gebhart/patrepeval huggingface dataset:
Scalable in-memory processing of omics workflows (2022)

We present a proof of concept implementation of the in-memory computing paradigm that we use to facilitate the analysis of metagenomic sequencing reads. In doing so we compare the performance of POSIX™file systems and key-value storage for omics data, and we show the potential for integrating high-performance computing (HPC) and cloud native technologies. We show that in-memory key-value storage offers possibilities for improved handling of omics data through more flexible and faster data processing. We envision fully containerized workflows and their deployment in portable micro-pipelines with multiple instances working concurrently with the same distributed in-memory storage. To highlight the potential usage of this technology for event driven and real-time data processing, we use a biological case study focused on the growing threat of antimicrobial resistance (AMR). We develop a workflow encompassing bioinformatics and explainable machine learning (ML) to predict life expectancy of a population based on the microbiome of its sewage while providing a description of AMR contribution to the prediction. We propose that in future, performing such analyses in 'real-time' would allow us to assess the potential risk to the population based on changes in the AMR profile of the community.
Fixed ratio or lower limit of normal for the FEV1/VC ratio: Relation to symptoms and extended lung function tests (2013)

There is no generally accepted agreement on the spirometric definition of chronic obstructive pulmonary disease (COPD). A fixed ratio FEV1/VC &lt;0.7 (FR) or a use of the age-related lower limit of normal for FEV1/VC (LLN) are the most common definitions. We analysed respiratory symptoms and extensive lung function in groups of subjects fulfilling none, either or both of the spirometric criteria for COPD. The study population comprised 450 subjects from a random population sample, who answered a questionnaire on respiratory symptom, underwent spirometry, body plethysmography, measurements of pulmonary reactance (AX) and diffusing capacity for CO (DL,CO). Results: Symptoms and lung function N - never-smokers (n=82) N - ever-smokers (n=236) FR+ (n=57) FR+LLN+ (n=66) Long-standing cough (%) 10 14 16 26 Dyspnoea on exertion (%) 20 26 38 52 FEV1/VC 0.79 ± 0.05 0.78 ± 0.05 0.68 ± 0.02 0.57 ± 0.08 FEV1 (% pred) 110 ± 16 103 ± 13 93 ± 15 78 ± 18 RV/TLC 96 ± 11 96 ± 13 101 ± 15 108 ± 18 AX (kPa L-1) 0.28 ± 0.38 0.36 ± 0.41 0.52 ± 0.56 0.77 ± 1.3 DL,CO (% pred) 89 ± 16 83 ± 15 79 ± 17 69 ± 20 Values are mean (SD). (N=ratio ≥0.7, FR+=ratio&lt;0.7, LLN+=ratio &lt;LLN) For symptoms, there was a significant (p&lt;0.05) difference between groups. For FEV1, RV/TLC and DL,CO there was a significant difference between FR+LLN+ and FR+ and between FR+ and normal ever-smokers. Conlusion: Subjects with FEV1/VC&lt;0.7 had worse lung function and more respiratory symptoms compared to subjects with normal ratio but less impairment and respiratory symptoms compared to subjects with FEV1/VC&lt;0.7 and &lt;LLN. Careful evaluation of respiratory symptoms and extensive lung function testing may be warranted if FEV1/VC&lt;0.7 and &gt;LLN.
Trap profiles of projector based optoelectronic tweezers (OET) with HeLa cells (2009)

In this paper we present trap profile measurements for HeLa cells in Optoelectronic Tweezers (OET) based on a data projector. The data projector is used as a light source to illuminate amorphous Si creating virtual electrodes which are used to trap particles through dielectrophoresis. We show that although the trap stiffness is typically greater at the edges of the optical spot it is possible to create a trap with constant trap stiffness by reducing the trap's size until it is similar to the object being trapped. We have successfully created a trap for HeLa cells with a constant trap stiffness of 3 x 10(-6) Nm-1 (capable of moving the cell up to 50 microms-1) with a 12 microm diameter trap. We also calculate the depth of the potential well that the cell will experience due to the trap and find that it to be 1.6 x 10(-16)J (4 x 10(4) kBT).
PROPOSAL OF A HANDY SETUP FOR DISCRIMINATING PARASITIC EFFECTS FOR THE MEASUREMENT OF IMPULSIVE THRUST FROM A MICROWAVE CAVITY (2020)

International audience
Analysis of Imperfect Rephasing in Photon Echo-Based Quantum Memories (2022)

Over the last two decades, quantum memories have been intensively studied for potential applications of quantum repeaters in quantum networks. Various protocols have also been developed. To satisfy no noise echoes caused by spontaneous emission processes, a conventional two-pulse photon-echo scheme has been modified. The resulting methods include double-rephasing, ac Stark, dc Stark, controlled echo, and atomic frequency comb methods. In these methods, the main purpose of modification is to remove any chance of a population residual on the excited state during the rephasing process. Here, we investigate a typical Gaussian rephasing pulse-based double-rephasing photon-echo scheme. For a complete understanding of the coherence leakage by the Gaussian pulse itself, ensemble atoms are thoroughly investigated for all temporal components of the Gaussian pulse, whose maximum echo efficiency is 26% in amplitude, which is unacceptable for quantum memory applications.
Two‐component “Onionlike” micelles with a PPO core, a PDMAEMA shell and a PEO corona: formation and crosslinking (2008)

Abstract BACKGROUND: Chemical or physical crosslinking of supramolecular assemblies gives them stability in a wide range of environments. Much attention is paid to multilayer (onion‐like) polymeric micelles because their functionality is higher than classic core‐shell micelles. This work reports on the formation and crosslinking of onion‐like micelles prepared by mixing two different block copolymers containing a crosslinkable poly(dimethylaminoethyl methacrylate) (PDMAEMA) block. RESULTS: Block copolymers of a crosslinkable PDMAEMA block were synthesized by atom transfer radical polymerization of 2‐(dimethylamino)ethyl methacrylate (DMAEMA) from poly(propylene oxide) (PPO) or poly(ethylene oxide) (PEO) macroinitiators. The (PDMAEMA 13 )‐ block ‐PPO 69 ‐ block ‐(PDMAEMA 13 ) triblock formed wormlike core‐shell micelles, which were converted into ellipsoidal onion‐like micelles on mixing with the PEO 45 ‐ block ‐P(DMAEMA 8 ‐ co ‐MMA 4 ) diblock. Onion‐like micelles were crosslinked by quaternization of DMAEMA units. CONCLUSION: Formation of onion‐like micelles by mixing two different AB (ABA) and B′C block copolymers and their subsequent crosslinking is a valuable approach towards stabilized supramolecular assemblies of a higher complexity and functionality than the individual constitutive components. Copyright © 2008 Society of Chemical Industry
Conformational properties of oligonucleotides. (1995)

Vast libraries of oligonucleotide sequences can be made. Such libraries have been screened and/or selected to identify individual molecules showing various properties, including high affinity/high specificity binding (to something) or new enzymatic activity. The SELEX protocol is used to identify these interesting oligonucleotides; two recent reviews of the SELEX protocol and its power have appeared recently. Oligonucleotides derived through the SELEX process have applications in diagnostics and therapeutics, and have additional value as research reagents and compounds that provide chemical plausibility to some ideas about evolution of the biosphere. Oligonucleotide conformations are shockingly robust and potent.
Valor pronóstico de la variación del segmento ST en aVR en el síndrome coronario agudo sin elevación del segmento ST (2021)

Introduccion : El analisis del segmento ST en la derivacion aVR frecuentemente se ignora en la lectura del electrocardiograma, aunque podria ofrecer informacion util en el contexto del sindrome coronario agudo. Objetivo : Determinar la contribucion de la variacion del ST en la derivacion aVR en pacientes con sindrome coronario agudo sin elevacion del segmento ST en la ocurrencia de eventos cardiovasculares adversos. Metodos : Estudio analitico, longitudinal en 2 799 pacientes con sindrome coronario agudo sin elevacion del segmento ST, ingresados en los hospitales Hermanos Ameijeiras y Enrique Cabrera entre mayo de 2011 y mayo de 2017. Resultados : Predominaron los pacientes de sexo masculino (52,9%), con edad media de 66,0 ± 8,0 anos y mas de dos enfermedades asociadas (92,2 %). La amplia variacion del segmento ST en aVR se asocio a clase Killip Kimbal avanzada, concentracion elevada de troponinas cardiacas, enfermedad coronaria compleja y peor funcion de ventriculo izquierdo. La variacion amplia del segmento ST en aVR estuvo relacionada con la ocurrencia de eventos cardiovasculares adversos. Conclusiones .  La amplia variacion del segmento ST en la derivacion aVR resulto ser una herramienta sensible que enriquece la prediccion de eventos cardiovasculares adversos.
LED-Based Photoacoustic Imaging for Monitoring Angiogenesis in Fibrin Scaffolds (2019)

Noninvasive imaging techniques provide insight into physiology that is complementary to tissue morphology obtained by invasive histology. Optical imaging techniques, such as laser speckle contrast analysis, are used <i>in vivo</i> to longitudinally evaluate vascularization. Despite their high spatial resolution, these techniques have a limited imaging depth. In this study, we demonstrate how a dual LED-based photoacoustic (PA) and ultrasound system can delineate changes in perfusion at depth within scaffolds containing basic fibroblast growth factor. Perfusion changes detected by PA corroborated with vessel density. PA imaging could be a noninvasive and sensitive method for evaluating vascularization at depth in larger constructs.
Trapping of Ultrashort Optical Pulse into Ultra-high-Q Photonic Nanocavity (2006)

A method of trapping of ultrashort pulse into an ultra-high Q nanocavity is investigated. Dynamic change in the coupling strength between the cavity and port leads to high efficiency trapping and holding.
Differentially protected .alpha.-aminoglycine (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDifferentially protected .alpha.-aminoglycineMark G. Bock, Robert M. DiPardo, and Roger M. FreidingerCite this: J. Org. Chem. 1986, 51, 19, 3718–3720Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/jo00369a035https://doi.org/10.1021/jo00369a035research-articleACS PublicationsRequest reuse permissionsArticle Views318Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
[Application value of combined organ radical resection in patients with recurrent gastric cancer]. (2016)

The combined organ radical resection can provide better survival for recurrent gastric cancer patients, while the indications should be controlled strictly with preoperative multidisciplinary assessment and precise surgical judgment in order to decrease the complication.
Solid state coordination chemistry: ligand influences on the structures of one-dimensional copper(i) cyanide–organodiimine solids (2001)

The structural consequences of introducing sterically demanding substituents have been investigated for composite organic–inorganic materials of the copper cyanide–organodiimine system. The hydrothermal reactions of copper(I) cyanide and KCN, with the appropriate chelating organodiimine ligands yield a series of one-dimensional copper cyanide chains decorated either with linear {(LL)Cu(CN)} (LL = organodiimine) side chains or with diimine ligands bound directly to the copper sites of the parent chain. The structures of [Cu3(CN)3(2,2′-bpy)] (1) (2,2′-bpy = 2,2′-bipyridine) and [Cu3(CN)3(phen)] (2) (phen = 1,10-phenanthroline) are similar to that of the previously reported [Cu4(CN)4(biquin)] (biquin = 2,2′-biquinoline), exhibiting the characteristic one-dimensional {Cu(CN)} chain with diimine–copper cyanide side arms. In contrast, the structures of [Cu3(CN)3(biquin)2] (3), [Cu2(CN)2(dpbp)], (4) (dpbp = 4,4′-diphenyl-2,2′-bipyridine), and [Cu(CN)(dpphen)] (5) (dpphen = 4,7-diphenyl-1,10-phenanthroline) are characterized by direct attachment of the organodiimine ligand to the copper cyanide chain.
Chapter 19 Iodinated Contrast Media as pH-Responsive CEST Agents (2017)

The application of paramagnetic metal ion complexes as MRIcontrast agents has an interesting history. Complexes developedinitially as T1 relaxivity agents contained paramagnetic Fe(III) and Mn(II), followed by studies on Gd(III) complexes [1]. Morerecently, complexes of lanthanide ions other than Gd(III) have beendeveloped asMRI contrast agents that operate by chemical exchangesaturation transfer (CEST) [2-4]. In particular, Eu(III), Tm(III), andYb(III) have been extensively used as CEST or paramagnetic CEST(paraCEST) agents as described in detail in Chapter 11. Why wouldone then want to develop transition metal ion paraCEST agentsbased on diﬀerent elements? In this chapter, we show that theunique coordination chemistry, tunable redox potentials as wellas suitable paramagnetic properties of transition metal ions makethem excellent candidates for the development as paraCEST agents.
Spatiotemporal Data Cleansing for Indoor RFID Tracking Data (2013)

The Radio Frequency Identification (RFID) is increasingly being deployed in indoor tracking systems, e.g., airport baggage monitoring. However, the “dirtiness” in raw RFID readings hinder the progress of applying meaningful high level applications that range from monitoring to analysis. Hence, it is indispensable to cleansing RFID data in such systems. In this paper, we focus on two quality aspects in raw indoor RFID data: temporal redundancy and spatial ambiguity. The former refers to the large number of repeated readings for the same object and the same RFID reader during a period of time. The latter refers to the undetermined whereabouts of an object due to multiple readings by different readers simultaneously. We investigate the spatiotemporal characteristics of indoor spaces as well as RFID reader deployment, and exploit them in designing effective data cleansing techniques. Specifically, we aggregate raw RFID readings to reduce temporal redundancy; we design a distance-aware graph to resolve spatial ambiguity with respect to the indoor topology and the RFID reader deployment captured in the graph. We evaluate the spatiotemporal data cleansing techniques using both real and synthetic datasets. The experimental results demonstrate that the proposed techniques are effective and efficient in cleansing indoor RFID tracking data.
Plasma myeloperoxidase level and polymorphonuclear leukocyte activation in horses suffering from large intestinal obstruction requiring surgery: preliminary results. (1999)

Myeloperoxidase (MPO) is a specific enzyme of neutrophil azurophilic granules with a strong oxidative activity. Thanks to a radioimmunoassay of equine myeloperoxidase, the authors have observed a significantly higher plasma level of MPO in horses operated for strangulation obstruction of the large intestine (n = 6) than in horses suffering from a non-strangulating displacement of the large intestine (n = 9). For the 2 groups, 3 phases were distinguished: reception (P1), intensive care (P2) and terminal phase (P3). The mean peak values of MPO for these phases were 121.6 ng/mL (P1), 168.6 ng/mL (P2), and 107.0 ng/mL (P3) for the non-strangulating group, and 242.6 ng/mL (P1); 426.0 ng/mL (P2), and 379.5 ng/mL (P3) for the strangulation group. The variations of the mean peak values of plasma MPO were significantly different between the 2 groups and between the different phases. A significant increase of the least square means of MPO was observed between P1 and P2. A significant decrease of the least square means of the number of circulating leukocytes was observed between P1 and P3. Polymorphonuclear neutrophil activation could play a major role in the pathogenesis of acute abdominal disease and endotoxic shock.
Oil Spraying as an Air Quality Improvement Technique in Livestock Buildings: Development and Utilisation of a Testing Device (2011)

Air quality is known to affect the production efficacy, health and welfare of different livestock species, as well as the health of farm workers. It is therefore important to improve air quality in facilities housing livestock to reduce the incidence and severity of respiratory diseases, improve animal welfare, production efficiency and reduce the potential occupational health and safety risks arising from exposure of farm workers to airborne pollutants in livestock facilities. This paper outlines the development of test equipment that enabled the standardised testing of different oil application rates (to be applied in bedded livestock buildings) on the resulting levels of dust suppression. Specifically the development of the equipment enabled optimum stirring and rotational speeds to be determined to give consistent levels of dust generation within the test chamber. This allowed for different oil inclusion rates to be determined in the oil/water mixture to achieve optimal dust reduction rates. Results showed that increased amounts of oil water mixture resulted in a decrease of airborne dust particles from the bedding material. However, an economically optimum rate was also identified, when the diminishing return (in terms of dust reduction rate) on the amount of oil applied was also considered. The paper also reviewed some previous studies conducted in Australia aimed at fine-tuning and applying oil spraying in livestock buildings to suppress dust.
Mechanics of post‐cam engagement during simulated dynamic activity (2013)

Posterior-stabilized (PS) total knee arthroplasty (TKA) components employ a tibial post and femoral cam mechanism to guide anteroposterior knee motion in lieu of the posterior cruciate ligament. Some PS TKA patients report a clicking sensation when the post and cam engage, while severe wear and fracture of the post; we hypothesize that these complications are associated with excessive impact velocity at engagement. We evaluated the effect of implant design on engagement dynamics of the post-cam mechanism and resulting polyethylene stresses during dynamic activity. In vitro simulation of a knee bend activity was performed for four cadaveric specimens implanted with PS TKA components. Post-cam engagement velocity and flexion angle at initial contact were determined. The experimental data were used to validate computational predictions of PS mechanics using the same loading conditions. A lower limb model was subsequently utilized to compare engagement mechanics of eight TKA designs, relating differences between implants to geometric design features. Flexion angle and post-cam velocity at engagement demonstrated considerable ranges among designs (23°-89°, and 0.05-0.22 mm/°, respectively). Post-cam velocity was correlated (r = 0.89) with tibiofemoral condylar design features. Condylar geometry, in addition to post-cam geometry, played a significant role in minimizing engagement velocity and forces and stresses in the post. This analysis guides selection and design of PS implants that facilitate smooth post-cam engagement and reduce edge loading of the post.
Association Between Imposition of a Maintenance of Certification Requirement and Ambulatory Care-Sensitive Hospitalizations and Health Care Costs (2014)

In 1990, the American Board of Internal Medicine (ABIM) ended lifelong certification by initiating a 10-year Maintenance of Certification (MOC) program that first took effect in 2000.
Abstract 44: Angiotensin-(1-9) Decreases Hypertension and Vascular Damage by Inhibiting Rhoa/rock Activity in Doca Hypertensive Rats (2013)

Previously, we found in experimental hypertension (DOCA salt model), that the RhoA/Rho-kinase pathway inhibition by fasudil decreases hypertension (HT), angiotensin (Ang) II levels and vascular remodeling. Besides, in this model fasudil increased ACE2 activity and Ang1-9 plasma levels. These results strongly suggest that in this experimental model, ROCK activity is more dependent on ACE2 and Ang-(1-9) than Ang II levels. There is no current evidence regarding the effect of Ang1-9 on ROCK activity of hypertensive rats. Aim: To determine the effect of the chronic administration of Ang1-9 on blood pressure (BP), vascular damage and activation of RhoA/ROCK pathway in deoxycorticosterone acetate (DOCA)-salt hypertensive rats. Methods: The DOCA-salt hypertensive model was used in Sprague-Dawley male rats (age: 5-6 weeks; 150±10 g). DOCA was administered twice a week (60 mg/kg, im) starting immediately after surgery. The animals also received 1% NaCl and 0.4% KCl in the drinking water. Controls (C) were uninephrectomized rats (Sham group, n=12). Hypertensive rats (D) were randomized to receive vehicle (n=10), Ang-(1-9) (600 ng/kg/min, n=12), Ang-(1-9) + the Mas blocker receptor A779 (100 ng kg−1 min−1,n=7) and Ang-(1-9) + the AT2R antagonist PD123319 (PD, 36 ng/Kg min) for 2 weeks. Systolic (S) and diastolic (D) BP, body mass (BM), heart weight (HW), heart mass relative to the length of the tibia (HMR), lumen area (LA), vascular reactivity assays (VRA % dilation at 10-9M AcCh) and ROCK activity by the ratio of phosphorylated vs total MYPT1 (MP/ MT) in the aortic wall were determined. Results: Compared to sham rats, in hypertensive rats VRA was significantly decreased (C: 15 ± 1.8 vs D: 2 ± 0.8), whereas SBP (C: 125 ± 2 vs D: 207 ± 7), AMT/LA (C: 0.32 ± 0.01 vs D: 0.4 ± 0.01) and MP/ MT (C: 1 ± 0.12 vs D: 1.77 ± 0.38) were significantly increased. In DOCA hypertensive rats, Ang1-9 significantly reduced SBP (161 ± 6), AMT/LA (0.37 ± 0.01) and aortic MP/ MT (0.65 ± 0.07) but increased VRA (25 ± 1.1). These beneficial effects of Ang-(1-9) were modified by PD123319 but not by A779. Conclusion: Ang1-9 reduces BP and vascular damage by inhibiting ROCK activity in this model of low renin HT. These effects seem be mediated by the AT2R. Fondecyt 1100874 and 1121060.
Crizotinib synergizes with cisplatin in preclinical models of ovarian cancer. (2017)

Crizotinib, a small molecule inhibitor of anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1) and c-MET (also called MET or hepatocyte growth factor receptor), has been approved by the Food and Drug Administration for the treatment of patients with advanced non-small cell lung cancer whose tumors have rearrangements in the ALK or ROS1 gene. However, the anticancer effect of crizotinib on ovarian cancer is still unclear. In this study, our data show that crizotinib can actively induce cell growth inhibition, cell cycle arrest at G2/M phase and apoptosis with the decreasing phosphorylation of the downstream signaling effectors AKT and ERK in human ovarian cancer cells. Crizotinib also increases the intracellular reactive oxidative species (ROS) levels, and pretreating with ROS scavenger N-acety-L-cysteine partially reverses crizotinib-induced apoptosis. Moreover, crizotinib can synergistically inhibit ovarian cancer cells growth <i>in vitro</i> and <i>in vivo when</i> combines with cisplatin. Altogether, crizotinib potently potentiates the activity of cisplatin in ovarian cancer, suggesting the synergistic effect of crizotinib and cisplatin may be valuable for ovarian cancer patients' treatment.