gebhart/patrepeval huggingface dataset:
Parallel Computation of the Minimal Elements of a Poset (2010)

Computing the minimal elements of a partially ordered finite set (poset) is a fundamental problem in combinatorics with numerous applications such as polynomial expression optimization, transversal hypergraph generation and redundant component removal, to name a few. We propose a divide-and-conquer algorithm which is not only cache-oblivious but also can be parallelized free of determinacy races. We have implemented it in Cilk++ targeting multicores. For our test problems of sufficiently large input size our code demonstrates a linear speedup on 32 cores.
Indiana Advanced Electric Vehicle Training and Education Consortium (I-AEVtec) (2013)

The Indiana Advanced Electric Vehicle Training and Education Consortium (I-AEVtec) is an educational partnership between six universities and colleges in Indiana focused on developing the education materials needed to support electric vehicle technology. The I-AEVtec has developed and delivered a number of degree and certificate programs that address various aspects of electric vehicle technology, including over 30 new or significantly modified courses to support these programs. These courses were shared on the SmartEnergyHub. The I-AEVtec program also had a significant outreach to the community with particular focus on K12 students. Finally, the evGrandPrix was established which is a university/college student electric go-kart race, where the students get hands-on experience in designing, building and racing electric vehicles. The evGrandPrix now includes student teams from across the US as well as from Europe and it is currently being held on Opening Day weekend for the Indy500 at the Indianapolis Motor Speedway.
43 PRODUCTION OF PORCINE EMBRYOS BY NUCLEAR TRANSFER OF BONE MARROW MESENCHYMAL STEM CELLS (2005)

Recent experimental evidence indicates that adult stem cells are more desirable than somatic cells for nuclear transfer (NT) because of their easy reprogrammability to resemble the genome of the zygote (Zhu et al . 2004 Biol. Reprod. 71, 1890-1897). Mesenchymal stem cells (MSCs) are a heterogeneous population of uncommitted and lineage-committed cells and may have a more flexible potential as donor cells for NT. The aim of this study was to characterize an isolated population of porcine MSCs from bone marrow and to compare the developmental potential of cloned (IVF) embryos with MSCs and porcine fetal fibroblasts (pFFs) by assessing the cleavage and blastocyst rate, total cell numbers, inner cell mass (ICM) ratio and apoptosis. MSCs were obtained from the aspirated bone marrow of 6-8-month-old pigs. Cells were centrifuged, resuspended, and plated in advanced-DMEM (ADMEM) supplemented with 5% fetal bovine serum (FBS). The differentiation potential was demonstrated by culture of MSCs (passage 3) under conditions that were favorable for adipogenic, osteogenic, and chondrogenic development (Pittenger et al . 1999 Science 284, 143-147). Oil red O staining revealed that MSCs produced lipid droplets after incubation in adipogenic media. Following osteoinduction, MSCs exhibited robust alkaline phosphatase activity and cells later transformed into mineralized nodules as demonstrated by von Kossa staining. Histological staining of proteoglycan indicated chondrogenic differentiation. Cumulus-oocyte complexes were matured, fertilized, and cultured by the following method (Abeydeera et al . 2000 Theriogenology 54, 787-797). NT embryos were produced as described by Kim et al . (2005 Mol. Rep. Dev. 70, 308-313). Cleavage rate was significantly ( P &amp;lt; 0.05) higher in IVF embryos than in NT embryos derived from MSCs and pFFs (84.5% ± 4.6 vs. 52.2% ± 5.4 and 50.8% ± 5.2, respectively). However, blastocyst rates in IVF embryos and NT embryos derived from MSCs (20.6% ± 2.5 and 18.5% ± 3.0) did not differ but these rates were significantly ( P &amp;lt; 0.05) higher than that for NT embryos derived from pFFs (9.5% ± 2.1). Total cell numbers and the ratio of ICM to total cells among embryos developed in NT from MSCs (29.4 ± 5.2 and 0.38 ± 0.08, respectively) were significantly ( P &amp;lt; 0.05) higher than for those from pFFs (22.6 ± 5.5 and 0.18 ± 0.12, respectively). Proportions of TUNEL-positive cells in NT embryos from pFFs (12.8 ± 2.5) were significantly ( P &amp;lt; 0.05) higher than in those from MSCs (8.6 ± 1.8) and in IVF embryos (4.6 ± 1.5). The results clearly demonstrate that multipotent bone marrow MSCs can make a suitable alternative to fibroblasts as donor cells and have a greater potential for producing viable cloned porcine embryos. This work was supported by Grant No. R05-2004-000-10702-0 from KOSEF, Republic of Korea.
Postgraduate Research Day in the West of Ireland [Society News] (2014)

Reports on recent trends and industry developments involving the CES society.
Clickable methyltetrazine-indocarbocyanine lipids: Novel toolkit for efficient modifications of cell membranes (2020)

Cell based therapeutics are one of the most promising and exciting breakthroughs in modern medicine. Modification of cell surface with ligands, biologics, drugs and nanoparticles can further enhance the functionality. Indocarbocyanine lipids are used in life sciences for labeling and tracking of cell membranes. Previously we described synthesis of dioctadecyl indocarbocyanine Cy3 analog (aminomethyl-DiI) for efficient and stable painting of mouse erythrocytes with small molecules, enzymes and biologics. Here we synthesized a near infrared aminomethyl dioctadecyl derivative of Cy7 (aminomethyl-DOCy7) and systematically compared it to aminomethyl-DiI as an anchor for modification of human erythrocytes, Jurkat cells and primary T cells with immunoglobulin G.&lt;br/&gt;To enable copper-free click chemistry modification of cell membranes, we conjugated methyltetrazine group to the amino indocyanine lipids via PEG linker (3400 Da). DOCy7-PEG3400-MTz showed over 99% painting efficiency of human erythrocytes at 25 u03bcM. Reaction of trans-cyclooctene (TCO) modified IgG with DOCy7-PEG4-MTz-painted RBCs (2-step painting) resulted in ~80,000 IgG molecules per erythrocyte as detected by immuno dot-blot. The number of IgG/RBC was controlled by concentration of IgG. The painting of RBCs with DiI-PEG3400-MTz resulted in a similar number of IgG/RBC. Painting of T-lymphocyte cell line Jurkat with IgG resulted in ~1x10&lt;sup&gt;6&lt;/sup&gt; IgG/cell with either the 1-step or 2-step method, and the painting efficiency was similar for DOCy7 and DiI constructs. Finally, we used DOCy7 and DiI constructs to demonstrate painting of primary CD3+T cells from healthy donors. The painting resulted in over 7x10&lt;sup&gt;6&lt;/sup&gt; IgG/cell, and the efficiency was similar for both dye constructs. In conclusion, click indocarbocyanine conjugates represent a novel multi-color chemical biology toolkit for efficient surface modification of different cells types and can be used for potential imaging and drug delivery applications involving engineered cells.
A microdischarge-based radiation detector utilizing stacked electrode arrays in a TO-5 package (2011)

This paper describes miniature discharge-based beta/gamma radiation detectors that use arrayed electrode structures to demonstrate a scalable path for increasing detection efficiency. The discharges are also used for wireless signaling. The device uses an in-package assembly scheme of stainless steel electrodes and a glass spacer structure within a TO-5 package. It is manufactured by leveraging commercial micromachining technologies e.g., photochemical etching of the electrodes and ultrasonic machining of the spacer structure. The detector diameter and height are 9 mm and 9.6 mm, respectively, and it weighs 1.01 g. The device performance has been characterized using a P-10 fill-gas near 710 Torr, with a 99 μCi <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">137</sup> Cs source (which is a beta and gamma emitter). The normalized gamma sensitivity is estimated to be 0.023 cps/mR/hr/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> as measured with the biasing arrangement described in the paper. Portable powering modules developed for these detectors are also presented. Rapid wireless transmissions with durations on the order of tens of ns have been measured.
Integrated security services for dynamic coalitions (2004)

Coalitions are collaborative networks of autonomous domains where resource sharing is achieved by the distribution of access permissions to coalition members based on negotiated resource-sharing agreements. The focus of our research is on dynamic coalitions, namely, coalitions where member domains may leave or new domains may join during the life of the coalition. We have developed a set of tools that integrate security services for dynamic coalitions, namely, services for (1) private and shared resource management, (2) identity and attribute certificate management, (3) secure group communication, and (4) joint administration for enforcing joint-action policies on shared critical resources. In this paper we give an overview of the architecture and implementation of our tools.
Endogenous and artificial miRNAs explore a rich variety of conformations: a potential relationship between secondary structure and biological functionality (2020)

Mature microRNAs are short non-coding RNA sequences which upon incorporation into the RISC ribonucleoprotein complex, play a crucial role in regulation of gene expression. However, miRNAs can exist within the cell also as free molecules fulfilling their biological activity. Therefore, it is emerging that in addition to sequence even the structure adopted by mature miRNAs might play an important role to reach the target. Indeed, we analysed by several spectroscopic techniques the secondary structures of two artificial miRNAs selected by computational tool (miR-Synth) as best candidates to silence c-MET and EGFR genes and of two endogenous miRNAs (miR-15a and miR-15b) having the same seed region, but different biological activity. Our results demonstrate that both endogenous and artificial miRNAs can arrange in several 3D-structures which affect their activity and selectivity toward the targets.
Ultra-High Endurance and Low I<inf>OFF</inf> Selector based on AsSeGe Chalcogenides for Wide Memory Window 3D Stackable Crosspoint Memory (2018)

New selector materials with very-low I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</inf> and optimum V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</inf> . based on As-Se-Ge chalcogenides are studied. An optimized composition is proposed, which achieves a good trade-off between thermal stability and cycling endurance and it is successfully integrated with PCM in a 3D stackable pillar structure. SET/RESET operation are demonstrated with ∼2V memory window. Selector is able to deliver 1mA ON current (7.9 MA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) and fast speed (10 ns). More than 1E12 read cycling endurance is achieved in 1S1R <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(\text{OTS}+\text{PCM})$</tex> device due to the excellent endurance of the selector.
Phase‐vanishing methods based on fluorous phase screen: A simple way for efficient execution of organic synthesis (2008)

The phase-vanishing (PV) method is based on spontaneous reaction controlled by diffusion of reagents into fluorous media, such as perfluorohexanes (FC-72) and polyperfluoroethers. Thus, the original PV reaction utilizes a triphasic test tube method composed of a bottom reagent phase, a middle fluorous phase, and a top substrate phase. In such a triphasic system, the fluorous phase acts as a liquid membrane to transport the bottom reagents to the top organic phase containing substrates. In the end, the bottom layer disappears and two phases remain. Since the first demonstration of the PV method by bromination of alkenes with molecular bromine, a number of applications have been developed thus far. These include halogenation of alcohols with SOBr(2) and PBr(3), demethylation of methoxyarenes with BBr(3), cyclopropanation of alkenes by CH(2)I(2)-AlEt(3), and Friedel-Crafts acylation of aromatic compounds with SnCl(4). A fluorous triphasic U-tube method is effective for chlorination of alcohols based on lighter (less dense) reagents such as SOCl(2) and PCl(3). A system using a solution containing reagents as a bottom phase is useful for oxidation with m-CPBA, which may be defined as a new category for the "extractive PV" method. Recent advances include a "quadraphasic" PV method, in which an aqueous "scavenger" phase is added to the original triphasic PV method to remove acidic by-products.
The t-SNAREs syntaxin 1 and SNAP-25 are present on organelles that participate in synaptic vesicle recycling. (1995)

Syntaxin 1 and synaptosome-associated protein of 25 kD (SNAP-25) are neuronal plasmalemma proteins that appear to be essential for exocytosis of synaptic vesicles (SVs). Both proteins form a complex with synaptobrevin, an intrinsic membrane protein of SVs. This binding is thought to be responsible for vesicle docking and apparently precedes membrane fusion. According to the current concept, syntaxin 1 and SNAP-25 are members of larger protein families, collectively designated as target-SNAP receptors (t-SNAREs), whose specific localization to subcellular membranes define where transport vesicles bind and fuse. Here we demonstrate that major pools of syntaxin 1 and SNAP-25 recycle with SVs. Both proteins cofractionate with SVs and clathrin-coated vesicles upon subcellular fractionation. Using recombinant proteins as standards for quantitation, we found that syntaxin 1 and SNAP-25 each comprise approximately 3% of the total protein in highly purified SVs. Thus, both proteins are significant components of SVs although less abundant than synaptobrevin (8.7% of the total protein). Immunoisolation of vesicles using synaptophysin and syntaxin specific antibodies revealed that most SVs contain syntaxin 1. The widespread distribution of both syntaxin 1 and SNAP-25 on SVs was further confirmed by immunogold electron microscopy. Botulinum neurotoxin C1, a toxin that blocks exocytosis by proteolyzing syntaxin 1, preferentially cleaves vesicular syntaxin 1. We conclude that t-SNAREs participate in SV recycling in what may be functionally distinct forms.
Morphology of basal plane dislocations in 4H-SiC homoepitaxial layers grown by chemical vapor deposition (2007)

The morphology of basal plane dislocations (BPDs) in 4H-SiC homoepitaxial layers has been investigated by plan-view transmission x-ray topography and molten KOH etching. Three types of BPDs are distinguished based on their morphologies. These include interfacial dislocations, curved dislocations, and circular loop dislocations around micropipes. Their characteristics are studied in detail and possible sources of their formation during epitaxy are discussed.
Radiation-enhanced expression of E6/E7 transforming oncogenes of human papillomavirus-16 in human cervical carcinoma (1998)

High doses of irradiation can induce a significant and long-lasting up-regulation of E6/E7 oncogenes and MHC Class I restriction elements on HPV positive cervical carcinoma cell lines. These effects by themselves suggest that irradiation could enhance local tumor immunogenicity in patients receiving radiation therapy. However, in contrast to this possible beneficial effect, sublethal tumor irradiation (up-regulating E6/E7 transforming oncoproteins) also could confer a significant growth advantage to radiation-resistant tumor cells. These findings, combined with the previously reported acquisition of a radiation-induced drug resistance, could provide a biologic basis for the poor prognosis of patients with cervical carcinoma recurrence after radiation therapy.
Turning RNA Into DNA: The Discovery That Revolutionized Biology and Biotechnology (2023)

Viruses are unique biological systems. They are parasites that use the cells of other organisms, called hosts, to multiply, often causing disease to the host. One of the most interesting features of viruses is that some of them contain RNA as their genetic material—all other known organisms use DNA. In the beginning of my career I worked on RNA viruses, trying to understand their basic behaviors and processes. When I focused on RNA viruses that are known to cause cancer, I discovered that they can make DNA from their RNA genomes, in a process called reverse transcription. That was a great discovery that changed the prevailing way of thinking and had profound implications in the fields of biology, medicine, and biotechnology. In this article, I will tell you about viruses, walk you through the discovery of reverse transcription, and describe some major implications of our findings in terms of improving or even saving many human lives.
6LB: Scalable and Application-Aware Load Balancing with Segment Routing (2018)

Network load-balancers generally either do not take the application state into account, or do so at the cost of a centralized monitoring system. This paper introduces a load-balancer running exclusively within the IP forwarding plane, ı.e., in an application protocol agnostic fashion - yet which still provides application-awareness and makes real-time, decentralized decisions. To that end, IPv6 Segment Routing is used to direct data packets from a new flow through a chain of candidate servers, until one decides to accept the connection, based solely on its local state. This way, applications themselves naturally decide on how to fairly share incoming connections, while incurring minimal network overhead, and no out-of-band signaling. A consistent hashing algorithm, as well as an in-band stickiness protocol, allow for the proposed solution to be able to be reliably distributed across a large number of instances. Performance evaluation by means of an analytical model and actual tests on different workloads (including a Wikipedia replay as a realistic workload) show significant performance benefits in terms of shorter response times, when compared with the traditional random load-balancer. In addition, this paper introduces and compares kernel bypass high-performance implementations of both 6LB and the state-of-the-art load-balancer, showing that the significant system-level benefits of 6LB are achievable with a negligible data-path CPU overhead.
Z- and Enantioselective Ring-Opening/Cross-Metathesis with Enol Ethers Catalyzed by Stereogenic-at-Ru Carbenes: Reactivity, Selectivity, and Curtin–Hammett Kinetics (2012)

The first instances of Z- and enantioselective Ru-catalyzed olefin metathesis are presented. Ring-opening/cross-metathesis (ROCM) reactions of oxabicyclic alkenes and enol ethers and a phenyl vinyl sulfide are promoted by 0.5-5.0 mol % of enantiomerically pure stereogenic-at-Ru complexes with an aryloxy chelate tethered to the N-heterocyclic carbene. Products are formed efficiently and with exceptional enantioselectivity (>98:2 enantiomer ratio). Surprisingly, the enantioselective ROCM reactions proceed with high Z selectivity (up to 98% Z). Moreover, reactions proceed with the opposite sense of enantioselectivity versus aryl olefins, which afford E isomers exclusively. Preliminary DFT calculations in support of Curtin-Hammett kinetics as well as initial models that account for the stereoselectivity levels and trends are provided.
Isolation of Bioactive Steroids from theStropharia rugosoannulataMushroom and Absolute Configuration of Strophasterol B (2013)

The absolute configuration of strophasterol B (1) isolated from the fruiting bodies of Stropharia rugosoannulata was determined by an X-ray crystallographic analysis. Three compounds (2 to 4) were isolated from the mushroom which suppressed or promoted lettuce growth.
Simulation of Postsynaptic Glutamate Receptors Reveals Critical Features of Glutamatergic Transmission (2011)

Activation of several subtypes of glutamate receptors contributes to changes in postsynaptic calcium concentration at hippocampal synapses, resulting in various types of changes in synaptic strength. Thus, while activation of NMDA receptors has been shown to be critical for long-term potentiation (LTP) and long term depression (LTD) of synaptic transmission, activation of metabotropic glutamate receptors (mGluRs) has been linked to either LTP or LTD. While it is generally admitted that dynamic changes in postsynaptic calcium concentration represent the critical elements to determine the direction and amplitude of the changes in synaptic strength, it has been difficult to quantitatively estimate the relative contribution of the different types of glutamate receptors to these changes under different experimental conditions. Here we present a detailed model of a postsynaptic glutamatergic synapse that incorporates ionotropic and mGluR type I receptors, and we use this model to determine the role of the different receptors to the dynamics of postsynaptic calcium with different patterns of presynaptic activation. Our modeling framework includes glutamate vesicular release and diffusion in the cleft and a glutamate transporter that modulates extracellular glutamate concentration. Our results indicate that the contribution of mGluRs to changes in postsynaptic calcium concentration is minimal under basal stimulation conditions and becomes apparent only at high frequency of stimulation. Furthermore, the location of mGluRs in the postsynaptic membrane is also a critical factor, as activation of distant receptors contributes significantly less to calcium dynamics than more centrally located ones. These results confirm the important role of glutamate transporters and of the localization of mGluRs in postsynaptic sites in their signaling properties, and further strengthen the notion that mGluR activation significantly contributes to postsynaptic calcium dynamics only following high-frequency stimulation. They also provide a new tool to analyze the interactions between metabotropic and ionotropic glutamate receptors.
Noise analysis of a current-mode read circuit for sensing magnetic tunnel junction resistance (2011)

Magnetologic circuits are digital logic circuits constructed using magnetic tunnel junction (MTJ) devices. These devices are non-volatile, robust, and scale favorably with process dimensions. Several approaches exist for building magnetologic circuits. We are investigating current-mode magnetologic circuits as a viable option. Current-mode circuits avoid charging/ discharging load capacitances and can be used to program a downstream device. Noise in a current-mode read circuit can affect the ability to correctly distinguish logic states in an MTJ. In this paper, we present a noise analysis of a current-mode read circuit or current conveyor. We derive analytical noise equations and verify them via simulation.