The apparent damage mechanism (which involved the creation of interface traps, oxide trapped charge, or both) and extent of damage were different for each of the three technologies investigated.
Transient erectile dysfunction associated with intramuscular injection of botulinum toxin type A. (2002)

Autonomic nervous system dysfunction occurs rarely after botulinum toxin type A (BTX-A) intramuscular injections. We report a case of a 23-year-old man with spastic diplegia who had transient erectile dysfunction after intramuscular injection of BTX-A (total dosage, 300 IU, body weight 95 kg) in both hamstring muscles. Some investigators believe that the local spread of the toxin is responsible for autonomic dysfunction, while others believe that the transportation of the toxin to the spinal cord via retrograde flow or via the blood flow after entering the circulation are possible mechanisms of neurologic side effects. On the basis of our case, a retrograde axoplasmic flow to the spinal cord could probably occur because the spinal cord level of hamstring muscles is close to spinal cord levels responsible for erection control.
The humoral response to Gardasil over four years as defined by Total IgG and competitive Luminex immunoassay (2011)

Safe and effective vaccines against anogenital human papillomaviruses (HPV) are now available. These vaccines, composed of virus-like particles (VLPs) made from the L1 major capsid protein of specific HPV types, induce a polyclonal antibody response directed against specific conformational and linear epitopes displayed on the VLP. Numerous studies indicated the importance of neutralizing antibodies in protection from infection. However, our understanding of the antibody responses to these vaccines is not complete, and there is no established immune correlate of protection nor antibody threshold that correlates with protection against HPV infection or disease. In the current study, antibody responses of young women to Gardasil®, the quadrivalent HPV 6, 11, 16 and 18 L1 VLP vaccine (qHPV), were assessed through 48 months (M) in total IgG and competitive Luminex immunoassays (total IgG LIA and cLIA). The total IgG LIA was developed as a research assay to evaluate preclinical multivalent HPV VLP vaccine formulations. The cLIA simultaneously evaluates the antibody response to a unique conformational, neutralizing epitope on each of the four HPV types present in the quadrivalent vaccine; HPV 6, 11, 16 and 18. The same sera from women vaccinated with the qHPV vaccine were tested in both the total IgG LIA and the cLIA assays. The proportion of vaccinated women achieving seropositivity and the anti-HPV VLP total IgG and cLIA geometric mean titers (GMTs) were summarized at M7, M24, M48 based on the serostatus cut-points defined for each immunoassay. Overall, greater than 99% of subjects seroconverted to all four vaccine types in both assays; GMTs peaked at M7. For all four HPV types, regardless of the immunoassay used, the most significant decline in GMTs was observed between M7 and M24. By M24, the antibody titers had reached a plateau and minimal declines in antibody titers were observed between M24 and M48 for all four HPV types in both immunoassays. Testing the same sera, seropositivity for M48 HPV18 remained high (96.7%) in the total IgG LIA, but was 64.8% in the cLIA. The current study illustrates potential important differences in serologic assays utilized in the clinical trials of the two currently available HPV VLP vaccines (quadrivalent and bivalent). Differences in seropositivity status are attributed to the measurement parameters and sensitivity of the individual immunoassays and do not indicate reduced anti-HPV18 protective antibodies.
Enhancement of post‐operative healing using platelet rich plasma (PRP) (2006)

Autologous platelet‐rich plasma (PRP), when applied to an oral surgical site, enhances bone and soft tissue healing. In a retrospective study of 902 mandibular molar extractions, with or without PRP, there was a significantly lower incidence of alveolar osteitis (AO). PRP diminished the incidence of AO for other related factors such as tooth position, tooth number, gender, birth control medications and smoking. The project also includes a prospective clinical study of the bilateral removal of mandibular third molars. One side received the PRP treatment with a gelatin medium, and the contra‐lateral side received the gelatin medium only. Both patients and clinical evaluators were blinded. Post‐operative pain, gingival and bone tissue healing were evaluated. PRP treatment did not alter pain perception, but PRP‐treated sites had improved soft tissue healing with less post‐operative bleeding and edema. Bone healing was evaluated with digital radiography and CAT scan analysis over a 6 month period. PRP treatment improved the rate and degree of bone formation versus contra lateral control sites. PRP use may also be beneficial in other oral surgical procedures.
A Fast and Effective Memristor-Based Method for Finding Approximate Eigenvalues and Eigenvectors of Non-negative Matrices (2018)

Throughout many scientific and engineering fields, including control theory, quantum mechanics, advanced dynamics, and network theory, a great many important applications rely on the spectral decomposition of matrices. Traditional methods such as the power iteration method, Jacobi eigenvalue method, and QR decomposition are commonly used to compute the eigenvalues and eigenvectors of a square and symmetric matrix. However, these methods suffer from certain drawbacks: in particular, the power iteration method can only find the leading eigen-pair (i.e., the largest eigenvalue and its corresponding eigenvector), while the Jacobi and QR decomposition methods face significant performance limitations when facing with large scale matrices. Typically, even producing approximate eigenpairs of a general square matrix requires at least O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) time complexity, where N is the number of rows of the matrix. In this work, we exploit the newly developed memristor technology to propose a low-complexity, scalable memristorbased method for deriving a set of dominant eigenvalues and eigenvectors for real symmetric non-negative matrices. The time complexity for our proposed algorithm is O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Δ) (where Δ governs the accuracy). We present experimental studies to simulate the memristor-supporting algorithm, with results demonstrating that the average error for our method is within 4%, while its performance is up to 1.78X better than traditional methods.
A Corpus and Cloze Evaluation for Deeper Understanding of Commonsense Stories (2016)

Nasrin Mostafazadeh, Nathanael Chambers, Xiaodong He, Devi Parikh, Dhruv Batra, Lucy Vanderwende, Pushmeet Kohli, James Allen. Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2016.
Effect of an AlN buffer layer on the epitaxial growth of InN by molecular-beam epitaxy (2001)

The effect of an AlN buffer layer on the epitaxial growth of InN by molecular-beam epitaxy (MBE) is studied. Using an AlN buffer layer can significantly improve the structural and electrical properties of InN. With increasing thickness of the AlN buffer layer, the Hall mobility of InN will monotonically increase while the electron carrier concentration decreases. The surface morphology of the film also improves. A Hall mobility of more than 800 cm2/V s with a carrier concentration of 2–3×1018 cm−3 at room temperature can be routinely obtained on ∼0.1 μm InN film. More importantly, it is found that under optimum growth conditions, by using an AlN buffer layer, InN films with comparable quality can be achieved by the conventional MBE technique compared to InN grown by migration-enhanced epitaxy. Increasing InN thickness also increases Hall mobility.
Metabolomics‐driven identification of adenosine deaminase as therapeutic target in a mouse model of Parkinson's disease (2019)

Abstract Neuroinflammation is one of the driving forces of progressive neurodegeneration in Parkinson’s disease (PD). The metabolomics approach has been proved highly useful in identifying potential therapeutic targets. Here, to identify inflammation‐relevant treatment targets for PD, mass spectrometry‐based untargeted metabolomics was applied to characterize metabolic changes in the striatum of mice with double‐hit PD induced by lipopolysaccharide plus 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP). Seven days after the final MPTP administration, metabolites from the purine metabolism pathway, including adenosine, 1‐methyladenosine, adenine, inosine, hypoxanthine, xanthine, xanthosine, and guanosine, were found to be significantly dysregulated. The metabolite–protein interaction network and changes in the concentration ratio of these metabolites indicated that adenosine and adenosine deaminase (ADA; EC 3.5.4.4) were the most promising therapeutic targets and adenosine augmentation might be a rational approach to slow PD progression. These findings were then verified in a subacute MPTP‐induced PD mouse model treated with ADA inhibition alone or in conjunction with antagonism of adenosine A 2A receptors (A 2A R). Behavioral, biochemical, and immunohistochemical analysis demonstrated that ADA inhibition significantly ameliorated the MPTP‐mediated motor disabilities, dopamine depletion, and dopaminergic cell death. Significantly enhanced neuroprotective effects were further observed when the ADA inhibitor was utilized in conjunction with an A 2A R antagonist. Together, our study indicated for the first time that ADA inhibitors protected against neurodegeneration induced by the neurotoxin MPTP, and ADA inhibitors in combination with A 2A R antagonists showed additive antiparkinsonian effects. image
Data Programming: Creating Large Training Sets, Quickly. (2016)

Large labeled training sets are the critical building blocks of supervised learning methods and are key enablers of deep learning techniques. For some applications, creating labeled training sets is the most time-consuming and expensive part of applying machine learning. We therefore propose a paradigm for the programmatic creation of training sets called <i>data programming</i> in which users express weak supervision strategies or domain heuristics as <i>labeling functions</i>, which are programs that label subsets of the data, but that are noisy and may conflict. We show that by explicitly representing this training set labeling process as a generative model, we can "denoise" the generated training set, and establish theoretically that we can recover the parameters of these generative models in a handful of settings. We then show how to modify a discriminative loss function to make it noise-aware, and demonstrate our method over a range of discriminative models including logistic regression and LSTMs. Experimentally, on the 2014 TAC-KBP Slot Filling challenge, we show that data programming would have led to a new winning score, and also show that applying data programming to an LSTM model leads to a TAC-KBP score almost 6 F1 points over a state-of-the-art LSTM baseline (and into second place in the competition). Additionally, in initial user studies we observed that data programming may be an easier way for non-experts to create machine learning models when training data is limited or unavailable.
Complexes of IgG and Plasma Proteins in Factor VIIIPreparations - a Possible Cause of Adverse Reactions (1985)

IgG in factor VIII preparations was studied as a possible cause of adverse reactions following infusion of hemophiliacs. Thin-layer immuno-gel filtration analysis of nine products from seven firms demonstrated aggregated and monomeric IgG at highly variable amounts and proportions. These factor VIII products contained from 20 to 700 mg IgG per 1000 IU of factor VIII; IgG-fibrinogen complexes were demonstrated by doubleantibody testing. A relationship is suggested between aggregated IgG and/or IgG complexes in factor VIII concentrates and adverse clinical reactions. They may also partially explain abnormalities and aberrations of the immune system previously reported in hemophiliacs.
Efficient two-pass rate control scheme based on adjusting distribution of discrete cosine transform coefficients (2010)

Video compression systems use rate control (RC) to achieve high visual quality under the constraint of a target bitrate. This work develops a two-pass variable bit rate (VBR) coding algorithm based on a group-of-picture (GOP) level ρ-domain model. The discrete cosine transform (DCT) coefficients distribution that is generated in the first pass is modified to select an appropriate quantisation parameter (QP) that is used in the second pass, according to the target bit budget of GOP. Besides, the other important parameters, such as the header bits, are also predicted in the second pass to improve the RC ability. If a scene change happens in the first pass coding, the QP value will be adjusted in the second pass coding. Then, the QP is refined based on the textural complexity of every macroblock (MB). Experimental results demonstrate that the proposed VBR methods can not only achieve excellent visual quality but also reduce the variation in distortion even if a scene change happens.
Synthesis of <scp>l</scp>-<i>β</i>-3‘-Deoxy-3‘,3‘-difluoro-4‘-thionucleosides (2006)

[Structure: see text] An efficient route to L-beta-3'-deoxy-3',3'-difluoro-4'-thionucleosides, thio-containing analogues of highly bioactive gemcitabine, is described. Our synthesis highlighted the installation of the thioacetyl group in high efficiency and construction of 3-deoxy-3,3-difluorothiofuranose skeleton in a novel method.
Tetralactam-modified gold electrodes for amperometric detection of acrylic acid (2008)

The presence of toxic acrylamide in a wide range of food products such as potato crisps, French fries or bread has been confirmed by Swedish scientists from Stockholm University. The neurotoxicity and possible carcinogenicity of this compound and its metabolites compel us to control them by quantitative and qualitative assays. Exposing acrylamide to pH extremes results in its hydrolysis to acrylic acid or its salt. In this work, we present the use of gold electrodes coated with self-assembled monolayers (SAMs) containing tetralactam molecules and its precursor as active elements for voltammetric detection of acrylic acid in water solution. The host molecules have been immobilised on the electrode surface by covalent Au–S bond or by embedment method into the thiol layer via hydrophobic and van der Waals interactions. Interactions with analytes were confirmed by Osteryoung square-wave voltammetry.