gebhart/patrepeval huggingface dataset:
Data from A Placenta-Specific Gene Ectopically Activated in Many Human Cancers Is Essentially Involved in Malignant Cell Processes (2023)

&lt;div&gt;Abstract&lt;p&gt;The identification and functional characterization of tumor-specific genes is a prerequisite for the development of targeted cancer therapies. Using an integrated data mining and experimental validation approach for the discovery of new targets for antibody therapy of cancer, we identified PLAC1. &lt;i&gt;PLAC1&lt;/i&gt; is a placenta-specific gene with no detectable expression in any other normal human tissue. However, it is frequently aberrantly activated and highly expressed in a variety of tumor types, in particular breast cancer. RNAi-mediated silencing of PLAC1 in MCF-7 and BT-549 breast cancer cells profoundly impairs motility, migration, and invasion and induces a G&lt;sub&gt;1&lt;/sub&gt;-S cell cycle block with nearly complete abrogation of proliferation. Knockdown of PLAC1 is associated with decreased expression of cyclin D1 and reduced phosphorylation of AKT kinase. Moreover, PLAC1 is localized on the surface of cancer cells and is accessible for antibodies which antagonize biological functions of this molecule. These features, in summary, make PLAC1 an attractive candidate for targeted immunotherapeutic approaches. [Cancer Res 2007;67(19):9528–34]&lt;/p&gt;&lt;/div&gt;
Data from Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition (2023)

&lt;div&gt;Abstract&lt;p&gt;Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between &lt;i&gt;MYCN&lt;/i&gt; amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of &lt;i&gt;MYCN&lt;/i&gt;. Genome-wide expression analysis showed downregulation of the MYCN transcriptional program accompanied by suppression of &lt;i&gt;MYCN&lt;/i&gt; transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knockdown phenocopied these effects, establishing BET bromodomains as transcriptional regulators of &lt;i&gt;MYCN&lt;/i&gt;. BET inhibition conferred a significant survival advantage in 3 &lt;i&gt;in vivo&lt;/i&gt; neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; Biomarkers of response to small-molecule inhibitors of BET bromodomains, a new compound class with promising anticancer activity, have been lacking. Here, we reveal &lt;i&gt;MYCN&lt;/i&gt; amplification as a strong genetic predictor of sensitivity to BET bromodomain inhibitors, show a mechanistic rationale for this finding, and provide a translational framework for clinical trial development of BET bromodomain inhibitors for pediatric patients with &lt;i&gt;MYCN&lt;/i&gt;-amplified neuroblastoma. &lt;i&gt;Cancer Discov; 3(3); 308–23. ©2012 AACR.&lt;/i&gt;&lt;/p&gt;&lt;p&gt;See related commentary by Schnepp and Maris, p. 255&lt;/p&gt;&lt;p&gt;This article is highlighted in the In This Issue feature, p. 239&lt;/p&gt;&lt;/div&gt;
Diffusion Processes for Retrieval Revisited (2013)

In this paper we revisit diffusion processes on affinity graphs for capturing the intrinsic manifold structure de-fined by pairwise affinity matrices. Such diffusion processes have already proved the ability to significantly improve sub-sequent applications like retrieval. We give a thorough overview of the state-of-the-art in this field and discuss ob-vious similarities and differences. Based on our observa-tions, we are then able to derive a generic framework for diffusion processes in the scope of retrieval applications, where the related work represents specific instances of our generic formulation. We evaluate our framework on sev-eral retrieval tasks and are able to derive algorithms that e. g. achieve a 100 % bullseye score on the popular MPEG7 shape retrieval data set. 1.
OFDM synthetic aperture radar based on fractional fourier transform (2016)

This paper investigates the use of fractional Fourier transform (FrFT)-based Orthogonal Frequency Division Multiplexing for Synthetic Aperture Radar (SAR) imaging for single point target and extended target. The geometry of synthetic aperture radar using FrFT-based OFDM is presented with the developing algorithm to process the raw data to reconstruct the image of the target in the range and in the Azimuth direction. In the simulation results, single point target is assumed to be at the center of swath width to show the performance of this approach as well as the point spread function in the range and Azimuth direction. Extended target with the shape of tank is used to show the capability of this method in resolving extended target images.
Scandium(III) Coordination Polymers Containing Capsules Based on Two p-Sulfonatocalix[4]arenes (2001)

Reactions of sodium p-sulfonatocalix[4]arene and scandium(III) tristriflate in the presence, and absence, of [18]crown-6 give the crystalline complexes [Sc2(mu-OH)2(H2O)10][Na4(H2O)8-[calix[4]arene(SO3)4]2).13 H2O and [[Sc2(mu-OH)2(H2O)8][Sc(H2O)4]2[calix[4]-arene(SO3)4-H+]2([18]crown-6).16H2O. Both complexes involve novel coordination polymers with calixarene units linked through sodium or scandium centers and also feature capsule assemblies through to the head-to-head association of calixarenes. A linear array of capsules associated with an infinite chain of aquo-bridged sodium ions, and an aquated hydroxy-bridged scandium(III) dimer, [Sc2(mu-OH)2(H2O)10]4+, are found in the absence of the crown ether. In the presence of [18]crown-6 both hydrated scandium monomers and dimers bridge between calixarenes in a two-dimensional coordination network. The crown ethers reside in cavities created by two calixarenes from adjacent polymeric sheets via a variety of supramolecular interactions(hydrogen-bonding, shape complementarity), and effectively add a third dimension to the network. The extended structure of both of these polymers is highly porous, and resembles a bilayer.
Development of High Performance Three-Way-Catalyst (2006)

&lt;div class="htmlview paragraph"&gt;In conventional gasoline engine vehicles, three-way catalysts are used to simultaneously remove HC, CO and NOx from the exhaust gas. The effectiveness of the catalyst to remove these harmful species depends strongly on the oxygen concentration in the exhaust gas. Deterioration of three-way catalyst results in a reduction in its purification activity and OSC (oxygen storage capacity). In this investigation, additive elements were used to enhance the durability and OSC of the catalyst support material. An optimized formulation of a CeO&lt;sub&gt;2&lt;/sub&gt;-ZrO&lt;sub&gt;2&lt;/sub&gt; and a ZrO&lt;sub&gt;2&lt;/sub&gt; material was developed to have excellent durability, improved OSC, enhanced interaction between precious metals and support materials, and increase thermal stability. Using these newly developed support materials, catalysts with increased performance was designed.&lt;/div&gt;
Reversible inactivation of the transcriptional function of P53 protein by farnesylation (2006)

Artificial protein farnesylation impaired the transcriptional activity of p53. This could be prevented by Farnesyl transferase inhibition. These data highlight the fact that the artificial prenylation of proteins provides a novel system for controlling the function of a transactivating factor.
An electrophoretic karyotype forSchizosaccharomyces pombeby pulsed field gel electrophoresis (1987)

The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs.
Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions (2012)

This study provides insights into the altered metabolism of P. putida in filament-inducing conditions, and indicates that the formation of filaments could potentially be utilized by P. putida as a survival strategy in its hostile, recurrently changing habitat.
Detection of High-Mass Biomolecules in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Theoretical and Experimental Investigations (1994)

A simple modification to an ion cyclotron resonance (ICR) cell for detection of high-mass ions with large spatial and kinetic energy distributions is described. The modification consists of a copper wire positioned inside the ICR cell running parallel to the magnetic field lines. The wire acts as an ion guide to position the ions at the exact center of the ion cell. Ion trajectories are calculated using SIMION, and the predictions based on the calculations are compared with the experimental results. The results presented in this paper show that the ion-guide ICR cell can be used to detect singly charged biomolecule ions of up to 157,000 Da.
Enhancing the low temperature hydrogen sensitivity of nanocrystalline SnO2 as a function of trivalent dopants (2007)

The effect of different indium doping concentrations on the room temperature hydrogen sensitivity of nano-SnO2 is investigated. The role of calcination temperature on the surface morphology, phase transformation, and subsequent impact on the gas sensing behavior of nanocrystalline doped SnO2 is presented. Differences in grain growth with varying doping amount give an explanation for enhanced sensing that is not always so obvious. Variation in the charge carrier density for indium doped nanocrystalline SnO2 is calculated as a function of indium concentration in the tin oxide lattice structure. The charge carrier density is correlated to the involved surface species of doped nanocrystalline SnO2 upon hydrogen gas exposure using Fourier transform infrared spectroscopy.
Self-supervised Deep Learning for Reading Activity Classification (2020)

Reading analysis can give important information about a user's confidence and habits and can be used to construct feedback to improve a user's reading behavior. A lack of labeled data inhibits the effective application of fully-supervised Deep Learning (DL) for automatic reading analysis. In this paper, we propose a self-supervised DL method for reading analysis and evaluate it on two classification tasks. We first evaluate the proposed self-supervised DL method on a four-class classification task on reading detection using electrooculography (EOG) glasses datasets, followed by an evaluation of a two-class classification task of confidence estimation on answers of multiple-choice questions (MCQs) using eye-tracking datasets. Fully-supervised DL and support vector machines (SVMs) are used to compare the performance of the proposed self-supervised DL method. The results show that the proposed self-supervised DL method is superior to the fully-supervised DL and SVM for both tasks, especially when training data is scarce. This result indicates that the proposed self-supervised DL method is the superior choice for reading analysis tasks. The results of this study are important for informing the design and implementation of automatic reading analysis platforms.
Arterial and aortic valve calcification inversely correlates with osteoporotic bone remodelling: a role for inflammation (2010)

This study provides direct in vivo evidence that in arteries and aortic valves, macrophage burden and calcification associate with each other, whereas inflammation inversely correlates with bone mineralization. Thus, understanding inflammatory signalling mechanisms may offer insight into selective abrogation of divergent calcific phenomena.
Exclusion of the COL2A1 gene as the mutation site in diastrophic dysplasia. (1989)

The involvement of the cartilage specific type II collagen gene (COL2A1) was studied in nine patients with diastrophic dysplasia in the Finnish population, where the prevalence of this chondrodystrophy clearly exceeds that reported for other populations. COL2A1 was chosen as the candidate gene based on previous morphological and chemical studies which suggested abnormal structure of type II collagen in diastrophic dysplasia. Southern analysis of the patients' DNA showed no disease related differences in any of the restriction fragments covering the 30 kb COL2A1 gene. As a second approach, the nine patients and their 74 relatives were studied for the inheritance of the type II collagen gene. Three of the patients with diastrophic dysplasia were not homozygous for the intragenic RFLP markers, which suggests that the disease is not linked to the type II collagen gene. Multipoint linkage analysis gave a lod score of -2.95, which conclusively excluded the COL2A1 gene as the mutation site in diastrophic dysplasia in these families.
Application of high‐throughput mini‐bioreactor system for systematic scale‐down modeling, process characterization, and control strategy development (2015)

High-throughput systems and processes have typically been targeted for process development and optimization in the bioprocessing industry. For process characterization, bench scale bioreactors have been the system of choice. Due to the need for performing different process conditions for multiple process parameters, the process characterization studies typically span several months and are considered time and resource intensive. In this study, we have shown the application of a high-throughput mini-bioreactor system viz. the Advanced Microscale Bioreactor (ambr15(TM) ), to perform process characterization in less than a month and develop an input control strategy. As a pre-requisite to process characterization, a scale-down model was first developed in the ambr system (15 mL) using statistical multivariate analysis techniques that showed comparability with both manufacturing scale (15,000 L) and bench scale (5 L). Volumetric sparge rates were matched between ambr and manufacturing scale, and the ambr process matched the pCO2 profiles as well as several other process and product quality parameters. The scale-down model was used to perform the process characterization DoE study and product quality results were generated. Upon comparison with DoE data from the bench scale bioreactors, similar effects of process parameters on process yield and product quality were identified between the two systems. We used the ambr data for setting action limits for the critical controlled parameters (CCPs), which were comparable to those from bench scale bioreactor data. In other words, the current work shows that the ambr15(TM) system is capable of replacing the bench scale bioreactor system for routine process development and process characterization.
Intense Ultraviolet Electroluminescence Properties of the High-Power InGaN-Based Light-Emitting Diodes Fabricated on Patterned Sapphire Substrates (2002)

The electroluminescence and photoluminescence characteristics of high-efficient InGaN multi-quantum-well ultraviolet light-emitting diodes have been investigated. There appeared a single emission band in the electroluminescence spectra at about 3.235 eV with a band width of 90 meV at room temperature under direct current. With increasing forward current, the luminescence intensity was not saturated, and increased linearly with increasing injection current up to 50 mA. Under pulsed current conditions at room temperature, the luminescence intensity increased linearly with increasing injection current up to 1000 mA, and a shift of the electroluminescence peak position was not observed. These results indicated that the injected carriers were confined efficiently in the active layer, and also suggested the possibility of realizing ultraviolet laser diodes. It was revealed that the forward-biased electroluminescence spectrum at 4 K reflected the distribution of hot electrons injected into the active layer. The maximum temperature of hot electrons was estimated to be about 350 K under a forward-biased pulsed current of about 500 mA, which was much higher than the lattice temperature.
Unraveling the glycosylated immunopeptidome with HLA-Glyco (2023)

Recent interest in targeted therapies has been sparked by the study of MHC-associated peptides (MAPs) that undergo post-translational modifications (PTMs), particularly glycosylation. In this study, we introduce a fast computational workflow that merges the MSFragger-Glyco search algorithm with a false discovery rate control for glycopeptide analysis from mass spectrometry-based immunopeptidome data. By analyzing eight large-scale publicly available studies, we find that glycosylated MAPs are predominantly presented by MHC class II. Here, we present HLA-Glyco, a comprehensive resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights, including high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between HLA allele groups. We integrate the workflow within the FragPipe computational platform and provide HLA-Glyco as a free web resource. Overall, our work provides a valuable tool and resource to aid the nascent field of glyco-immunopeptidomics.
In Vitro Biomimetic Model of the Human Immune System for Predictive Vaccine Assessments (2012)

The development of vaccines and immunotherapeutics is hampered by the lack of appropriate in vitro assays by which to test these compounds against the human immune system. By recognizing the key cellular elements (concentration and types of cells, cell motility, media, multicellular interactions, spatiotemporal cellular kinetics, cell expansion, and geometries) of immune tissues, such as the lymph node, we believed that we could recapitulate immune function in a biomimetic model of the human immune system, termed Modular Immune In vitro Construct (MIMIC®). We describe here the process we undertook to develop the MIMIC system by considering engineering design principles, the selection of cells to populate the system, immune functionality, the development of new antibody assays, and tissue construct automation. We also describe our approach toward using relevant challenges, such as influenza, as exemplars of different facets of immunity to test and validate the system. Through evaluating the MIMIC system with various experimental studies, we have demonstrated that the platform has the capacity to replicate known human immune response profiles. For example, we show here that influenza vaccine-induced antibody responses generated in a young adult and in the elderly donors in the MIMIC system can replicate the well-recognized immunosuppressed state of elderly donors. As well, we show the ability of the system to generate responses against variant antigens that are consistent with the response profiles observed in humans, but not in experimental animals. We believe that these studies highlight the potential of the MIMIC system for assessing human immune responses and suggest that it can serve as an ideal platform to disrupt translational research by reducing the time and cost requirements to bring new therapies to the clinic and the marketplace.
Ruthenium double perovskites: Transport and magnetic properties (2004)

The double perovskites ${\mathrm{La}}_{2}M{\mathrm{RuO}}_{6+\ensuremath{\delta}}$ contain ${M}^{2+}$ ions for $M=\mathrm{Mg},$ Zn, Co, and Ni and for $M=\mathrm{Mn}$ and Fe, ${M}^{3+}$ ions. Annealed samples have ordered ${M}^{2+}$ and Ru(IV), but samples with ${M}^{3+}$ ions are atomically disordered and remain oxidized $(\ensuremath{\delta}&gt;0)$ after annealing in a ${\mathrm{N}}_{2}$ atmosphere. A comparison of quenched, air-annealed, and ${\mathrm{N}}_{2}$-annealed ${\mathrm{La}}_{2}{\mathrm{MgRuO}}_{6+\ensuremath{\delta}}$ samples showed a persistence of a few cation vacancies in the presence of oxygen vacancies $(\ensuremath{\delta}&lt;0).$ In quenched samples, oxygen vacancies are preferentially located between two Ru atoms, where they form a deep two-electron trap state, whereas the two-electron trap state formed at an oxygen vacancy between an ${M}^{2+}$ and Ru(IV) is shallow. Magnetic as well as transport data indicate the \ensuremath{\pi}-bonding $4d$ electrons at the low-spin Ru atoms occupy itinerant-electron states of a ${\ensuremath{\pi}}^{*}$ band even in the atomically ordered samples, but strong correlations introduce magnetic transitions among the ${\ensuremath{\pi}}^{*}$ electrons. The $M=\mathrm{Co}$ and Ni samples exhibit a magnetic transition at some, if not all, of the ${\ensuremath{\pi}}^{*}$ electrons on the Ru array below a ${T}_{\mathrm{irr}}$ independent of magnetic ordering on the ${M}^{2+}$ ions, and below a ${T}_{N}\ensuremath{\approx}26\mathrm{K}&lt;{T}_{\mathrm{irr}},$ antiferromagnetic ordering of the ${M}^{2+}$-ion spins suppresses any spin on the intervening Ru(IV). The ${M}^{2+}{:e}^{2}\ensuremath{-}\mathrm{O}\ensuremath{-}\mathrm{Ru}(\mathrm{IV})\ensuremath{-}\mathrm{O}{\ensuremath{-}M}^{2+}{:e}^{2}$ antiferromagnetic superexchange interaction is stronger than the ferromagnetic ${M}^{2+}{:e}^{2}\ensuremath{-}\mathrm{O}\ensuremath{-}\mathrm{Ru}(\mathrm{IV}{):e}^{0}$ interaction because of a weak intraatomic exchange with the ${\ensuremath{\pi}}^{*}$-electron spins on the Ru(IV) atoms. On the other hand, disordered ${\mathrm{La}}_{2}{\mathrm{MnRuO}}_{6.17(1)}$ is ferromagnetic with a magnetization at 5 K of $2.85{\ensuremath{\mu}}_{B}$ per formula unit (f.u.) in a magnetic field of 50 kOe. This finding is interpreted with a model in which the \ensuremath{\pi}-bonding orbitals on both the Mn and Ru are coupled to form a common ferromagnetic ${\ensuremath{\pi}}^{*}$ band in which only the antibonding electrons are not spin paired. The strong next-nearest-neighbor interaction between Ru atoms made manifest in the ordered double perovskites provides an explanation of why the ${\ensuremath{\pi}}^{*}$ bandwidth of the perovskite system ${\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{Ca}}_{x}{\mathrm{RuO}}_{3}$ may increase with $x.$
Ultra-compact dispersion compensated femtosecond fiber oscillators and amplifiers (2005)

Dispersion-compensated fully integrated Er and Yb femtosecond fiber oscillators are described. Yb MOPAs produce 100 fs pulses at repetition rates of 60 MHz with average output powers up to 200 mW. Er MOPAs generate 100 fs pulses with average output powers up to 100 mW.
β-(Methoxy-(substitutedphenyl)-methyl)-γ-butyrolactones: A short synthesis from cinnamyl acetate (2016)

A simple and short synthesis has been revealed for the preparation of (±) β-(Methoxy-(substitutedphenyl)-methyl)-γ-butyrolactones. The reaction of cinnamyl acetate with Mn(OAc)3 · 2H2O in boiling acetic acid containing acetic anhydride gave the products 2 and 3, which further cyclized in 3% H2SO4/CH3OH to afford the butyrolactones (8a–e), which are intermediates of lignin, in good to moderate yields.
3 Serial verb constructions and motion semantics (2021)

This chapter investigates the expression of associated motion and directional motion in the form of serial verb constructions (SVCs). In a sample of 125 languages with SVCs, 101 have motion SVCs. The most common types are directional SVCs, in which a path-of-motion verb combines with another motion verb, and prior associated motion SVCs expressing motion prior to the activity or state predicated by the other verb in the construction. Concurrent motion and subsequent motion are much less common. In a prior motion SVC, the motion verb nearly always precedes the other verb, and the figure on the path of motion is the subject. In a directional SVC, the path-of-motion verb nearly always follows the other verb, and the grammatical function of the figure on the path of motion can vary according to the semantics of the main verb in the construction.