gebhart/patrepeval huggingface dataset:
Probabilistic interval-valued computation (2006)

Interval methods offer a general, fine-grain strategy for modeling correlated range uncertainties in numerical algorithms. We present a new, improved interval algebra that extends the classical affine form to a more rigorous statistical foundation. Range uncertainties now take the form of confidence intervals. In place of pessimistic interval bounds, we minimize the probability of numerical "escape"; this can tighten interval bounds by 10X, while yielding 10-100X speedups over Monte Carlo. The formulation relies on three critical ideas: liberating the affine model from the assumption of symmetric intervals; a unifying optimization formulation; and a concrete probabilistic model. We refer to these as probabilistic intervals, for brevity. Our goal is to understand where we might use these as a surrogate for expensive, explicit statistical computations. Results from sparse matrices and graph delay algorithms demonstrate the utility of the approach, and the remaining challenges.
Diagnostic value of comprehensive on-site and off-site coronary CT angiography for identifying hemodynamically obstructive coronary artery disease (2020)

In comprehensive on-site CCTA assessment, V<sub>sub</sub>/MLA2 demonstrated greatest diagnostic value for hemodynamically obstructive CAD and V<sub>sub</sub> was incremental to all evaluated CCTA indices. Additionally, adding FFR<sub>CT</sub> only minimally increased diagnostic performance, demonstrating that on-site CCTA assessment is a reasonable alternative to FFR<sub>CT</sub>.
Particle-in-cell simulations of optical injectors for plasma accelerators (2004)

Two possible methods of optically injecting electrons into a plasma accelerator are the self-modulated laser wakefield accelerator (SMLWFA) and laser ionization and ponderomotive acceleration (LIPA). A magnetic selection scheme is proposed to select a narrow band of energies from the intrinsically broad beam produced by the SML- WFA. The scheme is analyzed using 2D particle-in-cell (PIC) simulations and 3D ray tracing. The effects of space charge on the ideal LIPA distribution are examined using full 3D PIC simulations.
[N,N'-Bis(2-pyridylmethyl)ethylenediaminediacetato]cobalt(III) Perchlorate Monohydrate (1998)

The ligand N,N'-bis(2-pyridylmethyl)ethylenediamine-N,N'-diacetate coordinates to cobalt(III) in a distorted octahedral fashion with trans carboxylato groups. The structure of the cation is in good agreement with those reported for the isomorphous tetrafluoroborate monohydrate [Mandel & Douglas (1989). Inorg. Chim. Acta, 155, 55–69] and the hexafluorophosphate acetonitrile monohydrate [Caravan, Rettig & Orvig (1997). Inorg. Chem. 36, 1306–1315 and 4912].
Cell Wall Anchor Structure of BcpA Pili in Bacillus anthracis (2008)

Assembly of pili in Gram-positive bacteria and their attachment to the cell wall envelope are mediated by sortases. In Bacillus cereus and its close relative Bacillus anthracis, the major pilin protein BcpA is cleaved between the threonine and the glycine of its C-terminal LPXTG motif sorting signal by the pilin-specific sortase D. The resulting acyl enzyme intermediate is relieved by the nucleophilic attack of the side-chain amino group of lysine within the YPKN motif of another BcpA subunit. Cell wall anchoring of assembled BcpA pili requires sortase A, which also cleaves the LPXTG sorting signal of BcpA between its threonine and glycine residues. We show here that sortases A and D require only the C-terminal sorting signal of BcpA for substrate cleavage. Unlike sortase D, which accepts the YPKN motif as a nucleophile, sortase A forms an amide bond between the BcpA C-terminal carboxyl group of threonine and the side-chain amino group of diaminopimelic acid within the cell wall peptidoglycan of bacilli. These results represent the first demonstration of a cell wall anchor structure for pili, which are deposited by sortase A into the envelope of many different microbes.
Interfacial Electric Field Effects on a Carbene Reaction Catalyzed by Rh Porphyrins (2013)

An intramolecular reaction catalyzed by Rh porphyrins was studied in the presence of interfacial electric fields. 1-Diazo-3,3-dimethyl-5-phenylhex-5-en-2-one (2) reacts with Rh porphyrins via a putative carbenoid intermediate to form cyclopropanation product 3,3-dimethyl-5-phenylbicyclo[3.1.0]hexan-2-one (3) and insertion product 3,3-dimethyl-2,3-dihydro-[1,1'-biphenyl]-4(1H)-one (4). To study this reaction in the presence of an interfacial electric field, Si electrodes coated with thin films of insulating dielectric layers were used as the opposing walls of a reaction vessel, and Rh porphyrin catalysts were localized to the dielectric-electrolyte interface. The charge density was varied at the interface by changing the voltage across the two electrodes. The product ratio was analyzed as a function of the applied voltage and the surface chemistry of the dielectric layer. In the absence of an applied voltage, the ratio of 3:4 was approximately 10:1. With a TiO2 surface, application of a voltage induced a Rh porphyrin-TiO2 interaction that resulted in an increase in the 3:4 ratio to a maximum in which 4 was nearly completely suppressed (>100:1). With an Al2O3 surface or an alkylphosphonate-coated surface, the voltage caused a decrease in the 3:4 ratio, with a maximum effect of lowering the ratio to 1:2. The voltage-induced decrease in the 3:4 ratio in the absence of TiO2 was consistent with a field-dipole effect that changed the difference in activation energies for the product-determining step to favor product 4. Effects were observed for porphyrin catalysts localized to the electrode-electrolyte interface either through covalent attachment or surface adsorption, enabling the selectivity to be controlled with unfunctionalized Rh porphyrins. The magnitude of the selectivity change was limited by the maximum interfacial charge density that could be attained before dielectric breakdown.
Frequency Noise Reduction of Integrated Laser Source with On-Chip Optical Feedback (2017)

Integrated indium phosphide distributed-Bragg-reflector lasers with and without on-chip optical feedback are reported. The measured linewidth for the laser with coherent optical feedback is approximately 800 kHz, demonstrating an order of magnitude reduction.
Asynchronous Convergence in Multi-Task Learning via Knowledge Distillation from Converged Tasks (2022)

Weiyi Lu, Sunny Rajagopalan, Priyanka Nigam, Jaspreet Singh, Xiaodi Sun, Yi Xu, Belinda Zeng, Trishul Chilimbi. Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Industry Track. 2022.
Effectiveness of non-penetrating electroporation applicators to function as impedance spectroscopy electrodes (2009)

Electroporation is commonly performed to deliver drugs and genes to cells comprising tissues. A possible way to control and confirm delivery is through the use of impedance spectroscopy. Ideally, this tool should not interfere with delivery and should incorporate the use of electrodes, applicators, used for delivery. This work examines impedance spectra obtained with non-penetrating surface applicators commonly used for skin electroporation. After collecting and processing over 9,000 spectra from three animal models it was determined that the electrode systems tested would have no significant effect on the obtained spectra. Therefore, electroporation applicators currently in use could be used concurrently for the collection of impedance spectra.
Radiation Cystitis Modeling: a Comparative Study of Bladder Radiation‐Induced Fibrosis in Different Mouse Strains (2019)

Introduction and Objective Radiation cystitis (RC) is a severe side effect from radiation therapy that can occur in pelvic cancer survivors (e.g. cervical and prostate cancer) and results in a fibrotic bladder. However not all patients treated with pelvic radiation will develop RC. Different mouse strains can be used for exploring genetic variability with respect to human biology. We aimed to assess the fibrotic response of the bladder to radiation in various genetic mouse strains to determine if genetic background variation may explain differences in risk for patients developing RC after radiation treatment. Methods Female C57BL/6, C3H and Balb/c mice were given a single dose of 40 Gy irradiation using the Small Animal Radiation Research Platform (SARRP) to deliver a gamma‐irradiation to the bladder while limiting toxicity to neighboring tissue. Weekly micturition measurements were performed. Mice were sacrificed one‐year post irradiation and bladders were processed for histology. Fibrosis was determined using Mason's trichrome and Picrosirius Red stains. Results All mice tolerated the radiation treatment well ‐ no changes in weight or behavior were noted. Micturition measurements were performed in C57BL/6 and Balb/c mice only, as C3H mice destroyed the filter paper. Increased number of voids, and decreased average and primary void size developed in both strains, though occurred earlier in the C57BL/6 strain. Hematuria developed in all strains. Mild to severe radiation‐induced fibrosis was visible in Balb/c and C57Bl/6 mice, with the highest degree of fibrosis in the latter. Fibermetrics analysis indicated higher number of collagen fibers in C57Bl/6 and Balb/c mice, but only Balb/c mice showed increased collagen fiber length and diameter. Ongoing studies will determine changes in specific collagen proteins using antibody specific fluorescent staining. Conclusion Using SARRP, we can create bladder dysfunction in mice modeling symptoms of chronic human RC including hematuria, fibrosis, and micturition frequency. Radiation‐induced fibrosis in the bladder is strain dependent, suggesting that there may be a genetic predisposition to radiation sensitivity of the bladder. These results are essential in determining the right preclinical model for future RC studies and understanding which cancer patients are at risk for RC. Support or Funding Information This project was in part supported by the U Can‐Cer Vive Foundation, NIDDK K01 career development award DK114334 (BMMZ), NIDDK specialized center cooperative agreement award U54DK104310, and NIEHS predoctoral research award F31ES028594 (KW) This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
An Investigation on Number of Effective Taps for Multicarrier Schemes (2013)

In a wireless communication medium, the transmitted signal reaches to the receiver antenna after passing through multipath channel. The difference in path delays and mobility cause the transmitted signal spread both in time and frequency, resulting in inter-symbol (or adjacent block) and inter-carrier (or adjacent channel) interference, respectively. The pulse shaping and matching filters used in the transceivers also impact the level of dispersion in both time and frequency. In this study, the composite effects of wireless medium and the used filters are investigated on the equalization of multicarrier systems. For this purpose, considering a symbol-spaced tap model for the equalization, the number of effective taps in both time and frequency domains is obtained via Akaike information criterion (AIC) for different signal-to-noise ratios (SNRs). Subsequently, a method which characterizes the equalization complexity of the receiver as a function of the transmit pulse shape, communication medium, the receive filter response, and SNR is proposed.
Polarization State of Scattered Light in Apertureless Reflection-mode Scanning Near-Field Optical Microscopy (2013)

We studied the polarization state in an apertureless scanning near-field microscopy (a-SNOM) operating in reflection mode by using three-dimensional Finite-difference Time-domain (FDTD) method. As a result, the electric field around tip apex in the near-field region enhanced four times stronger than the incident light for ppolarization when the tip-sample separation was 10 nm. We find that the p- and s-polarization state is maintained for the scattered light when the probe is perpendicular to the sample. When the probe is not perpendicular to the sample, the polarization state of scattered light will rotate an angle that equals to the inclination angle of probe with p-polarization illumination. On the other hand, the polarization state will not rotate with s-polarization illumination.
MicroRNA signature in spermatozoa and seminal plasma of proven fertile men and in testicular tissue of men with obstructive azoospermia (2019)

MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.
Consistent Replication in Distributed Multi-Tier Architectures (2011)

Replication is commonly used to address the scalability and availability requirements of collaborative web applications in domains such as computer supported cooperative work, social networking, e-commerce and e-banking. While providing substantial benefits, replication also introduces the ov
Wideband efficiency improvement of fiber optic systems by carrier subtraction (1995)

Carrier subtraction from a weakly modulated optical signal is proposed, analyzed, and demonstrated to improve fiber-optic system efficiency. For constant photodetector current, an amount of carrier suppression results in an equal amount of RF gain. Improvement of 9-13 dB in link loss from 1 to 25 GHz is measured using a Fabry-Perot filter operating in the reflection mode. Measured induced harmonic distortion agrees with predicted values.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Method to Evaluate Lost Circulation Materials—Investigation of Effective Wellbore Strengthening Applications (2014)

Abstract With increased drilling activity in deeper, harsher, and more complex environments, controlling non-productive time (NPT) during drilling is critical to lowering the cost of well construction. Lost circulation (LC), one of the main contributors to NPT, is a widely discussed topic drawing industry attention, as is evident from recent publications and forums/workshops on the topic. The literature on LC reveals several means of mitigation, ranging from the simple use of Lost Circulation Materials (LCMs) to the use of gunk/chemical sealants and methods for altering near-wellbore stresses (stress caging or wellbore strengthening). There is a subtle difference between lost circulation and wellbore strengthening, and any research should help facilitate a better understanding of the two. Presented previously (Kumar et al. 2010; Savari et al. 2012) were novel insights into LCMs for wellbore strengthening applications. Continuing the research effort, this paper discusses another approach for designing LCMs to withstand higher wellbore pressures within a fracture. A property of Plug Breaking Pressure (PBP) was determined for different LCM combinations using a permeability plugging apparatus (PPA) with tapered slots. LCM combinations with differing mechanical properties behaved differently when compared using the PBP data. Particles, such as ground marble (GM), alone were not able to plug the tapered slot and hence the PBP was zero. Based on the previous work described by Savari et al. (2012), the addition of resilient graphitic carbon helped with plugging the tapered slot, with a PBP of approximately 900 psi. Adding fibers to the LCM combination was also evaluated. Plugging did not improve when fibers were added just to one other type of particulate LCM. But, the combination of ground marble, resilient graphitic carbon, and specific fibers was found to provide the most efficient plugging with the highest PBP of approximately 2,100 psi. This work confirms that all LCMs are not equal and that the LCM type plays a role in terms of both plugging and "toughness" that better withstands displacement pressures. It also validates that, most of the time, combinations of LCM work more effectively compared to using just one type alone. The novel PBP data on different LCM combinations can provide a qualitative comparison of their ability to withstand displacement and/or failure pressures when designing LCM combinations in wellbore strengthening applications.
Frequent Allelic Imbalance on Chromosome 18q21 in Early Superficial Colorectal Cancers (1999)

Genetic alterations in early superficial colorectal cancers have rarely been reported. In the present study, we searched for alterations in the APC and p53 genes in 27 superficial (20 depressed and 7 elevated) and 21 protruding colorectal cancers with submucosal invasion by means of PCR-single strand conformation polymorphism. Allelic imbalance (AI) on five loci, i.e., 1p34-36, 8p21-22, 14q32, 18q21 and 22q12-13, was also analyzed. Since a high incidence of 18q21 AI was detected in the superficial depressed cases, we further screened for alterations in Smad2, Smad4 and DCC. APC alterations were observed in three superficial depressed, one superficial elevated, and 11 protruding colorectal cancers, indicating that the frequency of APC alterations in superficial depressed cases was significantly lower than that in the protruding ones. There was no significant association between p53 alterations and macroscopic types. AI on 18q21 (13/20, 65%) was much higher than those on the other four loci in the superficial depressed cases. Moreover, the frequency of 18q21 AI in the superficial depressed cases was significantly higher than that in the protruding ones. Smad4 alterations were only detected in 1 of the 13 superficial depressed and 3 of the 17 protruding cases, while Smad2 and DCC alterations were not detected in any case examined. These data suggest that the carcinogenetic pathways of protruding and superficial depressed colorectal cancers are different, and that alterations of tumor suppressor gene(s) located on 18q21 other than Smad2, Smad4 and DCC might be associated with most superficial depressed colorectal cancers.
Branched Tertiary Amines from Aldehydes and α‐Olefins by Combined Multiphase Tandem Reactions (2022)

This study presents the transformation of olefins to branched amines by combining a hydroformylation/aldol condensation tandem reaction with the reductive amination in a combined multiphase system that can be recycled 9 times. The products are branched amines that are precursors for surfactants. Since the multiphase hydrofomylation/aldol condensation system has already been studied, the first step was to develop the partial hydrogenation of unsaturated aldehydes together with a subsequent reductive amination. The rhodium/phosphine catalyst is immobilized in a polar polyethylene phase which separates from the product phase after the reaction. Reaction and catalyst recycling are demonstrated by the conversion of the C<sub>14</sub> -aldehyde 2-pentylnonenal with the dimethylamine surrogate dimethylammonium dimethylcarbamate to the corresponding tertiary amine with yields up to 88 % and an average rhodium leaching of less than 0.1 % per recycling run. Furthermore, the positive influence of a Bronsted acid and carbon monoxide on the selectivity are discussed. Finally, the two PEG based systems have been merged in one recycling approach, by using the product phase of the hydroformylation aldol condensation reaction for the reductive amination reaction. The yields are stable during a nine recycling runs and the leaching low with 0.09 % over the two recycling stages.
Inhibitory Antibodies of the Proteases HGFA , Matriptase and Hepsin (2018)

Recent structural studies on inhibitory HGFA, matriptase and hepsin antibodies have greatly added to our understanding of how antibodies interfere with the catalytic machinery of these proteases. The structural details reveal a remarkable diversity of mechanisms by which enzyme catalysis is inhibited. The orthosteric type antibodies are competitive inhibitors and bind to the active site to obstruct substrate access. In contrast, the allosteric type antibodies bind outside the active site region and impose structural changes at the active site, which are detrimental to catalysis. In addition to being valuable research tools to decipher the biology of these proteases, the inhibitory antibodies have potential applications as diagnostics and as therapeutic agents in cancer.
Subgraph Homeomorphism via the Edge Addition Planarity Algorithm (2012)

This paper extends the edge addition planarity algorithm from Boyer and Myrvold to provide a new way of solving the subgraph homeomorphism problem for K2,3, K4, and K3,3. These extensions derive much of their behavior and correctness from the edge addition planarity algorithm, providing an alternative perspective on these subgraph homeomorphism problems based on affinity with planarity rather than triconnectivity. Reference implementations of these algorithms have been made available in an open source project (http://code.google.com/p/planarity).
Multi-dimensional optical data writing techniques for cloud-scale archival storage (2023)

The demand for long-term data storage in the cloud grows continuously into the zettabytes. Operating at such scales requires a fundamental re-thinking of how we build large-scale storage systems to archive data in a sustainable and costeffective manner. In Project Silica, a storage technology for the cloud is being designed and developed from the media up by leveraging the recent progress in ultrafast laser nano-structuring of the transparent media. Together with the advances in reading, decoding and error correction processes, high-density and high-throughput multi-dimensional volumetric optical data writing is achieved, enabling successful end-to-end proof-of-concept demonstrations of the technology. With exceptional media longevity, this could transform archival cloud storage. Here we briefly discuss the development of the technology, key metrics for cost-efficient optical data storage at scale, and successful proof-ofconcept demonstrations.
Peptide‐Decorated Dendrimers and Their Bioapplications (2016)

Peptide-decorated dendrimers (PDDs) are a class of spherical, regular, branched polymers that are modified by peptides covalently attached to their surface. PDDs have been used as protein mimetics, novel biomaterials, and in a wide range of biomedical applications. Since their design and development in the late eighties, poly-l-lysine has been a preferred core structure for PDDs. However, numerous recent innovations in polymer synthesis and ligation chemistry have re-energized the field and led to the emergence of well-defined peptide dendrimers with more diverse core structures and functions. This Minireview highlights the development of PDDs driven by significantly improved ligation chemistry incorporating structurally well-defined peptides and the emerging use of PDDs in imaging and drug development.