gebhart/patrepeval huggingface dataset:
Delay Minimization in Varying-Bandwidth Direct Multicast with Side Information (2013)

We study the delay minimization in a direct multicast communication scheme where a base station wishes to transmit a set of original packets to a group of clients. Each of the clients already has in its cache a subset of the original packets, and requests for all the remaining packets. The base station communicates directly with the clients by broadcasting information to them. Assume that bandwidths vary between the station and different clients. We propose a method to minimize the total delay required for the base station to satisfy requests from all clients.
Non-linear image registration for correction of motion artifacts during optical imaging of human hearts (2008)

Optical imaging of cardiac electrical activity can be used to elucidate patho-physiological mechanisms of cardiac arrhythmias. However, cardiac motion during optical imaging causes significant error in electrophysiological measurements such as action potential duration. In particular, cardiac tissue in fibrillation introduces highly non-linear imaging artifacts. We present a novel approach that uses non-linear image registration to correct for in-plane cardiac motion, particularly of non-linear origin found during cardiac arrhythmias. The algorithm is performed entirely post-acquisition and does not require a complicated optical setup. It is computationally fast, and available as open source. The algorithm was tested with images acquired from five excised dilated myopathic human hearts and the results show that the image registration method significantly reduces both non-linear and linear motion-related artifacts in both sinus rhythm and ventricular fibrillation. This algorithm corrects for non-linear imaging artifacts caused by cardiac motion that are impossible to correct using linear registration methods.
Simulation analysis of a miniaturized electron optics of the massively parallel electron-beam direct-write (MPEBDW) for multi-column system (2017)

In this study, a simulation analysis of a miniaturized electron optics for the Multi-Column Massively Parallel Electron Beam Writing system is demonstrated. Analytical evaluation of space charge effect with prototype Massively Parallel Electron Beam Writing (MPEBW) system showed 2.86 nm blur in radius occurs on each beam with a convergence half angle of 3 mrad. The angle of each beam was increased to 10 mrad to reduce the space charge effect, the coulomb blur amount can be kept to less than 1 nm in radius. However, there was limitation to increasing the angle due to a spherical aberration. Since the beam current density from the electron emitter array in the prototype MPEBW system was 100 &mu;A/cm<sup>2 </sup>and the total beam current was 1&mu;A with 100&times;100 array of 10&mu;m square emitter, the influence of coulomb blur was small. By contrast, considerably increasing the number of beams and the beam current are planned in near future in MPEBW. The coulomb blur and other aberrations will not be controlled by merely adjusting the beam convergence angle. In order to increase total beam current, miniaturized electron optics have been designed for Multi-beam+Multi-column system. Reduction lens in the designed miniaturized electron optics with crossover free to reduce the influence of coulomb repulsion with narrow convergence half angle. Unlike conventional methods, the electron beams as principal rays do not intersect at one point, so even if the beam becomes extremely narrow, the coulomb repulsion effect does not increase at the crossover area. The reduction of the entire size of parallel beams in the designed electron optics was confirmed by simulation software. The simulation results showed that least confusion disk of 6.5 nm size was obtained at the beam convergence half angles of 3 mrad corresponding to the incident beam of &plusmn;0.1 mrad divergence angle. It showed that the miniaturized electron optics was suitable for 10 nm order EB writing. The crossover free electron optics of the miniaturized electron optics is possible due to dispersing the intersection points of the principal rays by a combination of a concentric electron optics and a tapered lens electrode of the reduction lens.
A New Synthetic Approach to Indazole Synthesis (1997)

Stobbe condensation of 3-alkyl- or aryl-4-formylpyrazoles 3a-f with diethyl succinate in the presence of potassium t-butoxide, followed by intramolecular ring closure (Ac2O-NaOAc), afforded the corresponding indazole derivatives 5a-f in 65-85% overall yield. These compounds are good starting materials for transformation to biologically active molecules, such as new pyrazole analogs of the left-hand segment of the potent natural antineoplastic agent CC-1065.
Extraction of Data from a Hospital Information System to Perform Process Mining (2017)

The aim of this work is to share our experience in relevant data extraction from a hospital information system in preparation for a research study using process mining techniques. The steps performed were: research definition, mapping the normative processes, identification of tables and fields names of the database, and extraction of data. We then offer lessons learned during data extraction phase. Any errors made in the extraction phase will propagate and have implications on subsequent analyses. Thus, it is essential to take the time needed and devote sufficient attention to detail to perform all activities with the goal of ensuring high quality of the extracted data. We hope this work will be informative for other researchers to plan and execute extraction of data for process mining research studies.
Green Fluorescent Protein Variants as Ratiometric Dual Emission pH Sensors. 2. Excited-State Dynamics (2002)

In the preceding paper [Hanson, G. T., McAnaney, T. B., Park, E. S., Rendell, M. E. P., Yarbrough, D. K., Chu, S., Xi, L., Boxer, S. G., Montrose, M. H., and Remington, S. J. (2002) Biochemistry 41, 15477-15488], novel mutants of the green fluorescent protein (GFP) that exhibit dual steady-state emission properties were characterized structurally and discussed as potential intracellular pH probes. In this work, the excited-state dynamics of one of these new dual emission GFP variants, deGFP4 (C48S/S65T/H148C/T203C), is studied by ultrafast fluorescence upconversion spectroscopy. Following excitation of the high-energy absorption band centered at 398 nm and assigned to the neutral form of the chromophore, time-resolved emission was monitored from the excited state of both the neutral and intermediate anionic chromophores at both high and low pH and upon deuteration of exchangeable protons. The time-resolved emission dynamics and isotope effect appear to be very different from those of wild-type GFP [Chattoraj, M., King, B. A., Bublitz, G. U., and Boxer, S. G. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 8362-8367]; however, due to overlapping emission bands, the apparent difference can be analyzed quantitatively within the same framework used to describe GFP excited-state dynamics. The results indicate that the pH-sensitive steady-state emission characteristics of deGFP4 are a result of a pH-dependent modulation of the rate of excited-state proton transfer. At high pH, a rapid interconversion from the excited state of the higher energy neutral chromophore to the lower energy intermediate anionic chromophore is achieved by proton transfer. At low pH, excited-state proton transfer is slowed to the point where it is no longer rate limiting.
The von Hippel-Lindau Tumor Suppressor Protein Mediates Ubiquitination of Activated Atypical Protein Kinase C (2001)

The von Hippel-Lindau tumor-suppressor protein (pVHL) forms a protein complex (VCB-Cul2) with elongin C, elongin B, Cul-2, and Rbx1, which functions as a ubiquitin-protein ligase (E3). The alpha-subunits of the hypoxia-inducible factors have been identified as targets for the VCB-Cul2 ubiquitin ligase. However, a variety of cellular defects caused by the depletion of pVHL cannot be explained solely by the ubiquitin-mediated degradation of hypoxia-inducible factor-alpha. We show here that a member of the atypical protein kinase C (PKC) group, PKClambda, is ubiquitinated by the pVHL-containing E3 enzyme. An active PKClambda mutant is ubiquitinated more extensively than wild-type PKClambda in HEK293 cells, and the ubiquitination is further enhanced by the overexpression of pVHL. The activation of wild-type PKClambda by serum stimulation of cells enhances the ubiquitination of the protein, supporting the notion that active PKClambda is preferentially ubiquitinated by VCB-Cul2 ubiquitin ligase. Furthermore, we show that PKClambda can be ubiquitinated in vitro in a cell-free ubiquitination assay using purified recombinant components including VCB-Cul2. Given the known function of aPKC in the regulation of cell polarity and cell growth, PKClambda may be a target of pVHL in its function as a tumor suppressor.
Overexpression of SMYD2 relates to tumor cell proliferation and malignant outcome of esophageal squamous cell carcinoma (2009)

Although we have identified two putative targets, ATF3 and CENPF, for a frequently gained/amplified region around 1q32-q41 in esophageal squamous cell carcinoma (ESCC), it is possible that other amplification targets remain to be identified. In this study, we tested whether SET and MYND domain-containing protein 2 (SMYD2), located between those two genes and encoding a lysine methyltransferase for histone H3K36 and p53K370 that regulates transcription and inhibits transactivation activity, respectively, acts as a cancer-promoting gene through activation/overexpression in ESCC. Frequent overexpression of SMYD2 messenger RNA and protein was observed in KYSE150 cells with remarkable amplification at 1q32-41.1 and other ESCC cell lines (11/43 lines, 25.6%). Overexpression of SMYD2 protein was frequently detected in primary tumor samples of ESCC (117/153 cases, 76.5%) as well and significantly correlated with gender, venous invasion, the pT category in the tumor-lymph node-metastases classification and status of recurrence. Patients with SMYD2-overexpressing tumors had a worse overall rate of survival than those with non-expressing tumors, and SMYD2 positivity was independently associated with a worse outcome in the multivariate analysis. Knockdown of SMYD2 expression inhibited and ectopic overexpression of SMYD2 promoted the proliferation of ESCC cells in a TP53 mutation-independent but SMYD2 expression-dependent manner. These findings suggest that SMYD2 plays an important role in tumor cell proliferation through its activation/overexpression and highlight its usefulness as a prognosticator and potential therapeutic target in ESCC.
The Effects of Pharmacological Hypothermia Induced by Neurotensin Receptor Agonist ABS 201 on Outcomes of CPR (2018)

Neurotensin is an endogenous tridecapeptide that binds to neurotensin receptors in the brain, which induce hypothermia. The aim of this study was to investigate whether the receptor agonist ABS 201 could induce therapeutic hypothermia and improve postresuscitation outcomes in a ventricular fibrillation cardiac arrest (VFCA) rat model. VF was electrically induced in 12 rats. Defibrillation was achieved after 6 min of cardiopulmonary resuscitation. After successful resuscitation, animals were randomized to receive ABS 201 (8 mg/kg/h) or placebo. Postresuscitation myocardial function and neurological deficit scores (NDS) were assessed, and postresuscitation survival duration was observed for up to 72 h. After administration of ABS 201, blood temperature decreased significantly from 37°C to 34°C, and was maintained for 2.5 h. There was a significant improvement of postresuscitation myocardial dysfunction, NDS, and survival duration in animals treated with ABS 201. These results demonstrated that ABS 201 induces therapeutic hypothermia in a VFCA rat model, ameliorates postresuscitation myocardial-neurological dysfunction, and prolongs survival duration. ABS 201 may therefore be an alternative method to induce therapeutic hypothermia with current cooling methods and improve postresuscitation outcomes.
Corrosions induites par les micro-organismes en milieu marin (1991)

In contrast to the situation of a few years ago, the phenomenon of Microbiologic ally Induced Corrosion (MIC) is now generally accepted as being one of a number of mechanisms whereby corrosion of alloys in natural environments can occur. Experiments conducted in the laboratories with sterile or artificial medium inoculated with bacterial mono or co-cultures can lead to a better knowledge of the various mechanisms involved in MIC. However, the extrapolation of results obtained in such conditions to the natural environment is questionnable due to the complexity of these environments and the number of biological, physico-chemical and hydrodynamical parameters involved in material degradation.
Plug and play software for designing high-level speech processing systems (1998)

Software engineering for research and development in the area of signal processing is by no means unimportant. For speech processing, in particular, it should be a priority: given the intrinsic complexity of text-to-speech or recognition systems, there is little hope to do state-of-the-art research without solid and extensible code. This paper describes a simple and efficient methodology for the design of maximally reusable and extensible software components for speech and signal processing. The resulting programming paradigm allows software components to be advantageously combined with each other in a way that recalls the concept of hardware plug-andplay, without the need for incorporating complex schedulers to control data flows. It has been successfully used for the design of a software library for high-level speech processing systems at AT&T Labs, as well as for several other large-scale software projects.
Hydrothermal Synthesis and Crystal Structure of the New Manganese(II) Thioantimonate(III), Mn(en)<sub>3</sub>Sb<sub>4</sub>S<sub>7</sub> (1997)

Abstract The reaction of manganese with antimony and sulfur in an aqueous ethylenediamine (en) solution under hydrothermal conditions gives Mn(en) 3 Sb 4 S 7 . The structure of the title compound consists of Mn(en) 3 2+ cations and infinite one-dimensional (Sb 4 S 7 2- )„ anions forming slabs via long secondary interchain Sb···S bonds. A comparison between phases with polymeric (Sb 4 S 7 2- )„ anions shows in general a trend towards a lower dimensionality of the thioantimonate assembly with increasing cation size. In the title compound the lowest number of interchain Sb···S interactions is observed among other phases with chainlike Sb 4 S 7 2- anions.
An analytical algorithm for placement of arbitrarily sized rectangular blocks (1985)

This paper presents a novel mathematical formulation to the placement of arbitrarily sized rectangles that simultaneously account for the topological and geometrical characteristics of the placement problem. Special attention is paid to maintain the continuity of the formulation. Two examples are given to demonstrate the performance of the algorithm. Identical placement is obtained from two different initial placements of an example which has 8 movable components and 29 signal nets. For a practical example with 15 movable blocks and 142 signal nets, a final placement which is manual solution comparable is obtained using random initial positions.
Successful de-escalation antibiotic therapy using cephamycins for sepsis caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae bacteremia: A sequential 25-case series (2020)

Carbapenems are frequently used to treat infections caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), but carbapenem-resistant Enterobacteriaceae bacteria are a clinical concern. Although cephamycins (cefmetazole; CMZ) have been shown to be effective against mild cases of ESBL-E infection, data on their use for severe ESBL-E infections with sepsis or septic shock remain scarce. Herein, we discuss a de-escalation therapy to CMZ that could be used after empiric antibiotic therapy in ICU patients with sepsis or septic shock caused by ESBL-E bacteremia. A sequence of 25 cases diagnosed with sepsis or septic shock caused by ESBL-E bacteria was evaluated. The attending infectious disease specialist physicians selected the antibiotics and decided the de-escalation timing. The median SOFA (Sequential Organ Failure Assessment) and APACHE II (Acute Physiology and Chronic Health Evaluation II) severity scores were 8 and 30; the rate of septic shock was 60%. Infections originated most frequently with urinary tract infection (UTI) (56%) and <i>Escherichia coli</i> (85%). Eleven patients were de-escalated to CMZ after vital signs were stable, and all survived. No patients died of UTI regardless of with or without de-escalation. The median timing of de-escalation antibiotic therapy after admission was 4 days (range, 3-6 days). At the time of de-escalation, the median SOFA score fell from 8 to 5, the median APACHE II score from 28 to 22, and the rate of septic shock from 55% to 0%. We conclude that for sepsis in UTI caused by ESBL-E bacteremia, de-escalation therapy from broad-spectrum antibiotics to CMZ is a potential treatment option when vital signs are stable.
Significance of <i>BRCA2</i> and <i>RB1</i> Co-loss in Aggressive Prostate Cancer Progression (2019)

Our findings suggest that early identification of this aggressive form of prostate cancer offers potential for improved outcomes with early introduction of PARP inhibitor-based therapy.<i>See related commentary by Mandigo and Knudsen, p. 1784</i>.
Baseline host determinants of robust human HIV-1 vaccine-induced immune responses: A meta-analysis of 26 vaccine regimens (2022)

National Institute of Allergy and Infectious Diseases (UM1AI068635 to YH, UM1AI068614 to GDT, UM1AI068618 to MJM, and UM1 AI069511 to MCK), the Duke CFAR P30 AI064518 to GDT, and National Institute of Dental and Craniofacial Research (R01DE027245 to JJK). This work was also supported by the Bill and Melinda Gates Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding sources.
Quantification of weld size parameters for throat failure prevention in a brake flange axle weld subjected to torsional loading with structural stress approach (2018)

Purpose The brake reaction test performed on a rear axle assembly revealed that the brake flange weld could not sustain the load needed to pass the minimum requirement of the test. Evaluation of the failure mode indicated that the fracture of the weld originated at the root of the weld and cracked through the fusion zone of the weld instead of cracking through base material (toe failure). The paper aims to discuss these issues. Design/methodology/approach A computational methodology is presented to quantify the critical parameters to prevent throat failure. The torsion dominated loading created high in-plane shear stress on the weld which can contribute significantly to the premature failure. Findings The failure through the fusion zone, often termed as weld throat/root failure, was not accounted for during the design phase by numerical simulation which led to the wrong conclusion that the design will pass the test requirement. Although weld sizing and weld penetration depth can explain such unexpected failure modes, fatigue life of this particular failure was still over-predicted using the Master SN curve formulation of structural stress approach which is well established for Mode I type of failure. Accounting for the shear component in the structural stress approach led to good correlation with the test specimen. Weld throat depth is a significant parameter contributing to throat failure. Practical implications The failure of the weld joining the brake flange and the tube of an axle is a high severity failure mode which can result in loss of vehicle control and injury or death and hence the failure should be prevented at any cost. Originality/value Most of the previous work of welded components relates to Mode I loading. There is very few research performed to discuss the Mode III loading and failure. This research illustrates the importance of considering the throat failure mode and quantifies the weld parameters to prevent such failures in design applications.
Real-time optofluidic surface-enhanced Raman spectroscopy based on a graphene oxide/gold nanorod nanocomposite (2018)

We demonstrate a glass microcapillary fiber as an optofluidic platform for surface enhanced Raman spectroscopy (SERS), the inner walls of which are coated with a graphene oxide (GO)/gold nanorod (AuNR) nanocomposite. A simple thermal method is used for the coating, allowing for the continuous deposition of the nanocomposite without surface functionalization. We show that the AuNRs can be directly and nondestructively identified on the GO inside the capillaries via identification of the Au-Br SERS peak, as Br- ions from the AuNR synthesis remain on their surface. The coated microcapillary platform is, then, used as a stable SERS substrate for the detection of Rhodamine 6G (R6G) and Rhodamine 640 (RH640) at concentrations down to 10<sup>-7</sup> and 10<sup>-9</sup> M, respectively. As the required sample volumes are as low as a few hundred nanoliters, down to ~75 femtograms of analyte can be detected. The fiber also allows for the detection of the molecules at acquisition times as low as 0.05 s, indicating the platform's suitability for real-time sensing.
Synthesis, Structure, and Insertion Reactivity of Zirconium and Hafnium Amidate Benzyl Complexes (2010)

A series of amidate-ligated dibenzyl zirconium and hafnium complexes are accessed through protonolysis reactions of the amide proligands 2,6-dimethylphenylpivaloylamide, [DMP(NO)tBu]H (3), and 1,3-bis(1-adamantylamide)-2,2-dimethylpropane, Ad[O2N2]H2 (5), with Zr(CH2Ph)4 or Hf(CH2Ph)4. The resulting dibenzyl complexes [DMP(NO)tBu]2Zr(CH2Ph)2 (4), Ad[O2N2]Zr(CH2Ph)2(THF) (6), and Ad[O2N2]Hf(CH2Ph)2(THF) (7) are structurally characterized. Insertion reactions of 4 with isocyanides are investigated, resulting in the formation of an η2-iminoacyl species, [DMP(NO)tBu]2Zr(η2-2,6-Me2C6H3N═CCH2Ph)2 (8), which undergoes thermal C═C coupling to form an enediamido complex, [DMP(NO)tBu]2Zr(η4-ArNC(CH2Ph)═C(CH2Ph)NAr) (Ar = 2,6-Me2C6H3) (9). Analogous insertion of tBuN≡C into the Zr−C bonds of 4 results in the formation of a vinylamido complex, [DMP(NO)tBu]2Zr(N(tBu)CH═CHPh)2 (10), through a presumed 1,2-hydrogen migration mechanism from an iminoacyl intermediate similar to 8. Complexes 8 and 9 are also structurally characterized.