gebhart/patrepeval huggingface dataset:
PERK Pathway and Neurodegenerative Disease: To Inhibit or to Activate? (2021)

With the extension of life span in recent decades, there is an increasing burden of late-onset neurodegenerative diseases, for which effective treatments are lacking. Neurodegenerative diseases include the widespread Alzheimer's disease (AD) and Parkinson's disease (PD), the less frequent Huntington's disease (HD) and Amyotrophic Lateral Sclerosis (ALS) and also rare early-onset diseases linked to mutations that cause protein aggregation or loss of function in genes that maintain protein homeostasis. The difficulties in applying gene therapy approaches to tackle these diseases is drawing increasing attention to strategies that aim to inhibit cellular toxicity and restore homeostasis by intervening in cellular pathways. These include the unfolded protein response (UPR), activated in response to endoplasmic reticulum (ER) stress, a cellular affliction that is shared by these diseases. Special focus is turned to the PKR-like ER kinase (PERK) pathway of the UPR as a target for intervention. However, the complexity of the pathway and its ability to promote cell survival or death, depending on ER stress resolution, has led to some confusion in conflicting studies. Both inhibition and activation of the PERK pathway have been reported to be beneficial in disease models, although there are also some reports where they are counterproductive. Although with the current knowledge a definitive answer cannot be given on whether it is better to activate or to inhibit the pathway, the most encouraging strategies appear to rely on boosting some steps without compromising downstream recovery.
Directional neighbor discovery in 60 GHz indoor wireless networks (2009)

The unlicensed 60 GHz band brings the promise of multi-gigabit data rates to support new applications such as high definition video over wireless links. Signal propagation in the 60 GHz band significantly differs from that in the traditionally used 2.4 and 5 GHz bands. The propagation and penetration losses in the 60 GHz band are much higher. Furthermore, the signals are often reflected in indoor settings. Previous physical layer studies show that the use of directional antennas can significantly help in coping with these effects. In this paper, we address the problem of neighbor discovery in the 60 GHz band. We account for not only discovery via direct line-of-sight paths, but also via reflected beams. To the best of our knowledge, none of the previous efforts on higher layer protocols for use with directional antennas account for reflections. We consider two approaches for neighbor discovery (a) direct discovery where each node explicitly discovers its neighbors and, (b) gossip-based discovery where nodes exchange information with regards to their already discovered neighbors. We develop analytical models to capture the performance of the two approaches and validate the models via simulations in indoor settings with obstacles that reflect the transmitted signals. As one might expect, the gossip based discovery incurs a lower neighbor-discovery latency than direct discovery. We examine the impact of system parameters such as varying beamwidth and node density. Our study provides insights on the right choice of system parameters for efficient neighbor discovery in the 60 GHz regime.
Blockaid: Data Access Policy Enforcement for Web Applications (2022)

Modern web applications serve large amounts of sensitive user data, access to which is typically governed by data-access policies. Enforcing such policies is crucial to preventing improper data access, and prior work has proposed many enforcement mechanisms. However, these prior methods either alter application semantics or require adopting a new programming model; the former can result in unexpected application behavior, while the latter cannot be used with existing web frameworks. Blockaid is an access-policy enforcement system that preserves application semantics and is compatible with existing web frameworks. It intercepts database queries from the application, attempts to verify that each query is policy-compliant, and blocks queries that are not. It verifies policy compliance using SMT solvers and generalizes and caches previous compliance decisions for better performance. We show that Blockaid supports existing web applications while requiring minimal code changes and adding only modest overheads.
Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data. (2005)

Analysis of viral strand sequence data and viral replication capacity could potentially lead to biological insights regarding the replication ability of HIV-1. Determining specific target codons on the viral strand will facilitate the manufacturing of target-specific antiretrovirals. Various algorithmic and analysis techniques can be applied to this application. In this paper, we apply two techniques to a data set consisting of 317 patients, each with 282 sequenced protease and reverse transcriptase codons. The first application is recently developed multiple testing procedures to find codons which have significant univariate associations with the replication capacity of the virus. A single-step multiple testing procedure (Pollard and van der Laan 2003) method was used to control the family wise error rate (FWER) at the five percent alpha level as well as the application of augmentation multiple testing procedures to control the generalized family wise error (gFWER) or the tail probability of the proportion of false positives (TPPFP). We also applied a data adaptive multiple regression algorithm to obtain a prediction of viral replication capacity based on an entire mutant/non-mutant sequence profile. This is a loss-based, cross-validated Deletion/Substitution/Addition regression algorithm (Sinisi and van der Laan 2004), which builds candidate estimators in the prediction of a univariate outcome by minimizing an empirical risk. These methods are two separate techniques with distinct goals used to analyze this structure of viral data.
Bendable Zeolite Membranes: Synthesis and Improved Gas Separation Performance (2015)

Separation and sequestration of CO2 emitted from fossil energy fueled electric generating units and industrial facilities will help in reducing anthropogenic CO2, thereby mitigating its adverse climate change effects. Membrane-based gas separation has the potential to meet the technical challenges of CO2 separation if high selectivity and permeance with low costs for large-scale manufacture are realized. Inorganic zeolite membranes in principle can have selectivity and permeance considerably higher than polymers. This paper presents a strategy for zeolite growth within the pores of a polymer support, with crystallization time of an hour. With a thin coating of 200-300 nm polydimethylsiloxane (PDMS) on the zeolite-polymer composite, transport data for CO2/N2 separation indicate separation factors of 35-45, with CO2 permeance between 1600 and 2200 GPU (1 GPU = 3.35 × 10(-10) mol/(m(2) s Pa)) using dry synthetic mixtures of CO2 and N2 at 25 °C. The synthesis process results in membranes that are highly reproducible toward transport measurements and exhibit long-term stability (3 days). Most importantly, these membranes because of the zeolite growth within the polymer support, as contrasted to conventional zeolite growth on top of a support, are mechanically flexible.
An Automatic Hexahedral Mesh Generation System Using Feature Line Extraction Technique (2005)

A technique for automatically generating a hexahedral mesh of a complex solid model was developed. This technique can automate the interactive operations (such as model editing) that are carried out as a pretreatment for hexahedral-mesh generation. Consequently, the time taken by these interactive operations was significantly shortened, and high-speed generation of a hexahedral mesh was thus possible. Furthermore, the developed technique was applied to the generation of a hexahedral mesh of an engine-block model. And it was confirmed that the mesh generation time is shortened to one tenth of that for the conventional method.
Sulfated Escherichia coli K5 Polysaccharide Derivatives Inhibit Dengue Virus Infection of Human Microvascular Endothelial Cells by Interacting with the Viral Envelope Protein E Domain III (2013)

Dengue virus (DENV) is an emerging mosquito-borne pathogen that causes cytokine-mediated alterations in the barrier function of the microvascular endothelium, leading to dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). We observed that DENV (serotype 2) productively infects primary (HMVEC-d) and immortalized (HMEC-1) human dermal microvascular endothelial cells, despite the absence of well-described DENV receptors, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) or the mannose receptor on the cell surface. However, heparan sulfate proteoglycans (HSPGs) were highly expressed on these cells and pre-treatment of HMEC-1 cells with heparinase II or with glycosaminoglycans reduced DENV infectivity up to 90%, suggesting that DENV uses HSPGs as attachment receptor on microvascular endothelial cells. Sulfated Escherichia coli K5 derivatives, which are structurally similar to heparin/heparan sulfate but lack anticoagulant activity, were able to block DENV infection of HMEC-1 and HMVEC-d cells in the nanomolar range. The highly sulfated K5-OS(H) and K5-N,OS(H) inhibited virus attachment and subsequent entry into microvascular endothelial cells by interacting with the viral envelope (E) protein, as shown by surface plasmon resonance (SPR) analysis using the receptor-binding domain III of the E protein.
A Selectable and Excisable Marker System for the Rapid Creation of Recombinant Poxviruses (2011)

The system described here thus provides a faster, simpler and more efficient means to create clinic-ready recombinant poxviruses for therapeutic gene therapy applications.
Device Activity and Embedded Information Bit Detection Using AMP in Massive MIMO (2017)

Future cellular networks will support a massive number of devices as a result of emerging technologies such as Internet-of-Things and sensor networks. Enhanced by machine type communication (MTC), low-power low-complex devices in the order of billions are projected to receive service from cellular networks. Contrary to traditional networks which are designed to handle human driven traffic, future networks must cope with MTC based systems that exhibit sparse traffic properties, operate with small packets and contain a large number of devices. Such a system requires smarter control signaling schemes for efficient use of system resources. In this work, we consider a grant-free random access cellular network and propose an approach which jointly detects user activity and single information bit per packet. The proposed approach is inspired by the approximate message passing (AMP) and demonstrates a superior performance compared to the original AMP approach. Furthermore, the numerical analysis reveals that the performance of the proposed approach scales with number of devices, which makes it suitable for user detection in cellular networks with massive number of devices.
The insulin receptor C-terminus is involved in regulation of the receptor kinase activity (1993)

During the insulin receptor activation process, ligand binding and autophosphorylation induce two distinct conformational changes in the C-terminal domain of the receptor beta-subunit. To analyze the role of this domain and the involvement of the C-terminal autophosphorylation sites (Tyr1316 and Tyr1322) in receptor activation, we used (i) antipeptide antibodies against three different C-terminal sequences (1270-1281, 1294-1317, and 1309-1326) and (ii) an insulin receptor mutant (Y/F2) where Tyr1316 and Tyr1322 have been replaced by Phe. We show that the autophosphorylation-induced C-terminal conformational change is preserved in the Y/F2 receptor, indicating that this change is not induced by phosphorylation of the C-terminal sites but most likely by phosphorylation of the major sites in the kinase domain (Tyr1146, Tyr1150, and Tyr1151). Binding of antipeptide antibodies to the C-terminal domain modulated (activated or inhibited) both mutant and wild-type receptor-mediated phosphorylation of poly(Glu/Tyr). In contrast to the wild-type receptor, Y/F2 exhibited the same C-terminal configuration before and after insulin binding, evidencing that mutation of Tyr1316 and Tyr1322 introduced conformational changes in the C-terminus. Finally, the mutant receptor was 2-fold more active than the wild-type receptor for poly(Glu/Tyr) phosphorylation. In conclusion, the whole C-terminal region of the insulin receptor beta-subunit is likely to exert a regulatory influence on the receptor kinase activity. Perturbations of the C-terminal region, such as binding of antipeptides or mutation of Tyr1316 and Tyr1322, provoke alterations at the receptor kinase level, leading to activation or inhibition of the enzymic activity.
Multicasting schemes and performance issues of interconnection networks (1997)

One of the major challenges in the design of switching networks is the provision of multicast capability, or the ability to support point-to-multipoint connections, which is required in a wide range of applications such as tele-conferencing and video distribution systems. While many multistage multicast packet switches have been proposed to handle these connections in the switching context in which nodes are connected via a central packet switch, little effort has been spent on supporting multicast connections among nodes in a closed network. This thesis focuses on multicasting in the closed network scenario and investigates how this can be achieved in a systematic manner in arbitrary closed networks.
A multistage multicast packet switch is usually obtained by a cascade combination of a copy network and a point-to-point packet switch. In the closed network scenario, we can apply a similar methodology by splitting the multicast process into the replication phase and the routing phase in the time domain. In the replication phase, sufficient copies of a multicast packet are first generated by a replication algorithm. These copies are subsequently routed to their respective destinations in the routing phase. We show that by using a general replication algorithm for the replication phase, multicast capability can be incorporated into any closed interconnection networks. We will evaluate the performance of the general multicast network and derive a general throughput equation that relates the multicast throughput to the point-to-point routing delay. In this way, the performance of a multicast network can be obtained by making use of the results of the point-to-point analysis of the same network. Our analysis results indicate that the performance of a multicast network is affected by two detrimental phenomena known as deadlocks and network instability. To prevent such problems, we propose a deadlock-breaking mechanism and several access control schemes. With these protective measures, the maximum network throughput can be achieved. To complete the study, we investigate the memory requirements associated with the multicast scheme and discuss several alternatives in the destination address resolution process at the end of the packet replication phase. We will show that by properly choosing the locations for the destination address information, the amount of memory required can be significantly reduced at the cost of a slight reduction in network throughput.
Suction and Oscillatory Blowing Actuator Modeling and Validation (2008)

Enhancing the ability to control flows in different configurations and flow conditions can lead to improved flow-related, energy-efficient systems. Certain active flow control actuators are effective at low Mach numbers, but the momentum and vorticity they provide limits their utilization to low speeds. At higher Mach numbers, robust, unsteady, effective, and practical fluidic actuators are a critical, enabling technology in any flow control system, though they are largely missing. A new actuator concept, based on the combination of steady suction and oscillatory blowing, is presented. The actuator achieves near-sonic speeds at a frequency range from 10 Hz to at least 1 kHz. It has no moving parts and therefore is expected to have superior effectiveness and reliability. The operating principles of the new actuator are presented along with two computational models and their experimental validation.
Supplementary Figure 1 from Forkhead Box F1 Regulates Tumor-Promoting Properties of Cancer-Associated Fibroblasts in Lung Cancer (2023)

Supplementary Figure 1 from Forkhead Box F1 Regulates Tumor-Promoting Properties of Cancer-Associated Fibroblasts in Lung Cancer
Efficient and Precise Dynamic Construction of Control Flow Graphs (2019)

The extraction of high-level information from binary code is an important problem in programming languages, whose solution supports the detection of malware in binary code and the construction of dynamic program slices. The Control Flow Graph is one of the instruments used to represent the structure of binary programs. Most solutions to reconstruct CFGs from binary programs rely on purely static techniques, based either on data-flow analyses, or in type inference. In contrast, in this work we use a purely dynamic approach to such a purpose. Our technique can be used alone, or in combination with static analysis tools. We demonstrate that it is possible to verify completeness in several real-world programs. We also show how to combine our technique with DynInst, the current state-of-the-art static CFG reconstructor. By providing DynInst with extra information, we improve its capacity to deal with indirect jumps. Our dynamic CFG reconstructor has been implemented on top of valgrind. When applied on cBench, this implementation is able to completely cover 36% of all the functions available in that suite. It adds an average overhead of 43x onto the execution of the original programs. Although expressive, this overhead is almost four times lower than the overhead of DCFG, a tool distributed by Intel, and built on top of PinPlay.
A distributed opportunistic access scheme and its application to OFDMA systems (2009)

Multiuser systems can provide multiuser diversity gains by assigning channels to users with higher channel gains. To avoid the extensive information exchange with the access point for the uplink access in centralized approaches, we propose in this paper a distributed opportunistic access scheme. Through a judicious design of a novel backoff mechanism to utilize the channel information and reduce collisions, significant multiuser diversity gains are achieved. To a user, the higher the channel gain is, the smaller the backoff time-slot and, hence, the higher the access priority of that user is. In addition, for heterogeneous systems, our proposed scheme can realize multiuser diversity gains and achieve fairness among the users at the same time. Finally, we design two distributed opportunistic access schemes for OFDMA systems. Users contend on all sub-channels in the first scheme and only on several strongest sub-channels in the second scheme. Compared with traditional centralized OFDMA systems and other distributed access schemes, our proposed schemes reduce overhead and achieve a higher throughput.
Hybrid Beamforming Scheme for CDMA Systems to Overcome the Insufficient Pilot Power Problem in Correlated SIMO Channels (2005)

A hybrid beamformer composed of a direction-of-arrival (DOA) based scheme and maximal ratio combining (MRC) is proposed to overcome the degradation caused by inaccurate channel estimation due to insufficient pilot power, which happens in conventional single-input, multiple-output (SIMO) Code Division Multiple Access (CDMA) reverse link. The proposed scheme can provide more accurate channel estimation and interference reduction at the expense of diversity gain in the spatially correlated SIMO channel. As a result, the hybrid scheme outperforms conventional MRC beamformers for six or more antennas in the channel environment, in which the angle-of-spread (AOS) is within 30°.
A comparative study of lithium ion to lead acid batteries for use in UPS applications (2014)

Uninterruptible power supply (UPS) systems have incorporated in their structure an electrochemical battery which allows for smooth power supply when a power failure occurs. In general, UPS systems are based on lead acid batteries; mainly a valve regulated lead acid (VRLA) battery. Recently, lithium ion batteries are getting more and more attention for their use in the back-up power systems and UPSs, because of their superior characteristics, which include increased safety and higher gravimetric and volumetric energy densities. This fact allows them to be smaller in size and weight less than VRLA batteries, which are currently used in UPS applications. The main purpose of this paper is to analyze how Li-ion batteries can become a useful alternative to present VRLA. In this study, three different electrochemical battery technologies were investigated; two of the most appealing Li-ion chemistries, lithium iron phosphate (LFP) and lithium titanate oxide (LTO) were compared with lead acid batteries, in terms of their basics characteristics (e.g. capacity, internal resistance) and their dependence on the operating conditions.
Time-Varying Optimization-Based Consensus Control For Microgrid's Secondary Control (2021)

In this paper, a time-varying convex optimization-based consensus controller is utilized for the secondary control of Microgrid in islanded mode. During this mode, grid-forming units are responsible for controlling the frequency and voltage of the microgid. Hierarchical control structure based on droop control is utilized to provide these functionalities. In primary control level, the system stability is maintained through supplying required active and reactive power leaving a deviation in the frequency and voltage magnitudes. The secondary control level is introduced to restore the frequency and voltage to their nominal values. However, droop-based hierarchal control suffers from poor reactive power sharing due to voltage drop in the lines. The proposed controller aims to restore the frequency to its nominal value and voltage within a predefined limit while keeping the active and reactive power sharing difference between units to the minimum. The proposed controller employs consensus-based distributed communication where each unit only communicates with its neighbor. This paper provides optimality and consensus analysis of time-varying optimization-based consensus control as well as a design procedure of the controller. The proposed controller is validated through SIMULINK/ MATLAB simulation. The real-time convex optimization solver is provided by CVXGEN.