gebhart/patrepeval huggingface dataset:
Effects of Therapeutic Hypothermia on the Glial Proteome and Phenotype (2013)

Therapeutic hypothermia is a useful intervention against brain injury in experimental models and patients, but its therapeutic applications are limited due to its ill-defined mode of action. Glia cells maintain homeostasis and protect the central nervous system from environmental change, but after brain injury, glia are activated and induce glial scar formation and secondary injury. On the other hand, therapeutic hypothermia has been shown to modulate glial hyperactivation under various brain injury conditions. We considered that knowledge of the effect of hypothermia on the molecular profiles of glia and on their phenotypes would improve our understanding of the neuroprotective mechanism of hypothermia. Here, we review the findings of recent studies that examined the effect of hypothermia on proteome changes in reactive glial cells in vitro and in vivo. The therapeutic effects of hypothermia are associated with the inhibition of reactive oxygen species generation, the maintenance of ion homeostasis, and the protection of neurovascular units in cultured glial cells. In an animal model, a distinct pattern of protein alterations was detected in glia following hypothermia under ischemic/reperfusion conditions. In particular, hypothermia was found to exert a neuroprotective effect against ischemic brain injury by regulating specific glial signaling pathways, such as, glutamate signaling, cell death, and stress response, and by influencing neural dysfunction, neurogenesis, neural plasticity, cell differentiation, and neurotrophic activity. Furthermore, the proteins that were differentially expressed belonged to various pathways and could mediate diverse phenotypic changes of glia in vitro or in vivo. Therefore, hypothermia-modulated glial proteins and subsequent phenotypic changes may form the basis of the therapeutic effects of hypothermia.
Coulomb Blockade in Thin SOI Nanodevices (2002)

International audience
Elucidating dynamic behavior of synthetic supramolecular polymers in water by hydrogen/deuterium exchange mass spectrometry (2021)

Abstract A comprehensive understanding of the structure, self‐assembly mechanism, and dynamics of one‐dimensional supramolecular polymers in water is essential for their application as biomaterials. Although a plethora of techniques are available to study the first two properties, there is a paucity in possibilities to study dynamic exchange of monomers between supramolecular polymers in solution. We recently introduced hydrogen/deuterium exchange mass spectrometry (HDX‐MS) to characterize the dynamic nature of synthetic supramolecular polymers with only a minimal perturbation of the chemical structure. To further expand the application of this powerful technique some essential experimental aspects have been reaffirmed and the technique has been applied to a diverse library of assemblies. HDX‐MS is widely applicable if there are exchangeable hydrogen atoms protected from direct contact with the solvent and if the monomer concentration is sufficiently high to ensure the presence of supramolecular polymers during dilution. In addition, we demonstrate that the kinetic behavior as probed by HDX‐MS is influenced by the internal order within the supramolecular polymers and by the self‐assembly mechanism.
Solvation Rule for Solid‐Electrolyte Interphase Enabler in Lithium‐Metal Batteries (2020)

Abstract Despite the exceptionally high energy density of lithium metal anodes, the practical application of lithium‐metal batteries (LMBs) is still impeded by the instability of the interphase between the lithium metal and the electrolyte. To formulate a functional electrolyte system that can stabilize the lithium‐metal anode, the solvation behavior of the solvent molecules must be understood because the electrochemical properties of a solvent can be heavily influenced by its solvation status. We unambiguously demonstrated the solvation rule for the solid‐electrolyte interphase (SEI) enabler in an electrolyte system. In this study, fluoroethylene carbonate was used as the SEI enabler due to its ability to form a robust SEI on the lithium metal surface, allowing relatively stable LMB cycling. The results revealed that the solvation number of fluoroethylene carbonate must be ≥1 to ensure the formation of a stable SEI in which the sacrificial reduction of the SEI enabler subsequently leads to the stable cycling of LMBs.
Crystal structure of (E)-5,5-dimethyl-2-[3-(4-nitrophenyl)allylidene]cyclohexane-1,3-dione (2015)

In the title compound, C17H17NO4, the cylohexane-1,3-dione ring adopts an envelope conformation with the dimethyl-subsituted C atom as the flap. Its mean plane is inclined to the benzene ring by 7.99 (19)°. The mol-ecule has a trans conformation about the bridging C=C bonds of the ally-idene chain. In the crystal, mol-ecules are linked via pairs of C-H⋯O hydrogen bonds, forming inversion dimers. The dimers are linked by further C-H.·O hydrogen bonds, forming sheets lying parallel to (10-1).
Utility based sensor selection (2006)

Sensor networks consist of many small sensing devices that monitor an environment and communicate using wireless links. The lifetime of these networks is severely curtailed by the limited battery power of the sensors. One line of research in sensor network lifetime management has examined sensor selection techniques, in which applications judiciously choose which sensors' data should be retrieved and are worth the expended energy. In the past, many ad-hoc approaches for sensor selection have been proposed. In this paper, we argue that sensor selection should be based upon a tradeoff between application-perceived benefit and energy consumption of the selected sensor set. We propose a framework wherein the application can specify the utility of measuring data (nearly) concurrently at each set of sensors. The goal is then to select a sequence of sets to measure whose total utility is maximized, while not exceeding the available energy. Alternatively, we may look for the most cost-effective sensor set, maximizing the product of utility and system lifetime. This approach is very generic, and permits us to model many applications of sensor networks. We proceed to study two important classes of utility functions: submodular and supermodular functions. We show that the optimum solution for submodular functions can be found in polynomial time, while optimizing the cost-effectiveness of supermodular functions is NP-hard. For a practically important subclass of supermodular functions, we present an LP-based solution if nodes can send for different amounts of time, and show that we can achieve an O(log n) approximation ratio if each node has to send for the same amount of time. Finally, we study scenarios in which the quality of measurements is naturally expressed in terms of distances from targets. We show that the utility-based approach is analogous to a penalty-based approach in those scenarios, and present preliminary results on some practically important special cases.
Major human milk oligosaccharides are absorbed into the systemic circulation after oral administration in rats (2017)

Human milk oligosaccharides (HMO) are involved in many biological functions influencing infant health. Although HMO act locally at the intestine, recent evidence has demonstrated that HMO are partially incorporated into the systemic circulation of breast-fed infants. In the last few years, a large amount of research has been conducted using preclinical models to uncover new biological functions of HMO. The aim of this study was to evaluate the absorption and urine excretion of HMO in rats. We administered a single oral dose of the following HMO: 2'-fucosyllactose (2'-FL), 6'-sialyllactose and lacto-N-neotetraose at different concentrations to adult rats. The time course of absorption of HMO into the bloodstream and their appearance in urine was studied. Our results showed that rats, similar to human infants, are able to effectively absorb a portion of HMO from the intestine into plasma and to excrete them in urine. On the basis of this, we also conducted a specific kinetic absorption study with 2'-FL, the most predominant HMO in human milk, in 9-11-d-old rat pups. Our results confirmed that a significant amount of 2'-FL was absorbed into the systemic circulation and subsequently excreted in urine during lactation in rats in a dose-depended manner. We also found basal levels of these HMO in plasma and urine of adult rats as well as rat pups as a natural result of nursing. Our data suggest that the rat may be a useful preclinical model that provides new insights into the metabolism and functions of HMO.
[Diagnosis and staging of pleural mesothelioma]. (2009)

Accurate diagnosis and staging are very important for the treatment of pleural mesothelioma. In particular, surgical indications based on diagnosis and staging must be determined carefully, since extrapleural pneumectomy (EPP) is a highly invasive surgical mode. Sufficient biopsy specimens to make a differential diagnosis of this disease should be obtained during video-assisted thoracoscopic surgery (VATS). Currently, the final diagnosis of mesothelioma is based not only on the results of hematoxylin and eosin staining but also of immunostaining using several differential markers. The International Mesothelioma Interest Group (IMIG) classification is widely used for the TNM staging of pleural mesothelioma. The IMIG classification is now applied to clinical staging with the aid of computed tomography and positron-emission tomography images, but the accuracy and usefulness of this classification for surgical indications and outcomes must be improved in future. Extended preoperative staging, for example, mediastinoscopy, contralateral VATS, and laparoscopy, are now selectively performed for the precise diagnosis of potentially resectable mesothelioma.
Superluminal Pulse Propagation on a Silicon Chip (2008)

We demonstrate superluminal pulse propagation on a silicon chip using an all optical analog to electromagnetically induced absorption created by the coherent interaction between two micro-resonators. We show effective group indices tunable between −1158 and −312.
Pituitary microadenomas: diagnosis with two-and three-dimensional MR imaging at 1.5 T before and after injection of gadolinium. (1990)

The usefulness of different magnetic resonance (MR) imaging sequences (coronal and sagittal spin-echo [SE] and three-dimensional fast low-angle shot [3D FLASH]) in the detection of pituitary microadenomas before and after gadolinium injection was prospectively evaluated in 28 patients with surgical confirmation. When evaluated separately, the most useful sequences in the detection of these microadenomas were coronal pregadolinium T1-weighted SE, coronal pregadolinium 3D FLASH, coronal postgadolinium T1-weighted SE, and coronal postgadolinium 3D FLASH. The combination of pre- and postgadolinium T1-weighted sequences with pre-and postgadolinium 3D FLASH sequences produced the highest number of true-positive findings (90%) and the lowest number of false-positive findings (5%). When a 1.5-T imaging unit with a high signal-to-noise ratio allowing useful three-dimensional acquisition is used, the authors advocate a coronal T1-weighted SE sequence, followed (if necessary) by a coronal 3D FLASH sequence, both without injection of gadolinium, in the diagnosis of pituitary microadenomas. When no confident diagnosis is reached, the same sequences should be performed after the injection of gadolinium. The sagittal pre- and postgadolinium T1-weighted SE and long-TR SE sequences are useful only in specific cases.
An Evanescent-Mode Cavity-Backed High-Power Tunable Slot Antenna (2019)

In this paper, a new high-power and tunable cavity-backed slot antenna is introduced and experimentally investigated. The proposed antenna is composed of a frequency-tunable evanescent-mode cavity resonator loaded with an annular radiating slot on the cavity back side. Frequency tuning is performed by changing the critical gap size over the resonator's post through a piezotuner disk. A prototype copper-machined fabricated antenna represents about 25% tuning (2-2.57 GHz) of the antenna's 10 dB reflection coefficient when the cavity gap size is varied in the range of 17-171 μm. The introduced antenna depicts ≈5 dBi of gain and radiation efficiency of more than 85%. Moreover, the antenna successfully handles 80 W of input power which can also be increased using a closed loop actuating system. In addition, the proposed antenna shows a good linearity due to the mechanical tuning scheme. Hence, this antenna is promising for high-power applications, which, at the same time, can also be realized on printed circuit boards (PCBs), making it easy for integration with circuits.
Synthesis of cyclic nitrones by bromocyclization of unsaturated oximes (2006)

The bromocyclization of several ,-unsaturated oximes leads to respective bromomethylpyrroline N-oxides. Yields vary from 23 to 87 %, depending on the structural features. An unusual formal N-endo cyclization is found with a ,-enoxime. As a consequence, reversal of steps, i. e. addition of Br/OH to the C=C bond of the unsaturated aldehyde first, followed by oximation, opens access to 6-membered nitrones.
Analysis of a MIMO OFDMA heterogeneous feedback system employing joint scheduling and spatial diversity in Nakagami fading channels (2012)

We present a unified analytical framework to jointly examine spatial, spectral, and multiuser diversity in a general multiuser MIMO OFDMA system. Spectral diversity originates from frequency domain opportunistic scheduling enabled by the OFDMA technique, and is influenced by partial feedback design. We propose a heterogeneous partial feedback design method which adapts users' feedback resources to their frequency domain channel statistics. We investigate this adaptive feedback design by employing the best-M partial feedback strategy, and derive closed form expressions for the average spectral efficiency and bit error rate with different spatial diversity schemes under the generalized Nakagami-m fading channels. We also examine the interplay among the diversity effects using our heterogeneous feedback design as well as the channel fading effect through numerical results.
The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector (2017)

The development and operation of Liquid-Argon Time-Projection Chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.
Cloning and expression of recombinant Aspergillus fumigatus allergen I/a (rAsp f I/a) with IgE binding and type I skin test activity (1992)

Aspergillus fumigatus secretes an 18-kDa nonglycosylated IgE-binding protein. This protein was previously shown to be a ribotoxin, like alpha-sarcin and mitogillin. A 686-bp long A. fumigatus cDNA encoding an 18-kDa ribotoxin was cloned and expressed in Escherichia coli as a fusion protein with six adjacent histidines (rAsp f I/a). rAsp f I/a was purified to homogeneity by Ni(2+)-chelate affinity chromatography and refolded. The recombinant protein was enzymatically active resulting in the cleavage of 28S rRNA within a universally conserved region. rAsp f I/a was cytotoxic for EBV immortalized or PHA stimulated human PBMC. Furthermore, rAsp f I/a was recognized by murine mAb made against an 18-kDa ribotoxin. IgE of individuals allergic to A. fumigatus bound to rAsp f I/a as shown by ELISA, dot blots, and Western blots. rAsp f I/a elicited positive immediate type I skin reactions in individuals allergic to A. fumigatus but not in healthy control individuals. The results show that rAsp f I/a has similar functional characteristics when compared to the native 18-kDa ribotoxin. rAsp f I/a expressed in E. coli can therefore be used as a standardized Ag/allergen for serologic and clinical diagnosis of A. fumigatus-associated diseases.
Search for new phenomena in events with an energetic jet and missing transverse momentum in pp collisions at s=13  TeV with the ATLAS detector (2021)

Results of a search for new physics in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an integrated luminosity of 139 fb -1 at a center-of-mass energy of 13 TeV collected in the period 2015-2018 with the ATLAS detector at the Large Hadron Collider. Compared to previous publications, in addition to an increase of almost a factor of four in the data size, the analysis implements a number of improvements in the signal selection and the background determination leading to enhanced sensitivity. Events are required to have at least one jet with transverse momentum above 150 GeV and no reconstructed leptons (e, or ) or photons. Several signal regions are considered with increasing requirements on the missing transverse momentum starting at 200 GeV. Overall agreement is observed between the number of events in data and the Standard Model predictions. Model-independent 95% confidencelevel limits on visible cross sections for new processes are obtained in the range between 736 fb and 0.3 fb. Results are also translated into improved exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, supersymmetric particles in several compressed scenarios, axionlike particles, and new scalar particles in dark-energyinspired models. In addition, the data are translated into bounds on the invisible branching ratio of the Higgs boson.
An optimization approach to understanding structure-function relationships in the visual cortex (2009)

The relationship between structure and function is of central importance in neuroscience. Computational modeling techniques can play a crucial role in exploring this relationship. Neuroscientists have revealed an interesting patterning in the connectivity of visual cortical areas, where the receptive field sizes for feed-forward, lateral and feedback connections are monotonically increasing and these roughly double. In this paper, we use a computational modeling approach to understand the behavior of the visual system, and show that this observed connectivity pattern can be explained via a maximization of functional metrics based on separation and segmentation accuracies. We use an optimization function based on sparse spatiotemporal encoding and faithfulness of representation to derive the dynamical behavior of a multi-layer network of oscillatory units. The network behavior can be quantified in terms of its ability to separate and segment mixtures of inputs. We vary the topological connectivity between different layers of the simulated visual network and study its effect on performance in terms of separation and segmentation accuracy. We demonstrate that the best performance occurs when the topology of the simulated system is similar to that in the primate visual cortex where the receptive field sizes of feedforward, lateral and feedback connections are monotonically increasing. This explanation of the functional significance of topological connectivity provides a new perspective for the understanding of cortical function.
Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study (2021)

Long-term survival after Liver Transplantation (LT) is often compromised by infectious and metabolic complications. We aimed to delineate alterations in intestinal microbiome (IM) over time that could contribute to medical complications compromising long-term survival following LT. Fecal samples from LT recipients were collected at 3 months (3 M) and 6 months (6 M) post-LT. The bacterial DNA was extracted using E.Z.N.A. Stool DNA Kit and 16S rRNA gene sequencing at V4 hypervariable region was performed. DADA2 and Phyloseq was implemented to analyze the taxonomic composition. Differentially abundant taxa were identified by metagenomeSeq and LEfSe. Piphillin, an Inferred functional metagenomic analysis tool was used to study the bacterial functional content. For comparison, healthy samples were extracted from NCBI and analyzed similarly. The taxonomic & functional profiles of LT recipients were validated with metagenomic sequencing data from animals exposed to immunosuppressants using Venny. Our findings provide a new perspective on longitudinal increase in specific IM communities post-LT along with an increase in bacterial genes associated with metabolic and infectious disease.
Silk fibroin-based active optofluidics (2008)

The ancient silk fiber finds resurgence in a new paradigm of highly functional optofluidic devices embodied by an active oxygenation sensor comprising a hemoglobin infused cast silk integrated diffraction grating for spectral analysis.
Experimental and Theoretical Investigation of Gas/Oil Relative Permeability Hysteresis under Low Oil/Gas IFT and Mixed-Wet Conditions (2012)

Abstract Accurate determination of relative permeability values and their hysteresis is crucial for obtaining a reliable prediction of the performance of water-alternating-gas (WAG) injection in oil reservoirs. In this paper we report two series of gas/oil relative permeability curves obtained from coreflood experiments carried out in a mixed-wet core under a very low oil/gas interfacial tension (IFT) of 0.04mN.m−1. The first set of the corefloods began by oil injection (imbibition) in the core saturated with gas and immobile water (Swi). This was followed by a period of gas injection (drainage) and this sequential injection of oil and gas continued and in total, three imbibition and two drainage periods were carried out. In the second series of experiments, the core was initially saturated with oil and immobile water and the experiment started with a gas injection followed by cycles of drainage and imbibitions. The measured pressure drop and production data were history matched through simulation analysis to obtain krg and kro values for each of the imbibition and drainage cycles. The results show that both the oil and the gas relative permeability curves show cycle-dependent hysteresis despite the very low gas/oil IFT. Therefore, the current assumption in existing models (such as Land, Carlson and Killough) that the drainage scanning kr curves follow the preceding imbibition curve is not supported by our coreflood experiments. When compared to our measured data, Carlson model predictions for krg in imbibition direction are poor. Killough model predictions underestimate krg and overestimate kro especially near trapped gas saturation regions. Beattie et al. hysteresis model is able to capture the krg and kro behavior that we observed in our experiments qualitatively, but it is still unable to predict the value of the observed hysteresis. The results suggest that for mixed-wet systems, it is necessary to consider irreversible hysteresis loops for both the wetting and non-wetting phases. Such capability currently does not exist in reservoir simulators due to lack of appropriate predictive tools.