gebhart/patrepeval huggingface dataset:
Photonically Sintered PZT Energy Harvester (2015)

This paper reports an Aerosol-Jet printed micro scale Lead Zirconate Titanate (PZT) energy harvester directly sintered on a low melting point substrate in less than 1 msec using photonic sintering technology. To improve the output signal, d33 piezoelectric mode was employed by patterning silver electrodes as an interdigitated structure on top of a PZT film. The size of the device is 15.5 mm × 13.5 mm × 0.2 mm. Up to 2.4 V was measured at 145 MPa tensile bending stress level in the device after poling at 180 °C for 2 hours with an electric field of 30 kV/cm. Using an oscillating stress (∼2.5 Hz) of approximately 145 MPa, the power as a function of load was determined by connecting the device with various series resistive loads. A maximal power of 0.1 μW was generated when driving into a 10 MΩ load. A PZT energy harvester, for the first time, is demonstrated which has been directly printed and sintered on a low melting temperature flexible substrate without a film transfer processes. This not only dramatically simplifies the fabrication process, but expands the possible substrate materials for PZT energy harvesters.
Comments on electron relaxation time measurements from transient reflectances of metals (1991)

The measurement of nonequilibrium electron and lattice temperatures via transient reflectance (TR) technique is considered for metals. It is shown that TR is a function of the electronic relaxation time and the optical properties of the material. It is argued, that the photon energy of the transient reflectivity measurement should be chosen in the free electron domain and then the electron relaxation time may be determined quantitatively with the help of the temperature coefficients of the real and imaginary parts of the dielectric constant.
A Synthetic Probiotic Engineered for Colorectal Cancer Therapy Modulates Gut Microbiota (2020)

Abstract Background: Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used as anticancer agents, but efforts to utilize attenuated pathogenic bacteria suffer from the risk of toxicity or infection. Lactic acid bacteria are safe to eat and often confer health benefits, making them ideal candidates for live vehicles engineered to deliver anticancer drugs. Results: In this study, we developed an effective bacterial drug delivery system for colorectal cancer (CRC) therapy using the lactic acid bacterium Pediococcus pentosaceus . It is equipped with dual gene cassettes driven by a strong inducible promoter that encode the therapeutic protein P8 fused to a secretion signal peptide and a complementation system. In an inducible CRC cell-derived xenograft mouse model, our synthetic probiotic significantly reduced tumor volume and inhibited tumor growth relative to the control. Mice with colitis-associated CRC induced by azoxymethane and dextran sodium sulfate exhibited polyp regression and recovered taxonomic diversity when the engineered bacterium was orally administered. Further, the synthetic probiotic modulated gut microbiota and alleviated the chemically induced dysbiosis. Correlation analysis demonstrated that specific bacterial taxa potentially associated with eubiosis or dysbiosis, such as Akkermansia or Turicibacter , have positive or negative relationships with other microbial members. Conclusions: Taken together, our work illustrates that an effective and stable synthetic probiotic composed of P. pentosaceus and the P8 therapeutic protein can reduce CRC and contribute to rebiosis, and the validity and feasibility of cell-based designer biopharmaceuticals for both treating CRC and ameliorating impaired microbiota.
Repeat syphilis has a different immune response compared with initial syphilis: an analysis of biomarker kinetics in two cohorts (2017)

Repeat syphilis has a different clinical presentation and immunological response to initial infection.
The role of unanchored polyubiquitin chains and the TRIM E3-ubiquitin ligase family of proteins in the innate immune response to influenza virus infection (INM3P.402) (2015)

Abstract Intracellular innate immune responses are essential to protect host cells against pathogens. Upon infection, pattern recognition receptors detect incoming microbes and trigger downstream signaling pathways leading to production of antiviral type-I interferons (IFNs).These signaling pathways are regulated by different posttranslational modifications including the ubiquitin (Ub) system. Proteins covalently attached to K48-linked polyUb are targeted for degradation by the proteasome, whereas protein modification with K63-linked polyUb may have non-proteolytic activating functions. Unanchored Ub chains that are not covalently attached to any protein are also important for kinase activation. Tripartite motif (TRIM) proteins, which function as E3-ubiquitin ligases, have been implicated in antiviral activity. We found that TRIM6 is important in the synthesis of unanchored K48-linked polyUb chains, which activate the IKKε kinase for STAT1 phosphorylation and induction of an antiviral response. These polyUb chains and IKKε interact in vivo in an IFN-I signaling dependent manner upon virus infection in mice. To better understand the physiological role of unanchored polyUb during virus infection, we developed a system to isolate ubiquitin-interacting proteins from the lungs of influenza-infected mice. Using a proteomics approach we identified new cellular factors that interact with unanchored polyUb chains in vivo and may be involved in the innate immune antiviral response.
The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly (1998)

Escherichia coli RNase E, an essential single-stranded specific endoribonuclease, is required for both ribosomal RNA processing and the rapid degradation of mRNA. The availability of the complete sequences of a number of bacterial genomes prompted us to assess the evolutionarily conservation of bacterial RNase E. We show here that the sequence of the N-terminal endoribonucleolytic domain of RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria. Furthermore, we demonstrate that the Synechocystis sp. homologue binds RNase E substrates and cleaves them at the same position as the E. coli enzyme. Taken together these results suggest that RNase E-mediated mechanisms of RNA decay are not confined to E. coli and its close relatives. We also show that the C-terminal half of E. coli RNase E is both sufficient and necessary for its physical interaction with the 3'-5' exoribonuclease polynucleotide phosphorylase, the RhlB helicase, and the glycolytic enzyme enolase, which are components of a "degradosome" complex. Interestingly, however, the sequence of the C-terminal half of E. coli RNase E is not highly conserved evolutionarily, suggesting diversity of RNase E interactions with other RNA decay components in different organisms. This notion is supported by our finding that the Synechocystis sp. RNase E homologue does not function as a platform for assembly of E. coli degradosome components.
A Nanometer-Sized High-Spin Polyradical:  Poly(4-phenoxyl-1,2-phenylenevinylene) Planarily Extended in a Non-Kekulé Fashion and Its Magnetic Force Microscopic Images (2001)

A pi-conjugated, but non-Kekulé- and nondisjoint-type poly(1,2-phenylenevinylene) network bearing 4-substituted di-tert-butylphenoxyls was synthesized through a one-pot polycondensation of the star-shaped subpart and the subsequent oxidation, which was persistent even at room temperature. The polyphenoxyl radical with a spin concentration of 0.4 displayed an average S of 10/2. The polyradical with the molecular weight of 3.2 x 10(4) gave a disklike image of ca. 35 x 0.6 nm with both an atomic and a magnetic force microscopy: the molecular image was examined as a nanoscale and single-molecular-based magnetic dot.
Balancing burden and benefit (2013)

Mobile devices are increasingly powerful and flexible tools for computing and communication. When ICTD workers are given a mobile phone "for work", what else do they do? And to what extent can or should an employer shape that use? This note presents research in progress, focused on rules that development projects impose to govern use of mobile devices. This work maps these rules against actual instrumental (work-related, non-prescribed) and non-instrumental (personal) device use, and enforcement of these rules, in eight projects using a popular mobile-based job aid, CommCare. We present early insights from qualitative analysis of two such deployments in India identifying a range of often conflicting policy choices that affect device use for project mission and/or professional and personal empowerment. We explore tradeoffs for morale, work quality, mission, and device integrity. We identify user remote availability, soft intimidation, and validation as mechanisms to shift authority and credibility of information sources. The implications of our findings are increasingly important as governments and NGOs arm frontline workers with mobile devices as tools to improve service delivery.
Role of Hydrogen in Promoting the Splitting of Silicon Film during High Temperature Annealing of Porous Silicon (2011)

An attempt is made to explain the specific role of hydrogen in promoting thin film splitting from crystalline silicon wafers with buried voids transformed from pores or trenches during annealing at high temperature. It is suggested that the main effect of hydrogen is to speed up the breaking of lateral silicon straps separating the voids, causing their coalescence. Such an effect is related, through several mechanisms, to the chemistry of high temperature hydrogen diffusion in silicon. Straps between voids collapse by the pressure exerted by hydrogen molecules formed inside the voids, a process similar to exfoliation of hydrogen induced defects (HID) in single crystalline silicon supersaturated with hydrogen and annealed at high temperature. Also annealing in hydrogen reduces the cohesive strength of the void surface by forming low energy SiH complexes. Finally, chemical etching of the straps is envisaged with the presence of fluorine radicals and all species required for chemical etching of silicon.
PRINT: A Protein Bioconjugation Method with Exquisite N-terminal Specificity (2015)

Chemical conjugation is commonly used to enhance the pharmacokinetics, biodistribution, and potency of protein therapeutics, but often leads to non-specific modification or loss of bioactivity. Here, we present a simple, versatile and widely applicable method that allows exquisite N-terminal specific modification of proteins. Combining reversible side-chain blocking and protease mediated cleavage of a commonly used HIS tag appended to a protein, we generate with high yield and purity exquisitely site specific and selective bio-conjugates of TNF-α by using amine reactive NHS ester chemistry. We confirm the N terminal selectivity and specificity using mass spectral analyses and show near complete retention of the biological activity of our model protein both in vitro and in vivo murine models. We believe that this methodology would be applicable to a variety of potentially therapeutic proteins and the specificity afforded by this technique would allow for rapid generation of novel biologics.
Microwave-Assisted Synthesis, Characterization and Modeling of CPO-27-Mg Metal-Organic Framework for Drug Delivery (2021)

The coordination polymer CPO-27-Mg was rapidly synthesized under microwave irradiation. This material exhibits a sufficiently high drug loading towards aspirin (~8% wt.) and paracetamol (~14% wt.). The binding of these two molecules with the inner surface of the metal-organic framework was studied employing the Gaussian and Plane Wave approach of the Density Functional Theory. The structure of CPO-27-Mg persists after the adsorption of aspirin or paracetamol and their desorption energies, being quite high, decrease under solvent conditions.
Non-Abelian braiding of graph vertices in a superconducting processor (2023)

Indistinguishability of particles is a fundamental principle of quantum mechanics<sup>1</sup>. For all elementary and quasiparticles observed to date-including fermions, bosons and Abelian anyons-this principle guarantees that the braiding of identical particles leaves the system unchanged<sup>2,3</sup>. However, in two spatial dimensions, an intriguing possibility exists: braiding of non-Abelian anyons causes rotations in a space of topologically degenerate wavefunctions<sup>4-8</sup>. Hence, it can change the observables of the system without violating the principle of indistinguishability. Despite the well-developed mathematical description of non-Abelian anyons and numerous theoretical proposals<sup>9-22</sup>, the experimental observation of their exchange statistics has remained elusive for decades. Controllable many-body quantum states generated on quantum processors offer another path for exploring these fundamental phenomena. Whereas efforts on conventional solid-state platforms typically involve Hamiltonian dynamics of quasiparticles, superconducting quantum processors allow for directly manipulating the many-body wavefunction by means of unitary gates. Building on predictions that stabilizer codes can host projective non-Abelian Ising anyons<sup>9,10</sup>, we implement a generalized stabilizer code and unitary protocol<sup>23</sup> to create and braid them. This allows us to experimentally verify the fusion rules of the anyons and braid them to realize their statistics. We then study the prospect of using the anyons for quantum computation and use braiding to create an entangled state of anyons encoding three logical qubits. Our work provides new insights about non-Abelian braiding and, through the future inclusion of error correction to achieve topological protection, could open a path towards fault-tolerant quantum computing.
Reverse transcriptase and substrate dependence of the RNA hypermutagenesis reaction (1995)

G-->A hypermutation is a remarkable phenomenon resulting from retroviral reverse transcription in the presence of highly biased dNTP concentrations. Of the three reverse transcriptases (RTases) available, those of human immunodeficiency virus type 1 (HIV-1), avian myeloblastosis virus (AMV) and Moloney murine leukemia virus (MoMLV), the HIV-1 enzyme showed the greatest sensitivity to biased [dCTP]/[dTTP] ratios. The HIV-1 RTase was able to discriminate between dUTP, dITP and the four DNA precursors and was insensitive to pH. There was little preference for nucleotide contexts. A few exceptionally modified sequences were found presumably resulting from G-->A hypermutation and multiple strand transfer. This particular predilection of the HIV-1 and, by extrapolation, the lentiviral RTases towards G-->A hypermutation suggests that the phenomenon may have contributed to the remarkably elevated A content of these retroviral genomes.
Rotational Unit of Memory (2017)

The concepts of unitary evolution matrices and associative memory have boosted the field of Recurrent Neural Networks (RNN) to state-of-the-art performance in a variety of sequential tasks. However, RNN still have a limited capacity to manipulate long-term memory. To bypass this weakness the most successful applications of RNN use external techniques such as attention mechanisms. In this paper we propose a novel RNN model that unifies the state-of-the-art approaches: Rotational Unit of Memory (RUM). The core of RUM is its rotational operation, which is, naturally, a unitary matrix, providing architectures with the power to learn long-term dependencies by overcoming the vanishing and exploding gradients problem. Moreover, the rotational unit also serves as associative memory. We evaluate our model on synthetic memorization, question answering and language modeling tasks. RUM learns the Copying Memory task completely and improves the state-of-the-art result in the Recall task. RUM's performance in the bAbI Question Answering task is comparable to that of models with attention mechanism. We also improve the state-of-the-art result to 1.189 bits-per-character (BPC) loss in the Character Level Penn Treebank (PTB) task, which is to signify the applications of RUM to real-world sequential data. The universality of our construction, at the core of RNN, establishes RUM as a promising approach to language modeling, speech recognition and machine translation.
Software-based erasure codes for scalable distributed storage (2003)

This paper presents a new class of erasure codes, Lincoln Erasure codes (LEC), applicable to large-scale distributed storage that includes thousands of disks attached to multiple networks. A high-performance software implementation that demonstrates the capability to meet these anticipated requirements is described. A framework for evaluation of candidate codes was developed to support in-depth analysis. When compared with erasure codes based on the work of Reed-Solomon and Luby (2000), tests indicate LEC has a higher throughput for encoding and decoding and lower probability of failure across a range of test conditions. Strategies are described for integration with storage-related hardware and software.
Emergency Physicians Are Able to Detect Right Ventricular Dilation With Good Agreement Compared to Cardiology (2017)

Objective
Focused cardiac ultrasound (FOCUS) is a useful tool in evaluating patients presenting to the emergency department (ED) with acute dyspnea. Prior work has shown that right ventricular (RV) dilation is associated with repeat hospitalizations and shorter life expectancy. Traditionally, RV assessment has been evaluated by cardiologist-interpreted comprehensive echocardiography. The primary goal of this study was to determine the interrater reliability between emergency physicians (EPs) and a cardiologist for determining RV dilation on FOCUS performed on ED patients with acute dyspnea.

Methods
Prospective, observational study at two urban academic EDs; patients were enrolled if they had acute dyspnea and a computed tomographic pulmonary angiogram without acute disease. All patients had an EP-performed FOCUS to assess for RV dilation. RV dilation was defined as an RV to left ventricular ratio greater than 1. FOCUS interpretations were compared to a blinded cardiologist FOCUS interpretation using agreement and kappa statistics.

Results
Of 84 FOCUS examinations performed on 83 patients, 17% had RV dilation. Agreement and kappa, for EP-performed FOCUS for RV dilation were 89% (95% confidence interval [CI] 80-95%) and 0.68 (95% CI 0.48-0.88), respectively.

Conclusions
EP sonographers are able to detect RV dilation with good agreement when compared to cardiology. These results support the wider use of EP-performed FOCUS to evaluate for RV dilation in dyspneic ED patients.

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Discovery of a Pyrimidothiazolodiazepinone as a Potent and Selective Focal Adhesion Kinase (FAK) Inhibitor (2020)

Focal adhesion kinase (FAK) is a tyrosine kinase with prominent roles in protein scaffolding, migration, angiogenesis, and anchorage-independent cell survival and is an attractive target for the development of cancer therapeutics. However, current FAK inhibitors display dual kinase inhibition and/or significant activity on several kinases. Although multitargeted activity is at times therapeutically advantageous, such behavior can also lead to toxicity and confound chemical-biology studies. We report a novel series of small molecules based on a tricyclic pyrimidothiazolodiazepinone core that displays both high potency and selectivity for FAK. Structure-activity relationship (SAR) studies explored modifications to the thiazole, diazepinone, and aniline "tail," which identified lead compound BJG-03-025. BJG-03-025 displays potent biochemical FAK inhibition (IC<sub>50</sub> = 20 nM), excellent kinome selectivity, activity in 3D-culture breast and gastric cancer models, and favorable pharmacokinetic properties in mice. BJG-03-025 is a valuable chemical probe for evaluation of FAK-dependent biology.
PCEP Extension for Distribution of Link-State and TE information for Optical Networks (2000)

In order to compute and provide optimal paths, Path Computation
Elements (PCEs) require an accurate and timely Traffic Engineering
Database (TED). Traditionally this Link State and TE information has
been obtained from a link state routing protocol (supporting traffic
engineering extensions). This document extends the Path Communication
Element Communication Protocol (PCEP)_ with Link-State and TE
information for optical networks.
Effects of dietary vitamin E and fat supplementation on pork quality1 (2006)

The effects of dietary vitamin E (VE, alpha-tocopherol acetate) and fat supplementation on growth and carcass quality characteristics, oxidative stability of fresh and cooked pork patty in storage, fatty acid profiles of muscle and adipose tissue, and VE concentrations of plasma, muscle, and adipose tissue were studied. Six hundred pigs were allocated to 1 of 6 diets and fed for 63 d in a 3 x 2 factorial design. The dietary treatments included 3 fat levels (normal corn, high oil corn, high oil corn plus added beef tallow) and 2 levels of VE supplementation (40 IU/kg, normal VE supplementation; and 200 IU/kg, high VE supplementation). At 113 kg of BW, 54 pigs were slaughtered as a subsample to evaluate dietary effects on pork quality. Growth performance and meat quality characteristics did not differ (P > 0.05) among treatment groups. The high level of VE supplementation had a beneficial effect on the oxidative stability of pork as indicated by thiobarbituric acid reactive substance (TBARS) values. Lean tissue had lower (P < 0.05) TBARS in the group fed the high VE than in those fed the normal VE level. The TBARS values differed among storage periods (0 to 6 d) and also between fresh and cooked ground ham. Fat type did not significantly affect total saturated and unsaturated fatty acids proportions in the neutral and polar fraction of muscle. Adding VE acetate led to greater (P < 0.05) monounsaturated and total unsaturated fatty acid proportions in neutral lipids of muscle and adipose tissues. Increasing dietary levels of VE acetate increased the concentration of VE in plasma and muscle. These results indicate that dietary VE acetate supplementation increased (P < 0.05) lipid stability and the VE concentration of muscle.
One-Pot Synthesis of Azaindoles and Indoles (2006)

An efficient, Pd-catalyzed route to indoles and azaindoles via intermediate, non-isolable Sonogashira coupling products, is described. Starting with the readily available and inexpensive 2-chloroaniline and 3-amino-2-chloropyridine derivatives, obtained by reductive alkylation of the corresponding amino compounds with aldehydes and ketones, a palladium-catalyzed, copper-free Sonogashira coupling with X-Phos or dppb as ligands, followed by an in situ base-mediated indolization, was developed. The scope of this method is shown by a synthesis of 10 azaindoles with good to excellent yields (83-91%) and 4 indoles in moderate to good yields (50-84%) with relatively broad R2 and less general R1 and R3 substitution patterns.