gebhart/patrepeval huggingface dataset:
Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor (2007)

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.
Supplementary Figure 1 from Intravenous Injection of MVA Virus Targets CD8<sup>+</sup> Lymphocytes to Tumors to Control Tumor Growth upon Combinatorial Treatment with a TLR9 Agonist (2023)

&lt;p&gt;Supplementary Figure 1. CD3+ cells infiltration in tumor invasive margins.&lt;/p&gt;
Fouille de données à l'aide de HMM : Application à la détection de réitérations intragénomiques (2002)

Colloque avec actes et comité de lecture. nationale.
Scenario Reduction With Submodular Optimization (2016)

Stochastic programming methods have been proven to deal effectively with the uncertainty and variability of renewable generation resources. However, the quality of the solution that they provide (as measured by cost and reliability metrics) depends on the accuracy and the number of scenarios used to model this uncertainty and variability. Scenario reduction techniques are used to manage the computational burden by selecting representative scenarios. The common drawback of existing scenario reduction techniques is that the number of representative scenarios is a user-defined parameter. We propose a scenario reduction algorithm based on submodular function optimization to endogenously optimize the number of scenarios as well as rank these scenarios. This algorithm is compared, both qualitatively and quantitatively, with the state-of-the-art fast forward selection algorithm.
Factors Determining Yield Stress and Overrun of Whey Protein Foams (2002)

ABSTRACT: Foams were formed by whipping whey protein solutions (15% w/v protein) containing NaCl, CaCl 2 , lactose, or glycine. Foam overrun and yield stress were determined. Foams made from whey protein ingredients have greater overrun and yield stress if the concentration of β‐lactoglobulin is high relative to a‐lactalbumin. The presence of 0.4 M CaCl 2 in the foaming solution increases overrun and yield stress for β‐lactoglobulin and a‐lactalbumin. The high yield stress of β‐lactoglobulin and a‐lactalbumin foams made from solutions containing CaCl 2 suggests that CaCl 2 is altering rheological properties of the interfacial protein film and/or contributing to protein aggregation or network formation in the lamellae.
Preparation of Oxalate by Precipitation Method with Polyethylene Glycol and Formation Process of the Precipitate. (2000)

Fe3+とM2+(M=Ni,Cu,Co,Zn)を含む複シュウ酸塩を,金属硝酸塩水和物のポリエチレングリコール(以後PEGと略す)溶液を353 K,3h加熱処理することで調製した。シュウ酸塩は,PEG溶液中のPEG-陽イオン複合体が硝酸イオンによって酸化されることで生成した。得られたシュウ酸塩の構造と陽イオン組成は,出発物質であるPEG溶液の組成だけでなく,PEG分子量にも依存した。PEG分子量の増加により,得られたシュウ酸塩の結晶化度や粒子の大きさが増大した。これらの事実を理解するためにPEG溶液中のPEG-陽イオン複合体の生成過程について二つのモデルを検討した。それらは,Fe3+とM2+のPEGへの配位が独立に起こると仮定するものと協同的に起こると仮定するものである。これらのモデルを用いてPEG溶液の陽イオン組成と得られたシュウ酸塩の陽イオン組成の間の関係式を導いた。モデルから導かれた関係と実験結果を比較した結果,Fe3+がPEGに配位するとき,その近傍で常にM2+のPEGへの配位が起こることがわかった。
Author Correction: Transcriptional dysregulation of Interferome in experimental and human Multiple Sclerosis (2018)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Abstract TMP90: Frequency and Risk Factors for Early Neurological Deterioration Among Hyperacute Cerebral Ischemia Patients Treated With and Without Thrombolysis (2020)

Background: Early neurological deterioration (END) is a feared complication of acute cerebral ischemia. However, estimates of END frequency vary widely, rates have not been systematically examined in hyperacute patients presenting within the first 2h of onset, nor separately in patients treated with and without thrombolysis, and risk factors for END have not been well delineated. Methods: We analyzed patients with a final diagnosis of acute cerebral ischemia in the NIH FAST-MAG Phase 3 multicenter clinical trial. END was defined as worsening post-admission by ≥ 4 NIHSS points up to Day 4. We separately analyzed patients who did and did not receive IV tPA. Results: Among 1245 acute cerebral ischemia patients transported by EMS to 55 stroke centers, time from last known well (LKW) to ED arrival was median 59 mins (IQR 80-46), and 36.1% received IV tPA. Overall, 211 (16.9%) experienced END by Day 4, with a greater proportion of END in tPA than non-tPA patients (21.2% vs 14.5%, p=0.003). In multivariate analysis, from 26 candidate variables, among tPA recipients, independent predictors of END were: age (OR 1.03/year, 95%CI 1.01-1.05), diastolic BP (OR 1.01/mm Hg, 95%CI 1.00-1.03), prior stroke (OR 1.65, 95%CI 0.98-2.77), glucose (OR 11.06/10 fold increase, 95%CI 1.90-64.44), and worse ASPECTS score (OR 0.85/point, 95%CI 0.78-0.92). Among non-tPA recipients, independent predictors of END were: more severe NIHSS (OR 1.08/point, 95%CI 1.05-1.11), glucose (OR 8.88/10 fold increase, 95%CI 1.83-43.12), and h/o hypertension (OR 2.62/mm Hg, 95%CI 1.25-5.48), with Akaike information criteria identifying SBP, shorter LKW-to-ED time, and absence of anticoagulant agents as additional contributors. C statistics for these models were 0.68 for tPA patients and 0.73 for non-tPA patients. Conclusions: Among hyperacute cerebral ischemia patients, END occurs in 1 in 5 who receive tPA, and 1 in 7 who do not receive tPA. Greater initial stroke severity (on neurologic exam or imaging), higher glucose, and hypertension increase risk of END for both lytic and non-lytic patients, with older age and prior stroke additionally increasing END risk with tPA. Models based on these risk factors show fair to good performance identifying patients who will experience END after hospital admission.
Genetic variation in gonadal impairment in female survivors of childhood cancer: a PanCareLIFE study protocol (2018)

This international collaboration aims to enhance knowledge of genetic variation which may be included in risk prediction models for gonadal impairment in CCS.
CCN measurements at the Princess Elisabeth Antarctica research station during three austral summers (2019)

Abstract. For three austral summer seasons (2013–2016, each from December to February) aerosol particles arriving at the Belgian Antarctic research station Princess Elisabeth (PE) in Dronning Maud Land in East Antarctica were characterized. This included number concentrations of total aerosol particles (NCN) and cloud condensation nuclei (NCCN), the particle number size distribution (PNSD), the aerosol particle hygroscopicity, and the influence of the air mass origin on NCN and NCCN. In general NCN was found to range from 40 to 6700 cm−3, with a median of 333 cm−3, while NCCN was found to cover a range between less than 10 and 1300 cm−3 for supersaturations (SSs) between 0.1 % and 0.7 %. It is shown that the aerosol is dominated by the Aitken mode, being characterized by a significant amount of small, and therefore likely secondarily formed, aerosol particles, with 94 % and 36 % of the aerosol particles smaller than 90 and ≈35 nm, respectively. Measurements of the basic meteorological parameters as well as the history of the air masses arriving at the measurement station indicate that the station is influenced by both marine air masses originating from the Southern Ocean and coastal areas around Antarctica (marine events – MEs) and continental air masses (continental events – CEs). CEs, which were defined as instances when the air masses spent at least 90 % of the time over the Antarctic continent during the last 10 days prior to arrival at the measurements station, occurred during 61 % of the time during which measurements were done. CEs came along with rather constant NCN and NCCN values, which we denote as Antarctic continental background concentrations. MEs, however, cause large fluctuations in NCN and NCCN, with low concentrations likely caused by scavenging due to precipitation and high concentrations likely originating from new particle formation (NPF) based on marine precursors. The application of HYSPLIT back trajectories in form of the potential source contribution function (PSCF) analysis indicate that the region of the Southern Ocean is a potential source of Aitken mode particles. On the basis of PNSDs, together with NCCN measured at an SS of 0.1 %, median values for the critical diameter for cloud droplet activation and the aerosol particle hygroscopicity parameter κ were determined to be 110 nm and 1, respectively. For particles larger than ≈110 nm the Southern Ocean together with parts of the Antarctic ice shelf regions were found to be potential source regions. While the former may contribute sea spray particles directly, the contribution of the latter may be due to the emission of sea salt aerosol particles, released from snow particles from surface snow layers, e.g., during periods of high wind speed, leading to drifting or blowing snow. The region of the Antarctic inland plateau, however, was not found to feature a significant source region for aerosol particles in general or for cloud condensation nuclei measured at the PE station in the austral summer.
Survey of Analysis, Simulation and Modeling for Large Scale Logic Circuits (1981)

The purpose of this paper is to introduce recent developments in the time analysis, simulation and modeling of logic circuits. These advances which have taken place in the circuit and systems area augment the recent advances in logic time simulators. The latest trend has been to combine the approaches into a single system, a so called mixed simulation-analysis program. In this paper we review some of the circuit oriented techniques at a level understandable to the non circuit-theorist.
Adipose-immune interactions during obesity and caloric restriction: reciprocal mechanisms regulating immunity and health span (2008)

Increasing evidence suggests a tight coupling of metabolic and immune systems. This cross-talk mediated by neuroendocrine peptides as well as numerous cytokines and chemokines is believed to be responsible for integrating energy balance to immune function. These neuroendocrine-immune interactions are heightened during the state of chronic positive energy balance, as seen during obesity, and negative energy balance caused by caloric restriction (CR). Emerging evidence suggests that obesity may be associated with an immunodeficient state and chronic inflammation, which contribute to an increased risk of premature death. The direct interactions between expanded leukocyte populations within the adipose tissue during obesity and an increased number of adipocytes within an aging lymphoid microenvironment may constitute an important adaptive or pathological response as a result of change in energy balance. In stark contrast to obesity, CR causes negative energy balance and robustly prolongs a healthy lifespan in all of the species studied to date. Therefore, the endogenous neuroendocrine-metabolic sensors elevated or suppressed as a result of changes in energy balance may offer an important mechanism in understanding the antiaging and potential immune-enhancing nature of CR. Ghrelin, one such sensor of negative energy balance, is reduced during obesity and increased by CR. Ghrelin also regulates immune function by reducing proinflammatory cytokines and promotes thymopoiesis during aging and thus, may be a new CR mimetic target. The identification of immune effects and molecular pathways used by such orexigenic metabolic factors could offer potentially novel approaches to enhance immunity and increase healthy lifespan.
Enzymatic Glycosylation of Peptide Arrays on Gold Surfaces (2008)

Play it again, SAM. Peptide substrates immobilised on self-assembled monolayer (SAM)-coated gold surfaces were efficiently glycosylated with UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (ppGalNAcT2) to form the α-D-GalNAc threonine/serine linkage. Label-free analysis of the reactions were performed by using MALDI-ToF mass spectrometry.
Flying by Feeling: Communicating Flight Envelope Protection through Haptic Feedback (2021)

&lt;p&gt;Modern aircraft can be equipped with a flight envelope protection system: automation which modifies pilot control inputs to ensure that the aircraft remains within the allowable limits. Overruling the pilot inputs may lead to mode confusion, even when visual or auditory feedback is provided to alert pilots. We advocate using active control devices to make the flight envelope protection system tangible to the pilot. This paper presents the main findings of an evaluation of three haptic feedback designs for flight envelope protection. The first concept used both force feedback and vibro-tactile alerts, producing promising, yet inconclusive, results. The second concept used asymmetric vibrations to give directional alerting cues, which did not result in improved performance on initial use, but which did yield improved learning rate for the task. The third system employed force feedback to physically guide the pilot away from flight envelope limits, which yielded safety improvements from the first use, but created dependence: pilot performance degraded immediately after the force feedback was removed. From this, we advise to use asymmetric vibrations during training for flight envelope excursions, to leverage active control interfaces for providing force feedback during operation, and reevaluate a combination of both to combine their advantages for single-pilot operations.&lt;/p&gt;
Deep Learning-Based Adaptive Image Compression System for a Real-World Scenario (2020)

Deep Learning-based (DL) image compression has shown prominent results compared to standard image compression techniques like JPEG, JPEG2000, BPG and WebP. Nevertheless, neither DL nor standard techniques generally can cope with critical real-world scenarios, with stringent performance constraints. In order to explore the nature of this gap, we first introduce an industrial scenario, which contemplates real-time compression of high-resolution images, with strict requirements on a number of quality-performance indicators, namely: the output image quality, the hardware, and the compression complexity. Next, we propose a DL-based image compression model, i.e. a Convolutional Residual Autoencoder (CRAE). In particular, CRAE integrates some structural benefits of a deep neural network, including PReLU activation function and sub-pixel convolution, which have proven to be especially suitable for image compression tasks. We analyze the performance of the proposed CRAE approach by adopting two types of processing: (i) global and, (ii) patch-based processing of image data. To test the models, we exploit a dataset composed of high-resolution images provided by the MERMEC company composed of consecutive images of the railway track captured by a machine vision system called V-CUBE. Furthermore, the company provided strict compression requirements that needed to be met by the developed system. Preliminary results of an ongoing study indicates that the proposed image compression system can meet the requirements by MERMEC with reasonable performance, with a mild advantage observed for full-based CRAE. The obtained outcomes suggests that CRAE can adapt to the specific structure of the given dataset and extracts the salient recurrent patterns inside an image. In summary, this line of research represents the core of the future plug-and-play DL architecture for constrained image compression.
Sagittal focusing of high-energy synchrotron X-rays with asymmetric Laue crystals. II. Experimental studies (2001)

The use of bent asymmetric Laue crystals to focus synchrotron X-rays sagittally from 15 to 50 keV is described. A four-bar bender, bending a rectangular planar crystal, produced the necessary sagittal and meridional bending for this unique application. Adjustments of the tilt angle and height of the bent crystal resulted in first- and second-order corrections, respectively, to the dependence of the angle of diffraction on the horizontal position on the crystal. After these corrections, the remaining variation of the diffraction angle was of the order of 10 µrad. The theoretical sagittal focal length was verified. A prototype of a double-crystal sagittally focusing monochromator was constructed and tested, using two identical Laue crystals. A horizontal divergence of 3 mrad was focused to a horizontal dimension of about 0.4 mm. The X-ray flux density at the focus was a few hundred times larger than that of unfocused X-rays.
Water-Gated Transistor Using Ion Exchange Resin for Potentiometric Fluoride Sensing (2020)

We introduce fluoride-selective anion exchange resin sorbents as sensitisers into membranes for water-gated field effect transistors (WGTFTs). Sorbents were prepared via metal (La or Al)-loading of a commercial macroporous aminophosphonic acid resin, Puromet<sup>TM</sup> MTS9501, and were filled into a plasticised poly(vinyl chloride) (PVC) phase transfer membrane. We found a potentiometric response (membrane potential leading to WGTFT threshold shift) to fluoride following a Langmuir-Freundlich (LF) adsorption isotherm with saturated membrane potential up to ~480 mV, extremely low characteristic concentration c<sub>1/2</sub> = 1/K, and picomolar limit of detection (LoD), even though ion exchange did not build up charge on the resin. La-loading gave a superior response compared to Al-loading. Membrane potential characteristics were distinctly different from charge accumulating sensitisers (e.g., organic macrocycles) but similar to the Cs<sup>+</sup> (cation) selective ion-exchanging zeolite mineral 'mordenite'. We propose a mechanism for the observed threshold shift and investigate interference from co-solutes. Strong interference from carbonate was brought under control by 'diluting' metal loading in the resin. This work sets a template for future studies using an entirely new 'family' of sensitisers in applications where very low limit of detection is essential such as for ions of arsenic, mercury, copper, palladium, and gold.
QSAR Analysis for ADA upon Interaction with a Series of Adenine Derivatives as Inhibitors (2004)

The kinetic parameters of adenosine deaminase such as Km and Ki were determined in the absence and presence of adenine derivatives (R1-R24) in sodium phosphate buffer (50 mM; pH 7.5) solution at 27 degrees C. These kinetic parameters were used for QSAR analysis. As such, we found some theoretical descriptors to which the binding affinity of adenosine deaminase (ADA) towards several adenine nucleosides as inhibitors is correlated. QSAR analysis has revealed that binding affinity of the adenine nucleosides upon interaction with ADA depends on the molecular volume, dipole moment of the molecule, electric charge around the N1 atom, and the highest of positive charge for the related molecules.
A Dual Adversarial Calibration Framework for Automatic Fetal Brain Biometry (2021)

This paper presents a novel approach to automatic fetal brain biometry motivated by needs in low- and medium- income countries. Specifically, we leverage high-end (HE) ultrasound images to build a biometry solution for low-cost (LC) point-of-care ultrasound images. We propose a novel unsupervised domain adaptation approach to train deep models to be invariant to significant image distribution shift between the image types. Our proposed method, which employs a Dual Adversarial Calibration (DAC) framework, consists of adversarial pathways which enforce model invariance to; i) adversarial perturbations in the feature space derived from LC images, and ii) appearance domain discrepancy. Our Dual Adversarial Calibration method estimates transcerebellar diameter and head circumference on images from low-cost ultrasound devices with a mean absolute error (MAE) of 2.43mm and 1.65mm, compared with 7.28 mm and 5.65 mm respectively for SOTA.
An apparently high flux of primary cosmic-ray He-nuclei at 41 deg N mag. (1967)

Unexpected excess of primary cosmic ray helium nuclei flux value in nuclear photographic emulsions
Profiling Floats in SOCCOM: Technical Capabilities for Studying the Southern Ocean (2018)

Abstract We report on profiling float technology used in the Southern Ocean Carbon and Climate Observations and Models (SOCCOM) program, a 6 year study of the interaction of ocean physics and the carbon cycle in the Southern Ocean. A central part of this program is to produce and deploy 200 profiling floats equipped with CTD units and chemical sensors capable of measuring dissolved oxygen, nitrate, pH, chlorophyll fluorescence, and particulate backscatter. The performance of the first 63 floats deployed in SOCCOM is examined, and examples of the design criteria used in producing these floats are shown. Some of the sensors require surface measurements to be made in the dark at regular intervals, and the probability of ascending to the sea surface in the dark is estimated as a function of year‐day and latitude. An energy budget derived from laboratory measurements shows that only about 25% of the total energy stored in the batteries is used by the biogeochemical sensors, which bodes well for the long‐term survivability of the floats. The ice‐avoidance algorithm is discussed in detail, and it is shown that it is working as designed and allowing unprecedented numbers of profiles to be collected beneath the wintertime ice cover. The overall reliability of the first group of SOCCOM floats is compared with a much larger ensemble of Argo floats; the results show that the SOCCOM floats are surviving at a rate similar to the Argo floats, which have been shown to have lifetimes in excess of 5 years.
Pushing the boundaries of polytopal realizability (2011)

Let ∆(d, n) be the maximum possible diameter of the vertex-edge graph over all d-dimensional polytopes defined by n inequalities. The Hirsch bound holds for particular n and d if ∆(d, n) ≤ n − d. Francisco Santos recently resolved a question open for more than five decades by showing that ∆(d, 2d) = d + 1 for d = 43; the dimension was then lowered to 20 by Matchske, Santos and Weibel. This progress has stimulated interest in related questions. The existence of a polynomial upper bound for ∆(d, n) is still an open question, the best bound being the quasi-polynomial one due to Kalai and Kleitman in 1992. Another natural question is for how large n and d the Hirsch bound holds. Goodey showed in 1972 that ∆(4, 10) = 5 and ∆(5, 11) = 6, and more recently, Bremner and Schewe showed ∆(4, 11) = ∆(6, 12) = 6. Here we show that ∆(4, 12) = ∆(5, 12) = 7 and present strong evidence that ∆(6, 13) = 7.