gebhart/patrepeval huggingface dataset:
Discovery of prevalent, clinically actionable tumor neoepitopes via integrated biochemical and cell-based platforms (2022)

Summary Strategies for maximizing the potency and specificity of cancer immunotherapies have sparked efforts to identify recurrent epitopes presented in the context of defined tumor-associated neoantigens. Discovering these “neoepitopes” can be difficult owing to the limited number of peptides that arise from a single point mutation, a low number of copies presented on the cell surface, and variable binding specificity of the human leukocyte antigen (HLA) class I complex. Due to these limitations, many discovery efforts focus on identifying neoepitopes from a small number of cancer neoantigens in the context of few HLA alleles. Here we describe a systematic workflow to characterize binding and presentation of neoepitopes derived from 47 shared cancer neoantigens in the context of 15 HLA alleles. Through the development of a high-throughput neoepitope-HLA binding assay, we surveyed 24,149 candidate neoepitope-HLA combinations resulting in 587 stable complexes. These data were supplemented by computational prediction that identified an additional 257 neoepitope-HLA pairs, resulting in a total of 844 unique combinations. We used these results to build sensitive targeted mass spectrometry assays to validate neoepitope presentation on a panel of HLA-I monoallelic cell lines engineered to express neoantigens of interest as a single polypeptide. Altogether, our analyses detected 84 unique neoepitope-HLA pairs derived from 37 shared cancer neoantigens and presented across 12 HLA alleles. We subsequently identified multiple TCRs which specifically recognized two of these neoantigen-HLA combinations. Finally, these novel TCRs were utilized to elicit a T cell response suggesting that these neoepitopes are likely to be immunogenic. Together these data represent a validated, extensive resource of therapeutically relevant neoepitopes and the HLA context in which they can be targeted.
Bank-aware Dynamic Cache Partitioning for Multicore Architectures (2009)

As chip-multiprocessor systems (CMP) have become the predominant topology for leading microprocessors, critical components of the system are now integrated on a single chip. This enables sharing of computation resources that was not previously possible. In addition, the virtualization of these computational resources exposes the system to a mix of diverse and competing workloads. Cache is a resource of primary concern as it can be dominant in controlling overall throughput. In order to prevent destructive interference between divergent workloads, the last level of cache must be partitioned. In the past, many solutions have been proposed but most of them are assuming either simplified cache hierarchies with no realistic restrictions or complex cache schemes that are difficult to integrate in a real design. To address this problem, we propose a dynamic partitioning strategy based on realistic last level cache designs of CMP processors. We used a cycle accurate, full system simulator based on Simics and Gems to evaluate our partitioning scheme on an 8-core DNUCA CMP system. Results for an 8-core system show that our proposed scheme provides on average a 70% reduction in misses compared to non-partitioned shared caches, and a 25% misses reduction compared to static equally partitioned (private) caches.
Effects of dietary phosphorus and protein in dogs with chronic renal failure (1992)

Four diets were formulated to contain: 16% protein and 0.4% phosphorus--diet 1; 16% protein and 1.4% phosphorus--diet 2; 32% protein and 0.4% phosphorus--diet 3; and 32% protein and 1.4% phosphorus--diet 4. Forty-eight dogs were fed diet 1 for 3 months after surgical reduction of renal mass, then were allotted to 4 groups of 12 dogs each, with equal mean values for glomerular filtration rate (GFR). Dog of groups 1-4 were fed diets 1-4, respectively, for 24 months. Data collected from the dogs during and at termination of the study were analyzed statistically for effects of dietary protein, phosphorus (P), time, and interactions between these factors. During the 24 months of study, 24 dogs developed uremia and were euthanatized for necropsy. Necropsy also was performed on the remaining 24 dogs after they were euthanatized at the end of the study. Dog survival was significantly enhanced by 0.4% P diets (vs 1.4% P diets), but survival was not significantly influenced by amount of dietary protein. The 0.4% P diets (vs 1.4% P diets) significantly increased the period that GFR remained stable before it decreased, but dietary protein did not have significant effect. Significant blood biochemical changes attributed to P, protein, and time were identified during the study. Terminally, plasma parathyroid hormone concentration was significantly increased from prediet values in all groups of dogs. Urine protein excretion was not significantly affected by dietary amount of either protein or P, when measured by either timed urine collection or urine protein-to-creatinine ratio.(ABSTRACT TRUNCATED AT 250 WORDS)
Protection from liver fibrosis by a peroxisome proliferator-activated receptor δ agonist (2012)

Peroxisome proliferator-activated receptor delta (PPARδ), a member of the nuclear receptor family, is emerging as a key metabolic regulator with pleiotropic actions on various tissues including fat, skeletal muscle, and liver. Here we show that the PPARδ agonist KD3010, but not the well-validated GW501516, dramatically ameliorates liver injury induced by carbon tetrachloride (CCl(4)) injections. Deposition of extracellular matrix proteins was lower in the KD3010-treated group than in the vehicle- or GW501516-treated group. Interestingly, profibrogenic connective tissue growth factor was induced significantly by GW501516, but not by KD3010, following CCl(4) treatment. The hepatoprotective and antifibrotic effect of KD3010 was confirmed in a model of cholestasis-induced liver injury and fibrosis using bile duct ligation for 3 wk. Primary hepatocytes treated with KD3010 but not GW501516 were protected from starvation or CCl(4)-induced cell death, in part because of reduced reactive oxygen species production. In conclusion, our data demonstrate that an orally active PPARδ agonist has hepatoprotective and antifibrotic effects in animal models of liver fibrosis, suggesting a possible mechanistic and therapeutic approach in treating patients with chronic liver diseases.
Control of radiation angle by introducing symmetric end structure to oblique waveguide in three-dimensional photonic crystal (2016)

We investigate the radiation angle of an oblique waveguide in a stripe-stacked three-dimensional photonic crystal. We show that the output-light is radiated in a different direction from the oblique waveguide direction. Moreover, the radiation polar angle varies from 30° to 50° depending on the frequency. To inhibit the frequency dependence and obtain vertical radiation, we introduced a symmetric structure at the end of the waveguide. As a result of cancellation of the in-plane asymmetric wavenumber, the radiation polar angle is less than 6° from the surface-normal direction and does not depend on frequency.
Information-theoretic performance of quadrature mirror filters (1995)

Most existing quadrature mirror filters (QMFs) closely match the derived closed-form expression for an efficient class of QMFs. We use the closed-form expressions to derive the relationship between information-theoretic loss and the frequency selectivity of the QMF, by calculating first-order entropy as well as rate-distortion theoretic performance of a two band QMF system. We find that practical QMFs do not suffer a significant information-theoretic loss with first-order autoregressive Gaussian sources. With second-order autoregressive sources we find that practical QMFs suffer a notable information-theoretic loss when the bandwidth of the source is extremely narrow, but incur a small loss when the bandwidth is wider. We suggest that our results broadly apply to higher order autoregressive sources as well.
Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. (1996)

Nonhistone proteins 6A and 6B (NHP6A/B) are nonsequence-specific DNA-binding proteins from Saccharomyces cerevisiae that are related structurally and functionally to the mammalian high mobility group proteins 1 and 2. These DNA architectural proteins distort DNA structure severely and have been shown to promote assembly of specialized recombination complexes. Here we show that the yeast NHP6A/B proteins are required for the induction of a subset of genes transcribed by RNA polymerase II (pol II). Activation of the CUP1, CYC1, GAL1, and DDR2 genes was decreased or abolished completely in the delta nhp6A/B strain. No significant change in basal expression was observed for any of the 10 genes examined. Analysis of chimeric gene constructs localized the regions dependent on NHP6A/B to be primarily at the core promoters, although the GAL1 UAS also requires NHP6A/B for activity. In vitro, NHP6A stimulated transcription by pol II at the GAL1 promoter three- to fivefold above the level of activation by GAL4-VP16 alone. Gel mobility shift assays showed that NHP6A promotes the formation of a complex with TBP and TFIIA at the TATA box that has enhanced affinity for TFIIB.
Blue emission of Cerium doped Aluminum (oxy)-nitride thin film prepared by reactive sputtering technique (2016)

Recently, blue light emitting solid-state materials received high attention for use in white LEDs and other luminescent applications. In this direction, phosphors- doped nitrides and oxy-nitrides composites attracted much potential due to their thermal, chemical stability and the possibility to tune their electronic structure to adapt to the required applications. In particular, the III-nitrides (e.g. AlN, GaN) have been considered as a suitable host material for phosphors that emit in UV-visible range due to its large bandgap. Thus, the purpose of this study is to sensitize blue emission from rare earth doped AlN as a wide bandgap semiconductor.\nIn the present work, Cerium-doped aluminum nitride (Ce-AlN) thin films were prepared at room temperature using radio frequency (RF) reactive sputtering. X-ray diffraction and high resolution transmission electron microscopy (HRTEM) revealed a well crystalline textured microstructure with single &lt;002&gt; out-of-plane orientation. Strong blue emission from the prepared samples was detected when excited by 325 nm laser. Electron energy loss spectroscopy (EELS) has been used to reveal the dominant oxidation state of Ce atoms, which undergoes a change from of Ce(IV) to Ce(III) ions after annealing. The chemical composition was analyzed by simulation of Rutherford backscattering spectrometry (RBS) and compared to HRTEM images. A clear correlation between microstructure, composition and sample photoluminescence (PL) was established. It was found that surface oxidation during post-deposition annealing plays an important role in the PL response of the samples. We believe that the strong blue emission in this new (oxy)-nitride material holds great potentials for solid state lighting applications due to its thermal and chemical stability as well as the luminescence efficiency. Moreover, the comprehensive approach conducted within this study could serve as a guideline for better understanding and the design of the luminescence behavior in rare earth-doped (oxy)-nitride thin films.
Control plane integration for cloud services (2010)

This paper addresses the problem of control plane integration for management and control of cloud services. Unlike data plane integration, which ensures that services can exchange data during operation, control plane integration ensures proper configuration of services before their use. Examples of control plane integration include creating user accounts or establishing profiles in multiple services to allow them to work together during operation. The heterogeneity of service interfaces in the control plane arises from the different ways in which services are implemented and the different requirements they have for their use. Control plane integration is often needed for service bundling and ad-hoc compositions across services, such as for promotional campaigns that must be developed and deployed rapidly. In this paper, we propose a developer-centric approach to integration of services on the control plane. Our approach is based on using Java code annotation, which is introspected at runtime to create rich service models. A multi-layered architecture allows the rapid modeling, development and implementation of service integration scenarios. We demonstrate our approach with an example of a promotional campaign that uses two external service providers.
Is ultrasound axillary staging less accurate in invasive lobular breast cancer than in ductal breast cancer? (2012)

Objective: To determine the feasibility of excluding MRI from the preoperative diagnostic pathway of invasive lobular carcinoma (ILC) in women with low and low to moderate density breasts on mammography. Methods: A total of 179 cases of ILC were diagnosed between 2009 and 2012. Forty-eight cases were identified as low and low to moderate density breasts. The study group includes 32 cases who underwent MRI. Parameters scrutinised include size and number of lesions on mammography, ultrasound and MRI, second-look ultrasound, type of surgery, further surgery and histology. Results: Twenty-nine cases had low to moderate density breasts and three had purely low density breasts. Average age of women was 64. Size of lesions ranged between 2 and 50 mm with an average of 20.14 mm. In 25/32 cases (78.12%) conventional imaging matched MRI. MRI identified additional disease in 7/32 (21.8%). This was predominantly in the form of satellites around the index lesion resulting in multifocality in 6/7. Four resulted appropriately in mastectomy. Two led to wider WLE appropriately. In one case, multicentric disease was correctly detected and subjected to mastectomy. Second-look ultrasound was recommended in 4/7 cases. All these cases had low to moderate density breasts on mammography and 6/7 cases measured more than 15 mm in size. Ultrasound matched MRI in one mammographically occult case and was subjected to appropriate WLE. In two cases there was much more disease than anticipated from conventional imaging and MRI (6.25%). Conclusion: Even in low and low to moderate density breasts where mammography has a higher exclusion value, MRI identified additional disease in 21.8% (7/32).
Dissociation of connectivity for syntactic irregularity and perceptual ambiguity in musical chord stimuli (2020)

Abstract Previously syntactic irregularity has been most studied with chord sequences. However, the same chord may be interpreted as having different harmonic functions, implying perceptual ambiguity. Hence, syntactic irregularity and perceptual ambiguity may be processed simultaneously. We devised 3 different 5-chord sequences in which the ending chord differed with the tonic (T), submediant (SM), and supertonic (ST). In terms of syntactic regularity, T is most regular, ST is most irregular. However, in terms of perceptual ambiguity, the most irregular ST had the salient highest voice. Therefore, the SM was the most ambiguous condition. We investigated how the human brain separates syntactic irregularity and perceptual ambiguity in terms of effective connectivity in bilateral inferior frontal gyri (IFGs) and superior temporal gyri (STGs) with magnetoencephalography in 19 subjects. Correct rate was lower for the most ambiguous chord (SM) ( P = 0.020) as expected. Connectivity from the right to the left IFG was enhanced for the most irregular chord (ST) ( P = 0.024, false discovery rate (FDR) corrected), whereas connectivity from the right to the left STG was enhanced for the most ambiguous chord (SM) ( P &lt; 0.001, FDR corrected). The correct rate was negatively correlated with connectivity in the STG, further reflecting perceptual ambiguity ( P = 0.026). We found that syntactic irregularity and perceptual ambiguity in music are dissociated in connectivity between bilateral IFGs and STGs, respectively. Significance Statement We provide the first neurophysiological evidence of the processing of perceptual ambiguity, other than syntactic irregularity, implied in musical chords. We found that the notion of “perceptually ambiguity” is applicable to musical chord stimuli different in syntactic irregularity, and that perceptual ambiguity is separate from syntactic irregularity. Our data demonstrate that the brain interprets the three conditions of musical chords as both “from regular to irregular” and “from ambiguous to unambiguous” conditions simultaneously. This study is the first to unveil dissociation of connectivity by syntactic irregularity and perceptual ambiguity involved in musical chord stimuli.
Supplementary Table 2 from Signaling and Transcriptional Changes Critical for Transformation of Human Cells by Simian Virus 40 Small Tumor Antigen or Protein Phosphatase 2A B56γ Knockdown (2023)

Supplementary Table 2 from Signaling and Transcriptional Changes Critical for Transformation of Human Cells by Simian Virus 40 Small Tumor Antigen or Protein Phosphatase 2A B56γ Knockdown
Development and Testing of a Silver Chloride-Impregnated Activated Carbon for Aqueous Removal and Sequestration of Iodide (2005)

Silver impregnated activated carbon (SIAC) can effectively remove iodide from water and sequester it in the form of AgI(s)). Given the extremely insoluble nature of AgI(s), the spent SIAC can be safely disposed of in land burial facilities. However, when the molar ratio of silver to iodide is greater than one, which is typical for waters contaminated with iodide, unreacted silver on the SIAC leached into solution with decreasing pH. To minimize silver leaching, a silver chloride impregnated activated carbon (SIAC-Cl) was produced from a SIAC. Scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) and X-Ray Diffraction (XRD) analyses confirmed the presence of silver chloride on the SIAC-Cl. Batch isotherm experiments conducted at pH 5, 7 and 8 showed that the iodide uptakes of SIAC-Cl and SIAC were similar and independent of pH. SEM/EDX and XRD analyses after reaction with iodide indicated that chloride was exchanged with iodide to form AgI(s) on the SIAC-Cl. Batch leaching experiments demonstrated that leaching of silver from SIAC-Cl under acidic conditions was significantly lower than from SIAC. The performance of SIAC and SIAC-Cl for practical applications was evaluated by conducting column experiments using a radioactively contaminated groundwater that included 129I. SIAC and SIAC-Cl showed similar degrees of iodide uptake. However, a significant degree of silver leaching, about 50% of the total silver, occurred from the SIAC during the course of the column experiments, whereas silver leaching from SIAC-Cl was remarkably low (only 6% of the total silver). SIAC-Cl appears to be a suitable getter material to remove and sequester iodide from contaminated waste streams.
User Effects on MIMO Performance: From an Antenna to a Link Perspective (2011)

We investigate in this paper the effects of the user's presence on the performance of a multiple-input multiple-output (MIMO) system in data and in voice usage scenarios. The investigation studies the user effects on the antenna performance and how these are incorporated into the MIMO channel and the link characteristics. The antennas and the user are deterministic. These are then integrated into the statistical 3GPP spatial channel model (SCM) for a typical macrocell propagation environment setting. The channel performance is analyzed based on the average channel capacity, the average power transfer, the correlation, and the cumulative distribution function of the channel capacity as well as the link throughout and the error performance. The mentioned channel and link properties are tied to the MIMO antenna properties that are represented in the mutual coupling between the antennas, the power loss, the total radiated power, the mean effective gain (MEG), as well as the efficiency with emphasis on how the user affects each. It was found that the presence of the user contributed to a loss of up to 50% in the average channel power transfer. The data position was found to be the lowest in terms of channel capacity performance. The voice position performance showed a large dependence on the user orientation with respect to the line of sight path while the data position showed less dependence on the user's orientation. We also discuss through the examined antenna and channel properties the importance of the channel multipath on the MIMO performance. In some scenarios, it was found that a well-conditioned channel can compensate for losses due to the presence of the user, improving the overall system performance. The presented investigation at the link level also discusses the user effects in different MIMO transmission schemes.
Ontogenesis of mitochondrial reticulum in rat diaphragm muscle. (1981)

Ontogenesis of mitochrondrial reticulum discovered in rat diaphragm has been studied with an electron microscope by the serial section technique. The amount of mitochondrial material in the diaphragm of rat embryos was found to be small. There are rare inclusions of single mitochondria which form columns paralleling the long axis of muscle fiber. After birth, a progressive increase in the amount of mitochondrial material takes place. This process is accompanied by the appearance of new components inherent in the unitary system of mitochondrial reticulum, namely mitochondrial junctions, as well as branches and tubules of mitochondrial material paralleling Z-discs and localized on the levels of the isotropic regions of sarcomeres. The first mitochondrial junctions were found to appear as early as on the second day, and the mitochondrial branches between the second and the ninth days of postnatal development. For a one-month-old rat, a three-dimensional model of a part of mitochondrial reticulum corresponding to one sarcomere was reconstituted. It revealed columns of mitochondrial material crossing the anisotropic region of sarcomere. Such columns connect two networks of mitochondrial profiles localized on the levels of two isotropic regions of sarcomere. Formation of mitochondrial reticulum is completed within two postnatal months.
Increased Cathodic Kinetics in IT-SOFCs by Inserting Highly-Conductive Nanocrystalline Materials (2008)

One of the crucial factors for improving intermediate-temperature SOFC performance relies on reduction of the activation loss originating from limited electrode reaction kinetics. We investigated the properties and functions of nanocrystalline interlayer via quantum simulation (QS) and electrochemical impedance analyses. Electrode impedances were found to decrease several-fold as a result of introducing a nanocrystalline interlayer and this positive impact was the most significant when the interlayer was a highly ionic-conductive nanocrystalline material. Both exchange current density and maximum power density were highest in the ultra-thin SOFCs (fabricated with MEMS compatible technologies) consisting of a 50nm thick nano-GDC interlayer. Oxygen vacancy formation energies both at the surface and in the bulk of pure zirconia, ceria, yttria-stabilized zirconia (YSZ), and gadolinia doped ceria (GDC) were computed from density functional theory, which provided insight on surface oxygen vacancy densities.