gebhart/patrepeval huggingface dataset:
Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly, (2010)

In recent years, the opportunistic pathogen Pseudomonas aeruginosa has emerged as a major source of hospital-acquired infections. Effective treatment has proven increasingly difficult due to the spread of multidrug resistant strains and thus requires a deeper understanding of the biochemical mechanisms of pathogenicity. The central carbohydrate of the P. aeruginosa PAO1 (O5) B-band O-antigen, ManNAc(3NAc)A, has been shown to be critical for virulence and is produced in a stepwise manner by five enzymes in the Wbp pathway (WbpA, WbpB, WbpE, WbpD, and WbpI). Herein, we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) and product UDP-GlcNAc(3NH(2))A as the external aldimine at 1.9 A resolution. We also report the structures of WbpE in complex with PMP alone as well as the PLP internal aldimine and show that the dimeric structure of WbpE observed in the crystal structure is confirmed by analytical ultracentrifugation. Analysis of these structures reveals that the active site of the enzyme is composed of residues from both subunits. In particular, we show that a key residue (Arg229), which has previously been implicated in direct interactions with the alpha-carboxylate moiety of alpha-ketoglutarate, is also uniquely positioned to bestow specificity for the 6''-carboxyl group of GlcNAc(3NH(2))A through a salt bridge. This finding is intriguing because while an analogous basic residue is present in WbpE homologues that do not process 6''-carboxyl-modified saccharides, recent structural studies reveal that this side chain is retracted to accommodate a neutral C6'' atom. This work represents the first structural analysis of a nucleotide sugar aminotransferase with a bound product modified at the C2'', C3'', and C6'' positions and provides insight into a novel target for treatment of P. aeruginosa infection.
First demonstration of quasi phase matched generation of EUV high-harmonic radiation (2002)

High harmonic generation (HHG) is an excellent source of extreme ultraviolet (EUV) radiation that upconverts an intense laser pulse to much shorter wavelengths. Over the past decade, many experiments have studied this process, providing detailed insights into the physics of HHG. Phase matching the HHG process, either using a hollow waveguide,( 1 ) or using a near-plane-wave geometry, ( 2 , 3 ) increases the brightness of the source by orders of magnitude and generates and EUV beam with full spatial coherence.( 4 ) In this work, we experimentally demonstrate that phase-matching of HHG radiation can be extended to shorter wavelengths and higher pulse energies using a structured hollow waveguide. Moreover, this photonic structure results in the generation of a broad continuum that may support an isolated 250 attosecond EUV pulse, as has been previously predicted theoretically.( 5 ) This work is a compelling demonstration of the applicability of photonics technology concepts to a new region of the spectrum.
Phase I/II Study of an Anti-CD30 Monoclonal Antibody (MDX-060) in Hodgkin's Lymphoma and Anaplastic Large-Cell Lymphoma (2007)

MDX-060 was well tolerated at doses up to 15 mg/kg. MDX-060 has limited activity as a single agent, but the minimal toxicity observed and the significant proportion of patients with stable disease suggests that further study of MDX-060 in combination with other therapies is warranted.
Quantification of the Antiviral Effect of Interferon by Immunoassay of Vesicular Stomatitis Virus Proteins (1983)

A simple solid-phase immunoassay for quantification of vesicular stomatitis virus (VSV) is described. Infected cultures are lysed with deoxycholate. Samples of the lysates are transferred to PVC immunoassay plates and the amount of virus protein adsorbed to the plates is then quantified by sequential incubation with antiserum against VSV proteins and 125I-labelled Protein A. The decrease of VSV protein in interferon (IFN)-treated cultures is correlated with inhibition of formation of infectious virions; its quantification therefore allows accurate measurement of the antiviral effect. The applicability of the immunoassay for measuring the virus yield is not restricted to cells exhibiting a virus cytopathic effect. Moreover, since the decrease of virus protein is obtained at IFN concentrations lower than those that reduce cell killing by the virus, the assay provides a more sensitive measure for the IFN effect than that obtained by 'cytopathic effect inhibition' assays.
55‐1: Invited Paper : Passive Matrix Displays with Transfer‐Printed Microscale Inorganic LEDs (2016)

Displays that use direct light emission from microscale inorganic light emitting diodes (ILEDs) have the potential to be very bright and also very power efficient. High‐throughput assembly technologies that accurately and cost‐effectively deposit large arrays of ILEDs onto display substrates with high yield are key enablers for ILED displays. Transfer‐printing with elastomer stamps is a candidate assembly technology for making ILED displays. A variety of passive matrix ILED displays have been designed and fabricated using transfer‐printed microscale ILEDs.
Probabilistic construction of deterministic algorithms: Approximating packing integer programs (1986)

We consider the problem of approximating an integer program by first solving its relaxation linear program and "rounding" the resulting solution. For several packing problems, we prove probabilistically that there exists an integer solution close to the optimum of the relaxation solution. We then develop a methodology for converting such a probabilistic existence proof to a deterministic approximation algorithm. The methodology mimics the existence proof in a very strong sense.
Implementing machine learning methods with complex survey data: Lessons learned on the impacts of accounting sampling weights in gradient boosting (2023)

Despite the prominent use of complex survey data and the growing popularity of machine learning methods in epidemiologic research, few machine learning software implementations offer options for handling complex samples. A major challenge impeding the broader incorporation of machine learning into epidemiologic research is incomplete guidance for analyzing complex survey data, including the importance of sampling weights for valid prediction in target populations. Using data from 15, 820 participants in the 1988-1994 National Health and Nutrition Examination Survey cohort, we determined whether ignoring weights in gradient boosting models of all-cause mortality affected prediction, as measured by the F1 score and corresponding 95% confidence intervals. In simulations, we additionally assessed the impact of sample size, weight variability, predictor strength, and model dimensionality. In the National Health and Nutrition Examination Survey data, unweighted model performance was inflated compared to the weighted model (F1 score 81.9% [95% confidence interval: 81.2%, 82.7%] vs 77.4% [95% confidence interval: 76.1%, 78.6%]). However, the error was mitigated if the F1 score was subsequently recalculated with observed outcomes from the weighted dataset (F1: 77.0%; 95% confidence interval: 75.7%, 78.4%). In simulations, this finding held in the largest sample size (N = 10,000) under all analytic conditions assessed. For sample sizes <5,000, sampling weights had little impact in simulations that more closely resembled a simple random sample (low weight variability) or in models with strong predictors, but findings were inconsistent under other analytic scenarios. Failing to account for sampling weights in gradient boosting models may limit generalizability for data from complex surveys, dependent on sample size and other analytic properties. In the absence of software for configuring weighted algorithms, post-hoc re-calculations of unweighted model performance using weighted observed outcomes may more accurately reflect model prediction in target populations than ignoring weights entirely.
Bisindole-PBD regulates breast cancer cell proliferation via SIRT-p53 axis (2015)

In a previous study we reported the role of potent bisindole-PBD conjugate as an inclusion in the arsenal of breast cancer therapeutics. In breast cancer cell proliferation, PI3K/AKT/mTOR pathway plays a crucial role by prosurvival mechanism that inhibits programmed cell death. Here, 2 breast cancer cells lines, MCF-7 and MDA-MB-231 were treated with Vorinostat (suberoylanilide hydroxamic acid / SAHA) and bisindole-PBD (5b). We have investigated the effect on PI3K/AKT/mTOR pathway and SIRT expression including epigenetic regulation. There was consistent decrease in the level of PI3K, AKT, mTOR proteins upon treatment of 5b in both MCF-7 and MDA-MB-231 cell lines compared to untreated controls. Treatment with caspase inhibitor (Q-VD-OPH) confirmed that the effect of 5b on PI3K signaling was ahead of apoptosis. Real time PCR and western blot analysis showed profound reduction in the mRNA and protein levels of SIRT1 and SIRT2. Molecular docking studies also supported the interaction of 5b with various amino acids of SIRT2 proteins. Treatment with 5b caused epigenetic changes that include increase of acetylated forms of p53, increase of histone acetylation at p21 promoter as well as decrease in methylation state of p21 gene. Compound 5b thus acts as SIRT inhibitor and cause p53 activation via inhibition of growth factor signaling and activation of p53 dependent apoptotic signaling. This present study focuses bisindole-PBD on epigenetic alteration putting 5b as a promising therapeutic tool in the realm of breast cancer research.
Impact of Sinusoidal Co-channel CW Interference on the Spectral Efficiency of OTFS Modulation (2023)

The recently proposed Orthogonal Time Frequency Space (OTFS) modulation has been shown to be robust to mobility induced Doppler spread in next generation communication systems. Due to dense network deployment, next generation communication systems are expected to experience significant co-channel interference. Therefore, there is a need to study the robustness of OTFS modulation in the presence of co-channel interference. In this paper, we study the impact of sinusoidal co-channel continuous wave (CW) interference on the spectral efficiency (SE) of an Orthogonal Time Frequency Space (OTFS) modulation based communication system. In OTFS modulation, information symbols are embedded in the delay-Doppler (DD) domain. Analysis of the DD domain representation of the received CW interference shows that the interference received along a particular channel path is localized in a Doppler domain interval having width approximately twice the Doppler domain resolution (i.e., inverse of the OTFS frame time-duration). With fine Doppler domain resolution, the CW interference is localized to a small portion of the Doppler domain and is expected to interfere only with a small fraction of all information symbols. This observation is supported through simulations, where it is confirmed that the degradation in the OTFS SE performance is small when the Doppler domain resolution is fine.
Lipocalin-2 Deficiency Attenuates Neuroinflammation and Brain Injury after Transient Middle Cerebral Artery Occlusion in Mice (2014)

Lipocalin-2 (LCN2) is a secreted protein of the lipocalin family, but little is known about the expression or the role of LCN2 in the central nervous system. Here, we investigated the role of LCN2 in ischemic stroke using a rodent model of transient cerebral ischemia. Lipocalin-2 expression was highly induced in the ischemic brain and peaked at 24 hours after reperfusion. After transient middle cerebral artery occlusion, LCN2 was predominantly expressed in astrocytes and endothelial cells, whereas its receptor (24p3R) was mainly detected in neurons, astrocytes, and endothelial cells. Brain infarct volumes, neurologic scores, blood-brain barrier (BBB) permeabilities, glial activation, and inflammatory mediator expression were significantly lower in LCN2-deficient mice than in wild-type animals. Lipocalin-2 deficiency also attenuated glial neurotoxicity in astrocyte/neuron cocultures after oxygen-glucose deprivation. Our results indicate LCN2 has a critical role in brain injury after ischemia/reperfusion, and that LCN2 may contribute to neuronal cell death in the ischemic brain by promoting neurotoxic glial activation, neuroinflammation, and BBB disruption.
Impaired retinal microvascular function predicts long-term adverse events in patients with cardiovascular disease (2020)

Retinal arteriolar endothelial dysfunction is an independent predictor of MACE in patients with CAD or cardiovascular risk factors. Dynamic retinal vessel analysis may provide added benefit to traditional risk factors in stratifying patients at risk for cardiovascular events.
Comparison of Plantar Pressure of Different Prosthetic Feet in Able-Bodied Volunteers Simulating Active Foot Amputees during Locomotion (2020)

Active foot amputees may choose from a variety of prosthetic foot designs to accommodate their financial and daily lifestyles, yet it is unclear what design is similar to non-amputee gait, specifically in pressure distribution. The hypothesis is that there are differences in plantar pressure distributions for different types of prosthetic feet during gait and pressure distributions are comparable to able-bodied gait. The purpose of this study is to inform active foot amputees of what prosthetic foot designs can help them complete their daily tasks similar to non-amputees through plantar pressure comparisons. The study will be conducted by using an orthopedic boot system that attaches to different prosthetic foot designs. The orthopedic boot (OB) will be used by able-bodied-non-amputee volunteers, so that their foot is immobilized from the knee down to simulate active foot amputees. The three prosthetic foot designs that will be tested are the articulated foot, tec limbs, and Niagara foot and will be attached to the left orthopedic foot. The S.A.C.H foot will be the control group attached to the right boot. The prosthetic feet are put into a shoe that has the Tekscan F-scan sensors in the insole. This Tekscan system has been used clinically and in research to evaluate dynamic pressure distribution in gait and running. To our knowledge, it has not been used to evaluate dynamic pressure distribution in amputee gait. Preliminary results demonstrate differences exist and further research is recommended with this system.
Gut bacteria-derived serotonin promotes immune tolerance in early life (2022)

Abstract The gut microbiome promotes immune system development in early life, but the neonatal gut metabolome remains undefined. Here, we demonstrate that, distinct from adults, the neonatal mouse gut is enriched with neurotransmitters, and specific bacteria produce serotonin directly while downregulating monoamine oxidase A to limit serotonin breakdown. Serotonin inhibits mTOR activation to promote regulatory T cells and suppress T cell responses both ex vivo and in vivo in the neonatal intestine. Oral gavage of serotonin into neonatal mice leads to long-term immune tolerance toward both dietary antigens and commensal bacteria as well as alterations of the gut microbiome. Together, our study has uncovered unique microbiome-dependent mechanisms to maximize serotonin in the neonatal gut and a novel role for intestinal serotonin to promote immune tolerance in early life.
Non‐contrast‐enhanced peripheral angiography using a sliding interleaved cylinder acquisition (2014)

Non-contrast-enhanced angiography using SLINCYL can provide angiograms with improved artery-vein contrast in the lower extremities.
Erbium emission in highly doped tellurite and alumina-silica novelty fibers (2004)

We present a summary of emission properties of doped tellurite and alumina-silica fibers. The tellurite fiber offer higher and flatter signal gain over shorter lengths and the alumina-silica fiber, lower losses and better physical properties.
1027: Can Extended Lymph Node Dissection Improve Biochemical Disease Free Survival Following Radical Retropubic Prostatectomy for Tl-4N0M0 Prostate Cancer? (2005)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 24, 2005, 8:00 am - 12:00 pm1 Apr 20051027: Can Extended Lymph Node Dissection Improve Biochemical Disease Free Survival Following Radical Retropubic Prostatectomy for Tl-4N0M0 Prostate Cancer? Ying Hua, Carl K. Gjertson, Robert E. Mitchell, Aaron E. Katz, Eric T. Goluboff, Carl A. Olsson, Mitchell C. Benson, and James M. McKiernan Ying HuaYing Hua More articles by this author , Carl K. GjertsonCarl K. Gjertson More articles by this author , Robert E. MitchellRobert E. Mitchell More articles by this author , Aaron E. KatzAaron E. Katz More articles by this author , Eric T. GoluboffEric T. Goluboff More articles by this author , Carl A. OlssonCarl A. Olsson More articles by this author , Mitchell C. BensonMitchell C. Benson More articles by this author , and James M. McKiernanJames M. McKiernan More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)35183-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1027: Can Extended Lymph Node Dissection Improve Biochemical Disease Free Survival Following Radical Retropubic Prostatectomy for Tl-4N0M0 Prostate Cancer?." The Journal of Urology, 173(4S), p. 279 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 173Issue 4SApril 2005Page: 279 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Ying Hua More articles by this author Carl K. Gjertson More articles by this author Robert E. Mitchell More articles by this author Aaron E. Katz More articles by this author Eric T. Goluboff More articles by this author Carl A. Olsson More articles by this author Mitchell C. Benson More articles by this author James M. McKiernan More articles by this author Expand All Advertisement PDF DownloadLoading ...
Joint training of convolutional and non-convolutional neural networks (2014)

We describe a simple modification of neural networks which consists in extending the commonly used linear layer structure to an arbitrary graph structure. This allows us to combine the benefits of convolutional neural networks with the benefits of regular networks. The joint model has only a small increase in parameter size and training and decoding time are virtually unaffected. We report significant improvements over very strong baselines on two LVCSR tasks and one speech activity detection task.
Quality Factor Maximization Through Dynamic Balancing of Tuning Fork Resonator (2014)

This paper presents a method of dynamically balancing tuning fork microresonators, enabling maximization of quality factor (Q-factor) in structures with imperfections. Nonsymmetric tuning of stiffness in a coupled 2-DOF resonator is completed through the use of the negative electrostatic spring effect. This variable stiffness is shown to be able to adjust the reaction forces of the structure at the anchors, effectively balancing any spring imperfections caused by fabrication imperfections. Balancing the structure through stiffness matching minimizes the loss of energy through the substrate and maximizes Q-factor of the device's antiphase mode. The approach is experimentally demonstrated using a vacuum packaged microelectromechanical tuning fork resonator with operational frequency of 2.2 kHz and antiphase Q-factor of 0.6 million. By electrostatically tuning the reaction force at the anchors caused by fabrication imperfections, anchor loss can be suppressed, increasing the Q-factor to above 0.8 million. The experimentally validated analytical model of substrate dissipation is confirmed to be applicable to Q-factor tuning in antiphase driven resonators and gyroscopes.
A comparative study between polyclass and multiclass language models (1998)

In this work, we introduce the concept of Multiclass for language modeling and we compare it to the Polyclass model.The originality of the Multiclass is its capability to parse a string of classes/tags into variable length independent sequences.A few experimental tests were carried out on a class corpus extracted from the French « Le Monde » word corpus labeled automatically.This corpus contains a set of 43 million of words.In our experiments, Multiclass outperform first-order Polyclass but are slightly outperformed by second-order Polyclass.1.
Adsorption Behavior of Silk Fibroin on Amphiphilic Graphene Oxide (2016)

Graphene oxide-silk composites have gained a significant interest in the recent times because of the unique mechanical properties of both GO and silk and their ability to form layered structures that exhibit a striking resemblance to the layered (brick-mortar) composites found in nature. However, various aspects of the interaction between silk and graphene oxide (e.g., conformation and distribution of the silk chains on chemically heterogeneous GO surface) are not completely understood. In this study, we demonstrate that the interaction between the silk fibroin chains and GO can be modulated by altering the pH of the silk fibroin solution. We employed atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy to probe the distribution and the secondary structure of silk fibroin adsorbed on GO. In acidic pH conditions (i.e., pH < pI), a high density of silk chains were found to adsorb on the GO surface, whereas an increase in pH resulted in a progressive decrease in the density of the adsorbed silk chains. This pH-dependent adsorption is ascribed to the electrostatic interactions between the negatively charged GO surface and the tunable ionization of the silk molecules. The secondary structure of silk fibroin chains adsorbed on GO was also found to be highly dependent on the pH. This study provides a deeper understanding of the interaction between GO and silk fibroin that is critical for the design and fabrication of bioinspired nanocomposites with tailored mechanical properties.
Application of twin screw extrusion to the manufacture of cocrystals: scale-up of AMG 517–sorbic acid cocrystal production (2014)

The application of twin screw extrusion (TSE) in the scale-up of cocrystal production was investigated by using AMG 517-sorbic acid as a model system. Extrusion parameters that influenced conversion to the cocrystal such as temperature, feed rate and screw speed were investigated. Extent of conversion to the cocrystal was found to have a strong dependence on temperature and a moderate dependence on feed rate and screw speed. Cocrystals made by the TSE process were found to have superior mechanical properties than solution grown cocrystals. Additionally, moving to a TSE process eliminated the need for solvent.
Advanced Cooling Technologies II: Two-Phase Flow Cooling (2002)

As mentioned in Chapter 14, dielectric fluids are generally required for cooling of electronics, especially in direct-immersion cooling. Dielectric liquids such as Freon from Dupont and Fluorinert (FC series) from 3M Company are the most popular fluids used in direct cooling of electronics. The basic characteristics of those fluids are as follows: