gebhart/patrepeval huggingface dataset:
A New Fault-Tolerant Routing Methodology for KNS Topologies (2016)

Exascale computing systems are being built with thousands of nodes. A key component of these systems is the interconnection network. The high number of components significantly increases the probability of failure. If failures occur in the interconnection network, they may isolate a large fraction of the machine. For this reason, an efficient fault-tolerant mechanism is needed to keep the system interconnected, even in the presence of faults. A recently proposed topology for these large systems is the hybrid KNS family that provides supreme performance and connectivity at a reduced hardware cost. This paper present a fault-tolerant routing methodology for the KNS topology that degrades performance gracefully in the presence of faults and tolerates a reasonably large number of faults without disabling any healthy node. In order to tolerate network failures, the methodology uses a simple mechanism: for some source-destination pairs, only if necessary, packets are forwarded to the destination node through a set of intermediate nodes (without being ejected from the network) which allow avoiding faults. The evaluation results shows that the methodology tolerates a large number of faults. Furthermore, the methodology offers a gracious performance degradation. For instance, performance degrades only 1% for a 2D-network with 1024 nodes and 1% faulty links.
A Glucocorticoid Receptor Gene Haplotype (TthIII1/ER22/23EK/9β) Is Associated with a More Aggressive Disease Course in Multiple Sclerosis (2009)

MS patients carrying the haplotype 6 (TthIIII, ER22/23EK, and 9beta) have a more aggressive disease course. This is probably due to the presence of the polymorphism ER22/23EK, which causes a decreased GC sensitivity.
New purine derivatives as P2X3 receptor antagonists (2012)

P2X3 receptors (P2X3Rs) play an important role in neuropathic and chronic pain pathways; hence, novel P2X3R antagonists are potential agents for the treatment of chronic pain conditions and migraine. Based on molecular modeling studies, a new series of 2,6-diaminopurine derivatives bearing a substituted benzyl chain in 9-position and lipophilic substituents in N6-position were synthesized. The new derivatives were evaluated on rat P2X3Rs by using patch clamp recording from HEK-transfected cells, and some selected ones were also tested at human and at native P2X3Rs expressed by trigeminal ganglion (TG) sensory neurons in culture. Furthermore, since P2X3Rs expressing sensory neurons such as TG neurons are known to express also 5-HT and GABA receptors, this property was used to evaluate the selectivity of the new molecules. Biological results showed that the new compounds behave as antagonists of P2X3Rs; one of themappears to be potent on both recombinant and native P2X3Rs and, besides that, to substantially inhibit the 5-HT3 receptor subtype. Since studies with 5-HT3 receptor antagonists and knockout mice revealed that these receptors are positively involved in nociception and pain transduction, the novel antagonist might produce an analgesic effect due to the block of not only P2X3 but also 5-HT3 receptors of sensory neurons.
Tamoxifen induces stem-like phenotypes and multidrug resistance by altering epigenetic regulators in ERα+ breast cancer cells (2020)

In the present study, we conclude that the treatment with tamoxifen induces multiple epigenetic alterations that lead to the development of MDR and stem-like phenotypes in breast cancers. Therefore, our study provides better insights to develop novel treatment regime to control the progression of breast cancer.
Improvement of SiO<sub>2</sub>/4H-SiC(0001) Interface Properties by H<sub>2</sub> and Ar Mixture Gas Treatment Prior to SiO<sub>2</sub> Deposition (2018)

We investigated the impact of high-temperature H 2 /Ar mixture gas treatment of 4H-SiC(0001) surfaces before SiO 2 deposition on the electrical properties of SiO 2 /SiC interfaces. Physical characterizations revealed that the SiC surface treated by the H 2 /Ar mixture gas exhibited a (√3×√3) R 30° structure composed of Si-O bonds, indicating that a well-ordered and stable silicate adlayer was formed by the treatment to passivate SiC(0001) surface. Electrical defects at the CVD-grown SiO 2 /SiC interface was significantly reduced by the treatment. Consequently, a peak electron mobility in SiC-MOSFETs with the deposited gate oxides was enhanced to 24.9 cm 2 /Vs.
Cyclopropylacetylene (2003)

Abstract Cyclopropylacetylene solvent: 250 mL of cyclohexane product: cyclopropylacetylene
The History of Writing Reflects the Effects of Education on Discourse Structure: Implications for Literacy, Orality, Psychosis and the Axial Age (2020)

The educational pathways of oral and literate traditions are structurally divergent, with a decreasing range of recurrence in the former, and an increasing range of recurrence in the latter. Education is seemingly the driving force underlying discourse maturation.
The promise of graphene-based transistors for democratizing multiomics studies (2021)

As biological research has synthesized genomics, proteomics, metabolomics, and transcriptomics into systems biology, a new multiomics approach to biological research has emerged. Today, multiomics studies are challenging and expensive. An experimental platform that could unify the multiple omics approaches to measurement could increase access to multiomics data by enabling more individual labs to successfully attempt multiomics studies. Field effect biosensing based on graphene transistors have gained significant attention as a potential unifying technology for such multiomics studies. This review article highlights the outstanding performance characteristics that makes graphene field effect transistor an attractive sensing platform for a wide variety of analytes important to system biology. In addition to many studies demonstrating the biosensing capabilities of graphene field effect transistors, they are uniquely suited to address the challenges of multiomics studies by providing an integrative multiplex platform for large scale manufacturing using the well-established processes of semiconductor industry. Furthermore, the resulting digital data is readily analyzable by machine learning to derive actionable biological insight to address the challenge of data compatibility for multiomics studies. A critical stage of systems biology will be democratizing multiomics study, and the graphene field effect transistor is uniquely positioned to serve as an accessible multiomics platform.
Cu Sub-Nanoparticles on Cu/CeO2 as an Effective Catalyst for Methanol Synthesis from Organic Carbonate by Hydrogenation (2015)

Cu/CeO2 works as an effective heterogeneous catalyst for hydrogenation of dimethyl carbonate to methanol at 433 K and even at low H2 pressure of 2.5 MPa, and it provided 94% and 98% methanol yield based on the carbonyl and total produced methanol, respectively. This is the first report of high yield synthesis of methanol from DMC by hydrogenation with H2 over heterogeneous catalysts. Characterization of the Cu/CeO2 catalyst demonstrated that reduction of Cu/CeO2 produced Cu metal with <1.0 nm (subnanoparticles). Cu metal subnanoparticles are easily formed by the interaction with the CeO2 surface, which is responsible for the high catalytic performance.
Molecular and cellular reorganization of neural circuits in the human lineage (2017)

To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. Integration with human single-cell transcriptomic data revealed global, regional, and cell-type-specific species expression differences in genes representing distinct functional categories. We validated and further characterized the human specificity of genes enriched in distinct cell types through histological and functional analyses, including rare subpallial-derived interneurons expressing dopamine biosynthesis genes enriched in the human striatum and absent in the nonhuman African ape neocortex. Our integrated analysis of the generated data revealed diverse molecular and cellular features of the phylogenetic reorganization of the human brain across multiple levels, with relevance for brain function and disease.
In-Situ TEM Studies on Nanoparticle Interactions with Bacterial Cells (2022)

Journal Article In-Situ TEM Studies on Nanoparticle Interactions with Bacterial Cells Get access Abhijit H Phakatkar, Abhijit H Phakatkar Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA Search for other works by this author on: Oxford Academic Google Scholar Pankaj Ghildiyal, Pankaj Ghildiyal Department of Chemical Engineering and Materials Science, University of California Riverside, CA, USA Search for other works by this author on: Oxford Academic Google Scholar Yujie Wang, Yujie Wang Department of Chemical Engineering and Materials Science, University of California Riverside, CA, USA Search for other works by this author on: Oxford Academic Google Scholar Michael R Zachariah, Michael R Zachariah Department of Chemical Engineering and Materials Science, University of California Riverside, CA, USA Search for other works by this author on: Oxford Academic Google Scholar Tolou Shokuhfar, Tolou Shokuhfar Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA Corresponding authors: tolou@uic.edu, rsyassar@uic.edu. Search for other works by this author on: Oxford Academic Google Scholar Reza Shahbazian-Yassar Reza Shahbazian-Yassar Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL, USA Corresponding authors: tolou@uic.edu, rsyassar@uic.edu. Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 1104–1106, https://doi.org/10.1017/S1431927622004676 Published: 01 August 2022
Front Cover: Quantifying and Adjusting Plasmon‐Driven Nano‐Localized Temperature Field around Gold Nanorods for Nucleic Acids Amplification (Small Methods 5/2021) (2021)

In article number 2001254, Srikanth Singamaneni, Feng Xu, and co-workers demonstrated a novel method to quantify the nano-localized temperature field around AuNR by combining experimental measurement and numerical simulation. By precisely controlling the nano-localized temperature field, a plasmon-driven isothermal amplification is successfully performed in the nano-localized environment of AuNRs.
A novel device to preserve intestinal tissue Ex-Vivo by cold peristaltic perfusion (2014)

In the past two decades, much advancement has been made in the area of organ procurement and preservation for the transplant of kidneys, livers, and lungs. However, small intestine preservation remains unchanged. We propose a new preservation system for intestinal grafts that has the potential to increase the viability of the organ during transport. When experimented with porcine intestine, our device resulted in superior tissue quality than tissue in standard of care.
Interaction of immune sera with synthetic peptides corresponding to the structural protein region of hepatitis C virus. (1992)

Comparison of the deduced amino acid sequence from the structural region of the Hutchinson strain of hepatitis C virus (HCV-H) with four other HCV isolates clearly divides the five isolates into two groups based on sequence homology. The first group includes HCV-H, HCV-1, and HC-J1, while the second includes HCV-J1 and HC-J4. Among the five isolates the first 190 residues (putative nucleocapsid) are highly conserved whereas residues 196-513 exhibit significant diversity and include a hypervariable region encompassing residues 386-404. A series of overlapping decapeptides were synthesized by solid-phase pin technology according to sequence from HCV-H (amino acids 1-513), HC-J4 (amino acids 181-513), and regions from the three other isolates which exhibited sequence variation. A modified ELISA was used to measure immunoreactivity of sera from clinical posttransfusion cases and experimentally infected chimpanzees. Comparison of pre- and postinfection samples revealed 16 clusters of immunoreactive peptides within the structural region, none of which was found in the hypervariable region. Only one cluster (amino acids 73-89) was recognized by all human and chimpanzee sera. Clear variation in the immune response was observed between individuals, although no obvious difference in reactivity between acute and chronic cases was observed. Within individual profiles, the reactivity to each peptide cluster and the total number of reactive clusters increased over time.
Surface femtochemistry of CO/O2/Pt(111): The importance of nonthermalized substrate electrons (1998)

We studied the surface femtochemistry of CO/O2/Pt(111) induced with 0.3 ps laser pulses over a wide range of wavelength and fluence. Below 10 μJ/mm2, the yields depend linearly on fluence. Above 10 μJ/mm2, the yields scale nonlinearly in the fluence. From the dependence of the yields on wavelength, we determine that the nonlinear surface femtochemistry is influenced by nonthermal substrate electrons.
Implicit gaze based annotations to support second language learning (2014)

This paper explores if implicit gaze based annotations can support reading comprehension tasks of second language learners. We show how to use eye tracking to add implicit annotations to the text the user reads and we start by annotating physical features (reading speed, re-reading, number of fixation areas) to documents using eye tracking.
A Facile C—C Bond Cleavage in Epoxides and Its Use for the Synthesis of Oxygenated Heterocycles by a Ring Expansion Strategy (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Background data organisation for the low-power implementation in real-time of a digital audio broadcast receiver on a SIMD processor (2003)

In this work we illustrates the strong interaction between the data organisation in background memory and the data format required for sub-word level acceleration. The impact of such interaction is demonstrated on the implementation of a Digital Audio Broadcast Channel Decoder on a TriMedia processor where data format transformations applied on the background memory data enable a substantially better exploitation of the available Single Instruction Multiple Data instructions. As a result, a factor two reduction for both execution time and data memory energy is achieved.
PATIS: Using partial configuration to improve static FPGA design productivity (2010)

Reconfigurable hardware development and debugging tools aspire to provide software-like productivity. A major impediment, however, is the lack of a module linkage capability permitting hardware blocks to be compiled concurrently, limiting the effective use of multi-core and multiprocessor platforms. Although modular and incremental design flows can reuse the layouts of unmodified blocks, non-local changes to the logical hierarchy or physical layout, or addition of debug circuitry, generally force complete re-implementation. We describe the PATIS dynamic floorplanner, targeting development environments in which some circuit speed and area optimization may be sacrificed for improved implementation and debug turnaround. The floorplan consists of partial modules with structured physical interfaces observable through configuration readback rather than synthesized logic analysis circuitry, allowing module ports to be passively probed without disturbing the layout. Although PATIS supports incremental design, complete re-implementation is still rapid because the partial bitstream for each block is generated by independent and concurrent invocations of the standard Xilinx tools running on separate cores or hosts. A continuous background task proactively generates floorplan variants to accelerate global layout changes. The partial reconfiguration design flow is easier to automate in PATIS because run-time module swapping is not required, suggesting that partial reconfiguration may serve a useful role in large-scale static design.
Assessment of performance and implementation characteristics of rapid point of care SARS-CoV-2 antigen testing (2022)

<ns3:p> <ns3:bold>Background</ns3:bold> : The COVID-19 pandemic has resulted in a need for rapid identification of infectious cases. Testing barriers have prohibited adequate screening for SARS-CoV-2, resulting in significant delays in commencement of treatment and outbreak control measures. This study aimed to generate evidence on the performance and implementation characteristics of the BD Veritor™ Plus System rapid antigen test as compared to reverse transcription polymerase chain reaction (RT-PCR) for diagnosis of SARS-CoV-2 in Kenya. </ns3:p> <ns3:p> <ns3:bold>Methods</ns3:bold> : This was a field test performance evaluation in adults undergoing testing for SARS-CoV-2. Recruited participants were classified as SARS-CoV-2-positive based on RT-PCR carried out on nasopharyngeal swabs. Antigen tests were performed with simultaneous RT-PCR on 272 participants, allowing estimation of sensitivity, specificity, positive and negative predictive values for the rapid antigen test. Implementation characteristics were assessed. </ns3:p> <ns3:p> <ns3:bold>Results: </ns3:bold> We enrolled 97 PCR negative symptomatic and 128 PCR negative asymptomatic, and 28 PCR positive symptomatic and 19 PCR positive asymptomatic participants. Compared to RT-PCR, the sensitivity of the rapid antigen test was 94% (95% confidence interval [CI] 86.6 to 100.0) while the specificity was 98% (95% CI 96 to 100). There was no association between sensitivity and symptom status, or between the cycle threshold value and sensitivity of the BD Veritor. The rapid test had a quick turnaround time, required minimal resources, and laboratory personnel conducting testing found it easier to use than RT-PCR. </ns3:p> <ns3:p>The relatively high sensitivity of BD Veritor may be partially attributed to shortages of RT-PCR testing materials, resulting in specimen analysis delays and potential degradation of viral genetic material. Therefore, in resource-constrained settings, rapid antigen tests may perform better than the reference RT-PCR, resulting in prompt institution of isolation and treatment measures. </ns3:p> <ns3:p> <ns3:bold>Conclusion:</ns3:bold> The BD Veritor rapid antigen test’s high sensitivity should be interpreted with consideration to the challenges occasioned by RT-PCR testing in resource-constrained settings. </ns3:p>
Thin epitaxial quartz films with tunable textures on silicon. (2015)

9-13 March 2015
Evidence for intestinal chloride secretion (2010)

Intestinal fluid secretion is pivotal in the creation of an ideal environment for effective enzymatic digestion, nutrient absorption and stool movement. Since fluid cannot be actively secreted into the gut, this process is dependent on an osmotic gradient, which is mainly created by chloride transport by the enterocyte. A pathological dysbalance between fluid secretion and absorption leads to obstruction or potentially fatal diarrhoea. This article reviews the widely accepted model of intestinal chloride secretion with an emphasis on the molecular players involved in this tightly regulated process.
The Effect of Thermal Barrier Coating Roughness Magnitude on Heat Transfer With and Without Flowpath Surface Steps (2003)

An experimental study has been performed to investigate the convective heat transfer coefficients resulting from differing magnitudes of surface roughness for ceramic thermal barrier coatings (TBC) of the type used to protect gas turbine hot section components. A flat plate wind tunnel test is employed with zero freestream pressure gradient, and levels of freestream turbulence from 4.5 to 6.5%. The TBC applied in these tests is an air plasma sprayed, yttriastabalized zirconia-oxide. Average test surface Reynolds numbers are varied from 400,000 to 2,200,000. Average roughness values (RA) for the TBC surfaces are varied by degrees of polishing from 10 μm to 1 μm, resulting in roughness Reynolds numbers of up to 70. Baseline comparison tests use smooth metal surfaces. The changing physical and heat transfer character of the TBC surfaces with polishing is demonstrated. Results show a significant effect of polishing degree on the surface heat transfer coefficients. Such surfaces were also tested with varying magnitudes of forward facing flowpath steps to model the potential interruptions seen at component interfaces. Flowpath steps are shown to produce quite elevated levels of heat transfer for the smooth surfaces, with little or no further additional enhancement due to increased TBC roughness levels.
Preferential Charging of tRNAMetf in Escherichia coli K12 (1978)

The charging of tRNA-Met-f and tRNA-Met-m in vivo and in vitro and initiation of polysomes during methionine limitation were studied in two strains of Escherichia coli K12. In the wild-type strain the distribution of polysomes as well as the kinetic parameters of methionyl-tRNA synthetase indicate preferential acylation of tRNA-Met-f. This preferential charging of tRNAM-et-f does not take place in a mutant strain which is also defective in initiation of polysomes during methionine limitation.
220,000‐r/min, 2‐kW PM motor drive for turbocharger (2007)

Abstract This paper describes an ultrahigh‐speed permanent‐magnet synchronous motor drive, which is embedded in a turbocharger of an internal‐combustion engine. The electrical drive makes it possible to enhance output power of the turbocharger in a motoring mode and to retrieve combustion energy from exhaust gas in a regenerating mode. Computer simulations and experimental tests are conducted to examine various operation characteristics of a prototype. The experimental data demonstrate 220,000‐r/min operation at 2.2‐kW inverter output power, in good agreement with the simulation results and proving the feasibility of the proposed system. © 2007 Wiley Periodicals, Inc. Electr Eng Jpn, 161(3): 31–40, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20408
Highly Sensitive Room Temperature Heterodyne Detection with Stabilized Qc Lasers (2022)

A heterodyne detection system, made with unipolar devices operating @4.5µm, reaches a record noise equivalent power of 200 fW at room temperature. Key elements of this setup are frequency stabilized QC lasers and high-speed detectors.
Nonlinear Observer-Based Control of Load Transitions in Homogeneous Charge Compression Ignition Engines (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper presents a model-based nonlinear feedback controller designed to regulate the crank angle at 50% fuel burned $(\theta_{CA50})$ for a gasoline homogeneous charge compression ignition engine model during load transitions. The regulation of the combustion timing is based on manipulating the charge temperature through internal dilution, which is achieved by controlling the lift of a secondary opening of the exhaust valve, also known as the rebreathing lift. The nonlinear feedback controller developed is based on a positive semidefinite Lyapunov function using a simplified control model which contains only the cycle-to-cycle temperature dynamics. The nonlinear feedback controller depends on measurement of the combustion timing $\theta_{CA50}$ and estimation of the temperature at intake valve closing. Closed-loop simulation of the full-order engine model shows that the nonlinear feedback controller, along with a nonlinear observer, is able to regulate the combustion timing $\theta_{CA50}$ by stabilizing the temperature dynamics during load transitions. The closed-loop system with the observer-based feedback controller is shown to be robust to some classes of model uncertainty and measurement noise through simulation and an estimate of the region of attraction. </para>