gebhart/patrepeval huggingface dataset:
Proto-oncogenic properties of the DP family of proteins. (1995)

The cellular transcription factor DRTF1/E2F is implicated in the control of cellular proliferation due to its interaction with key regulators of cell cycle progression, such as the retinoblastoma tumour suppressor gene product, cyclins and cyclin-dependent kinases. DRTF1/E2F is a heterodimeric DNA binding activity which arises when a member of two distinct families of proteins, DP and E2F, interact as DP/E2F heterodimers, for example, DP-1 and E2F-1. In DRTF1/E2F the activity of DP-1 is under cell cycle control, possibly by phosphorylation, and in many types of cells it is a frequent, if not general DNA binding component of DRTF1/E2F. The expression of other DP proteins, such as DP-2, is tissue-restricted. Here, we show that DP-1 and DP-2 are integrated with another growth regulating pathway which involves signal transduction emanating from activated Ras protein. Thus, activated Ha-ras can co-operate with DP-1 or DP-2 in the transformation of rat embryo fibroblasts, establishing for the first time that DP proteins are endowed with proto-oncogenic activity. Moreover, an analysis of a dominant-negative and mutant DP-1 proteins suggests that the primary target through which DP-1 mediates its oncogenic activity is unlikely to be due to the regulation of E2F site-transcription, suggesting an E2F-independent effector function for DP-1. These results therefore establish DP genes as proto-oncogenes and thus argue that deregulating the normal control of DP protein activity will be important in promoting aberrant cellular proliferation.
Body sway reflects leadership in joint music performance (2017)

The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers' ratings of the "goodness" of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships.
Epicardial Fibrosis Explains Increased Transmural Conduction in a Computer Model of Atrial Fibrillation (2016)

Recent work has shown that the transition from persistent to permanent AF in goats coincides with an increase in fibrosis in the outer millimeter of the atrial wall. Macroscopically this leads to reduced electrical conductivity orthogonal to the dominant fiber orientation.
BayesRank (2015)

Advances in online and computer supported education afford exciting opportunities to revolutionize the classroom, while also presenting a number of new challenges not faced in traditional educational settings. Foremost among these challenges is the problem of accurately and efficiently evaluating learner work as the class size grows, which is directly related to the larger goal of providing quality, timely, and actionable formative feedback. Recently there has been a surge in interest in using peer grading methods coupled with machine learning to accurately and fairly evaluate learner work while alleviating the instructor bottleneck and grading overload. Prior work in peer grading almost exclusively focuses on numerically scored grades -- either real-valued or ordinal. In this work, we consider the implications of peer ranking in which learners rank a small subset of peer work from strongest to weakest, and propose new types of computational analyses that can be applied to this ranking data. We adopt a Bayesian approach to the ranked peer grading problem and develop a novel model and method for utilizing ranked peer-grading data. We additionally develop a novel procedure for adaptively identifying which work should be ranked by particular peers in order to dynamically resolve ambiguity in the data and rapidly resolve a clearer picture of learner performance. We showcase our results on both synthetic and several real-world educational datasets.
Supplementary Figure 1 from Enhanced Effector Responses in Activated CD8<sup>+</sup> T Cells Deficient in Diacylglycerol Kinases (2023)

&lt;p&gt;PDF file - 52K, MesoCAR-transduced dgkzeta-deficient T cells demonstrate resistance to multiple inhibitory stimuli&lt;/p&gt;
Promoting effects of Sn on NO dissociation and NO reduction with H2on Rh–Sn/SiO2catalysts (1993)

K. Tomishige, K. Asakura and Y. Iwasawa, J. Chem. Soc., Chem. Commun., 1993, 184 DOI: 10.1039/C39930000184
Nonlinear studies of semiconductor doped glasses (1989)

Saturation of two-photon absorption (2PA) in Corning CS-368 semiconductor doped glass has been experimentally observed via standard nonlinear transmission measurements and nonlinear refraction was observed using the newly developed "Z-scan" technique. 1 We found that the saturation of the absorption for this glass follows the form α = α 0 (1 + I / I sat ) −1/2 , where I sat = 10 MW/cm 2 and α 0 = 4.7 cm −1 are extracted from the experimental data. At much higher irradiance levels, nonlinear absorption sets in consistent with a combination of two-photon absorption (2PA) and excited carrier absorption. A 2PA coefficient, β 2 = 0.04 cm / GW was obtained for input irradiances ≃20 GW/cm 2 . From Z-scan measurements, the contribution to nonlinear refraction was studied. A self-defocusing nonlinearity was observed at incident irradiances ≃1 GW/cm 2 giving a value of Δ n = −1.5 × 10 −5 . This defocusing increased for higher irradiances. Theoretical studies were conducted by extending Maxwell Garnett and Mie theories to account for nonlinear [χ (3) ] effects observed in several of these Corning semiconductor doped glasses. The theories predict an enhancement of the nonlinear absorption coefficient, β 2 , which we may or may not be observing depending on how well the particle number density of the semiconductor in glass and the actual microparticle radius is known.
Characterization of the Human Diaphragm Muscle with Respect to the Phrenic Nerve Motor Points for Diaphragmatic Pacing (2004)

Diaphragm pacing from laparoscopically placed electrodes is an alternative to conventional phrenic pacers that use electrodes placed in direct contact with the nerve in the neck or chest. The challenge with the laparoscopic approach is determining where to implant the electrodes, as the phrenic nerves are not visible from the abdomen. The objective of this study was to locate the phrenic nerve "motor points" in the human diaphragm muscle from an abdominal perspective. Twenty-five cadavers were examined by excising the diaphragm muscle and assessing for the thickness of the muscle, the motor point area, and the accessibility of the motor point from the abdominal approach. The data indicate the average thickness of the muscle in the motor point region was 3.0 mm for the left and 2.9 mm for the right hemidiaphragm. The average motor point area was 73 mm2 for the left and 58.7 mm2 for the right hemidiaphragm. The motor points were accessible from an abdominal approach, but the motor point on the right hemidiaphragm was located on the central tendon in many cases (12 of 25). Thus, although the nerves branch prior to entry into the muscle on the right side, several well-placed electrodes could still activate the entire nerve. In this study, we have characterized the human diaphragm muscle in the motor point region and found that it is feasible to place laparoscopically intramuscular electrodes in the motor point region. This is the foundation for the laparoscopically placed diaphragm pacing device that has been utilized in a small series of patients.
Intermittent polaron dynamics: Born-Oppenheimer out of equilibrium (2004)

We consider the non-equilibrium dynamics of a molecular level interacting with local phonon modes in the case of a strong polaronic shift which prevents a perturbative treatment of the problem. Instead, we find that in an adiabatic regime when the electronic states react faster than the phonon modes it is possible to provide a fully non-perturbative treatment of the phonon dynamics including random noise and dissipation. The result shows intermittent switching between bistable states of the oscillator with an effective random telegraph noise.
Analysis of Stresses in Metal Sheathed Thermocouples in High-Temperature, Hypersonic Flows (2020)

Near-wall flow temperature sensing remains important for many hypersonic aerodynamics and propulsion applications. Flight test applications, in particular, demand robust and accurate sensing, making thermocouple sensors attractive. Even for these extremely well-developed sensors, the prediction of stresses within thermocouple sheaths for custom-configured probes remains a topic of great concern for ensuring adequate lifetime of sensors. In contemporary practice, high-fidelity simulations must be run to prove if a new design will work at all, albeit at significant time and expense. Given the time and money it takes to run high-fidelity simulations, rapid optimization of sensor configurations is often impossible, or at minimum, impractical. The developments presented in this paper address the need for hypersonic flow temperature sensor structural predictions which are compatible with rapid design iteration. The derivation and implementation of a new analytical, low-order model to predict stresses within the sheath of a thermocouple are provided. The analytical model is compared to high-fidelity ANSYS mechanical simulations as well as simplified experimental data. The predictions using the newly developed structural low-order model are in excellent agreement with the numerically simulated results and experimental results with an absolute maximum percent error of approximately 4% and 9.5%, respectively, thus validating the model.
Combined MvdXML and Semantic Technologies for Green Construction Code Checking (2019)

The construction process plays a key role in sustainable development of the environment. With the concept of sustainable construction being put forward in the world, some countries released green construction standards to strengthen the requirements in the construction phase. Green construction code checking needs to integrate semantic information embedded in green construction standards and model information involved in Industry Foundation Classes (IFC) and/or Model View Definition (MVD), which are generated separately and lead to difficulty in information integration for green construction code checking. At present, the existing code-checking methods cannot be directly used for green construction. Related practitioners need an efficient and convenient method for green construction code checking urgently. To ameliorate this situation, this research proposes an innovative approach to organize, store, and re-use green construction knowledge by combining mvdXML and semantic technologies. The code checking of green construction is classified into four types based on the difficulty level to meet the requirements of the clauses in green construction standard. Depending on the characteristics of each inspection type, mvdXML or semantic technology is adopted for the appropriate inspection type. This paper demonstrates the deployment and validation of such automated checking procedures in a case study. Based on these experiences, a detailed discussion about the identified issues is provided as the starting point for future research.
Immunologie moléculaire (1999)

Qu’en est-il de l’immunologie moléculaire ? S’agit-il stricto sensu de l’étude des molécules du système immunitaire et de leurs interactions ? Sans doute. Une partie importante de l’immunologie s’occupe de récepteurs et de leurs ligands, et de la transmission des signaux depuis la surface des cellules jusqu’à leur noyau. C’est aujourd’hui l’un des champs de la biologie où on voit le mieux comment des agrégats moléculaires s’assemblent et se dissocient dans des combinatoires hautement spécifiques. Mais ce n’est pas cette vision restrictive que je retiens. L’immunologie moléculaire n’est pas un domaine spécialisé de l’immunologie. Elle désigne, au contraire, l’inscription de l’immunologie dans la mouvance de la biologie moléculaire ; ce qui, de fait, en élargit le cadre.
Origin of Electrochromism in High-Performing Nanocomposite Nickel Oxide (2013)

Electrochromic effects of transition metal oxides provide a great platform for studying lithium intercalation chemistry in solids. Herein, we report on an electronically modified nanocomposite nickel oxide (i.e., Li2.34NiZr0.28Ox) that exhibits significantly improved electrochromic performance relative to the state-of-the-art inorganic electrochromic metal oxides in terms of charge/discharge kinetics, bleached-state transparency, and optical modulation. The knowledge obtained from O K-edge X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS) suggests that the internally grown lithium peroxide (i.e., Li2O2) species plays a major role in facilitating charge transfer thus enabling optimal electrochromic performance. This understanding is relevant to recent theoretical studies concerning conductivity in Li2O2 for lithium-air batteries (as cited in the main text). Furthermore, we elucidate the electrochromism in modified nickel oxide in lithium ion electrolyte with the aid of Ni K-edge XAS and Ni L-edge XAS studies. The electrochromism in the nickel oxide materials arises from the reversible formation of hole states on the NiO6 units, which then impacts the Ni oxidation state through the Ni3d-O2p hybridization states. This study sheds light on the lithium intercalation chemistry for general energy storage and semiconductor applications.
A ubiquitous enhancer shared by two promoters in the human aldolase A gene (1991)

The human aldolase A gene is transcribed from three different promoters, which are all clustered within a 1.6 kbp DNA domain. Two of these, PN and PH, are ubiquitous and seem to be co-regulated in most tissues while the third one, PM, is specific to adult skeletal muscle. We investigated the sequences involved in the ubiquitous activity of the PN and PH promoters of the human aldolase A gene. Deletion analysis, performed by transient expression assays of chloramphenicol acetyltransferase reporter genes in human HepG2 hepatoma cells, indicated that PH activity results from the interaction of an upstream activating region with two distinct core promoters. The upstream activating region was able to stimulate transcription from the HSV tk promoter as efficiently as the SV40 enhancer in all cell types tested. It appears, therefore, to be a strong ubiquitous enhancer. DNAsel footprinting revealed protections covering sequences scattered along the enhancer, including Sp1 and AP1 motifs. Importantly, we found that this enhancer was also necessary to activity of the other ubiquitous promoter of the aldolase A gene, PN. These studies demonstrate that expression of the human aldolase A gene is mediated by a complex interplay of enhancer and promoter elements.
BLC (CXCL13) is expressed by different dendritic cell subsets in vitro and in vivo (2001)

Dendritic cells (DC) attract both T and B lymphocytes to induce an efficient antigen-specific immune response. Recently, it was shown that naïve T cells are attracted to DC by dendritic cell chemokine 1 (DC-CK1, CCL18). The potent B lymphocyte chemoattractant BLC (CXCL13) was previously shown to be essential for homing of lymphocytes into secondary lymphoid organs and for the development of B cell follicles. As the cells that produce BLC are largely unknown and BLC could be a candidate chemokine for the recruitment of B cells to DC, we analyzed different DC subsets for expression of BLC. Here we demonstrate that monocyte-derived DC as well as activated blood DC indeed express and secrete BLC. Interestingly, ligation of the CD40 molecule down-regulated BLC expression in monocyte-derived DC. Staining of tonsilar sections indicated that BLC is expressed by follicular dendritic cells and germinal center dendritic cells (GCDC) in vivo. Real-time quantitative PCR confirmed the expression of BLC in isolated GCDC. Since both B cells and activated T cells express the receptor for BLC, our findings implicate an important role for BLC in establishing the interaction of DC with T cells and B cells. Furthermore, CD40/CD40 ligand interactions could modulate this process by down-regulating the expression of BLC.
Statistical distributions that arise in constrained beamforming with incomplete channel information (2010)

We examine the statistical distribution of received power when a subscriber terminal with multiple transmit antennas beamforms on the uplink of a wireless orthogonal frequency-division multiplexing system to a base station with multiple receive antennas. We assume that a time-division duplex terminal has incomplete uplink channel knowledge obtained by measuring the downlink channel during base station transmissions. The base station transmissions employ cyclic delay diversity, of which the terminal is unaware. The distribution of uplink power received at the base station, with and without downlink cyclic delay diversity and with various types of power constraints at the terminal, allow us to make some surprising conclusions about how the power constraints and cyclic delay influence the performance of beamforming. We show that beamforming gains need to be examined critically beyond simple average performance metrics to conclude that they are superior to simpler channel-unaware methods. We also conclude that cyclic delay on the downlink is very beneficial to beamforming on the uplink, even with restrictive types of power constraints.
Isotropic perfect absorber in optical frequencies using vertical split-ring resonators (2014)

Plasmonic metamaterials are composed of artificial metamolecules exhibiting unusual optical properties such as negative refraction index, and toroidal dipolar response that can lead to applications that are otherwise unattainable in nature, such as sub-diffraction imaging, and optical and spectrum manipulation.
Two-layer integrated photonic architectures with multiport photodetectors for high-fidelity and energy-efficient matrix multiplications (2022)

Photonic integrated circuits (PICs) are emerging as a promising tool for accelerating matrix multiplications in deep learning. Previous PIC architectures, primarily focusing on the matrix-vector multiplication (MVM), have large hardware errors that increase with the device scale. In this work, we propose a novel PIC architecture for MVM, which features an intrinsically small hardware error that does not increase with the device scale. Moreover, we further develop this concept and propose a PIC architecture for the general matrix-matrix multiplication (GEMM), which allows the GEMM to be directly performed on a photonic chip with a high energy efficiency unattainable by parallel or sequential MVMs. This work provides a promising approach to realize a high fidelity and high energy efficiency optical computing platform.
Hyperglucagonemia in youth is associated with high plasma free fatty acids, visceral adiposity, and impaired glucose tolerance (2019)

Hyperglucagonemia in childhood obesity is associated with hyperinsulinemia, high plasma FFAs, high plasma triglycerides, visceral adiposity, and IGT. The glucagonotropic effect of FFAs on isolated human islets provides a potential mechanism linking high fasting plasma FFAs and glucagon levels.
Sparse basis selection, ICA, and majorization: towards a unified perspective (1999)

Sparse solutions to the linear inverse problem Ax=Y and the determination of an environmentally adapted overcomplete dictionary (the columns of A) depend upon the choice of a "regularizing function" d(x) in several previously proposed procedures. We discuss the interpretation of d(x) within a Bayesian framework, and the desirable properties that "good" (i.e., sparsity ensuring) regularizing functions, d(x) might have. These properties are: Schur-concavity (d(x) is consistent with majorization); concavity (d(x) has sparse minima); parameterizability (d(x) is drawn from a large, parameterizable class); and factorizability of the gradient of d(x) in a certain manner. The last property (which naturally leads one to consider separable regularizing functions) allows d(x) to be efficiently minimized subject to Ax=Y using an affine scaling transformation (AST)-like algorithm "adapted" to the choice of d(x). A Bayesian framework allows the algorithm to be interpreted as an independent component analysis (ICA) procedure.
Supplementary figures s1-s15 from Cyst Fluid Telomerase Activity Predicts the Histologic Grade of Cystic Neoplasms of the Pancreas (2023)

&lt;p&gt;Figure S1: Coefficient of variation telomerase assay. Figure S2: Telomerase assay controls Figure S3; Serial dilution, limit of detection telomerase assay, Figure S4; Protein extraction and assay performance; Figure S5; Lack of telomerase activity in supernatants. Figure S6; input protein and telomerase activity. Figure S7; Discovery set cyst fluid results effects of thawing. Figure S8 discovery set cyst fluid results. Figure S9 validation set results. Figure S10; telomerase results in previously thawed cyst fluids. Figure S11; Telomerase activity in all discovery set samples. Figure S12; Effect of cyst fluid on telomerase activity. Figure S13; SCN telomerase activity and cyst fluid appearance. Figure S14; Pathologic diagnosis according to cyst imaging group (high risk, worrisome etc). Figure S15: telomerase activity in EUS FNA samples&lt;/p&gt;
Design of defect-chemical properties and device performance in memristive systems (2020)

Future development of the modern nanoelectronics and its flagships internet of things, artificial intelligence, and neuromorphic computing is largely associated with memristive elements, offering a spectrum of inevitable functionalities, atomic level scalability, and low-power operation. However, their development is limited by significant variability and still phenomenologically orientated materials' design strategy. Here, we highlight the vital importance of materials' purity, demonstrating that even parts-per-million foreign elements substantially change performance. Appropriate choice of chemistry and amount of doping element selectively enhances the desired functionality. Dopant/impurity-dependent structure and charge/potential distribution in the space-charge layers and cell capacitance determine the device kinetics and functions. The relation between chemical composition/purity and switching/neuromorphic performance is experimentally evidenced, providing directions for a rational design of future memristive devices.