gebhart/patrepeval huggingface dataset:
Human Cathelicidin Peptide LL-37 Modulates the Effects of IFN-γ on APCs (2009)

The human cathelicidin peptide LL-37 is a multifunctional immunomodulatory and antimicrobial host defense peptide of the human immune system. LL-37 modulates host cell responses to microbial stimuli and also affects the action of other endogenous immune mediators such as IL-1beta and GM-CSF. This activity of LL-37 is known to be complex, with the functional outcomes being dependent on the cell type and activation status, timing of exposure, and other immune mediators present. It was demonstrated in this study that LL-37 inhibited cellular responses to IFN-gamma, the key cytokine of Th1-polarized immunity. The inhibitory activity of LL-37 on IFN-gamma responses was characterized in monocytes, macrophages, dendritic cells, and B lymphocytes, showing suppression of cell activation, proliferation, and production of proinflammatory and Th1-polarizing cytokines, and Abs. It was further shown that in monocytes the suppressive effects of LL-37 were mediated through inhibition of STAT1-independent signaling events, involving both the p65 subunit of NF-kappaB and p38 MAPK. This study suggests that LL-37 modulates IFN-gamma responses during both the innate and adaptive phases of immune responses, indicating a new immunomodulatory role for this endogenous peptide. These effects on IFN-gamma activity should be taken into consideration in the development of cathelicidin-based peptides for therapeutic applications as immunomodulatory or microbicidal agents.
Adversarial Training for Multilingual Acoustic Modeling (2019)

Multilingual training has been shown to improve acoustic modeling performance by sharing and transferring knowledge in modeling different languages. Knowledge sharing is usually achieved by using common lower-level layers for different languages in a deep neural network. Recently, the domain adversarial network was proposed to reduce domain mismatch of training data and learn domain-invariant features. It is thus worth exploring whether adversarial training can further promote knowledge sharing in multilingual models. In this work, we apply the domain adversarial network to encourage the shared layers of a multilingual model to learn language-invariant features. Bidirectional Long Short-Term Memory (LSTM) recurrent neural networks (RNN) are used as building blocks. We show that shared layers learned this way contain less language identification information and lead to better performance. In an automatic speech recognition task for seven languages, the resultant acoustic model improves the word error rate (WER) of the multilingual model by 4% relative on average, and the monolingual models by 10%.
<title>Statistical real-time video channels over a multiaccess network</title> (1994)

Video frames are usually compressed before their transmission through a network. Due to this compression, some frames will be more important than others when the images are reconstructed at the receiver node, i.e., frames are not independent of one another. Although it is desirable to keep the miss rate of these important frames as low as possible, it is not always appropriate to give them higher priority than other real-time traffic since the performance guarantees of real-time channels could otherwise be compromised. We propose a scheme which can provide performance guarantees to all real-time traffic and also improve the overall frame reconstruction rate without compromising the performance guarantees of inter- dependent video frame streams. Basically, we use a statistical real-time channel to deliver each video stream and dynamically extend the due data of a frame as long as the frame is still useful after its previously-assigned due date. Channels originating from the same source node are multiplexed so that the overall network utilization can be improved. We have simulated the proposed scheme using MPEG-coded frames of the movie Star Wars and the scheme is shown to be able to effectively improve the overall frame reconstruction rate, successfully reduce the link capacity necessary for an MPEG channel to an average level from the worst-case level needed for a channel of the same quality without channel multiplexing, and at the same time provide performance guarantees.
Large domain graphene (2010)

Graphene growth by chemical vapor deposition has received a lot of attention recently owing to the ease with which large area films can be grown, but growth of large domain or equivalently large grain size has not been reported yet. In this brevia, we report on a CVD process that yields graphene with domains of hundreds of micrometers, by very low pressure CVD, less than 50 mTorr, and very low precursor flow rates using methane as the source of carbon on the inside of copper foil enclosures at high temperature, around 1000 oC. The carrier mobility for the large-domain graphene films is up to 21,000 cm2/Vs.
Validation of a second generation Type 3 generic wind model (2014)

This paper presents the validation method and results of a second generation Type 3 generic wind turbine model for dynamic voltage regulation and reactive power control. A staged field test at the wind farm point of interconnection was conducted and the measured response is compared with the second generation generic model as well as the first generation generic model and the GE-specific model. The simulated response of each model closely matches the measured response, demonstrating that the Type 3 models provide a reasonable representation of actual performance.
Deep levels in Co-doped InP (1982)

Co-doped LEC InP was studied using resistivity and Hall measurements, thermal and optical capacitance spectroscopy, photoluminescence (PL) and PL-excitation (PLE) techniques. The derived activation energy for n-type conduction is about 0.50 eV in semiinsulating InP:Co samples of resistivity 106 to 107 Omega cm. The same level at Ec-0.53 eV is found in high concentration in DLTS measurements. A hole trap at Ev+0.3 eV in similar concentrations is detected in optical DLTS and photocapacitance experiments. Relationships between optical cross sections for transitions to the valence band and to the Gamma and L regions of the conduction band are derived for the 0.53 eV level. Co is shown to substitute for In in InP from the observation of the 4T2(F)4 to 4A2(F) (F) crystal field transition of Co2+ (d7) at 474.0 meV in photoluminescence. Furthermore, PLE is used to show that the Co2+ charge state is presented in n-type and semi-insulating InP:Co from observation of the 4A2(F)-4T1(F) transition of Co2+ at 785.8 meV. M From these results and the electrical and capacitance measurements, the level at Ec-0.53 eV is identified with the transition Co2+ to Co3++e, whereas the level at Ev+0.3 eV is attributed to either Co4 + to Co3++h or to a transition involving a Co-related complex. The trends of the ionisation energies of 2+ charge states of transition metals in III-V semiconductors are discussed and it is concluded that the value for Co2+ in InP (0.53 eV) is anomalously low.
Loss of transgene expression limits liver gene therapy in primates (2022)

Introductory Paragraph Efforts to improve liver gene therapy have focused on next-generation adeno-associated virus (AAV) vector capsids, transgene delivery, and immunomodulating drugs, such as corticosteroids, to avoid destructive T-cell responses. We conducted a detailed characterization of AAV transduction in nonhuman primate liver across multiple capsids and transgenes to better define interactions that may limit stable and efficient transgene expression. We show that the initial transduction of hepatocytes is high, but the transduction rapidly diminishes to a lower stable baseline of &lt;1% of cells, even though ~10% of the cells retain vector DNA that is localized within the nucleus. Further characterization showed genomic vector integration at frequencies of 1/100 to 1/1,000 genomes, suggesting that one mechanism for stable expression may occur via genome integration. These studies suggest that strategies to enhance durable transgene expression by activating retained nuclear episomes or by increasing the frequency of vector integrations may improve liver directed AAV gene therapy.
Frontal convergence and vertical velocities measured by drifters in the Alboran Sea (2020)

Trabajo presentado en la AGU Fall Meeting (2020), celebrada online del 1 al 17 de diciembre de 2020.
Prevalence and characteristics of hyporeflective preretinal tissue in vitreomacular interface disorders (2015)

Hyporeflective preretinal tissue was found with significant frequency in eyes with LMH, FTMH and ERM, with a particularly high incidence in LMH. The increased presence of this tissue in cases of LMH may signify a particular subtype of LMH. More research is needed to better understand the implications of the presence of this tissue for visual and surgical outcomes.
Activity and Safety of the Antiestrogen EM-800, the Orally Active Precursor of Acolbifene, in Tamoxifen-Resistant Breast Cancer (2004)

EM-800 produced responses in a significant proportion of patients with tamoxifen-resistant breast cancer, thus showing that this highly potent, selective estrogen receptor modulator, which lacks estrogenic activity in the mammary gland and endometrium, has incomplete cross-resistance with tamoxifen, thus suggesting additional benefits in the treatment of breast cancer.
Optimum Design of a Piezo-Actuated Triaxial Compliant Mechanism for Nanocutting (2017)

A novel piezo-actuated compliant mechanism is developed to obtain triaxial translational motions with decoupled features for nanocutting. Analytical modeling of the working performance followed by Pareto-based multiobjective optimization is conducted for determining dimensions of the mechanism. Finite element analysis on the designed mechanism verifies the accuracy of the developed model, accordingly demonstrating the effectiveness of the optimal design process. Open-loop test on the prototype shows that proper strokes with low coupling and high natural frequencies are obtained as estimated. Low tracking error in closed-loop test suggests that the developed mechanism can precisely follow the desired trajectory to form complicated nanostructures. Finally, closed-loop based nanosculpturing is conducted, demonstrating the effectiveness of the developed triaxial motion system for nanocutting well.
Supplementary Table 1 from miR-31 Is a Broad Regulator of β1-Integrin Expression and Function in Cancer Cells (2023)

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Ordering in Blends of Diblock Copolymers (1998)

The morphology of binary blends of poly(styrene)−poly(2-vinylpyridine) (PS−PVP) diblock copolymers of the type (A−B)α + (A−B)β was examined in a thin-film geometry using neutron reflection (NR), transmission electron microscopy (TEM), and self-consistent field (SCF) calculations. Blends of symmetric diblock copolymers (fA,α ≈ fA,β ≈ 0.5) revealed a localization of the lower molecular weight diblock copolymer and stretching of the higher molecular weight diblock copolymer near the AB interface that is qualitatively consistent with the data of a prior study by Mayes and co-workers. Blends of asymmetric diblock copolymers of the type fA,α < 0.5 and fA,β > 0.5 having similar molecular weights (Nα ≈ Nβ) and with ∼50% overall composition of a chemically similar block in the blend, 〈fA〉 ≈ 0.5, revealed molecular-level mixing of the two components and the formation of a single-phase morphology. A lamellar morphology was formed even when the individual components exhibit a nonlamellar morphology in the pure melt state. In general, the morphological characteristics are well anticipated by SCF calculations. After accounting for fluctuations at the interface, spatial distributions of the individual components in the blend obtained by SCF calculations were in close agreement with the NR data. For diblock copolymers near the order−disorder transition, a χ value higher than the bulk was necessary to fit the experimental data, suggesting an enhancement of ordering in the thin films near the transition due to the presence of the surfaces.
Predicting Visual Semantic Descriptive Terms From Radiological Image Data: Preliminary Results With Liver Lesions in CT (2014)

We describe a framework to model visual semantics of liver lesions in CT images in order to predict the visual semantic terms (VST) reported by radiologists in describing these lesions. Computational models of VST are learned from image data using linear combinations of high-order steerable Riesz wavelets and support vector machines (SVM). In a first step, these models are used to predict the presence of each semantic term that describes liver lesions. In a second step, the distances between all VST models are calculated to establish a nonhierarchical computationally-derived ontology of VST containing inter-term synonymy and complementarity. A preliminary evaluation of the proposed framework was carried out using 74 liver lesions annotated with a set of 18 VSTs from the RadLex ontology. A leave-one-patient-out cross-validation resulted in an average area under the ROC curve of 0.853 for predicting the presence of each VST. The proposed framework is expected to foster human-computer synergies for the interpretation of radiological images while using rotation-covariant computational models of VSTs to 1) quantify their local likelihood and 2) explicitly link them with pixel-based image content in the context of a given imaging domain.
Search for high-mass dilepton resonances in pp collisions at √s = 8 TeV with the ATLAS detector (2014)

The ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to dielectron or dimuon final states. Results are presented from an analysis of proton-proton (pp) collisions at a center-of-mass energy of 8 TeV corresponding to an integrated luminosity of 20.3fb-1 in the dimuon channel. A narrow resonance with Standard Model Z couplings to fermions is excluded at 95% confidence level for masses less than 2.79 TeV in the dielectron channel, 2.53 TeV in the dimuon channel, and 2.90 TeV in the two channels combined. Limits on other model interpretations are also presented, including a grand-unification model based on the E6 gauge group, Z_ bosons, minimal Z_ models, a spin-2 graviton excitation from Randall-Sundrum models, quantum black holes, and a minimal walking technicolor model with a composite Higgs boson.
Passive radiative cooling of a body (2023)

A metallic waveguide tuned to an infrared region of interest provides spectral and spatial control over emitted/absorbed thermal radiation. The ratio of the depth of the waveguide to the smallest lateral dimension thereof is such that that the lateral dimension provides spectral selectivity and that the waveguide is deep enough for a fixed lateral dimension to establish directionality but is not so deep that it incurs severe ohmic losses. A panel with an array of such waveguides directs thermal radiation from a body in a specific direction and with a spectral response that is the result of the physical dimensions of the individual waveguides that make up the waveguide array and the arrangement of the waveguides in the array. The waveguide axis may be obliquely oriented with respect to the substrate normal so as to impart non-normal directionality to the emitted radiation with respect to the substrate normal surface.
Performance analysis of k -ary n -cube interconnection networks (1987)

Abstmct-VLSI communication networks are wire-limited. The cost of a network is not a function of the number of switches required, but rather a function of the wiring density required to construct the network. This paper analyzes commu-nication networks of varying dimension under the assumption of constant wire bisection. Expressions for the latency, average case throughput, and hot-spot throughput of k-ary n-cube networks with constant bisection are derived that agree closely with experi-mental measurements. It is shown that low-dimensional networks (e.g., tori) have lower latency and higher hot-spot throughput than high-dimensional networks (e.g., binary n-cubes) with the same bisection width. Index Terms- Communication networks, concurrent comput-ing, interconnection networks, message-passing multiprocessors, parallel processing, VLSI. I.
ExTuNe: Explaining Tuple Non-conformance (2020)

In data-driven systems, we often encounter tuples on which the predictions of a machine-learned model are untrustworthy. A key cause of such untrustworthiness is non-conformance of a new tuple with respect to the training dataset. To check conformance, we introduce a novel concept of data invariant, which captures a set of implicit constraints that all tuples of a dataset satisfy: a test tuple is non-conforming if it violates the data invariants. Data invariants model complex relationships among multiple attributes; but do not provide interpretable explanations of non-conformance. We present ExTuNe, a system for Explaining causes of Tuple Non-conformance. Based on the principles of causality, ExTuNe assigns responsibility to the attributes for causing non-conformance. The key idea is to observe change in invariant violation under intervention on attribute-values. Through a simple interface, ExTuNe produces a ranked list of the test tuples based on their degree of non-conformance and visualizes tuple-level attribute responsibility for non-conformance through heat maps. ExTuNe further visualizes attribute responsibility, aggregated over the test tuples. We demonstrate how ExTuNe can detect and explain tuple non-conformance and assist the users to make careful decisions towards achieving trusted machine learning.
Understanding and Minimizing VOC Losses in All‐Perovskite Tandem Photovoltaics (2022)

Abstract Understanding performance losses in all‐perovskite tandem photovoltaics is crucial to accelerate advancements toward commercialization, especially since these tandem devices generally underperform in comparison to what is expected from isolated layers and single junction devices. Here, the individual sub‐cells in all‐perovskite tandem stacks are selectively characterized to disentangle the various losses. It is found that non‐radiative losses in the high‐gap subcell dominate the overall recombination in the baseline system, as well as in the majority of literature reports. Through a multi‐faceted approach, the open‐circuit voltage ( V OC ) of the high‐gap perovskite subcell is enhanced by 120 mV. Employing a novel (quasi) lossless indium oxide interconnect, this enables all‐perovskite tandem solar cells with 2.00 V V OC and 23.7% stabilized efficiency. Reducing transport losses as well as imperfect energy‐alignments boosts efficiencies to 25.2% and 27.0% as identified via subcell selective electro‐ and photo‐luminescence. Finally, it is shown how, having improved the V OC , improving the current density of the low‐gap absorber pushes efficiencies even further, reaching 25.9% efficiency stabilized, with an ultimate potential of 30.0% considering the bulk quality of both absorbers measured using photo‐luminescence. These insights not only show an optimization example but also a generalizable evidence‐based optimization strategy utilizing optoelectronic sub‐cell characterization.
The Compound SBI-0090799 Inhibits Zika Virus Infection by Blocking De Novo Formation of the Membranous Replication Compartment (2021)

Zika virus (ZIKV) is a mosquito-borne pathogen classified by the World Health Organization (WHO) as a public health emergency of international concern in 2016, and it is still identified as a priority disease. Although most infected individuals are asymptomatic or show mild symptoms, a risk of neurologic complications is associated with infection in adults. Additionally, infection during pregnancy is directly linked to microcephaly and other congenital malformations. Since there are no currently available vaccines or approved therapeutics for this virus, there is a critical unmet need in developing treatments to prevent future ZIKV outbreaks. Toward this end, we performed a large-scale cell-based high-content screen of 51,520 chemical compounds to identify potential antiviral drug candidates. The compound (2E)-N-benzyl-3-(4-butoxyphenyl)prop-2-enamide (SBI-0090799) was found to inhibit replication of multiple ZIKV strains and in different cell systems. SBI-0090799 did not affect viral entry or RNA translation but suppressed RNA replication by preventing the formation of the membranous replication compartment. Selection of drug-resistant viruses identified single-amino-acid substitutions in the N-terminal region of nonstructural protein NS4A, arguing this is the likely drug target. These resistance mutations rescued viral RNA replication and restored the formation of the membranous replication compartment. This mechanism of action is similar to clinically approved NS5A inhibitors for hepatitis C virus (HCV). Taken together, SBI-0090799 represents a promising lead candidate for the development of an antiviral treatment against ZIKV infection for the mitigation of severe complications and potential resurgent outbreaks of the virus. <b>IMPORTANCE</b> This study describes the elucidation of (2E)-N-benzyl-3-(4-butoxyphenyl)prop-2-enamide (SBI-0090799) as a selective and potent inhibitor of Zika virus (ZIKV) replication using a high-throughput screening approach. Mapping and resistance studies, supported by electron microscopy observations, indicate that the small molecule is functioning through inhibition of NS4A-mediated formation of ZIKV replication compartments in the endoplasmic reticulum (ER). Intriguingly, this defines a novel nonenzymatic target and chemical matter for the development of a new class of ZIKV antivirals. Moreover, chemical modulation affecting this nonstructural protein mirrors the identification and development of hepatitis C virus (HCV) NS5A inhibitor daclatasvir and its derivatives, similarly interfering with the formation of the viral replication compartment and also targeting a protein with no enzymatic activity, which have been part of a curative strategy for HCV.
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors (2022)

Despite the growing number of G protein-coupled receptor (GPCR) structures, only 39 structures have been cocrystallized with allosteric inhibitors. These structures have been studied by protein mapping using the FTMap server, which determines the clustering of small organic probe molecules distributed on the protein surface. The method has found druggable sites overlapping with the cocrystallized allosteric ligands in 21 GPCR structures. Mapping of Alphafold2 generated models of these proteins confirms that the same sites can be identified without the presence of bound ligands. We then mapped the 394 GPCR X-ray structures available at the time of the analysis (September 2020). Results show that for each of the 21 structures with bound ligands there exist many other GPCRs that have a strong binding hot spot at the same location, suggesting potential allosteric sites in a large variety of GPCRs. These sites cluster at nine distinct locations, and each can be found in many different proteins. However, ligands binding at the same location generally show little or no similarity, and the amino acid residues interacting with these ligands also differ. Results confirm the possibility of specifically targeting these sites across GPCRs for allosteric modulation and help to identify the most likely binding sites among the limited number of potential locations. The FTMap server is available free of charge for academic and governmental use at https://ftmap.bu.edu/.