gebhart/patrepeval huggingface dataset:
Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types (2018)

FoxP3<sup>+</sup> T regulatory (Treg) cells are central elements of immunologic tolerance. They are abundant in many tumors, where they restrict potentially favorable antitumor responses. We used a three-pronged strategy to identify genes related to the presence and function of Tregs in the tumor microenvironment. Gene expression profiles were generated from tumor-infiltrating Tregs (TITRs) of both human and mouse tumors and were compared with those of Tregs of lymphoid organs or normal tissues from the same individuals. A computational deconvolution of whole-tumor datasets from the Cancer Genome Atlas (TCGA) was performed to identify transcripts specifically associated with Tregs across thousands of tumors from different stages and locations. We identified a set of TITR-differential transcripts with striking reproducibility between tumor types in mice, between mice and humans, and between different human patients spanning tumor stages. Many of the TITR-preferential transcripts were shared with "tissue Tregs" residing in nonlymphoid tissues, but a tumor-preferential segment could be identified. Many of these TITR signature transcripts were confirmed by mining of TCGA datasets, which also brought forth transcript modules likely representing the parenchymal attraction of, or response to, tumor Tregs. Importantly, the TITR signature included several genes encoding effective targets of tumor immunotherapy. A number of other targets were validated by CRISPR-based gene inactivation in mouse Tregs. These results confirm the validity of the signature, generating a wealth of leads for understanding the role of Tregs in tumor progression and identifying potential targets for cancer immunotherapy.
Resolution of HLA‐B*44:02:01G, ‐DRB1*14:01:01G and ‐DQB1*03:01:01G reveals a high allelic variability among 12 European populations (2014)

Within the framework of the EU-funded HLA-NET action, an analysis of three G-group alleles, HLA-B*44:02:01G, DRB1*14:01:01G and DQB1*03:01:01G, was undertaken in 12 European populations. Ambiguities were resolved by polymerase chain reaction-sequence-specific amplification (PCR-SSP) or PCR-sequence-based typing (PCR-SBT) in a total of 5095 individuals. The results of the DRB1*14:01/14:54 ambiguity showed high relative ratios (24-53%) of DRB1*14:01 in Bulgarians, Croatians, Greeks, Italians and Slovenians, contrasting with low ratios (6-13%) in Austrians, Finnish, French, Hungarians, Norwegians and Swiss. Resolution of the B*44:02/44:27 ambiguity showed that B*44:27 had a high relative ratio in Slovenians (25.5%) and Bulgarians (37%) and low in French and Swiss (0.02-1%), and was not observed in Greeks and Italians. The highest relative ratio of DQB1*03:19 was found in Portuguese (11%), by contrast with low ratios (0-3%) in the other five populations. Analysis of the A, B, DRB1 phenotypes and family-derived haplotypes in 1719 and 403 individuals positive for either HLA-B*44:02G or DRB1*14:01G ambiguities, respectively, showed some preferential associations, such as A*26∼DRB1*14:01, B*35∼DRB1*14:01, B*38∼DRB1*14:01 and B*44:27∼DRB1*16. Because these ambiguities are located outside the peptide-binding site, they may not be recognized by alloreactive T-cells. However, because of strong linkage disequilibrium (LD), the DRB1*14:01 vs DRB1*14:54 and the B*44:02 vs B*44:27 mismatches are associated to DRB3-, and C-mismatches, respectively. These results are informative for algorithms searching unrelated hematopoietic stem cell donors. For B*44:27-positive patients, searches are expected to be more successful when requesting donors from Southeastern-European ancestry. Furthermore, the introduction of human leukocyte antigen (HLA)-typing strategies that allow resolving exon 4 (for class I) and exon 3 (for class II) polymorphisms can be expected to contribute significantly to population genetics studies.
Joint Analysis of Success and Outage Probability in 5G Multi-Tier Heterogeneous Network (2022)

The evolving high-performance communication gadgets and applications will demand higher reliability, accessibility or coverage to achieve the massive data rate requirement. Consequently, the 5G cellular network is embracing the multi-tier heterogeneous network that incorporates the dense deployment of small cells or multiple-tiers of small cells i.e. pico and femto cells under macro cells to offer sufficient coverage and service quality. The research, therefore, aimed to measure and maximize the success probability and minimize the outage probability of a tier of multi-tier network in terms of network resource i.e. transmission power, bias, densities, etc. offer optimal success and outage probability to the user to ensure a better quality of service.
2-(2′-((Dimethylamino)methyl)-4′-(fluoroalkoxy)-phenylthio)benzenamine Derivatives as Serotonin Transporter Imaging Agents (2007)

A novel series of ligands with substitutions at the 5-position on phenyl ring A and at the 4'-position on phenyl ring B of 2-(2'-((dimethylamino)methyl)-4'-(fluoroalkoxy)phenylthio)benzenamine (4'-2-fluoroethoxy derivatives 28-31 and 4'-3-fluoropropoxy derivatives 40-42) were prepared and tested as serotonin transporter (SERT) imaging agents. The new ligands displayed high binding affinities to SERT (Ki ranging from 0.03 to 1.4 nM). The corresponding 18F labeled compounds, which can be prepared readily, showed excellent brain uptake and retention after iv injection in rats. The hypothalamus region showed high uptake values between 0.74% and 2.2% dose/g at 120 min after iv injection. Significantly, the hypothalamus to cerebellum ratios (target to nontarget ratios) at 120 min were 7.8 and 7.7 for [18F]28 and [18F]40, respectively. The selective uptake and retention in the hypothalamus, which has a high concentration of SERT binding sites, demonstrated that [18F]28 and [18F]40 are promising positron emission computed tomography imaging agents for mapping SERT binding sites in the brain.
Etch proximity correction by integrated model-based retargeting and OPC flow (2007)

Model-based Optical Proximity Correction (OPC) usually takes into consideration optical and resist process proximity effects. However, the etch bias proximity effect usually can not be completely eliminated by etch process optimization only and needs to be compensated for in OPC flow for several critical layers. Since the understanding of the etch process effect is getting better and accurate etch bias modeling is available now, lithographers start to migrate from rule-based correction to model-based correction. Conventionally when etch bias is considered in model-based correction, optical/resist/etch effect is corrected in one step by using the input layout as the final etch target. In this paper, we proposed a new flow in which etch and optical/resist process effect are separated in both model calibration and layout correction. This double separation allows easier control over etch and resist target, resulting in drastic reduction of OPC runtime. In addition it enables post-OPC verification at both resist and etch level. Advantages of the new integrated model-based retarget/OPC flow in RET implementation are also discussed.
Vanadium interferes with siderophore-mediated iron uptake in Pseudomonas aeruginosa (2000)

Vanadium is a metal that under physiological conditions can exist in two oxidation states, V(IV) (vanadyl ion) and V(V) (vanadate ion). Here, it was demonstrated that both ions can form complexes with siderophores. Pseudomonas aeruginosa produces two siderophores under iron-limiting conditions, pyoverdine (PVD) and pyochelin (PCH). Vanadyl sulfate, at a concentration of 1-2 mM, strongly inhibited growth of P. aeruginosa PAO1, especially under conditions of severe iron limitation imposed by the presence of non-utilizable Fe(III) chelators. PVD-deficient mutants were more sensitive to vanadium than the wild-type, but addition of PVD did not stimulate their growth. Conversely, PCH-negative mutants were more resistant to vanadium than the wild-type strain. Both siderophores could bind and form complexes with vanadium after incubation with vanadyl sulfate (1:1, in the case of PVD; 2:1, in the case of PCH). Although only one complex with PVD, V(IV)-PVD, was found, both V(IV)- and V(V)-PCH were detected. V-PCH, but not V-PVD, caused strong growth reduction, resulting in a prolonged lag phase. Exposure of PAO1 cells to vanadium induced resistance to the superoxide-generating compound paraquat, and conversely, exposure to paraquat increased resistance to V(IV). Superoxide dismutase (SOD) activity of cells grown in the presence of V(IV) was augmented by a factor of two. Mutants deficient in the production of Fe-SOD (SodB) were particularly sensitive to vanadium, whilst sodA mutants deficient for Mn-SOD were only marginally affected. In conclusion, it is suggested that V-PCH catalyses a Fenton-type reaction whereby the toxic superoxide anion O(2)- is generated, and that vanadium compromises PVD utilization.
Downlink Training in Cell-Free Massive MIMO: A Blessing in Disguise (2019)

Cell-free Massive MIMO (multiple-input multiple-output) refers to a distributed Massive MIMO system where all the access points (APs) cooperate to coherently serve all the user equipments (UEs), suppress inter-cell interference and mitigate the multiuser interference. Recent works demonstrated that, unlike co-located Massive MIMO, the channel hardening is, in general, less pronounced in cell-free Massive MIMO, thus there is much to benefit from estimating the downlink channel. In this study, we investigate the gain introduced by the downlink beamforming training, extending the previously proposed analysis to non-orthogonal uplink and downlink pilots. Assuming single-antenna APs, conjugate beamforming and independent Rayleigh fading channel, we derive a closed-form expression for the per-user achievable downlink rate that addresses channel estimation errors and pilot contamination both at the AP and UE side. The performance evaluation includes max-min fairness power control, greedy pilot assignment methods, and a comparison between achievable rates obtained from different capacity-bounding techniques. Numerical results show that downlink beamforming training, although increases pilot overhead and introduces additional pilot contamination, improves significantly the achievable downlink rate. Even for large number of APs, it is not fully efficient for the UE relying on the statistical channel state information for data decoding.
Serial bipolar androgen therapy (sBAT) using cyclic supraphysiologic testosterone (STP) to treat metastatic castration-resistant prostate cancer (mCRPC) (2019)

During prostate carcinogenesis, molecular changes occur in prostate epithelial cells such that their Androgen Receptor (AR) protein expression increases significantly (i.e. >5 fold).
Cobalt porphyrin-Mediated Oxygen Transport in a Polymer Membrane: Effect of the Cobalt porphyrin Structure on the Oxygen-Binding Reaction, Oxygen-Diffusion Constants, and Oxygen-Transport Efficiency (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCobalt porphyrin-Mediated Oxygen Transport in a Polymer Membrane: Effect of the Cobalt porphyrin Structure on the Oxygen-Binding Reaction, Oxygen-Diffusion Constants, and Oxygen-Transport EfficiencyHiroyuki Nishide, Takayuki Suzuki, Hiroyoshi Kawakami, and Eishun TsuchidaCite this: J. Phys. Chem. 1994, 98, 19, 5084–5088Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/j100070a023https://doi.org/10.1021/j100070a023research-articleACS PublicationsRequest reuse permissionsArticle Views319Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Radiative properties of multicarrier bound excitons in GaAs (2015)

Excitons in semiconductors can have multiple lifetimes due to spin-dependent oscillator strengths and interference between different recombination pathways. In addition, strain and symmetry effects can further modify lifetimes via the removal of degeneracies. We present a convenient formalism for predicting the optical properties of $k=0$ excitons with an arbitrary number of charge carriers in different symmetry environments. Using this formalism, we predict three distinct lifetimes for the neutral acceptor bound exciton in GaAs, and confirm this prediction through polarization dependent and time-resolved photoluminescence experiments. We find the acceptor bound-exciton lifetimes to be ${T}_{o}\ifmmode\times\else\texttimes\fi{}(1,3,\frac{3}{4})$, where ${T}_{o}=(0.61\ifmmode\pm\else\textpm\fi{}0.12)\phantom{\rule{4.pt}{0ex}}\text{ns}$. Furthermore, we provide an estimate of the intralevel and interlevel exciton spin-relaxation rates.
RELACIONES ENTRE EL CONTEXTO CINEMATOGRÁFICO ESPAÑOL Y EL LATINOAMERICANO: ESTUDIO DEL CINE MEXICANO DE LOS AÑOS 40 VISTO A TRAVÉS DE LA REVISTA PRIMER PLANO. (2016)

Resumen: Este trabajo trata de analizar el discurrir de la cinematografia latinoamericana (mas concretamente la mexicana) en Espana durante la decada de los cuarenta a traves de la publicacion cinematografica espanola Primer Plano , teniendo en cuenta el particular contexto politico de ambos paises (ausencia de relaciones diplomaticas); y de que manera la coyuntura internacional y los vinculos culturales entre ambas naciones; marcaron el discurrir de las relaciones entre ambas cinematografias. Abstract: This paper attempts to analyze the flow of Latin American cinema (specifically Mexico) in Spain during the forties through the Spanish Film Spotlight publication, taking into account the particular political context of both countries (absence of diplomatic relations); and how the international situation and cultural ties between the two nations; they marked the passage of relations between the two film industries.
On Unifying Deep Generative Models (2017)

Deep generative models have achieved impressive success in recent years. Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs), as emerging families for generative model learning, have largely been considered as two distinct paradigms and received extensive independent studies respectively. This paper aims to establish formal connections between GANs and VAEs through a new formulation of them. We interpret sample generation in GANs as performing posterior inference, and show that GANs and VAEs involve minimizing KL divergences of respective posterior and inference distributions with opposite directions, extending the two learning phases of classic wake-sleep algorithm, respectively. The unified view provides a powerful tool to analyze a diverse set of existing model variants, and enables to transfer techniques across research lines in a principled way. For example, we apply the importance weighting method in VAE literatures for improved GAN learning, and enhance VAEs with an adversarial mechanism that leverages generated samples. Experiments show generality and effectiveness of the transferred techniques.
Signal processing for DNA sequencing (2002)

Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
Curious gain-switching operation of GaInN blue-violet laser diodes producing high-peak-power picosecond optical pulses (2009)

We found new kinds of phenomena in blue-violet GaInN laser diodes. In strong gain-switching operation, 10-W peak-power and 10-ps optical pulses were generated, and laser light injection into laser diodes further enhanced the peak power.
Creating porosity in a trianglimine macrocycle by heterochiral pairing (2021)

Macrocycles are usually non-porous or barely porous in the solid-state because of their small intrinsic cavity sizes and tendency to close-pack. Here, we use a heterochiral pairing strategy to introduce porosity in a trianglimine macrocycle, by co-crystallising two macrocycles with opposing chiralities. The stable racemic trianglimine crystal contains an interconnected pore network that has a Brunauer-Emmett-Teller (BET) surface area of 355 m2 g-1.
Organic Transistors Incorporating Lipid Monolayers for Drug Interaction Studies (2019)

Abstract Cell membranes are fundamental for cellular function as they protect the cell and control passage in and out of the cell. Despite their clear significance, cell membranes are often difficult to study, due to their complexity and the lack of available technologies to interface with them and transduce their functions. Overcoming this complexity by developing simple, reductionist models can facilitate their study. Indeed, lipid layers represent a simplified yet representative model for a cell membrane. Lipid layers are highly insulating, a property that is directly affected by changes in lipid packing or membrane fluidity. Such physical changes in the membrane models can be characterized by coupling them with an electronic transducer. Herein, a lipid monolayer that is stabilized between two immiscible solvents is integrated with an organic electrochemical transistor, which is capable of operating in a biphasic solvent mixture. The platform is used to evaluate how lidocaine, a widely used anesthetic the working mechanism of which is still a matter of debate, interacts with the cell membrane. The present study provides evidence that the anesthetic directly interacts with the lipids in the membrane, affecting their packing and therefore the monolayer permeability. The proposed platform provides an elegant solution for studying compound–membrane interactions.
Preparation and evaluation of alpha-phenyl-n-tert-butyl nitrone (PBN)-encapsulated chitosan and PEGylated chitosan nanoparticles. (2009)

Alpha-phenyl-n-tert-butyl nitrone (PBN) shows its major effect by scavenging free radicals formed in the ischemia and it has the ability to penetrate through the blood brain barrier easily. The in vivo stability of PBN is very low and when administered systemically, it has a mean plasma half life of about three hours. Therefore, formulations which are able to prolong the plasma residence time of PBN are of major interest, because oxygen radicals are usually continuously formed under pathological conditions. In this study, PBN, a nitrone compound having neuroprotective properties, was encapsulated in chitosan (CS) and chitosan-poly(ethylene glycol) (CS-PEG) nanoparticles for treatment of diseases such as stroke, in which sustained free radical production is reported. The nanoparticles were characterized through particle size determination, zeta potential, encapsulation efficiency, surface morphology determinations and in vitro release studies. The surface morphologies were evaluated by transmission electron microscopy (TEM) and nanoparticles having spherical shapes were characterized. The particle size distribution was between approximately 97 nm and approximately 322 nm; and the zeta potentials varied between approximately 9 mV and approximately 33 mV. Size of the nanoparticle formulations was important for the release of PBN from nanoparticles. The quantitative determination of PBN has been evaluated by a validated analytical HPLC method. The presented chitosan-based nanotechnology opens new perspectives for testing antioxidant activity in vivo.
InGaN self‐organized quantum dots grown by metalorganic chemical vapour deposition (MOCVD) (2003)

InGaN self-organized quantum dots (QDs) have been grown on sapphire (0001) substrates by low-pressure metalorganic chemical vapor deposition (MOCVD). Atomic force microscopy (AFM) measurements revealed the formation of InGaN QDs grown at 760 °C on a very thin AlN template. No InGaN QDs were formed when the amount of InGaN deposited was less than 5 monolayers (MLs), whereas self-organized QDs appear on the surface with further increase in the number of InGaN MLs. For the typical 15 MLs InGaN QDs grown by this technique, the average diameter and height of the QDs are 19.5 and 7.5 nm, respectively, with a dot density of about 1.3 × 1011 cm−2. Room temperature microphotolumi-nescence measurements show blue (2.86 eV) to green (2.31 eV) emission when the InGaN QDs deposited on the thin AlN layer increased from 15 to 35 MLs.
Flexible Crossbar‐Structured Phase Change Memory Array via Mo‐Based Interfacial Physical Lift‐Off (2018)

Abstract Inorganic phase change memories (PCMs) have attracted substantial attention as a next‐generation storage node, due to their high‐level of performance, reliability, and scalability. To integrate the PCM on plastic substrates, the reset power should be minimized to avoid thermal degradation of polymers and adjacent cells. Additionally, flexible phase change random access memory remains unsolved due to the absence of the optimal transfer method and the selection device. Here, an Mo‐based interfacial physical lift‐off transfer method is introduced to realize a crossbar‐structured flexible PCM array, which employs a Schottky diode (SD) selection device and conductive filament PCM storage node. A 32 × 32 parallel array of 1 SD‐1 CFPCM, which utilizes a Ni filament as a nanoheater for low power phase transition, is physically exfoliated from the glass substrate at the face‐centered cubic/body‐centered cubic interface within the sacrificial Mo layer. First principles density functional theory calculations are utilized to understand the mechanism of the Mo‐based exfoliation phenomena and the observed metastable Mo phase. The flexible 1 SD‐1 CFPCM shows reliable operations (e.g., large resistance ratio of 17, excellent endurance over 100 cycles, and long retention over 10 4 s) with excellent flexibility. Furthermore, the random access operation is confirmed by addressing tests of characters “KAIST.”
21‐1: Active Circular Polarizer OLED E‐Mirror (2019)

Due to the inherent reflective property of OLED (organic light‐emitting diode) displays, the use of an active circular polarizer technology has been previously reported to provide an OLED E‐Mirror (Electronic‐Mirror). This paper focuses on the optimization of the active circular polarizer technology to improve the dynamic reflection dimming range.
ChemInform Abstract: In situ Preparation of a Multifunctional Chiral Hybrid Organic—Inorganic Catalyst for Asymmetric Multicomponent Reactions. (2013)

Abstract The utilized catalyst is made of a chiral mesoporous organosilica material incorporating a urea‐based cinchona derivative and propylamine groups, generated by a co‐condensation method.
Photochemical bonding of epithelial cell-seeded collagen lattice to rat muscle layer for esophageal tissue engineering: a pilot study (2005)

The photochemical bonding of cell-seeded collagen lattice to muscle layer in rat, was investigated for esophageal tissue engineering. The esophageal epithelial cells of the rat were seeded on collagen lattice and together with the latissimus dorsi muscle layer, were exposed to a photosensitizer rose Bengal at the bonding surface. The photochemical bonding was found to significantly increase the adherence at the bonding interface without compromising the cell viability. The results show integration of the collagen lattice with the muscle layer at the bonding interface although the subsequent surgical manipulation disturbed the integration at some region.