gebhart/patrepeval huggingface dataset:
Integrin Activation Controls Regulatory T Cell–Mediated Peripheral Tolerance (2018)

Maintenance of the regulatory T (Treg) cell pool is essential for peripheral tolerance and prevention of autoimmunity. Integrins, heterodimeric transmembrane proteins consisting of α and β subunits that mediate cell-to-cell and cell-to-extracellular matrix interactions, play an important role in facilitating Treg cell contact-mediated suppression. In this article, we show that integrin activation plays an essential, previously unappreciated role in maintaining murine Treg cell function. Treg cell-specific loss of talin, a β integrin-binding protein, or expression of talin(L325R), a mutant that selectively abrogates integrin activation, resulted in lethal systemic autoimmunity. This dysfunction could be attributed, in part, to a global dysregulation of the Treg cell transcriptome. Activation of integrin α<sub>4</sub>β<sub>1</sub> led to increased suppressive capacity of the Treg cell pool, suggesting that modulating integrin activation on Treg cells may be a useful therapeutic strategy for autoimmune and inflammatory disorders. Taken together, these results reveal a critical role for integrin-mediated signals in controlling peripheral tolerance by virtue of maintaining Treg cell function.
Estimation of 3-D conduction velocity vector fields from cardiac mapping data (2000)

A method to estimate three-dimensional (3-D) conduction velocity vector fields in cardiac tissue is presented. The speed and direction of propagation are found from polynomial "surfaces" fitted to space-time (x, y, z, t) coordinates of cardiac activity. The technique is applied to sinus rhythm and paced rhythm mapped with plunge needles at 396-466 sites in the canine myocardium. The method was validated on simulated 3-D plane and spherical waves. For simulated data, conduction velocities were estimated with an accuracy of 1%-2%. In experimental data, estimates of conduction speeds during paced rhythm were slower than those found during normal sinus rhythm. Vector directions were also found to differ between different types of beats. The technique was able to distinguish between premature ventricular contractions and sinus beats and between sinus and paced beats. The proposed approach to computing velocity vector fields provides an automated, physiological, and quantitative description of local electrical activity in 3-D tissue. This method may provide insight into abnormal conduction associated with fatal ventricular arrhythmias.
Test of dynamic closed-loop baroreflex and autoregulatory control of total peripheral resistance in intact and conscious sheep (2004)

This is the first study able to examine and delineate the actual actions of the physiological mechanisms responsible for the dynamic couplings between cardiac output (CO), arterial pressure (Pa), right atrial pressure (PRA), and total peripheral resistance (TPR) in an individual subject without altering the underlying regulatory mechanisms. Eight conscious male sheep were used, where both types of baroreceptors were independently exposed to simultaneous beat-to-beat pressure perturbations under intact closed-loop conditions while CO, Pa, PRA, and TPR were measured. We applied the cardiovascular system identification method proposed in a companion paper (4) to quantitatively characterize the dynamic closed-loop transfer relations CO-->Pa, PRA-->Pa, Pa-->TPR, and PRA-->TPR from the measured signals. To validate the dynamic properties of the estimated transfer relations, the essential parts of the linear dynamics of the model were independently and comprehensively evaluated via error model cross-validation, and the overall model's steady-state behavior was compared with a separate random effects regression approach. In addition to numerous physiological findings, we found that the cardiovascular system identification results were exceptionally consistent with the analytically derived solutions previously discussed in Ref. 4. In conclusion, this study presents the first time validation of a cardiovascular system identification method by means of experimentally acquired animal data in the intact and conscious animal and offers a set of powerful quantitative tools essential to advancing our knowledge of cardiovascular regulatory physiology.
Analysis of exome sequences with and without incorporating prior biological knowledge (2011)

Next-generation sequencing technology provides new opportunities and challenges in the search for genetic variants that underlie complex traits. It will also presumably uncover many new rare variants, but exactly how these variants should be incorporated into the data analysis remains a question. Several papers in our group from Genetic Analysis Workshop 17 evaluated different methods of rare variant analysis, including single-variant, gene-based, and pathway-based analyses and analyses that incorporated biological information. Although the performance of some of these methods strongly depends on the underlying disease model, integration of known biological information is helpful in detecting causal genes. Two work groups demonstrated that use of a Bayesian network and a collapsing receiver operating characteristic curve approach improves risk prediction when a disease is caused by many rare variants. Another work group suggested that modeling local rather than global ancestry may be beneficial when controlling the effect of population structure in rare variant association analysis.
Apps Gone Rogue: Maintaining Personal Privacy in an Epidemic (2020)

Containment, the key strategy in quickly halting an epidemic, requires rapid identification and quarantine of the infected individuals, determination of whom they have had close contact with in the previous days and weeks, and decontamination of locations the infected individual has visited. Achieving containment demands accurate and timely collection of the infected individual's location and contact history. Traditionally, this process is labor intensive, susceptible to memory errors, and fraught with privacy concerns. With the recent almost ubiquitous availability of smart phones, many people carry a tool which can be utilized to quickly identify an infected individual's contacts during an epidemic, such as the current 2019 novel Coronavirus crisis. Unfortunately, the very same first-generation contact tracing tools have been used to expand mass surveillance, limit individual freedoms and expose the most private details about individuals. We seek to outline the different technological approaches to mobile-phone based contact-tracing to date and elaborate on the opportunities and the risks that these technologies pose to individuals and societies. We describe advanced security enhancing approaches that can mitigate these risks and describe trade-offs one must make when developing and deploying any mass contact-tracing technology. With this paper, our aim is to continue to grow the conversation regarding contact-tracing for epidemic and pandemic containment and discuss opportunities to advance this space. We invite feedback and discussion.
Cardiovascular and Renal Complications of Type 2 Diabetes in Obesity:Role of Sympathetic Nerve Activity and Insulin Resistance (2010)

Overweight and obesity is a growing "world-wide epidemic problem". Because as many as, two-thirds of the adult population and a growing number of children are overweight. The prevalence of diabetes, especially type 2 diabetes and hypertension have significantly increased with the prevalence of obesity. Obesity accompanying type 2 diabetes and hypertension are known to be closely linked with insulin resistance and elevated sympathetic nervous activity. It has been well documented that obesity, hypertension, and diabetes are high risk factors for subsequent cardiovascular and renal complications. Many patients are both diabetic and hypertensive, while they are obese, but not all diabetic patients have hypertension, indicating that insulin resistance is not only a mechanism for blood pressure elevation in diabetic-hypertensive patients. Several investigators have reported that sympathetic nervous activation relates to cardiovascular complications in patients with hypertension, diabetes, and obesity, and that sympathetic nerve activity accompanying insulin resistance is closely linked with left ventricular hypertrophy in healthy subjects. In addition, sympathetic nerve activation may predict future renal injury in healthy normotensive subjects. These findings suggest that elevated sympathetic nerve activity associated with insulin resistance may contribute to the onset and maintenance of cardiovascular and renal complications in diabetes, and hypertension in obesity. Further, genetic polymorphisms of the beta2- and beta3-adrenoceptor gene have been associated with type-2 diabetes and insulin resistance in many epidemiological studies and might be another factor responsible for the close relationship between insulin resistance and heightened sympathetic nerve activity. Thus, focusing on the interactions between insulin resistance, sympathetic nervous activity and beta-adrenoceptor polymorphisms might help in understanding the precise relationships between insulin resistance and sympathetic nerve activity in type 2 diabetes and obesity-related hypertension. The purpose of this article is to provide a synthesis of the current findings on the mechanisms of the onset and maintenance of cardiovascular and renal complications in obesity, diabetes and hypertension. A better understanding of the relationships of sympathetic nervous system activity and insulin resistance might help with the clinical treatment of diabetes and hypertension in obesity. Further, to clarify the pathogenesis and mechanisms of the association between obesity, diabetes, and hypertension may lead to reductions in cardiovascular and renal risk.
Quantifying turning behavior and gait in Parkinson’s disease using mobile technology (2018)

Gait and balance impairments associated with Parkinson's disease (PD) are often refractory to traditional treatments. Objective, quantitative analysis of gait patterns is crucial in successful management of these symptoms. This project aimed to 1) determine if biomechanical metrics from a mobile device inertial measurement unit were sensitive enough to characterize the effects of anti-parkinsonian medication during the Timed Up and Go (TUG) Test, and 2) develop the Cleveland Clinic Mobility and Balance application (CC-MB) to provide clinicians with objective report following completion of the TUG. The CC-MB captured 3-dimensional acceleration and rotational data from people with PD (pwPD) to characterize center of mass movement while performing the TUG. Trials were segmented into four components: Sit-to-Walk, Gait, Turning, and Stand-to-Sit. Thirty pwPD were tested On and Off (12 h) anti-PD medication. Significant improvements (p < 0.05) between On versus Off conditions included: reduction in MDS-UPDRS III motor scores (10.7%), faster trial times (9.3%), more dynamic walking as evident by increased normalized jerk scores (vertical: 17.3%, medial-lateral: 12.3%), shorter turn durations (10.4%), and faster turn velocities (8%). Measures in Sit-to-Walk and Stand-to-Sit did not show significant changes. Trial time and turn velocity showed excellent test-retest reliability (ICC range: 0.83-0.96) across both medication states. A mobile device platform provided quantitative measures of gait and turning during the TUG that detected significant improvements from anti-parkinsonian medications. This platform is a low-cost, easy-to-use tool that can provide objective reports immediately following the clinical assessments, making it ideal for use in and outside the clinical setting.
R/G/B/Natural White Light Thin Colloidal Quantum Dot‐Based Light‐Emitting Devices (2014)

Bright, low-voltage driven colloidal quantum dot (QD)-based white light-emitting devices (LEDs) with practicable device performances are enabled by the direct exciton formation within quantum-dot active layers in a hybrid device structure. Detailed device characterization reveals that white-QLEDs can be rationalized as a parallel circuit, in which different QDs are connected through the same set of electrically common organic and inorganic charge transport layers.
Demonstration of 2-dimensional data transcription between 8x8 arrays of completely-depleted optical thyristors (1995)

Differential pairs of PnpN optical thyristors are among the most promising devices for digital parallel optical information processing systems. Very recently it has been shown that these AlGaAs based detector-emitter type of devices can be cascaded at 50 MHz with only 7.2 fJ external optical input energy [1], and that this optical input energy scales with device area resulting in a record sensitivity of 15 aJ/μm 2 [2]. The layer structure of these optical thyristors has been designed such that all free carriers can be extracted from the center p- and n-type layers by applying a small negative anode-to-cathode voltage pulse (complete depletion for a turn-off voltage of - 4V), while switching on the device requires a break-over voltage of 2.7 V. To be of use in practical systems the device has also been engineered to be cascadable. In this way, an optical thyristor operating as a detector is sensitive to the light that an identical element, working as an emitter, generates. Moreover, a differential pair configuration has been adopted to increase the optical input sensitivity [3]. Finally, correct operation of 8*8 monolithic arrays (see Fig la) of these completely depleted, cascadable differential pairs has been demonstrated [4].
СОСТОЯНИЕ АКТИВНЫХ КОМПОНЕНТОВ НА ПОВЕРХНОСТИ КАТАЛИЗАТОРА НИЗКОТЕМПЕРАТУРНОГО ОКИСЛЕНИЯ МОНООКСИДА УГЛЕРОДА PDCL2 CUCL2 -AL2O3 (2012)

Методами спектроскопии рентгеновского поглощения (XAS), порошковой рентгеновской дифракции (XRD), растровой электронной микроскопии (РЭМ), ИК-Фурье-спектроскопии диффузного рассеяния (DRIFTS) изучено состояние активных компонентов свежеприготовленного катализатора для низкотемпературного окисления монооксида углерода молекулярным кислородом. Показано, что на поверхности находятся медь в виде кристаллической фазы Cu2Cl(OH)3 со структурой минерала паратакамита и хлорид палладия в аморфном состоянии. По данным XAS локальное окружение палладия состоит из четырех атомов хлора, которые образуют плоский квадрат с увеличенным расстоянием между палладием и одним из атомов хлора. Рассмотрена эволюция локального окружения меди и палладия при переходе от исходных солей к пропиточным растворам и к хлоридам на поверхности . Обсуждена роль в формировании фазы Cu2Cl(OH)3. Методом DRIFTS показано, что при адсорбции CO на поверхности катализатора образуются линейная (2114 см-1) и мостиковые (1990 и 1928 см-1) формы координированного монооксида углерода. Обнаружено образование CO2 при взаимодействии координированного CO с кислородом воздуха. На поверхности свежеприготовленного катализатора отсутствуют активные центры, включающие медь и палладий.
H-infinity control based scheduler for the deployment of Small Cell Networks (2011)

In this work, we address the joint problem of traffic scheduling and interference management related to the deployment of Small Cell Networks (SCNs). The Base Stations of the SCNs (which we will refer to as Micro Base Stations, MBSs) are low power devices with limited buffer size. They are connected to a Central Scheduler (CS) with limited capacity backhaul links. In this scenario, traffic has to be scheduled from the network to the MBS queues in such a way that the queue-length at MBS remains as close as possible to a given target queue-length. The challenge is to design a scheduler which is oblivious to the wireless link between the MBSs and the User Terminals (UTs). For the traffic arriving at the MBS, we need to efficiently transmit it over the wireless channel to the UTs with minimum power in an interference limited environment. Additionally, real time centralized interference management techniques will not be feasible. In this paper, we decouple the joint scheduling and interference management into two separate parts. For the scheduling problem, we propose a H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sup> control based scheduler which regulates the arrival rates to the queues at the MBS. For the problem of power minimization and decentralized interference management over the wireless link, we propose a multi-cell beamforming technique in which MBSs need to exchange only the channel statistics of their UTs. We use tools from the field Random Matrix Theory to formulate our algorithm. Our simulation results show that the H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sup> based queue length control algorithm stabilizes the queue-lengths at the MBS and keeps the variation of the queue-length around the target to a minimum.
Towards Fine-grained Flow Forecasting: A Graph Attention Approach for Bike Sharing Systems (2020)

As a healthy, efficient and green alternative to motorized urban travel, bike sharing has been increasingly popular, leading to wide deployment and use of bikes instead of cars. Accurate bike-flow prediction at the individual station level is essential for bike sharing service. Due to the spatial and temporal complexities of traffic networks and the lack of data-driven design for bike stations, existing methods cannot predict the fine-grained bike flows to/from each station.
DNA as a Supramolecule for Long-Distance Charge Transport (2000)

Electron transport through DNA occurs over very long distances (100 Å and more). The process follows a hopping mechanism and depends upon the DNA sequence. The efficiency of the charge transport is only slightly distance dependent because in most cases the H2O trapping of the charge is slower than the electron transfer. These findings show the potential of substituted DNAs as new materials for nanoelectronics in the future.
Dynamic Posted-Price Mechanisms for the Blockchain Transaction Fee Market (Invited Talk) (2022)

In recent years, prominent blockchain systems such as Bitcoin and Ethereum have experienced explosive growth in transaction volume, leading to frequent surges in demand for limited block space and causing transaction fees to fluctuate by orders of magnitude. Existing systems sell space using first-price auctions; however, users find it difficult to estimate how much they need to bid in order to get their transactions accepted onto the chain. If they bid too low, their transactions can have long confirmation times. If they bid too high, they pay larger fees than necessary. In light of these issues, new transaction fee mechanisms have been proposed, most notably EIP-1559, aiming to provide better usability. EIP-1559 is a history-dependent mechanism that relies on block utilization to adjust a base fee. We propose an alternative design - a dynamic posted-price mechanism - which uses not only block utilization but also observable bids from past blocks to compute a posted price for subsequent blocks. We show its potential to reduce price volatility by providing examples for which the prices of EIP-1559 are unstable while the prices of the proposed mechanism are stable. More generally, whenever the demand for the blockchain stabilizes, we ask if our mechanism is able to converge to a stable state. Our main result provides sufficient conditions in a probabilistic setting for which the proposed mechanism is approximately welfare optimal and the prices are stable. Our main technical contribution towards establishing stability is an iterative algorithm that, given oracle access to a Lipschitz continuous and strictly concave function f, converges to a fixed point of f.
Interference Mitigation via Rate-Splitting and Common Message Decoding in Cloud Radio Access Networks (2019)

Cloud-radio access networks (C-RAN) help in overcoming the scarcity of radio resources by enabling dense deployment of base-stations (BSs) and connecting them to a central-processor (CP). This paper considers the downlink of a C-RAN, where the cloud is connected to the BSs via limited-capacity backhaul links. We propose and optimize a C-RAN transmission scheme that combines rate splitting, common message decoding, and beamforming vectors design and clustering. To this end, this paper optimizes a transmission scheme that combines rate splitting (RS), common message decoding (CMD), and clustering and coordinated beamforming. In this paper, we focus on maximizing the weighted sum-rate subject to per-BS backhaul capacity and transmit power constraints, so as to jointly determine the RS-CMD mode of transmission, the cluster of BSs serving private and common messages of each user, and the associated beamforming vectors of each user private and common messages. This paper proposes solving such a complicated non-convex optimization problem using $l_{0}$ -norm relaxation techniques, followed by inner-convex approximations (ICA), so as to achieve stationary solutions to the relaxed non-convex problem. The numerical results show that the proposed method provides significant performance gain as compared to conventional interference mitigation techniques in C-RAN which simply treat interference as noise (TIN).
Targeted gene therapy for rat glomerulonephritis using HVJ‐immunoliposomes (2002)

This study has demonstrated that systemic delivery of HVJ-liposomes coupled with OX-7 results in efficient ODN transfer in rat glomeruli. NF-kappaB, but not SD decoy ODN administered systemically via HVJ-liposomes complexed with OX-7 showed clear therapeutic potential for glomerulonephritis. This novel ODN transfer method combined with decoy strategy has the potential to lead to the establishment of a new therapeutic approach to glomerular diseases.
Room Temperature Pulsed Operation of Nitride Based Multi-Quantum-Well Laser Diodes with Cleaved Facets on Conventional C-Face Sapphire Substrates (1996)

We demonstrate room temperature pulsed operation of nitride based multi-quantum-well (MQW) laser diodes with cleaved mirror facets grown on a conventional C-face sapphire substrate. Cleavage was performed along the &lt;11*BAR*2*BAR*0&gt; direction of the sapphire substrate, and the resultant facet was analyzed using an atomic force microscope (AFM) and theoretical calculation. A single peak emisson, at a wavelength of 417.5 nm, with a full width at half-maximum of 0.15 nm, was obtained. The threshold current density of the laser was 50 kA/cm 2 and a voltage for the threshold current was 20 V.
Learning Domain Randomization Distributions for Training Robust Locomotion Policies (2019)

Domain randomization (DR) is a successful technique for learning robust policies for robot systems, when the dynamics of the target robot system are unknown. The success of policies trained with domain randomization however, is highly dependent on the correct selection of the randomization distribution. The majority of success stories typically use real world data in order to carefully select the DR distribution, or incorporate real world trajectories to better estimate appropriate randomization distributions. In this paper, we consider the problem of finding good domain randomization parameters for simulation, without prior access to data from the target system. We explore the use of gradient-based search methods to learn a domain randomization with the following properties: 1) The trained policy should be successful in environments sampled from the domain randomization distribution 2) The domain randomization distribution should be wide enough so that the experience similar to the target robot system is observed during training, while addressing the practicality of training finite capacity models. These two properties aim to ensure the trajectories encountered in the target system are close to those observed during training, as existing methods in machine learning are better suited for interpolation than extrapolation. We show how adapting the domain randomization distribution while training context-conditioned policies results in improvements on jump-start and asymptotic performance when transferring a learned policy to the target environment.