gebhart/patrepeval huggingface dataset:
Distributed and Lumped Parameter Models for the Characterization of High Throughput Bioreactors (2016)

Next generation bioreactors are being developed to generate multiple human cell-based tissue analogs within the same fluidic system, to better recapitulate the complexity and interconnection of human physiology [1, 2]. The effective development of these devices requires a solid understanding of their interconnected fluidics, to predict the transport of nutrients and waste through the constructs and improve the design accordingly. In this work, we focus on a specific model of bioreactor, with multiple input/outputs, aimed at generating osteochondral constructs, i.e., a biphasic construct in which one side is cartilaginous in nature, while the other is osseous. We next develop a general computational approach to model the microfluidics of a multi-chamber, interconnected system that may be applied to human-on-chip devices. This objective requires overcoming several challenges at the level of computational modeling. The main one consists of addressing the multi-physics nature of the problem that combines free flow in channels with hindered flow in porous media. Fluid dynamics is also coupled with advection-diffusion-reaction equations that model the transport of biomolecules throughout the system and their interaction with living tissues and C constructs. Ultimately, we aim at providing a predictive approach useful for the general organ-on-chip community. To this end, we have developed a lumped parameter approach that allows us to analyze the behavior of multi-unit bioreactor systems with modest computational effort, provided that the behavior of a single unit can be fully characterized.
The design of a potent inhibitor of the hepatitis C virus NS3 protease: BILN 2061—From the NMR tube to the clinic (2004)

The virally encoded serine protease NS3/NS4A is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. Until very recently, the design of inhibitors for the HCV NS3 protease was limited to large peptidomimetic compounds with poor pharmacokinetic properties, making drug discovery an extremely challenging endeavor. In our quest for the discovery of a small-molecule lead that could block replication of the hepatitis C virus by binding to the HCV NS3 protease, the critical protein-polypeptide interactions between the virally encoded NS3 serine protease and its polyprotein substrate were investigated. Lead optimization of a substrate-based hexapeptide, guided by structural data, led to the understanding of the molecular dynamics and electronic effects that modulate the affinity of peptidomimetic ligands for the active site of this enzyme. Macrocyclic beta-strand scaffolds were designed that allowed the discovery of potent, highly selective, and orally bioavailable compounds. These molecules were the first HCV NS3 protease inhibitors reported that inhibit replication of HCV subgenomic RNA in a cell-based replicon assay at low nanomolar concentrations. Optimization of their biopharmaceutical properties led to the discovery of the clinical candidate BILN 2061. Oral administration of BILN 2061 to patients infected with the hepatitis C genotype 1 virus resulted in an impressive reduction of viral RNA levels, establishing proof-of-concept for HCV NS3 protease inhibitors as therapeutic agents in humans.
BSA Adsorption on Differently Charged Polystyrene Nanoparticles using Isothermal Titration Calorimetry and the Influence on Cellular Uptake (2011)

BSA adsorption onto negatively and positively charged polystyrene nanoparticles was investigated. The nanoparticles were characterized in terms of particle size, zeta potential, surface group density, and morphology. The adsorption behavior of BSA on the particle surface, as a function of pH and overall charge of the particle, was studied using ITC. Different thermodynamic data such as enthalpy changes upon binding and stoichiometry of the systems were determined and discussed. The degree of surface coverage with BSA was calculated using the thermodynamic data. The cellular uptake of particles before and after BSA adsorption was studied using HeLa cells in the presence and absence of supplemented FCS in the cell culture medium.
On the delay of network coding over line networks (2009)

We analyze a simple network where a source and a receiver are connected by a line of erasure channels of different reliabilities. Recent prior work has shown that random linear network coding can achieve the min-cut capacity and therefore the asymptotic rate is determined by the worst link of the line network. In this paper we investigate the delay for transmitting a batch of packets, which is a function of all the erasure probabilities and the number of packets in the batch. We show a monotonicity result on the delay function and derive simple expressions which characterize the expected delay behavior of line networks. Further, we use a martingale bounded differences argument to show that the actual delay is tightly concentrated around its expectation.
New Optimization Technique for Operational Setpoints of Activated Sludge Process Using Genetic Algorithm. (2003)

A new optimization technique for establishing control setpoints for an activated sludge process based on Activated Sludge Model No.2d (ASM2d) and Genetic Algorithm (GA) has been developed. Process performance predicted by ASM2d, which was compared with the data measured at an existing wastewater treatment plant and confirmed to be sufficiently reliable, was used as the objective function in determining new setpoints by the proposed optimization technique. It has been shown that this technique can determine the combinations of good setpoints that would yield effluent nitrogen and phosphorus concentrations below 10mg-N·l-1 and 1mg-P·l-1, respectively. Moreover, these setpoints were found to be economically advantageous in comparison with other operational conditions. The proposed new optimization technique is expected to make significant contributions to the enhancement of biological nutrient removal in the activated sludge process.
Synthesis Design and Structure of a Multipore Zeolite with Interconnected 12- and 10-MR Channels (2012)

A new molecular sieve, ITQ-38, containing interconnected large and medium pores in its structure has been synthesized. The rational combination of dicationic piperidine-derivative molecules as organic structure directing agents (OSDAs) with germanium and boron atoms in alkaline media has allowed the synthesis of ITQ-38 zeolite. High-resolution transmission electron microscopy (HRTEM) has been used to elucidate the framework topology of ITQ-38, revealing the presence of domains of perfect ITQ-38 crystals as well as very small areas containing nanosized ITQ-38/ITQ-22 intergrowths. The structure of ITQ-38 is highly related to ITQ-22 and the recently described polymorph C of ITQ-39 zeolite. It shares a common building layer with ITQ-22 and contains the same building unit as the polymorph C of ITQ-39. All three structures present similar framework density, 16.1 T atoms/1000 Å(3).
Lactam Coupling as a Versatile Route to Indoprofen Analogs (2010)

A convergent synthesis of indoprofen via a Buchwald coupling approach is reported. Using this methodology, indoprofen and a set of analogs of indoprofen were readily prepared.
A randomized phase II, open-label study of sipuleucel-T with concurrent or sequential abiraterone acetate (AA) in metastatic castrate-resistant prostate cancer (mCRPC). (2013)

114 Background: Sipuleucel-T and AA are both FDA approved for mCRPC. Given that androgen deprivation therapy is immunostimulatory, increased suppression of the androgen axis with AA could provide synergy in combination with sipuleucel-T; however, AA is given with prednisone (P), which may be immunosuppressive. In order to evaluate the impact of concurrent AA + P on product characteristics, a study of sipuleucel-T with concurrent or sequential AA + P was undertaken. Methods: Pts aged ≥18 yrs with asymptomatic or minimally symptomatic mCRPC, and ECOG PS 0/1 were randomized (1:1) to sipuleucel-T (3 infusions at approx 2-week intervals) with up to 26 weeks of AA + P (AA 1000mg QD + P 5mg BID) starting 1 day after the first sipuleucel-T infusion (concurrent arm) or at week 10 (sequential arm). The primary endpoint was cumulative CD54 upregulation (measure of antigen presenting cell activation); secondary and tertiary endpoints included CD54 + cell and total nucleated cell (TNC) counts (measures of product potency), safety and efficacy. Results: 29 pts have been enrolled. 16 pts in the concurrent arm (A) and 13 pts in the sequential arm (B) have completed sipuleucel-T treatment at the time of this interim analysis (7 Sept 2012). 27/29 pts received all 3 infusions of sipuleucel-T; 2 pts (both arm A) received only 1 infusion due to insufficient TNC count (n=1) and disease progression 8 days after randomization (n=1). No significant differences in median cumulative CD54 upregulation (31.6 vs 36.6) and CD54 + count (1.9 vs 2.1 x10 9 ) were observed between arms A and B, respectively. Increased CD54 upregulation with the 2 nd and 3 rd treatments were indicative of a prime boost effect in both arms. Similarly, the TNC profile over time was similar for both arms. The overall incidence of adverse events (AEs) was similar in arms A (81%) and B (77%). Common all-grade AEs included muscle spasms (31% vs 23%), oral paresthesia (19% vs 31%), chills (31% vs 8%) and cough (19% vs 15%). Conclusions: These data suggest that sipuleucel-T can be manufactured during treatment with AA + P with product potency and prime boost similar to that of sipuleucel-T alone. Clinical trial information: NCT01487863.
A 1.1- $\mu \text{m}$ 33-Mpixel 240-fps 3-D-Stacked CMOS Image Sensor With Three-Stage Cyclic-Cyclic-SAR Analog-to-Digital Converters (2017)

In this paper, a 1.1-μm-pitch 33-Mpixel 240-fps backside-illuminated 3-D-stacked CMOS image sensor with three-stage cyclic-cyclic-successive-approximation-register (SAR) analog-to-digital converters (ADCs) is developed. The narrow-pitch interconnection technology that connects the pixels and arrayed ADCs inside the pixel area is described. The 3-D-stacked architecture, constructed using the interconnection technology, makes it possible to place a 1932 (H) × 4 (V) correlated-double-sampling/ADC array underneath the pixel area. Furthermore, the pipelined and parallel operation of the three-stage cyclic-cyclic-SAR ADC architecture effectively reduces the conversion time period and power consumption and achieves 12-b precision within one horizontal scan time of 0.92 μs. As a result, the interconnection technology and ADC architecture achieved a high frame rate of 240 fps in 33 Mpixels. Random noise of 3.6 e- and low power consumption of 3.0 W were attained at an extremely high pixel rate of 7.96 Gpixel/s. A good figure of merit is achieved compared with recently developed image sensors.
Active model matching in range images (2005)

A general three dimensional image analysis environment is presented. The environment proved extremely flexible, and a three dimensional object recognition system was designed using this environment. The recognition system addresses all the issues associated with view independent object recognition. The particular concentration of this paper is the development of an active model matching approach called a procedural model The procedural model uses the surface geometry available in a range image to limit the amount of searching that must be done. The surface geometry is determined by solving an eigensystem, and utilized to determine the pose of the object.
Quadratic approach for single-channel noise reduction (2020)

Abstract In this paper, we introduce a quadratic approach for single-channel noise reduction. The desired signal magnitude is estimated by applying a linear filter to a modified version of the observations’ vector. The modified version is constructed from a Kronecker product of the observations’ vector with its complex conjugate. The estimated signal magnitude is multiplied by a complex exponential whose phase is obtained using a conventional linear filtering approach. We focus on the linear and quadratic maximum signal-to-noise ratio (SNR) filters and demonstrate that the quadratic filter is superior in terms of subband SNR gains. In addition, in the context of speech enhancement, we show that the quadratic filter is ideally preferable in terms of perceptual evaluation of speech quality (PESQ) and short-time objective intelligibility (STOI) scores. The advantages, compared to the conventional linear filtering approach, are particularly significant for low input SNRs, at the expanse of a higher computational complexity. The results are verified in practical scenarios with nonstationary noise and in comparison to well-known speech enhancement methods. We demonstrate that the quadratic maximum SNR filter may be superior, depending on the nonstationary noise type.
A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli (2017)

We made a coupled genetic reporter that detects rare transcription misincorporation errors to measure RNA polymerase transcription fidelity in <i>Escherichia coli</i> Using this reporter, we demonstrated <i>in vivo</i> that the transcript cleavage factor GreA, but not GreB, is essential for proofreading of a transcription error where a riboA has been misincorporated instead of a riboG. A <i>greA</i> mutant strain had more than a 100-fold increase in transcription errors relative to wild-type or a <i>greB</i> mutant. However, overexpression of GreB in Δ<i>greA</i> cells reduced the misincorporation errors to wild-type levels, demonstrating that GreB at high concentration could substitute for GreA in RNA proofreading activity <i>in vivo</i>.
Impact of Passive In-Home Health Status Monitoring Technology in Home Health: Outcome Pilot (2006)

This paper describes a study designed to assess the impacts of passive health status monitoring technology in home health. Monitoring systems were installed in the homes of 13 home health clients to track physiological parameters (heart rate, breathing rate, and gait), the activities of daily living (ADLs) and key alert conditions of residents, such as falls. Activity reports and alert notifications were sent to professional caregivers in order to refine and target the care administered to clients participating in the study. Informal caregivers of participants were provided with access to the ongoing wellness status of their loved ones. The potential diagnostic utility of the monitoring data, the subjects' quality of life and health related quality of life, as well as the quality of life, strain and burden levels of the informal caregivers were assessed. Pre- and post-installation scores were compared. The results suggest that monitoring technologies could provide care coordination tools that have a positive impact on the perceived quality of life of monitored individuals, as well as a reduction in the strain levels of their informal caregivers, and may have a positive impact on the participants' health related quality of life
CL1-SR39: A Noninvasive Molecular Imaging Model of Prostate Cancer Suicide Gene Therapy Using Positron Emission Tomography (2002)

Molecular based imaging of sr39tk transfected prostate cancer tumors and adenoviral delivered HSV1-tk suicide gene therapy based on the selective conversion and intracellular trapping of F-FHBG by sr39tk is feasible. Potential applications include noninvasive monitoring of the location, duration and intensity of gene constructs, which may contribute to the safety of clinical gene therapy protocols, and noninvasive imaging of the prostate cancer xenograft response to experimental therapy.
Semiconductor optical amplifiers: a key technology to control the packet power variation (2002)

Semiconductor optical amplifiers have already been identified as a key technology for fast switching. We demonstrate that a proper exploitation of the saturation area can provide concrete solutions to control the power variations between consecutive packets.
Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function (2021)

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.
Thermometry Using Thermal Activation of Josephson Junctions at MilliKelvin Temperatures (2005)

We use the thermal activation of Josephson junctions as a thermometer to investigate heat flow from a hot resistor at milliKelvin temperatures on a silicon chip used for superconducting qubit experiments. The experiments are compared to computer simulations and agree well. These results indicate that on-chip resistors can be used below a certain power level, but not above that level.
TRICK (2006)

Compilers, during compilation, analyze the application being compiled and build up extensive knowledge about the program. This knowledge is essential for the compiler to produce correct object code. Though some part of this knowledge is retained in the generated object files as symbol table information to be used by the linker and/or debugger, most of it is discarded after the compilation is done. In this paper, we introduce the TRICK framework, which is an attempt to retain and reuse this internal information generated by the compiler as part of its program analysis, in building new tools or enhancing existing tools as well for reuse by the compiler for continuous program optimization. We present examples of how development and maintenance of various program analysis tools can be simplified by using the TRICK framework describing tools developed by our group as well as how TRICK framework can be employed in continuous program optimization by the compiler. TRICK framework can be part of both static and dynamic compilation system, though our current usage model is in the context of a static compilation system,
Residual Stress Measurement in Steel Plates and Welds Using Critically Refracted Longitudinal (LCR) Waves (1996)

Abstract The application of acoustoelasticity using critically refracted longitudinal (LCR) waves is described for measuring residual stress in welded steel plates. Residual stresses are self-equilibrating and may exist in a material that has been deformed in a nonhomogeneous manner. When unknown residual stress is present in a structure, the true stress may become significantly greater than the working stress. In a corrosive environment, highly stressed areas that have not been properly stress relieved are prone to stress corrosion cracking. Areas near welds are particularly susceptible to stress corrosion cracking. Two welded plates were investigated for the present work: one hot-rolled and the other cold-rolled. Residual stresses are usually greatest after welding. Further, longitudinal stress (i.e., stress parallel to the weld bead) is typically greater than the component transverse to the weld bead. Since the acoustoelastic behavior of the LCR wave is largest when propagated parallel to a uniaxial stress, the LCR wave traveling parallel to the weld bead was used to investigate the stress changes after stress relieving of the welded plates. Both 1 MHz and 2.25 MHz probe frequencies were used in this study. The stress changes in the welds and in the cold-rolled plate were clearly indicated by the LCR data. Two verification methods were used: hole drilling (HD) and neutron diffraction (ND). The stress relief was verified by the hole-drilling technique. While the HD technique showed about the same stress magnitude as found by the LCR results, the orientation was reversed. The stress orientation was probably caused by the grinding process used to flatten the weld bead. Texture was also investigated using a neutron diffraction (ND) technique on the (001)[110] texture. The through-the-thickness technique yields an average of the orientation distribution of the (110) planes. At locations in the parent metal and in the weld, the distribution was found to be very similar, indicating uniform texture throughout the weld and parent metal zones.
Design of variable-resistance class E inverters for load modulation (2012)

Single-switch inverters such as the conventional class E inverter are often highly load sensitive, and maintain zero-voltage switching over only a narrow range of load resistances. This paper introduces a design methodology that enables rapid synthesis of class E inverters that maintain ZVS operation over a wide range of resistive loads. We also show how the proposed methodology relates to circuit transformations on traditional class E designs. The proposed methodology is demonstrated and experimentally validated on a design at 27.12 MHz that operates efficiently over an 8:1 load resistance range.
The Effect of the Solvation Ability Towards Mg 2+ -ion on the Kinetic Behavior of Mg 3 Bi 2 Electrode (2022)

Intermetallic compounds are expected to be used as the negative electrode for Mg-ion batteries, due to their relatively large capacity and the excellent electrochemical performance in the non-ethereal solutions. In the present study, the reaction mechanism of Mg 3 Bi 2 is focused. By comparing the reactivity towards the same electrode sheet in various electrolyte solutions, it is found that the effect of MgF 2 based surface film, which is formed by the decomposition of Mg(N(CF 3 SO 2 ) 2 ) 2 (Mg(TFSA) 2 ), is not large necessarily. The reactivity in Mg(TFSA) 2 +crown ether/acetonitrile solution fairly varies by the size of crown ethers. From the results, it is indicated that the de-solvation process will also be the critical factor for the Mg 2+ -ion insertion/extraction into the Mg 3 Bi 2 electrode.
Revenue Driven Virtual Machine Management in Green Datacenter Networks Towards Big Data (2016)

The big data era is presenting unprecedented opportunities for generating new revenues in various sectors ranging from health care, economics, life science, to manufacturing. Datacenters (DCs) are widely deployed to provision various application services as well as to process big data. Since more and more servers are installed in DCs, the cost of electricity incurs a financial burden for the DC operators. Many DCs are equipped with renewable energy to reduce the electricity bill. However, the locations of the energy demands do not match the locations of the renewable energy generation. This mismatch may be addressed by virtual machine (VM) migration. The DCs, which lack renewable energy, can migrate their workloads to other DCs, which have abundant renewable energy. In addition, DC operators always want to maximize revenue and minimize operation cost. In this paper, the problem of maximizing revenue and minimizing operation cost of a green DC network enabled with and without VM migration is formulated by integer linear programming. Simulation results show that optimal results can be reached for small size problems. Two heuristic algorithms are proposed to efficiently solve large size problems. To our best knowledge, this is the first study of the revenue driven VM management problem in green DC networks towards big data with VM migration.