gebhart/patrepeval huggingface dataset:
Mutation ofBAX occurs infrequently in acquired immunodeficiency syndrome-related non-Hodgkin's lymphomas (2000)

Acquired immunodeficiency syndrome (AIDS)-related non-Hodgkin's lymphomas (AIDS-NHLs) consistently derive from B cells, are histologically heterogeneous, and are associated with distinct molecular pathways depending upon histology. Recently, it has been proposed that inactivating mutations of the bax death agonist may contribute to the pathogenesis of human tumors. In particular, among B-cell malignancies, BAX mutations have been detected at a certain frequency in Burkitt lymphomas. This study is aimed at defining the status of the BAX gene throughout the clinicopathologic spectrum of AIDS-NHL (n = 54), including AIDS-related Burkitt lymphoma (n = 14), AIDS-related Burkitt-like lymphoma (n = 8), AIDS-related diffuse large cell lymphoma (n = 15), AIDS-related primary central nervous system lymphoma (n = 6), and AIDS-related primary effusion lymphoma (n = 11). All 6 BAX exons and flanking sequences were subjected to mutational analysis by polymerase chain reaction-single strand conformation polymorphism followed by DNA direct sequencing of positive cases. Mutations of BAX among AIDS-NHL were restricted to a cell line of AIDS-related primary effusion lymphoma, which harbored a frameshift mutation causing the introduction of a proximal stop codon. All other AIDS-NHL displayed wild-type BAX alleles. In order to investigate whether BAX inactivation in AIDS-NHL may occur through mechanisms other than gene mutation, bax protein expression was investigated by Western blot analysis or immunohistochemistry in selected cases. All AIDS-NHL analyzed expressed normal bax proteins. Overall, this study indicates that deregulation of apoptotic control in AIDS-NHL is not caused by BAX alterations. Genes Chromosomes Cancer 27:177-182, 2000.
Immunogenicity comparison of a multi-antigenic peptide bearing V3 sequences of the human immunodeficiency virus type 1 with TAB9 protein in mice (2000)

The multiple antigenic peptide system (MAP) has been proposed as a novel and valuable approach for eliciting antibodies for peptides and developing synthetic vaccines. Multi-epitope polypeptides (MEP) have also been developed as an alternative to the recombinant approach for vaccines. The V3 loop from the HIV type 1 (HIV-1) external glycoprotein (gp120) contains the principal neutralization domain (PND). Antibodies against this region neutralize HIV-1 in vitro and in vivo. In this work, a novel presentation of di-epitope MAP was synthesized. A monomeric MAP carrying two identical JY1 V3 sequences as B-cell epitopes and the 830-843 region of tetanus toxoid as a T-helper cell epitope was synthesized. This basic structure was covalently linked to produce a four-JY1-branched homodimer (JY1-MAP4). Additionally, six different monomeric MAPs, bearing four copies of V3 from isolates LR150, JY1, RF, MN, BRVA and IIIB, were synthesized. These monomers were conveniently linked among themselves to produce homodimeric and heterodimeric MAPs of eight V3 branches (V3-MAP8). JY1-MAP8 elicited higher antibody titers in Balb/c mice than JY1-MAP4. The immunogenicity of two different, hexavalent V3-MAP8 mixtures and the MEP TAB9, which tandems the same six V3 sequences in a single molecule, were compared. The antibody response against the mixtures of the heterodimeric MAP showed a wider recognition pattern of the V3 region, while the homodimeric cocktail showed an intermediate pattern. Antibodies elicited by TAB9 recognized only the JY1, LR150 peptides. These results emphasize the influence of V3 epitope presentation upon the characteristics of the antibody response generated.
Novel Bioactive Antimicrobial Lignin Containing Coatings on Titanium Obtained by Electrophoretic Deposition (2014)

Hydroxyapatite (HAP) is the most suitable biocompatible material for bone implant coatings; its brittleness, however, is a major obstacle, and the reason why research focuses on creating composites with biopolymers. Organosolv lignin (Lig) is used for the production of composite coatings, and these composites were examined in this study. Titanium substrate is a key biomedical material due to its well-known properties, but infections of the implantation site still impose a serious threat. One approach to prevent infection is to improve antimicrobial properties of the coating material. Silver doped hydroxyapatite (Ag/HAP) and HAP coatings on titanium were obtained by an electrophoretic deposition method in order to control deposited coating mass and morphology by varying applied voltage and deposition time. The effect of lignin on microstructure, morphology and thermal behavior of biocomposite coatings was investigated. The results showed that higher lignin concentrations protect the HAP lattice during sintering, improving coating stability. The corrosion stability was evaluated in simulated body fluid (SBF) at 37 °C. Newly formed plate-shaped carbonate-HAP was detected, indicating enhanced bioactive performance. The antimicrobial efficiency of Ag/HAP/Lig was confirmed by its higher reduction of bacteria Staphylococcus aureus TL (S. aureus TL) than of HAP/Lig coating. Cytotoxicity assay revealed that both coatings can be classified as non-toxic against healthy immunocompetent peripheral blood mononuclear cells (PBMC).
Design Optimization of Passive Gyroscopic Damper by Genetic Algorithms. Monte Carlo Optimization under Random Excitations. (1996)

In this study, genetic algorithms (GAs) are utilized as a framework for Monte Carlo optimizations of the passive gyroscopic damper (PGD). The PGD is an effective damping mechanism for rotational vibrations, however, it shows considerable nonlinearity under strong excitations. The response to the random excitations can not be precisely analyzed by any conventional approximate method. The Monte Carlo approach exploits numerical simulations using pseudorandom numbers as the excitations and a numerical integration algorithm. The Monte Carlo estimations of the station ary response to white noise excitations are combined with the GAs. The quasi-continuous generation model with an algebraic crossover is customized for noisy Monte Carlo estimations, and it realizes a stochastic hillclimber. The gimbal spring constant and the giambal damper coefficient are optimized to minimize the stationary variance of the main system angle, as in the previous study of the same authors, wherein the Fokker-Planck method was employed together with a nonlinear programming algorithm. The GA solutions are again verified by the Monte Carlo estimations to prove their superiority to the previous ones.
Measurement Results for Millimeter Wave Pure LOS MIMO Channels (2017)

In this paper we present measurement results for pure line-of-sight MIMO links operating in the millimeter wave range. We show that the estimated condition numbers and capacities of the measured channels are in good agreement with the theory for various transmission distances and antenna setups. Furthermore, the results show that orthogonal channel vectors can be observed if the spacing criterion is fulfilled, thus facilitating spatial multiplexing and achieving high spectral efficiencies even over fairly long distances. Spacings generating ill-conditioned channel matrices show on the other hand significantly reduced performance.
S346 Enrollment Rate of African Americans in a Colon Cancer Screening Trial at a Historically Black College and University Is Similar to Other Patient Populations (2021)

Introduction: Clinical trials often have low enrollment of minorities, particularly African-Americans (AAs), which may limit the generalizability of research findings. Previously identified barriers to AAs recruitment include historical abuses leading to mistrust, communication issues with providers, socio-economic factors, and a lack of access to clinical trials. In a Historically Black College and University (HBCU) serving a primarily AA population at a large safe-net hospital, we evaluated the enrollment of eligible AA patients for a colorectal cancer (CRC) screening clinical trial. This was compared to the enrollment rates across other study sites. Methods: A large, prospective, multi-centered clinical trial to validate a blood-based test for early detection of CRC (PREEMPT-CRC) was initiated at a HBCU, where 84% of patients are AAs. To maximize study recruitment, culturally sensitive methods were employed including racially congruent recruitment staff as well as synchronized timing of consent/study procedures with pre-endoscopy COVID testing/clinic visits. Detailed information for all eligible subjects was recorded. Demographic and socio-economic data including census information for enrolled and not enrolled subjects were compared. The enrollment rate (defined as enrolled/eligible patients) over the first 6 weeks at the HBCU and that of the other study sites providing screening logs was analyzed. Results: The enrollment rate at the HBCU was 55% (44 out of 80 eligible patients; 95% CI 43.5-66.2%), compared to 49.8% (258 out of 518 eligible patients; 95% CI 45.4- 54.2%) at the other 26 study sites. While age and gender of enrolled patients at the HBCU were comparable to other sites, the main difference was race: at the HBCU the study participants were 79.5% AAs and 9.1% whites, while at the other sites the participants were 11.5% AAs and 82.8% whites (p< 0.001). At the HBCU, the demographic characteristics and socio-demographic data including income, marital status, insurance status/type, and census tract median household income of the 44 enrolled and 36 not-enrolled subjects were similar (Table 1). Conclusion: Contrary to conventional belief that AAs do not want to be involved in clinical trials, we find their enrollment is similar to a predominant white study population when offered the opportunity in a culturally sensitive setting. Future trials should consider including HBCU sites in order to attain adequate AA enrollment to improve the generalizability of research findings.Table 1.: Baseline Patient Demographic and Sociodemographic Information
Utilization of Epigenome-wide DNA Methylation for Longitudinal Comparison of White Blood Cell Proportions Across Preeclamptic and Normotensive Pregnancy by Self-Reported Race (2020)

Abstract Objective We utilized epigenome-wide DNA methylation data to estimate/compare white blood cell (WBC) proportions in plasma across preeclamptic (case) and uncomplicated, normotensive (control) pregnancy. Methods We previously collected methylation data using Infinium® MethylationEPIC Beadchips during the three trimesters in 28 cases and 28 controls (21 Black, 7 White participants/group). We employed Houseman’s regression calibration method to estimate and compare neutrophil, monocyte, B cell, NK cell, CD4+ T and CD8+ T cell proportions across pregnancy and between cases and controls. Results We observed changes in WBC proportions across pregnancy within cases and controls that varied by cell type and race. Neutrophils represented the largest WBC mean proportion in all three trimesters for cases (Mean±SD: 67.2±9.6% – 74.4±12%) and controls (64.2±11% – 74.0±7.9%). Mean B cell proportions were significantly lower in cases than controls in Trimester 1 (5.25±0.02% versus 6.30±0.02%, p =0.02). The remaining mean cell proportions did not significantly differ in the overall sample. Stratified analyses revealed race-specific differences. In White participants (n=14): (1) neutrophil proportions were significantly higher in cases in Trimester 1 ( p =0.04), but significantly lower in Trimester 2 ( p =0.02), (2) B cell proportions were significantly lower in cases in Trimester 1 ( p =0.001). No significant differences were detected among Black participants (n=42). Conclusions Although chronic inflammation characterizes preeclampsia, few studies have investigated WBCs across pregnancy. We report differences between cases and controls across pregnancy. Our findings in a small sample demonstrate the need for additional studies investigating the relationship between race and WBCs in pregnancy, which could provide insight into preeclampsia pathophysiology.
First-Principles Approach to Calculating Energy Level Alignment at Aqueous Semiconductor Interfaces (2014)

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.
Hybrid Music Perception Outcomes: Implications for Melody and Timbre Recognition in Cochlear Implant Recipients (2019)

Recipients of hybrid cochlear implants demonstrate music perception abilities superior to those observed in traditional cochlear implant recipients. Results from the present study support the notion that electric-acoustic stimulation confers advantages related to the availability of low-frequency acoustic hearing, most particularly for melody recognition. However, timbre recognition remains more limited for both hybrid and traditional cochlear implant users. Opportunities remain for new coding strategies to improve timbre perception.
Advantages of Incorporating Perceptual Component Models into a Machine Learning framework for Prediction of Display Quality (2018)

Recent work in prediction of overall HDR and WCG display quality has shown that machine learning approaches based on physical measurements performs on par with more advanced perceptually transformed measurements. While combining machine learning with the perceptual transforms did improve over using each technique separately, the improvement was minor. However, that work did not explore how well these models performed when applied to display capabilities outside of the training data set. This new work examines what happens when the machinelearning approaches are used to predict quality outside of the training set, both in terms of extrapolation and interpolation. While doing so, we consider two models &#x2013; one based on physical display characteristics, and a perceptual model that transforms physical parameters based on human visual system models. We found that the use of the perceptual transforms particularly helps with extrapolation, and without their tempering effects, the machine learning-based models can produce wildly unrealistic quality predictions.
RESULTS FROM BEAM COMMISSIONG OF AN SRF PLUG-GUN CAVITY PHOTOINJECTOR (2013)

Superconducting rf photo-electron injectors (SRF photoinjectors) hold the promise to deliver high brightness, high average current electron beams for future light sources or other applications demanding continuous wave operation of an electron injector. This paper discusses results from beam commissioning of a hybrid SRF photoinjector based on a Pb coated plug and a Nb rf gun cavity for beam energies up to 2.5 MeV at Helmholtz-Zentrum Berlin (HZB). Emittance measurements and transverse phase space characterization with solenoid-scan and slitmask methods will be presented.
Flexible Multielectrode Array for Skeletal Muscle Conditioning, Acetylcholine Receptor Stabilization and Epimysial Recording After Critical Peripheral Nerve Injury (2019)

Complete re-innervation after a traumatic injury severing a muscle's peripheral nerve may take years. During this time, the denervated muscle atrophies and loses acetylcholine receptors, a vital component of the neuromuscular junction, limiting functional recovery. One common clinical treatment for atrophy is electrical stimulation; however, epimysial electrodes currently used are bulky and often fail due to an excessive inflammatory response. Additionally, there remains a need for a device providing <i>in vivo</i> monitoring of neuromuscular regeneration and the maintenance of acetylcholine receptors. Here, an implantable, flexible microelectrode array (MEA) was developed that provides surface neuromuscular stimulation and recording during long-term denervation. <b>Methods:</b> The MEA uses a flexible polyimide elastomer and an array of gold-based microelectrodes featuring Peano curve motifs, which together maintain electrode flexibility. The devices were implanted along the denervated gastrocnemius muscles of 5 rats. These rats underwent therapeutic stimulation using the MEA daily beginning on post-operative day 2. Another 5 rats underwent tibial nerve resection without implantation of MEA. Tissues were harvested on post-operative day 14 and evaluated for quantification of acetylcholine receptors and muscle fiber area using immunofluorescence and histological staining. <b>Results:</b> The Young's modulus was 1.67 GPa, which is comparable to native tendon and muscle. The devices successfully recorded electromyogram data when implanted in rats. When compared to untreated denervated muscles, MEA therapy attenuated atrophy by maintaining larger muscle fiber cross-sectional areas (p < 0.05). Furthermore, the acetylcholine receptor areas were markedly larger with MEA treatment (p < 0.05). <b>Conclusions:</b> This proof-of-concept work successfully demonstrates the ability to combine conformability, tensile strength-enhancing metal micropatterning, electrical stimulation and recording into a functional implant for both epimysial stimulation and recording.
Patterns and Reuse in Document Engineering (2002)

is evolving as a new discipline for specifying, designing, and implementing the electronic documents that request or provide interfaces to business processes via Web-based services. The essence of Document Engineering is the analysis and design methods that yield formal models to describe the information these processes or services require. Good Document Engineering practice emphasizes the reuse of existing models wherever possible and requires that new models be described in ways that encourage their reuse by others. Reusable patterns in Document Engineering are found at both the implementation level in the form of EDI and XML libraries and also at the conceptual level in terms of libraries of models that describe common business processes and the organization of activities between businesses. Re-using patterns at these more abstract levels facilitates interoperability between different technology implementations.
Supplementary Data from Antihistamine Drug Ebastine Inhibits Cancer Growth by Targeting Polycomb Group Protein EZH2 (2023)

&lt;p&gt;Supplementary Data File&lt;/p&gt;
Capillary-Channeled Polymer Fibers as a Stationary Phase for Desalting of Protein Solutions for Electrospray Ionization Mass Spectrometry Analysis (2006)

Micropipet solid-phase extraction (SPE) tips have been used to desalt and purify proteins and peptides from mixtures of buffers and biological solutions. Removing salts and buffers prior to electrospray ionization mass spectrometry (ESI-MS) characterization improves the detection limits and the sensitivity of the protein analyses. Recently, capillary-channeled polymer (C-CP) fibers have been investigated as stationary phases for high-performance liquid chromatography separations of proteins. Polypropylene C-CP fibers incorporated as sorbent materials in micro-SPE tips are shown to effectively remove both inorganic and organic buffers from proteins in defined solutions. The architecture of the fibers provides large surface areas in comparison to conventional round fibers and is readily packed into capillaries that can be affixed to micropipet tips. Desalting of protein solutions is demonstrated for ESI-MS analysis through increased signal-to-noise ratios and reduced spectral complexity.
Identification and characterization of <i>in vitro</i> and <i>in vivo</i> fidarestat metabolites: Toxicity and efficacy evaluation of metabolites (2021)

The progression of diabetic complications can be prevented by inhibition of aldose reductase and fidarestat considered to be highly potent. To date, metabolites of the fidarestat, toxicity, and efficacy are unknown. Therefore, the present study on characterization of hitherto unknown in vitro and in vivo metabolites of fidarestat using liquid chromatography-electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS) is undertaken. In vitro and in vivo metabolites of fidarestat have been identified and characterized by using LC/ESI/MS/MS and accurate mass measurements. To identify in vivo metabolites, plasma, urine, and feces samples were collected after oral administration of fidarestat to Sprague-Dawley rats, whereas for in vitro metabolites, fidarestat was incubated in human S9 fraction, human liver microsomes, and rat liver microsomes. Furthermore, in silico toxicity and efficacy of the identified metabolites were evaluated. Eighteen metabolites have been identified. The main in vitro phase I metabolites of fidarestat are oxidative deamination, oxidative deamination and hydroxylation, reductive defluroniation, and trihydroxylation. Phase II metabolites are methylation, acetylation, glycosylation, cysteamination, and glucuronidation. Docking studies suggest that oxidative deaminated metabolite has better docking energy and conformation that keeps consensus with fidarestat whereas the rest of the metabolites do not give satisfactory results. Aldose reductase activity has been determined for oxidative deaminated metabolite (F-1), and it shows an IC50 value of 0.44 μM. The major metabolite, oxidative deaminated, did not show any cytotoxicity in H9C2, HEK, HEPG2, and Panc1 cell lines. However, in silico toxicity, the predication result showed toxicity in skin irritation and ocular irritancy SEV/MOD versus MLD/NON (v5.1) model for fidarestat and its all metabolites. In drug discovery and development research, it is distinctly the case that the potential for pharmacologically active metabolites must be considered. Thus, the active metabolites of fidarestat may have an advantage as drug candidates as many drugs were initially observed as metabolites.
Domain III of the envelope protein as a dengue vaccine target (2010)

A dengue vaccine should induce long-lasting, simultaneous protection to the four dengue viruses while avoiding the immune enhancement of viral infection. Domain III of the dengue envelope protein has been implicated in receptor binding, and is also the target of specific neutralizing antibodies. Domain III has emerged as a promising region for a subunit vaccine candidate. Here, we review the current state of knowledge on vaccine candidates based on domain III. Due to the results obtained concerning the immune response and protection in mice and monkeys, particular attention is paid to the chimeric protein domain III fused to p64k of Neisseria meningitidis.
Tuning phase transition between quantum spin Hall and ordinary insulating phases (2007)

An effective theory is constructed for analyzing a generic phase transition between the quantum spin Hall and the insulator phases. Occurrence of degeneracies due to closing of the gap at the transition are carefully elucidated. For systems without inversion symmetry the gap closing occurs at $\ifmmode\pm\else\textpm\fi{}{\stackrel{P\vec}{k}}_{0}(\ensuremath{\ne}\stackrel{P\vec}{G}∕2)$ while for systems with inversion symmetry, the gap can close only at wave numbers $\stackrel{P\vec}{k}=\stackrel{P\vec}{G}∕2$, where $\stackrel{P\vec}{G}$ is a reciprocal lattice vector. In both cases, following a unitary transformation which mixes spins, the system is represented by two decoupled effective theories of massive two-component fermions having masses of opposite signs. Existence of gapless helical modes at a domain wall between the two phases directly follows from this formalism. This theory provides an elementary and comprehensive phenomenology of the quantum spin Hall system.