gebhart/patrepeval huggingface dataset:
Impact of Antibiotic-Resistant Bacteria on Immune Activation and Clostridioides difficile Infection in the Mouse Intestine (2020)

Antibiotic treatment of patients undergoing complex medical treatments can deplete commensal bacterial strains from the intestinal microbiota, thereby reducing colonization resistance against a wide range of antibiotic-resistant pathogens. Loss of colonization resistance can lead to marked expansion of vancomycin-resistant <i>Enterococcus faecium</i> (VRE), <i>Klebsiella pneumoniae</i>, and <i>Escherichia coli</i> in the intestinal lumen, predisposing patients to bloodstream invasion and sepsis. The impact of intestinal domination by these antibiotic-resistant pathogens on mucosal immune defenses and epithelial and mucin-mediated barrier integrity is unclear. We used a mouse model to study the impact of intestinal domination by antibiotic-resistant bacterial species and strains on the colonic mucosa. Intestinal colonization with <i>K. pneumoniae</i>, <i>Proteus mirabilis</i>, or <i>Enterobacter cloacae</i> promoted greater recruitment of neutrophils to the colonic mucosa. To test the hypothesis that the residual microbiota influences the severity of colitis caused by infection with <i>Clostridioides difficile</i>, we coinfected mice that were colonized with ampicillin-resistant bacteria with a virulent strain of <i>C. difficile</i> and monitored colonization and pathogenesis. Despite the compositional differences in the gut microbiota, the severity of <i>C. difficile</i> infection (CDI) and mortality did not differ significantly between mice colonized with different ampicillin-resistant bacterial species. Our results suggest that the virulence mechanisms enabling CDI and epithelial destruction outweigh the relatively minor impact of less-virulent antibiotic-resistant intestinal bacteria on the outcome of CDI.
Lifetime measurements on silicon-on-insulator wafers (1993)

We report noncontact measurements of the effective minority carrier lifetime in the superficial silicon layer of silicon-on-insulator wafers. The carriers are excited by a pulse of short-wavelength photons (λ≤350 nm), all of which are absorbed in the first 500 Å of the silicon layer. The carriers are detected by the change in microwave reflectance in a resonant circuit to which the wafer is coupled. The results obtained vary from ∼3 μs for a three year old separation by implanted oxygen (SIMOX) wafer to ∼25 μs for current vendor SIMOX and bond-etchback samples. The variation in free surface recombination velocity is eliminated by HF passivating the samples prior to measurement.
Probing the Reactivity and Radical Nature of Oxidized Transition Metal-Thiolate Complexes by Mass Spectrometry (2013)

Transition metal thiolate complexes such as [PPN](+)[RuL3](-) (PPN = bis(triphenylphosphoranylidene) ammonium and L = diphenylphosphinobenzenethiolate) are known to undergo addition reactions with unsaturated hydrocarbons via the formation of new C-S bonds in solution upon oxidation. The reaction mechanism is proposed to involve metal-stabilized thiyl radical intermediates, a new type of distonic ions such as [RuL3](+) ion in the case of [PPN](+)[RuL3](-). This study presents the reactivity and structure investigation of [RuL3](+) by mass spectrometry (MS) in conjunction with ion/molecule reactions. The addition reactions of [RuL3](+) with alkenes or methyl ketones in the gas phase are indeed observed, in agreement with the proposed mechanism. Such reactivity is also maintained by several fragment ions of [RuL3](+), indicating the preserved thiyl diradical core structure is responsible for the addition reaction. The thiyl radical nature of [RuL3](+) was further verified by the ion/molecule reaction of [RuL3](+) with dimethyl disulfide, in which the characteristic CH3S• transfer occurs, both at atmospheric pressure and also at low pressure (~mTorr). These results provide, for the first time, clear mass spectrometric evidence of the radical nature of [RuL3](+) (i.e., the distonic ion structure of [RuL3](+)), arising from the oxidation of non-innocent thiolate ligands of the complex [PPN](+)[RuL3](-). Similar thiolate complexes, including ReL3 and NiL2, were also examined. Although reactions of oxidized ReL3 or NiL2 with CH3SSCH3 take place at atmospheric pressure, the corresponding reaction did not occur in vacuum. Consistent with these data, the addition of ethylene was not observed either, indicating lower reactivities of [ReL3](+) and [NiL2](+) in comparison to [RuL3](+).
The Projected GSURE for Automatic Parameter Tuning in Iterative\n Shrinkage Methods (2010)

Linear inverse problems are very common in signal and image processing. Many\nalgorithms that aim at solving such problems include unknown parameters that\nneed tuning. In this work we focus on optimally selecting such parameters in\niterative shrinkage methods for image deblurring and image zooming. Our work\nuses the projected Generalized Stein Unbiased Risk Estimator (GSURE) for\ndetermining the threshold value lambda and the iterations number K in these\nalgorithms. The proposed parameter selection is shown to handle any degradation\noperator, including ill-posed and even rectangular ones. This is achieved by\nusing GSURE on the projected expected error. We further propose an efficient\ngreedy parameter setting scheme, that tunes the parameter while iterating\nwithout impairing the resulting deblurring performance. Finally, we provide\nextensive comparisons to conventional methods for parameter selection, showing\nthe superiority of the use of the projected GSURE.\n
Subtilisin inhibitors in <i>Canavalia</i> and <i>Vicia faba</i> seeds. A comparative study (1989)

Abstract Subtilisin isoinhibitors (SI) were isolated from jack bean ( Canavalia ensiformis L ) and broad bean ( Vicia faba L ) seeds. Jack beans contain three isoinhibitors (pI 6.6, 6.3 and 6.0) that constitute 0.021 g per 100 g of dry seeds, while the two active proteins from broad beans (pI 5.7 and 5.1) represent 0.028%. The molecular weight, determined by gel filtration, is around 8000 D in both legumes. Large variations in specific activity of SI against subtilisin Carlsberg were detected in six species of the Canavalia genus, whereas only slight changes were found among six cultivars of C ensiformis. Antibodies raised against SI isolated from jack beans are specific for SI from different varieties of this and other species of the Canavalia genus. However, they do not recognise SI from broad beans and other legume seeds tested. In broad beans the variability between cultivars is significant. Cv Canaria has two active bands and four are detected in the ‚dark’︁ variety, which is 2.7 times less active than the former. SI are specific towards microbial serine proteases, showing high affinity for proteinase K. No appreciable activity against animal proteases or plant thiol enzymes can be detected. SI are also inactive against 4 alpha‐amylases of different origins. Reversible limited proteolysis of the reactive site bond suggests that SI interact with subtilisin by the ‚standard mechanism’︁ usually accepted for the inhibition of trypsin by its proteinaceous inhibitors.
Density Functional Theory Study on the Cleavage Mechanism of the Carbonyl Bond in Amides on Flat and Stepped Ru Surfaces: Hydrogen-Induced or Direct C–O Bond Breaking? (2012)

We have performed density functional theory (DFT) calculations to investigate the reaction mechanism of the cleavage of the carbonyl bond in amides on both flat and stepped Ru surfaces. The simplest amide molecule, N,N-dimethylacetamide (DMA), was used as the exemplar model molecule. Through the calculations, the most stable transition states (TSs) in all the pathways on both flat and stepped Ru surfaces are identified. Comparing the energy profiles of different reaction pathways, we find that a direct cleavage mechanism is always energetically favored as compared with an alternative hydrogen-induced mechanism on either the flat or stepped Ru surface. It is easier for the dissociation process to occur on the stepped surface than on the flat surface. However, as compared with the terrace, the superiority of step sites boosting the C–O bond dissociation is not as evident as that on CO dissociation.
Channel Sounding Pilot Overhead Reduction for TDD Multiuser MIMO Systems (2009)

Coordinated linear transmit-receive processing with beam selection is a method to utilize all degrees of freedom available in multiuser multiple-input multiple-output (MIMO) cellular systems in order to increase system capacity. By applying channel state information in the transmitter (CSIT), the base station (BS) is able to spatially multiplex downlink data streams for different users. In the time division duplex (TDD) mode, CSIT for the BS is provided by means of uplink CSI sounding pilots. However, antenna-specific uplink pilot streams cause an extensive overhead that restricts the size of the practical user group and the terminal antenna setup that can be handled within the same time-frequency slot. We propose to reduce the required overhead by letting the terminals form pilot beams by transmit precoding, based on the knowledge of the user-specific MIMO channels obtained via a downlink common pilot signal. The achievable rate of the system is evaluated in conjunction with channel estimation and linear receivers. According to the results, the performance loss induced by the incomplete sounding is minor, as the beamforming gain provided by multiple terminal antennas, and the multiuser diversity seen by the BS are retained. When taking into account the CSI estimation error in the BS, the overhead reduction turns out to improve robustness and even increase the average system capacity.
Mechanically Stabilized Tetrathiafulvalene Radical Dimers (2011)

Two donor-acceptor [3]catenanes-composed of a tetracationic molecular square, cyclobis(paraquat-4,4'-biphenylene), as the π-electron deficient ring and either two tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) containing macrocycles or two TTF-butadiyne-containing macrocycles as the π-electron rich components-have been investigated in order to study their ability to form TTF radical dimers. It has been proven that the mechanically interlocked nature of the [3]catenanes facilitates the formation of the TTF radical dimers under redox control, allowing an investigation to be performed on these intermolecular interactions in a so-called "molecular flask" under ambient conditions in considerable detail. In addition, it has also been shown that the stability of the TTF radical-cation dimers can be tuned by varying the secondary binding motifs in the [3]catenanes. By replacing the DNP station with a butadiyne group, the distribution of the TTF radical-cation dimer can be changed from 60% to 100%. These findings have been established by several techniques including cyclic voltammetry, spectroelectrochemistry and UV-vis-NIR and EPR spectroscopies, as well as with X-ray diffraction analysis which has provided a range of solid-state crystal structures. The experimental data are also supported by high-level DFT calculations. The results contribute significantly to our fundamental understanding of the interactions within the TTF radical dimers.
Phase-Field Simulation of Li-Ion Diffusion and Stress Evolution in Cathode Materials in NCA-Type Li-Ion Batteries (2020)

The crack propagation in a positive electrode of lithium (Li)-ion batteries degrades the performance of Li-ion batteries. The crack propagation is driven by the Li intercalation- and deintercalation-induced stress-field in the electrode. In order to prevent the degradation of Li-ion battery performance, it is essential to understand the Li-ion diffusion and stress evolution in the positive electrode during the charging and discharging processes. Phase-field (PF) method has been widely used as a powerful numerical simulation methodology for analyzing micro- and meso-scale phenomena including electrochemical reactions. In this study, we develop a PF model for simulating the Li-ion diffusion and stress evolution in a positive electrode in a LiNi 1- x - y Co x Al y O 2 (NCA)-type Li-ion battery, which attracts attentions as a high-capacity cathode material. In the PF model, the Li-ion diffusion in the NCA electrode is treated by the Cahn-Hilliard equation which incorporates the Butler-Volmer equation. The stress evolution is analyzed based on the PF microelasticity theory. The elastic constants and lattice misfit strains of NCA electrode used in the PF model were obtained from first-principles calculation. Using the developed PF model, we investigate the Li-ion diffusion and stress evolution in a NCA second-particle, which strongly depends on the distribution and crystal orientation of primary NCA particles in the second-particle.
DeepRadioID: Real-Time Channel-Resilient Optimization of Deep\n Learning-based Radio Fingerprinting Algorithms (2019)

Radio fingerprinting provides a reliable and energy-efficient IoT\nauthentication strategy. By mapping inputs onto a very large feature space,\ndeep learning algorithms can be trained to fingerprint large populations of\ndevices operating under any wireless standard. One of the most crucial\nchallenges in radio fingerprinting is to counteract the action of the wireless\nchannel, which decreases fingerprinting accuracy significantly by disrupting\nhardware impairments. On the other hand, due to their sheer size, deep learning\nalgorithms are hardly re-trainable in real-time. Another aspect that is yet to\nbe investigated is whether an adversary can successfully impersonate another\ndevice fingerprint. To address these key issues, this paper proposes\nDeepRadioID, a system to optimize the accuracy of deep-learning-based radio\nfingerprinting algorithms without retraining the underlying deep learning\nmodel. We extensively evaluate DeepRadioID on a experimental testbed of 20\nnominally-identical software-defined radios, as well as on two datasets made up\nby 500 ADS-B devices and by 500 WiFi devices provided by the DARPA RFMLS\nprogram. Experimental results show that DeepRadioID (i) increases\nfingerprinting accuracy by about 35%, 50% and 58% on the three scenarios\nconsidered; (ii) decreases an adversary's accuracy by about 54% when trying to\nimitate other device fingerprints by using their filters; (iii) achieves 27%\nimprovement over the state of the art on a 100-device dataset.\n
Detection of ALK, RET, ROS1, NTRK1 and MET rearrangements and actionable mutations using next generation sequencing in patients with non-small cell lung cancer (2018)

Background: Targeted therapies have been developed this last decade and considerably improved PFS and OS of patients with NSCLC. Next-Generation Sequencing (NGS) is commonly used for the detection of actionable mutations in a panel of genes and FISH or IHC are the gold-standard assay for the detection of rearrangements of ALK, RET, ROS1, NTRK1 and MET. The aim of this study is to evaluate the suitability and reliability of NGS assay for the detection of rearrangements compared to the results obtained using FISH and IHC. Methods: 86 FFPE samples, primary tumors or micro biopsies of patients with NSCLC, were analyzed in 7 European labs for this study. All samples were qualified by a senior pathologist prior to analysis. DNA and RNA were extracted from FFPE samples using Qiagen AllPrep kit. TruSight™ Tumor 15 and INCa panel kits were used for DNA library preparation and Archer® FusionPlex® panel kit for RNA library preparation. Both libraries were finally pooled and analyzed using illumina MiSeq sequencing system. Data were finally analyzed using Variant Studio software or Biomedical Genomics Workbench and Ingenuity Variant Analysis for SNV or indel and Archer Analysis software for rearrangements. SNV, indel and rearrangements found for each sample were finally compared to FISH and IHC results and previous DNA sequencing data when available in the labs. Results: 86 DNA and RNA libraries were sequenced. Among 86 samples 8 failed fusion quality control, due to too low amount or too degraded input RNA. No FISH and IHC results were available for 12 samples. Rearrangements were found for 28 samples, 22, 5 and 1 with an ALK, ROS1 and RET rearrangements respectively. Among 74 samples with previously known rearrangements, all samples showed full concordance with previous methods. Conclusions: RNA based NGS is a suitable and reliable alternative to FISH and/or IHC for the detection of rearrangements of ALK, RET, ROS1, NTRK1 and MET genes for the theragnostic management of patients with NSCLC. Further investigations are needed to determine if an “all NGS strategy” is more likely cost-effective and faster than a “FISH and NGS strategy”. Legal entity responsible for the study: Institut de Cancérologie de Lorraine. Funding: Illumina. Disclosure: A. Harlé: All reagents used in this study were provided free of charge by Illumina and Archer. I. Vogl: Works at Genolytic GmbH. All other authors have declared no conflicts of interest.
Transcriptional Activities of Reovirus RNA Polymerase in Recoated Cores (2000)

The particle-associated reovirus polymerase synthesizes mRNA within only certain viral particle types. Reovirus cores, subviral particles lacking outer capsid proteins mu1, sigma3, and sigma1, produce mRNA and abortive transcripts. Reovirus virions, which contain complete outer capsids, cannot produce mRNA and produce few abortive transcripts. Recoated cores are virion-like particles generated by the addition of recombinant outer capsid proteins to cores. We used recoated cores to analyze transcriptional regulation by reovirus outer capsid proteins. Partially recoated particles, containing less than virion amounts of mu1 and sigma3, synthesized mRNA at levels inversely proportional to outer capsid protein levels. Fully recoated cores exhibited undetectable mRNA synthesis levels, as did virions. However, recoated cores produced high levels of abortive transcripts. Recoated core abortive transcripts remained particle-associated and appeared to inhibit further abortive transcript production. Proteolysis of recoated cores removing mu1 and sigma3 released accumulated abortive transcripts and relieved inhibition of mRNA and abortive transcript synthesis. These results suggest transcriptional elongation, but not initiation, is blocked by virion-like amounts of mu1 and sigma3. Particle-associated abortive transcripts may down-regulate transcriptional initiation. Minor outer capsid protein sigma1 had no demonstrable effect on transcriptional activities. Transcriptional regulation may ensure progeny virions do not compete with transcribing particles for ribonucleoside triphosphates.
Finite Element Analysis on Non-Isothermal Glass Molding (2012)

Glass molding is a high-volume fabrication method for producing optical components. Non-isothermal glass molding press (NGM) was proposed to fabricate optical glass, and its characteristics were studied by finite element method (FEM) simulation. The coupled thermo-mechanical analysis was carried out to analyze the key factors such as temperature distribution, stress distribution and strain distribution. The non-isothermal and isothermal glass molding (IGM) was studied, and optimal temperature match between glass and mold was obtained.
Time to Steroid Independence After Laser Interstitial Thermal Therapy vs Medical Management for Treatment of Biopsy-Proven Radiation Necrosis Secondary to Stereotactic Radiosurgery for Brain Metastasis (2022)

These data suggest that LITT for treatment of biopsy-proven RN after SRS for BM significantly decreases time to steroid independence. Prospective trials should be designed to further validate the utility of LITT for RN and its impact on steroid-induced morbidity.
Machine Learning in Python: Main Developments and Technology Trends in Data Science, Machine Learning, and Artificial Intelligence (2020)

Smarter applications are making better use of the insights gleaned from data, having an impact on every industry and research discipline. At the core of this revolution lies the tools and the methods that are driving it, from processing the massive piles of data generated each day to learning from and taking useful action. Deep neural networks, along with advancements in classical machine learning and scalable general-purpose graphics processing unit (GPU) computing, have become critical components of artificial intelligence, enabling many of these astounding breakthroughs and lowering the barrier to adoption. Python continues to be the most preferred language for scientific computing, data science, and machine learning, boosting both performance and productivity by enabling the use of low-level libraries and clean high-level APIs. This survey offers insight into the field of machine learning with Python, taking a tour through important topics to identify some of the core hardware and software paradigms that have enabled it. We cover widely-used libraries and concepts, collected together for holistic comparison, with the goal of educating the reader and driving the field of Python machine learning forward.
Functional analysis of the sucrose phosphate synthase gene family in Arabidopsis (2015)

Poster presentado en el XXI Reunion de la Sociedad Espanola de Fisiologia Vegetal y el XIV Congreso Hispano-Luso Fisiologia Vegetal, celebrado en Toledo del 14 al 17 de junio de 2015.
A short synthesis of (R)-(+)-frontalin and Latia luciferin using new organosilicon reagents (1978)

P. Magnus and G. Roy, J. Chem. Soc., Chem. Commun., 1978, 297 DOI: 10.1039/C39780000297
MMP levels in the response to degradable implants in the presence of a hydroxamate‐based matrix metalloproteinase sequestering biomaterial <i>in vivo</i> (2009)

The inflammatory response to an implanted tissue engineered construct alters the remodeling that occurs and this can diminish the intended therapeutic effect. It was hypothesized that the use of a hydroxamate-based matrix metalloproteinase (MMP) sequestering biomaterial (MI) in the form of approximately 200 microm microspheres would lower the amount and activity of MMP in vivo in response to a subcutaneous, degradable implant (gelatin or Integra disc). MMP degrade extracellular matrix, facilitating inflammatory cell migration and local remodeling of the implant environment. Gelatin or Integra discs were implanted subcutaneously in the backs of CD1 mice together with 30 mg of MI microspheres or with 30 mg of similarly sized control poly(methyl methacrylate) (PMMA) microspheres in a paired study. To sample the implant space, weakly adsorbed protein or attached cells were recovered from explanted discs by soaking the discs in PBS overnight at 4 degrees C. Unexpectedly, MMP-2, -8, -9, and TIMP-1 levels were surprisingly similar in this recovered fluid for the two treatments. Also, there were significantly more (and at day 4 an order of magnitude more) leukocytes recovered from the gelatin discs coimplanted with the MI microspheres than with the PMMA control. It is suggested that the MI microspheres disturbed the natural MMP control pathway leading to high-leukocyte numbers, especially at early times. These results highlight the challenge associated with controlling the fate of tissue engineered constructs in vivo.
Pacing-associated cardiomyopathy in adult congenital heart disease (2020)

In a cohort of patients with ACHD followed long-term post-pacing, 24% developed cardiomyopathy that was significantly associated with a higher burden of ventricular pacing (VP ≥70%). Given promising response rates to CRT, patients with ACHD expected to pace in the ventricle should be closely monitored for systemic ventricular decline.