gebhart/patrepeval huggingface dataset:
Essentials for ATP Synthesis by F1F0 ATP Synthases (2009)

The majority of cellular energy in the form of adenosine triphosphate (ATP) is synthesized by the ubiquitous F(1)F(0) ATP synthase. Power for ATP synthesis derives from an electrochemical proton (or Na(+)) gradient, which drives rotation of membranous F(0) motor components. Efficient rotation not only requires a significant driving force (DeltamuH(+)), consisting of membrane potential (Deltapsi) and proton concentration gradient (DeltapH), but also a high proton concentration at the source P side. In vivo this is maintained by dynamic proton movements across and along the surface of the membrane. The torque-generating unit consists of the interface of the rotating c ring and the stator a subunit. Ion translocation through this unit involves a sophisticated interplay between the c-ring binding sites, the stator arginine, and the coupling ions on both sides of the membrane. c-ring rotation is transmitted to the eccentric shaft gamma-subunit to elicit conformational changes in the catalytic sites of F(1), leading to ATP synthesis.
A limited-memory quasi-Newton algorithm for bound-constrained non-smooth optimization (2017)

We consider the problem of minimizing a continuous function that may be non-smooth and non-convex, subject to bound constraints. We propose an algorithm that uses the L-BFGS quasi-Newton approximation of the problem's curvature together with a variant of the weak Wolfe line search. The key ingredient of the method is an active-set selection strategy that defines the subspace in which search directions are computed. To overcome the inherent shortsightedness of the gradient for a non-smooth function, we propose two strategies. The first relies on an approximation of the ε-minimum norm subgradient, and the second uses an iterative corrective loop that augments the active set based on the resulting search directions. While theoretical convergence guarantees have been elusive even for the unconstrained case, we present numerical results on a set of standard test problems to illustrate the efficacy of our approach, using an open-source Python implementation of the proposed algorithm.
Totally green (2012)

The environmental impact of servers and datacenters is an important future challenge. System architects have traditionally focused on operational energy as a proxy for designing green servers, but this ignores important environmental implications from server production (materials, manufacturing, etc.). In contrast, this paper argues for a lifecycle focus on the environmental impact of future server designs, to include both operation and production. We present a new methodology to quantify the total environmental impact of system design decisions. Our approach uses the thermodynamic metric of exergy consumption, adapted and validated for use by system architects. Using this methodology, we evaluate the lifecycle impact of several example system designs with environment-friendly optimizations. Our results show that environmental impact from production can be important (around 20% on current servers and growing) and system design choices can reduce this component (by 30--40%). Our results also highlight several, sometimes unexpected, cross-interactions between the environmental impact of production and operation that further motivate a total lifecycle emphasis for future green server designs.
Sparsity in the Delay-Doppler Domain for Measured 60 GHz Vehicle-to-Infrastructure Communication Channels (2019)

We report results from millimeter wave vehicle-to-infrastructure (V2I) channel measurements conducted on Sept. 25, 2018 in an urban street environment, down-town Vienna, Austria. Measurements of a frequency-division multiplexed multiple-input single-output channel have been acquired with a time-domain channel sounder at 60 GHz with a bandwidth of 100 MHz and a frequency resolution of 5 MHz. Two horn antennas were used on a moving transmitter vehicle: one horn emitted a beam towards the horizon and the second horn emitted an elevated beam at 15-degrees up-tilt. This configuration was chosen to assess the impact of beam elevation on V2I communication channel characteristics: propagation loss and sparsity of the local scattering function in the delay-Doppler domain. The measurement results within urban speed limits show high sparsity in the delay-Doppler domain.
Is speech recognition becoming mainstream? (2002)

The Web's connectivity, wireless technology and handheld devices - combined with effective grammar-based speech recognition in a VoiceXML infrastructure may finally bring speech recognition to mass-market prominence.
Syntax-based alignment of multiple translations (2003)

We describe a syntax-based algorithm that automatically builds Finite State Automata (word lattices) from semantically equivalent translation sets. These FSAs are good representations of paraphrases. They can be used to extract lexical and syntactic paraphrase pairs and to generate new, unseen sentences that express the same meaning as the sentences in the input sets. Our FSAs can also predict the correctness of alternative semantic renderings, which may be used to evaluate the quality of translations.
EU FP7 INFSO-ICT-247223 ARTIST4G, D5.1 Scenarios, Key Performance Indicators and Evaluation Methodology for Advanced Cellular Systems (2010)

The following document states what performance indicators,\nevaluation scenarios and evaluation methodologies should be used within the ARTIST4G project in order to meet the overall objective: an increased and more uniform quality of service within the radio network.
Optimal sampling and reconstruction of MRI signals resulting from sinusoidal gradients (1991)

The optimum continuous time filter and its various discrete time implementations for free induction delay signals resulting from sinusoidal gradients of magnetic resonance imaging (MRI) are formulated. It is found that the estimation error associated with implementation based on linear temporal sampling, or, equivalently, nonlinear spatial frequency sampling, is smaller than that of nonlinear temporal sampling. It is shown that the optimal maximum likelihood estimator for sinusoidal gradients has higher error variance than that of constant gradients. Experimental results verifying the theoretical predictions are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-Temperature IGZO Technology on Transparent Plastic Foil by Atmospheric Spatial Atomic Layer Deposition (2019)

We use sALD to deposit IGZO and Al2O3 layers in top-gated self-aligned TFTs, achieving a low-temperature process flow (d200oC). We attain mobility of 8 cm2/Vs and switch-on voltage of -0.1 V for transistors with channel lengths down to 1 μm, enabling a 200 ppi QVGA display on transparent PEN foil.
Dynamics of the super pinch electron beam and fusion energy perspective (2021)

The characterization of a high current, relativistic electron beam, designated the Super Pinch electron beam, has been performed using compact pulsed-power accelerators of various architectures with a novel diode geometry. The Thunderbird accelerator has an initial $1.5\text{\ensuremath{-}}\ensuremath{\mu}\mathrm{s}$ rise time and 150-kA peak current. The drive voltage is compressed to produce a 12-ns 500-kV voltage pulse generating a $\ensuremath{\sim}40\text{\ensuremath{-}}\mathrm{kA}$ electron beam, which apparently exceeds the Alv\'en current limit although the useful current at small radius is an order of magnitude less. Using an insulated hollow cathode with a 0.5-cm anode-cathode gap, the large current is enabled by the evolution of plasma from the dielectric sleeve enveloping the cathode and a 0.5-mm wire anode. Post-shot recovery of the anode target and measurements of its deformation and damage allow an evaluation of the enhanced electron-beam focusing whereby significant beam energy is delivered to the record small, microscopic volume inside the anode target. The electron beam is seen to have conditions favorable to those needed to ignite compressed fuel in inertial confinement fusion. These results motivated a deeper insight using theoretical modeling with hybrid particle-in-cell codes. The modeling presented in this paper shows an electron beam radius of $&lt;10\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$ containing a current of 3--6 kA or $&gt;500\text{ }\text{ }\mathrm{MA}/{\mathrm{cm}}^{2}$ current density. Scaling up the accelerator, such preferred focusing, target penetration, and affordability of the pulsed power generated electron beams open a new opportunity for the application of the mainstream pulsed power devices in the research and development of fusion energy.
TNF-induced intracellular signaling leading to gene induction or to cytotoxicity by necrosis or by apoptosis. (1997)

TNF-induced apoptosis, e.g. in murine PC60 cells, requires the TNF receptor p55 (TNF-R55) and the TNF receptor p75 (TNF-R75); the latter even does not have to be triggered. The intracellular domain of TNF-R55 can be activated in the cytosol by linking it to the trimeric CAT protein; induction of this fusion protein leads to a full TNF response. A new MAP kinase, p38, has been shown to be also activated by TNF. This activation is essential for gene induction, but not for cytotoxicity in L929 cells. TNF treatment of L929 leads to reactive oxygen formation in the mitochondria, resulting in cell death by necrosis. TNF treatment of many other cell types results in apoptosis, and this process involves activation of one or more ICE homologs (IHO). In the mouse, seven cysteine proteases of the IHO family have been cloned and partially characterized. One or more of these IHOs is involved in cell killing by proteolysis of critical substrate(s). One substrate, which may be a key effector molecule in the apoptotic process, is PITSLRE kinase.
Anti-CD19 CAR T cells in combination with ibrutinib for the treatment of chronic lymphocytic leukemia (2022)

In chronic lymphocytic leukemia (CLL) patients who achieve a complete remission (CR) to anti-CD19 chimeric antigen receptor T cells (CART-19), remissions are remarkably durable. Preclinical data suggesting synergy between CART-19 and the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib prompted us to conduct a prospective single-center phase 2 trial in which we added autologous anti-CD19 humanized binding domain T cells (huCART-19) to ibrutinib in patients with CLL not in CR despite ≥6 months of ibrutinib. The primary endpoints were safety, feasibility, and achievement of a CR within 3 months. Of 20 enrolled patients, 19 received huCART-19. The median follow-up for all infused patients was 41 months (range, 0.25-58 months). Eighteen patients developed cytokine release syndrome (CRS; grade 1-2 in 15 of 18 subjects), and 5 developed neurotoxicity (grade 1-2 in 4 patients, grade 4 in 1 patient). While the 3-month CR rate among International Working Group on CLL (iwCLL)-evaluable patients was 44% (90% confidence interval [CI], 23-67%), at 12 months, 72% of patients tested had no measurable residual disease (MRD). The estimated overall and progression-free survival at 48 months were 84% and 70%, respectively. Of 15 patients with undetectable MRD at 3 or 6 months, 13 remain in ongoing CR at the last follow-up. In patients with CLL not achieving a CR despite ≥6 months of ibrutinib, adding huCART-19 mediated a high rate of deep and durable remissions. ClinicalTrials.gov number, NCT02640209.
Multi-Level Group Testing with Application to One-Shot Pooled COVID-19 Tests (2020)

A key requirement in containing contagious diseases, such as the Coronavirus disease 2019 (COVID-19) pandemic, is the ability to efficiently carry out mass diagnosis over large populations. Some of the leading testing procedures, such as those utilizing qualitative polymerase chain reaction, involve using dedicated machinery which can simultaneously process a limited amount of samples. A candidate method to increase the test throughput is to examine pooled samples comprised of a mixture of samples from different patients. In this work we study pooling based tests which operate in a one-shot fashion, while providing an indication not solely on the presence of infection, but also on its level, without additional pool tests, as often required in COVID-19 testing. As these requirements limit the application of traditional group-testing (GT) methods, we propose a multi-level GT scheme, which builds upon GT principles to enable accurate recovery using much fewer tests than patients, while operating in a one-shot manner and providing multi-level indications. We provide a theoretical analysis of the proposed scheme and characterize conditions under which the algorithm operates reliably and at affordable computational complexity. Our numerical results demonstrate that multi level GT accurately and efficiently detects infection levels, while achieving improved performance over previously proposed one-shot COVID-19 pooled-testing methods.
Using the Universal Software Radio Peripheral (USRP N210) as a RF Front-End for a Wide-Band Multi-Constellation GNSS Signal Receiver (2012)

This paper has implemented a wide-band multi-constellation GNSS signal receiver in conjunction with a universal software radio peripheral (USRP N210). This paper aims at designing this full-constellation GNSS receiver by utilizing a cost effective, readily available, and flexible front-end. This front-end should be wide enough to capture the frequency from 1555 MHz to 1607 MHz, more than 50MHz. Compass E2, Galileo E1, GPS L1 and GLONASS G1 is taken into account. After comparing different GNSS front-end options, universal software radio peripheral (USRP N210) platform is selected as the appropriate RF front-end. However, two main shortcomings appear in USRP N210. First, its unstable onboard TCXO oscillator is not sufficient for GNSS applications. We, finally, use a high-quality external OCXO oscillator as the USRP N210 reference clock when conducting the GNSS applications. Second, it has limited sample capture bandwidth 25MHz that is not wide enough for recording 50MHz full-constellation GNSS signals. Therefore, we reconfigure USRP N210 platform and develop our custom wide-band firmware. An experimental system was set up to record wide-band multi-constellation GNSS data. Final results achieved wide-band full-constellation GNSS satellites signals acquisition and tracking; concluding with the GPS and GLONASS position solutions.
The Association Between Self-Reported Anxiety Symptoms and Suicidality (2009)

This cross-sectional study assessed the association between self-reported anxiety symptoms and self-reported suicidality among a mixed diagnostic sample of psychiatric outpatients. Data were obtained from chart review of 2,778 outpatients who completed a routine diagnostic clinical interview and a standardized self-report of psychiatric symptoms on admission. Bivariate analyses indicated that those with >or= moderate anxiety symptoms were over three times as likely to report >or= moderate difficulty with suicidality. Self-reported anxiety symptoms were associated with a 2-fold increased likelihood of reporting suicidality after controlling for confounding (demographics, depressive symptoms, and diagnoses). These data are consistent with a growing literature demonstrating an association between anxiety symptoms and suicidality, and suggest that this association is not accounted for by coexisting mood symptoms or diagnoses. A single item, self-report may be a useful screening tool for symptoms that are pertinent to assessment of suicide risk.
Material microenvironmental properties couple to induce distinct transcriptional programs in mammalian stem cells (2018)

Variations in a multitude of material microenvironmental properties have been observed across tissues in vivo, and these have profound effects on cell phenotype. Phenomenological experiments have suggested that certain of these features of the physical microenvironment, such as stiffness, could sensitize cells to other features; meanwhile, mechanistic studies have detailed a number of biophysical mechanisms for this sensing. However, the broad molecular consequences of these potentially complex and nonlinear interactions bridging from biophysical sensing to phenotype have not been systematically characterized, limiting the overall understanding and rational deployment of these biophysical cues. Here, we explore these interactions by employing a 3D cell culture system that allows for the independent control of culture substrate stiffness, stress relaxation, and adhesion ligand density to systematically explore the transcriptional programs affected by distinct combinations of biophysical parameters using RNA-seq. In mouse mesenchymal stem cells and human cortical neuron progenitors, we find dramatic coupling among these substrate properties, and that the relative contribution of each property to changes in gene expression varies with cell type. Motivated by the bioinformatic analysis, the stiffness of hydrogels encapsulating mouse mesenchymal stem cells was found to regulate the secretion of a wide range of cytokines, and to accordingly influence hematopoietic stem cell differentiation in a Transwell coculture model. These results give insights into how biophysical features are integrated by cells across distinct tissues and offer strategies to synthetic biologists and bioengineers for designing responses to a cell's biophysical environment.
Morin enhances auranofin anticancer activity by up‐regulation of DR4 and DR5 and modulation of Bcl‐2 through reactive oxygen species generation in Hep3B human hepatocellular carcinoma cells (2019)

Evidence suggests that auranofin (AF) exhibits anticancer activity by inhibiting thioredoxin reductase (TrxR). Here, in this study, we have investigated the synergistic effects of AF and morin and their mechanism for the anticancer effects focusing on apoptosis in Hep3B human hepatocellular carcinoma cells. We assessed the anticancer activities by annexin V/PI double staining, caspase, and TrxR activity assay. Morin enhances the inhibitory effects on TrxR activity of AF as well as reducing cell viability. Annexin V/PI double staining revealed that morin/AF cotreatment induced apoptotic cell death. Morin enhances AF-induced mitochondrial membrane potential (ΔΨm) loss and cytochrome c release. Further, morin/AF cotreatment upregulated death receptor DR4/DR5, modulated Bcl-2 family members (upregulation of Bax and downregulation of Bcl-2), and activated caspase-3, -8, and -9. Morin also enhances AF-induced reactive oxygen species (ROS) generation. The anticancer effects results from caspase-dependent apoptosis, which was triggered via extrinsic pathway by upregulating TRAIL receptors (DR4/DR5) and enhanced via intrinsic pathway by modulating Bcl-2 and inhibitor of apoptosis protein family members. These are related to ROS generation. In conclusion, this study provides evidence that morin can enhance the anticancer activity of AF in Hep3B human hepatocellular carcinoma cells, indicating that its combination could be an alternative treatment strategy for the hepatocellular carcinoma.
Polymer photocatalysts with plasma-enhanced activity (2020)

Plasma treatment was used as a new method to enhance the photocatalytic performance of a hydrophobic polymer photocatalyst.
Implantable Cardioverter-Defibrillators in Heart Failure Patients with Reduced Ejection Fraction and Diabetes (2018)

Among patients with HF and diabetes, primary prevention ICD in combination with medical therapy vs. medical therapy alone was not significantly associated with a reduced risk of all-cause death. Further studies are needed to evaluate the effectiveness of ICDs among patients with diabetes.
High-Resolution NMR Studies at 270 MHz of Alternating Poly(γbenzyl D-L-glutamate) in Double-Stranded Helical Conformations (1977)

Current self-report medication adherence measures often provide heavily skewed results with limited variance, suggesting that most participants are highly adherent. This contrasts with findings from objective adherence measures. We argue that one of the main limitations of these self-report measures is the limited range covered by the behaviors assessed. That is, the items do not match the adherence behaviors that people perform, resulting in a ceiling effect. In this paper, we present a new self-reported medication adherence scale based on the Rasch model approach (the ProMAS), which covers a wide range of adherence behaviors. The ProMAS was tested with 370 elderly receiving medication for chronic conditions. The results indicated that the ProMAS provided adherence scores with sufficient fit to the Rasch model. Furthermore, the ProMAS covered a wider range of adherence behaviors compared to the widely used Medication Adherence Report Scale (MARS) instrument, resulting in more variance and less skewness in adherence scores. We conclude that the ProMAS is more capable of discriminating between people with different adherence rates than the MARS.
Ultrafast transport dynamics of p-i-n photodetectors under high-power illumination (1998)

We studied ultrafast transport dynamics of highspeed p-i-n photodetectors under high illumination using an electrooptic sampling technique. Under high illumination, saturation nonlinearities were found to be dominated by a space-charge-screening effect. A transient forward external current was also observed, which was attributed to an underdamped plasma oscillation. The external bias required to compensate these nonlinear effects increased with increased illumination.
Design and Measurement Techniques for an 80 Gb/s 1-Tap Decision Feedback Equalizer (2013)

A millimeter wave frequency mixed-signal design of a 1-tap half-rate look-ahead decision feedback equalizer for 80 Gb/s short-reach optical communication systems is presented. On-wafer tests are developed to determine the maximum operating bit rate of the equalizer. Results are also presented for intersymbol interference mitigation at 80 Gb/s for a 20 GHz bandwidth-limited channel. Further improvements on the architecture of the 80 Gb/s equalizer are discussed and used in the design and on-wafer measurement of a 110 Gb/s equalizer. The equalizers are designed in a 0.13 μm SiGe:C BiCMOS technology. The 80 and 110 Gb/s versions dissipate 4 and 5.75 W, respectively and occupy 2 and 2.56 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , respectively.
Seven‐tesla phase imaging of acute multiple sclerosis lesions: A new window into the inflammatory process (2013)

Ultrahigh-field MRI and, especially, phase contrast, are highly sensitive to tissue changes in acute MS lesions, which differ from the patterns seen in chronic lesions. In acute lesions, the hypointense phase rim reflects the expanding inflammatory edge and may directly correspond to inflammatory byproducts and sequelae of blood-brain barrier opening.
The α1 Chain of Chick Type VI Collagen Is a Hybrid Molecule Made of One Short Collagen and Three von Willebrand Factor Type A‐like Domainsa (1990)

Type VI collagen is a major component of the interstitial matrices.' It consists of molecules composed of three different chains with apparent M, in sodium dodecyl sulfatepolyacrylamidegelsofabout 150,000(al), 140,000(a2), and260,000(~3): We have used the pEXl plasmid expression vector to isolate and characterize cDNA clones encoding the a1 chain.