gebhart/patrepeval huggingface dataset:
Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies (2013)

Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes.
DaPanda: Detecting Aggressive Push Notifications in Android Apps (2019)

Mobile push notifications have been widely used in mobile platforms to deliver all sorts of information to app users. Although it offers great convenience for both app developers and mobile users, this feature was frequently reported to serve malicious and aggressive purposes, such as delivering annoying push notification advertisement. However, to the best of our knowledge, this problem has not been studied by our research community so far. To fill the void, this paper presents the first study to detect aggressive push notifications and further characterize them in the global mobile app ecosystem on a large scale. To this end, we first provide a taxonomy of mobile push notifications and identify the aggressive ones using a crowdsourcing-based method. Then we propose sc DaPanda, a novel hybrid approach, aiming at automatically detecting aggressive push notifications in Android apps. sc DaPanda leverages a guided testing approach to systematically trigger and record push notifications. By instrumenting the Android framework, sc DaPanda further collects all notification-relevant runtime information to flag the aggressive ones. Our experimental results show that sc DaPanda is capable of detecting different types of aggressive push notifications effectively in an automated way. By applying sc DaPanda to 20,000 Android apps from different app markets, it yields over 1,000 aggressive notifications, which have been further confirmed as true positives. Our in-depth analysis further reveals that aggressive notifications are prevalent across different markets and could be manifested in all the phases in the lifecycle of push notifications. It is hence urgent for our community to take actions to detect and mitigate apps involving aggressive push notifications.
Avian Influenza H5N1: Risks at the Human–Animal Interface (2007)

To most effectively decrease the risk of a pandemic, the public health and animal health sectors--those which are responsible for protecting and improving the health of humans and animals, respectively--must collaborate to decrease human exposure to HPAI virus, both by controlling virus circulation among poultry and by assessing the risks of human exposure to avian influenza virus at the human-animal interface from primary production through consumption of poultry and poultry products, and implementing risk-based mitigation measures.
Vacuum mechatronics and self-contained manufacturing for microelectronics processing (2003)

The Center for Robotic Systems in Microelectronics (CRSM) has developed the core of a self-contained automated robotic factory (SCARF). This includes a central chamber with various transfer and monitoring ports, a vacuum-compatible robot for wafer transfer, and a particle monitoring system, all under automation. The cylindrical coordinate SCARF vacuum-compatible robot is unique due to its fully vacuum-compatible motors, closed-loop control, and configuration which makes it an ideal central component for a self contained manufacturing system. The CRSM is currently developing a color vision system for in-vacuum inspection and measurement which will be an integral part of SCARF. Details of the SCARF system and robot are discussed, as well as the key technical issues facing the development of self-contained manufacturing systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
State of hepatitis B virus DNA in hepatocytes of patients with hepatitis B surface antigen-positive and -negative liver diseases. (1981)

Using the Southern blot technique and cloned hepatitis B virus (HBV) DNA as a probe, we studied the state of HBV DNA in the liver of 13 patients with hepatocellular carcinoma, 17 patients with chronic hepatitis, and 2 patients with acute hepatitis. The hybridization results were compared with the serological and immunohistological data. Integration of HBV DNA in cellular DNA of the liver from patients with hepatocellular carcinoma was demonstrated. In two patients from which tumorous and nontumorous liver tissue samples were available the integration patterns were different. In one patient with hepatitis B e antigen (HBeAg)-positive early hepatocellular carcinoma, free viral DNA was present in the liver. In some patients with HBeAg-negative chronic hepatitis, without tumor, integration of HBV DNA in cellular DNA was also demonstrated. This suggests that HBV is not the only factor involved in the development of a tumor. In patients with HBeAg-positive chronic hepatitis, free viral DNA was detected in the liver. In the two acute hepatitis patients analyzed, the restriction endonuclease patterns strongly suggested HBV DNA integration. Therefore, viral DNA integration seems to occur early in infection. Whatever the form of the disease, discrete bands were observed, suggesting the existence of limited and specific integration sites in host cellular DNA. The presence of integrated or free DNA sequences has implications for antiviral therapy. In addition, detection of HBV DNA in the liver is another sensitive viral marker that could be useful for diagnostic purposes.
Accelerated volumetric MRI with a SENSE/GRAPPA combination (2006)

The proposed SENSE/GRAPPA combination for 3D imaging allows the GRAPPA method to be applied in combination with 2D undersampling. Because the SENSE/GRAPPA combination is not based on knowledge of spatial coil sensitivities, it should be the method of choice whenever it is difficult to extract the sensitivity information.
Male and female <i>Fmr1</i> knockout mice on C57 albino background exhibit spatial learning and memory impairments (2010)

Impaired spatial learning is a prominent deficit in fragile X syndrome (FXS). Previous studies using the Fmr1 knockout (KO) mouse model of FXS have not consistently reported a deficit in spatial learning. Fmr1 KO mice bred onto an albino C57BL/6J-Tyr(c-Brd) background showed significant deficits in several primary measures of performance during place navigation and probe trials in the Morris water maze. Fmr1 KO mice were also impaired during a serial reversal version of the water maze task. We examined fear conditioning as an additional cognitive screen. Knockout mice exhibited contextual memory deficits when trained with unsignaled shocks; however, deficits were not found in a separate group of KO mice trained with signaled shocks. No potentially confounding genotypic differences in locomotor activity were observed. A decreased anxiety-like profile was apparent in the open field, as others have noted, and also in the platform test. Also as previously reported, startle reactivity to loud auditory stimuli was decreased, prepulse inhibition and social interaction increased in KO mice. Female Fmr1 KO mice were tested along with male KO mice in all assays, except for social interaction. The female and male KO exhibited very similar impairments indicating that sex does not generally drive the behavioral symptoms of the disorder. Our results suggest that procedural factors, such as the use of albino mice, may help to reliably detect spatial learning and memory impairments in both sexes of Fmr1 KO mice, making it more useful for understanding FXS and a platform for evaluating potential therapeutics.
Ultrahigh-transparency, ultrahigh-haze nanograss glass with fluid-induced switchable haze (2017)

Optoelectronic applications such as solar cells and light-emitting diodes would benefit from glass substrates with both high transparency and high haze to improve power conversion and extraction efficiencies, respectively. In this Letter, we demonstrate glass with grass-like nanostructures that displays ultrahigh transparency and ultrahigh haze (both over 95% at wavelength 550 nm). The nanograss is fabricated by a scalable maskless reactive ion etching process in fused silica where the height is controlled via the etch time. We demonstrate that shorter nanograss ( 6  μm height), though the transmission decreases slightly to less than 92%. Finally, we demonstrate that various fluids with a similar index of refraction as the glass may be used to switch the haze of these substrates.
Comparison of Methods for Target Detection and Applications Using Polarimetric SAR Image (2008)

Abstract — Polarimetric SAR (PolSAR) is sensitive to the orientation and characters of object and polarimetry could yield several new descriptive radar target detection parameters and lead to the improvement of radar detection algorithms. Target decomposition theory has been used for information extraction in PolSAR, and it can also explore the phase message in PolSAR data. In this paper, a comparison of polarimetric target decomposition methods is proposed. We generate a validity test for these methods using DLR ESAR L-band full polarized data. Results show that among many target decomposition algorithms, the coherent and incoherent formulations are quite comparable in distinguishing natural targets and man-made buildings. Pauli decomposition, Cameron decomposition and Freeman decomposition are suitable for the detection of natural targets. On the other hand, SDH decomposition, OEC decomposition, and Four-component model, in particular, are very useful for man-made target extraction. 1.
Structural and Energetic Basis of Carbohydrate–Aromatic Packing Interactions in Proteins (2013)

Carbohydrate-aromatic interactions mediate many biological processes. However, the structure-energy relationships underpinning direct carbohydrate-aromatic packing interactions in aqueous solution have been difficult to assess experimentally and remain elusive. Here, we determine the structures and folding energetics of chemically synthesized glycoproteins to quantify the contributions of the hydrophobic effect and CH-π interactions to carbohydrate-aromatic packing interactions in proteins. We find that the hydrophobic effect contributes significantly to protein-carbohydrate interactions. Interactions between carbohydrates and aromatic amino acid side chains, however, are supplemented by CH-π interactions. The strengths of experimentally determined carbohydrate CH-π interactions do not correlate with the electrostatic properties of the involved aromatic residues, suggesting that the electrostatic component of CH-π interactions in aqueous solution is small. Thus, tight binding of carbohydrates and aromatic residues is driven by the hydrophobic effect and CH-π interactions featuring a dominating dispersive component.
A technique of mathematical expression structure analysis for the handwriting input system (1999)

We propose a new practical user interface to input mathematical expressions into a computer using a data tablet or an electron board. The system recognizes mathematical expressions of high school level (until the first year of university), and the results are output in LATEX-source format. For the character recognition, we use a 3/spl times/5-mesh directional element feature and some additional features which are robust against the distortion. As for the segmentation of characters and the structure analysis of mathematical expressions, our method is considerably robust against the touching of characters and the deviation of positions in the wide range.
Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries (2009)

Abstract Background The development and maintenance of the prostate is dependent on androgens and the androgen receptor. The androgen pathway continues to be important in prostate cancer. Here, we evaluated the transcriptome of prostate cancer cells in response to androgen using long serial analysis of gene expression (LongSAGE) libraries. Results There were 131 tags (87 genes) that displayed statistically significant (p ≤ 0.001) differences in expression in response to androgen. Many of the genes identified by LongSAGE (35/87) have not been previously reported to change expression in the direction or sense observed. In regulatory regions of the promoter and/or enhancer regions of some of these genes there are confirmed or potential androgen response elements (AREs). The expression trends of 24 novel genes were validated using quantitative real time-polymerase chain reaction (qRT-PCR). These genes were: ARL6IP5, BLVRB, C19orf48, C1orf122, C6orf66, CAMK2N1, CCNI, DERA, ERRFI1, GLUL, GOLPH3, HM13, HSP90B1, MANEA, NANS, NIPSNAP3A, SLC41A1, SOD1, SVIP, TAOK3, TCP1, TMEM66, USP33 , and VTA1 . The physiological relevance of these expression trends was evaluated in vivo using the LNCaP Hollow Fibre model. Novel androgen-responsive genes identified here participate in protein synthesis and trafficking, response to oxidative stress, transcription, proliferation, apoptosis, and differentiation. Conclusion These processes may represent the molecular mechanisms of androgen-dependency of the prostate. Genes that participate in these pathways may be targets for therapies or biomarkers of prostate cancer.
PITX2c Is Expressed in the Adult Left Atrium, and Reducing Pitx2c Expression Promotes Atrial Fibrillation Inducibility and Complex Changes in Gene Expression (2011)

These findings demonstrate a physiological role for PITX2 in the adult heart and support the hypothesis that dysregulation of PITX2 expression can be responsible for susceptibility to AF.
A Decision-Making Framework for Ozone Pollution Control (2009)

In this paper, an intelligent decision-making framework (DMF) is developed to help decision makers identify cost-effective ozone control policies. High concentrations of ozone at the ground level continue to be a serious problem in numerous U.S. cities. Our DMF searches for dynamic and targeted control policies that require a lower total reduction of emissions than current control strategies based on the “trial and error” approach typically employed by state government decision makers. Our DMF utilizes a rigorous stochastic dynamic programming (SDP) formulation and incorporates an atmospheric chemistry module to model how ozone concentrations change over time. Within the atmospheric chemistry module, methods from design and analysis of computer experiments are employed to create SDP state transition equation metamodels, and critical dimensionality reduction is conducted to reduce the state-space dimension in solving our SDP problem. Results are presented from a prototype DMF for the Atlanta metropolitan region.
Mapping Genes Conferring Resistance to Phytophthora Root Rot of Soybean, Rps1a and Rps7 (2001)

A linkage map was constructed for two Phytophthora sojae Kauf. +Gerd. root rot resistance genes, Rps1a and Rps7, in soybean (Glycine max (L.) Merr.) using microsatellite or simple sequence repeat (SSR) markers. An F2 population consisting of 81 individuals derived from a cross between OX281, which carries Rps7, and Mukden, which carries Rps1a, was used as the mapping population. A linkage map consisting of 10 SSR markers was first constructed using the computer software MapMaker/EXP 3.0. Rps1a and Rps7 were then placed at two different loci in the same linkage group with LOD scores of 2.88 and 9.16, respectively. Rps1a and Rps7 were linked at a distance of 13.8 cM. Rps1a was flanked by Satt159 (0.7 cM) and Satt009 (3.2 cM). Rps7 was flanked by Satt009 (10.6 cM) and Satt125 (29.1 cM).
FACT - Fine grained Assessment of web page CredibiliTy (2019)

With more than a trillion web pages, there is a plethora of content available for consumption. Search Engine queries invariably lead to overwhelming information, parts of it relevant and some others irrelevant. Often the information provided can be conflicting, ambiguous, and inconsistent contributing to the loss of credibility of the content. In the past, researchers have proposed approaches for credibility assessment and enumerated factors influencing the credibility of web pages. In this work, we detailed a WEBCred framework for automated genre-aware credibility assessment of web pages. We developed a tool based on the proposed framework to extract web page features instances and identify genre a web page belongs to while assessing it's Genre Credibility Score ( GCS). We validated our approach on `Information Security' dataset of 8,550 URLs with 171 features across 7 genres. The supervised learning algorithm, Gradient Boosted Decision Tree classified genres with 88.75% testing accuracy over 10 fold cross-validation, an improvement over the current benchmark. We also examined our approach on `Health' domain web pages and had comparable results. The calculated GCS correlated 69% with crowdsourced Web Of Trust ( WOT) score and 13% with algorithm based Alexa ranking across 5 Information security groups. This variance in correlation states that our GCS approach aligns with human way ( WOT) as compared to algorithmic way (Alexa) of web assessment in both the experiments.
Circuit termination methodologies and their characteristics (2002)

All five commonly used passive termination techniques have application implementations in high performance digital designs. Selecting which termination type to implement for a given design is based upon matching the primary design goals and application characteristics to the characteristics of the termination techniques. Additional information, including more detailed discussions, design equations, and characteristic information for the various termination techniques, is available from CMD's Data Book and numerous Application Notes.
Recording slope and curvature contours of flexed plates using a grating shearing interferometer (1977)

A diffraction grating shearing interferometer is presented which, depending on the recording procedure, can be used to measure directly the slopes and curvatures of specularly reflecting flexed plates. Three system arrangements are described: two for slope measurement and one for curvature. One slope arrangement yields results in real time but, in general, does not compensate for initial model curvature. The second requires an additional spatial filtering step but does compensate for the initial curvature. A diffraction theory approach is used to arrive at expressions for the complex field amplitude of the light at the output plane. This leads to expressions for the fringe values. Experimental results for three types of model are also presented. Errors of 2-4% were found for the various system arrangements. In addition, an analytical expression is derived and verified experimentally, which shows that when the system is used for measuring slope, the curvature of the model limits the measuring sensitivity. The theoretical analysis shows that this is a fundamental property of grating interferometers in general. This property is then exploited as the basis of the curvature measuring technique.
Dose and Fractionation in Radiation Therapy of Curative Intent for Non-Small Cell Lung Cancer: Meta-Analysis of Randomized Trials (2016)

In trials with concurrent chemotherapy, higher radiation therapy doses resulted in poorer survival, possibly caused, at least in part, by high levels of toxicity. Where radiation therapy was given without chemotherapy, progressively higher radiation therapy doses resulted in progressively longer survival, and no upper dose level was found above which there was no further benefit. These findings support the consideration of further radiation therapy dose escalation trials, making use of modern treatment methods to reduce toxicity.
Recent Developments on the Use of Polymers as Corrosion Inhibitors - A Review (2014)

The use of corrosion inhibitors is the one the most economical and practical means of controlling metallic corrosion in different corrosive media. Interest on the use of eco-friendly organic compounds as corrosion inhibitors has extended to the use of polymers to inhibit metallic corrosion. The use of polymers as corrosion inhibitors has attracted attention and has gained wide acceptance in recent times. This has been attributed to a number of factors namely: (i) they are low cost and stable to metallic materials in acid media, (ii) they possess multiple adsorption sites, (iii) through their functional groups, they form complexes with metal ions and on the metal surface these complexes occupy a large area, thereby blanketing the surface and protecting the metal from corrosive agents present in the solution. A number of synthetic and natural polymers as metallic corrosion inhibitors have been investigated and reported. As an update to previous review work on the use of polymers as corrosion inhibitors, the present review presents most of the contributions made to the literature on the use of polymers as corrosion inhibitors of diverse metals in different corrosive media in the last four (2010-2013) years.
Field/frequency lock monitor for signal averaging with high resolution NMR spectrometers (1975)

A method for monitoring the field/frequency lock condition of a high resolution NMR spectrometer and suspending signal averaging in the event of loss or degradation of the lock is described. This procedure involves amplification and conditioning of the absorption mode lock signal, followed by analog-to-digital conversion under control of the data acquisition computer, or by a binary comparison of the lock signal amplitude with a chosen threshold value with analog circuitry.