gebhart/patrepeval huggingface dataset:
From In Vitro to In Vivo: A Rational Flowchart for the Selection and Characterization of Candidate Probiotic Strains in Intestinal Disorders (2023)

Experimental and clinical evidence has demonstrated the potential of probiotic strains in the prevention or treatment of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). However, there is little data on what the methodology leading to the identification of such strains should be. In this work, we propose a new flowchart to identify strains with probiotic potential for the management of IBS and IBD, which we tested on a collection of 39 lactic acid bacteria and Bifidobacteria strains. This flowchart included in vitro tests of immunomodulatory properties on intestinal and peripheral blood mononuclear cells (PBMCs), assessment of the barrier-strengthening effect by measuring transepithelial electric resistance (TEER) and quantification of short-chain fatty acids (SCFAs) and aryl hydrocarbon receptor (AhR) agonists produced by the strains. The in vitro results were then combined in a principal component analysis (PCA) to identify strains associated with an anti-inflammatory profile. To validate our flowchart, we tested the two most promising strains identified in the PCA in mouse models of post-infectious IBS or chemically induced colitis to mimic IBD. Our results show that this screening strategy allows the identification of strains with potential beneficial effects on colonic inflammation and colonic hypersensitivity.
Vibrational energy redistribution in glyoxal following internal conversion (1979)

The vibrational redistribution of energy following internal conversion in glyoxal has been studied in a molecular beam using the ’’pump-and-probe’’ technique. A beam of glyoxal is initially pumped from So to a selected vibronic level of S1. After internal conversion occurs, a tunable dye laser is used to probe the hot band absorption of the molecules by re-excitation into S1. The total fluorescence as a function of probe laser wavelength is observed. The excitation spectrum is broad and featureless in the red but shows sharp structure in the vicinity of the pump laser wavelength. However, the sharp structure depends on the portion of the rotational contour excited. The experimental results show that the redistribution of energy is nonstatistical among the isoenergetic levels. This is explained by assuming that combination bands of low quanta of vibrations are the accepting levels in the internal conversion process and that these accepting levels undergo slow energy redistribution.
Signal conditioning for polar all-digital OFDM wireless transmitters (2014)

A novel scheme for conditioning OFDM modulated signals is proposed to facilitate the implementation of mixerless all-digital transmitter using polar RF Digital to Analog Converters (RFDACs). The signal conditioning is applied to the OFDM signal to avoid phase discontinuities, thus mitigating the effects of bandwidth expansion in polar decomposition. The absence of mixers and filters offers wide RF bandwidth and takes the design a step closer to reconfigurable transmitter. To validate this concept, the signal conditioning is applied to an LTE signal and sent to a phase modulator circuit. The performance of the phase modulator in terms of signal quality is assessed using Normalized Mean Square Error (NMSE) metric. It is concluded that the signal conditioning results in a signal that may not comply with the existing standards, but is spectrally efficient and thus enables the use of polar architectures for wideband signals.
Lamellae orientation in dynamically sheared diblock copolymer melts (1992)

Two distinct lamellae orientaitons have been identified by small-angle neutron scattering (SANS) in dynamically sheared poly(ethylene-propylene)-poly(ethylethylene) (PEP-PEE) diblock copolymer melts. Near the order-disorder transition temperature, T↦TODT, and at low shear frequencies, the lamellae arrange with unit normal perpendicular to the flow direction and parallel to the velocity gradient direction (parallel orientation). Higher frequency processing leads to lamellae with unit normal permendicular to both the flow and velocity gradient directions (perpendicular orientation). The crossover from low to high frequency behavior occurs at ω≈τ-1 where τ is the relaxation time for local domain deformations. At temperatures further from the ODT, T ≪TODT, the parallel orientation is obtained at all shearing frequencies. Based on dynamic and steady shear rheological measurements we propose two mechanisms to account for these results. The perpendicular orientation is proposed to arise from shear-induced disordering, followed by reordering in the perpendicular direction due to the effect of vorticity. Parallel lamellae are believed to be a manifestation of defect mediated stress relaxation. These findings are supported by additional experiments on various other shear-oriented polyolefin diblock copolymers.
Verifying network protocols using temporal logic (1980)

Programs that implement computer communications protocols can exhibit extremely complicated behavior, and neither informal reasoning nor testing is reliable enough to establish their correctness. In this paper we discuss the application of program verification techniques to protocols. This approach is more reliable than informal reasoning, but has the advantage over formal reasoning based on finite-state models that the complexity of the proof does not grow unmanageably as the size of the program increases. Certain tools of concurrent program verification that are especially useful for protocols are presented: history variables that record sequences of input and output values, temporal logic for expressing properties that must hold in a future system state (such as eventual receipt of a message), and module specification and composition rules. The use of these techniques is illustrated by verifying a simple data transfer protocol from the literature.
Classification of SD-OCT Volumes Using Local Binary Patterns: Experimental Validation for DME Detection (2016)

This paper addresses the problem of automatic classification of Spectral Domain OCT (SD-OCT) data for automatic identification of patients with DME versus normal subjects. Optical Coherence Tomography (OCT) has been a valuable diagnostic tool for DME, which is among the most common causes of irreversible vision loss in individuals with diabetes. Here, a classification framework with five distinctive steps is proposed and we present an extensive study of each step. Our method considers combination of various preprocessing steps in conjunction with Local Binary Patterns (LBP) features and different mapping strategies. Using linear and nonlinear classifiers, we tested the developed framework on a balanced cohort of 32 patients. Experimental results show that the proposed method outperforms the previous studies by achieving a Sensitivity (SE) and a Specificity (SP) of 81.2% and 93.7%, respectively. Our study concludes that the 3D features and high-level representation of 2D features using patches achieve the best results. However, the effects of preprocessing are inconsistent with different classifiers and feature configurations.
Comparative genomics of the Rab protein family in Apicomplexan parasites (2008)

Rab genes encode a subgroup of small GTP-binding proteins within the ras super-family that regulate targeting and fusion of transport vesicles within the secretory and endocytic pathways. These genes are of particular interest in the protozoan phylum Apicomplexa, since a family of Rab GTPases has been described for Plasmodium and most putative secretory pathway proteins in Apicomplexa have conventional predicted signal peptides. Moreover, peptide motifs have now been identified within a large number of secreted Plasmodium proteins that direct their targeting to the red blood cell cytosol, the apicoplast, the food vacuole and Maurer's clefs; in contrast, motifs that direct proteins to secretory organelles (rhoptries, micronemes and microspheres) have yet to be defined. The nature of the vesicle in which these proteins are transported to their destinations remains unknown and morphological structures equivalent to the endoplasmic reticulum and trans-Golgi stacks typical of other eukaryotes cannot be visualised in Apicomplexa. Since Rab GTPases regulate vesicular traffic in all eukaryotes, and this traffic in intracellular parasites could regulate import of nutrient and drugs and export of antigens, host cell modulatory proteins and lactate we compare and contrast here the Rab families of Apicomplexa.
Stereochemistry of vinylallene cycloadditions (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of vinylallene cycloadditionsHans J. Reich, Eric K. Eisenhart, Wesley L. Whipple, and Martha J. KellyCite this: J. Am. Chem. Soc. 1988, 110, 19, 6432–6442Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://pubs.acs.org/doi/10.1021/ja00227a024https://doi.org/10.1021/ja00227a024research-articleACS PublicationsRequest reuse permissionsArticle Views704Altmetric-Citations75LEARN 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
CCR2 Regulates the Immune Response by Modulating the Interconversion and Function of Effector and Regulatory T Cells (2017)

Abstract Chemokines and chemokine receptors establish a complex network modulating immune cell migration and localization. These molecules were also suggested to mediate the differentiation of leukocytes; however, their intrinsic, direct regulation of lymphocyte fate remained unclear. CCR2 is the main chemokine receptor inducing macrophage and monocyte recruitment to sites of inflammation, and it is also expressed on T cells. To assess whether CCR2 directly regulates T cell responses, we followed the fates of CCR2−/− T cells in T cell–specific inflammatory models. Our in vitro and in vivo results show that CCR2 intrinsically mediates the expression of inflammatory T cell cytokines, and its absence on T cells results in attenuated colitis progression. Moreover, CCR2 deficiency in T cells promoted a program inducing the accumulation of Foxp3+ regulatory T cells, while decreasing the levels of Th17 cells in vivo, indicating that CCR2 regulates the immune response by modulating the effector/regulatory T ratio.
Expanded Analysis of 20 Pneumococcal Serotypes Associated With Radiographically Confirmed Community-acquired Pneumonia in Hospitalized US Adults (2021)

The current analysis using UAD2 identified a sizeable proportion of hospitalized adult CAP associated with PCV20-unique serotypes. PCV20 may therefore address the burden of CAP caused by the additional serotypes present in the vaccine.
Carbon black grade influence on strain controlled fatigue life of natural rubber (2019)

Rubber material fatigue and effective prediction thereof has been a topic of interest for countless years. Strain life curves perhaps have the longest historic interest. However, many of these historic publications relate to tests at constant loading levels of carbon black or relate to specific part applications. The current study focuses on a series of 10 carbon blacks and 2 pre-reacted silica compounds at an equivalent durometer and utilizes a universally relatable dumbbell specimen, ASTM D412 Die D. A Power Law function is fit for each unique compound to compare the carbon black and silica across strain levels. These measured fatigue cycle counts are associated with other inherent compound parameters to confirm their ability to be predicted effectively.
On linear frequency domain turbo-equalization of non linear Volterra channels (2014)

This article deals with iterative Frequency Domain Equalization (FDE) for Single Carrier (SC) transmissions over Volterra non linear satellite channels. SC-FDE has gained much importance in recent research for its efficient implementation at the receiver and its interesting low Peak to Average Power Ratio (PAPR) at the transmitter. However, nearly saturated power amplifiers on board satellites generate linear and non linear Inter Symbol Interference (ISI) at the receiver. It is thus interesting to investigate the implementation of SC-FDE for non linear channels. To do so, a frequency domain equivalent satellite channel is derived based on the time domain Volterra series representation of the non linear channel. Then a Minimum Mean Square Error (MMSE)-based iterative frequency domain equalizer is designed. It is shown that the proposed equalizer consists of a Soft Interference Canceller (SIC) which subtracts both the linear and non-linear soft frequency symbols. The equalizer performance is then compared to the equivalent time domain implementation. Results show that a channel-memory independent efficient implementation is achieved at the price of a negligible spectral efficiency loss due to cyclic prefix insertion.
Structure-Guided Design of a Fluorescent Probe for the Visualization of FtsZ in Clinically Important Gram-Positive and Gram-Negative Bacterial Pathogens (2019)

Addressing the growing problem of antibiotic resistance requires the development of new drugs with novel antibacterial targets. FtsZ has been identified as an appealing new target for antibacterial agents. Here, we describe the structure-guided design of a new fluorescent probe (BOFP) in which a BODIPY fluorophore has been conjugated to an oxazole-benzamide FtsZ inhibitor. Crystallographic studies have enabled us to identify the optimal position for tethering the fluorophore that facilitates the high-affinity FtsZ binding of BOFP. Fluorescence anisotropy studies demonstrate that BOFP binds the FtsZ proteins from the Gram-positive pathogens Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae with K<sub>d</sub> values of 0.6-4.6 µM. Significantly, BOFP binds the FtsZ proteins from the Gram-negative pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii with an even higher affinity (K<sub>d</sub> = 0.2-0.8 µM). Fluorescence microscopy studies reveal that BOFP can effectively label FtsZ in all the above Gram-positive and Gram-negative pathogens. In addition, BOFP is effective at monitoring the impact of non-fluorescent inhibitors on FtsZ localization in these target pathogens. Viewed as a whole, our results highlight the utility of BOFP as a powerful tool for identifying new broad-spectrum FtsZ inhibitors and understanding their mechanisms of action.
Bio-inspired dental fillings (2009)

Human teeth are anisotropic composites. Dentin as the core material of the tooth consists of nanometer-sized calcium phosphate crystallites embedded in collagen fiber networks. It shows its anisotropy on the micrometer scale by its well-oriented microtubules. The detailed three-dimensional nanostructure of the hard tissues namely dentin and enamel, however, is not understood, although numerous studies on the anisotropic mechanical properties have been performed and evaluated to explain the tooth function including the enamel-dentin junction acting as effective crack barrier. Small angle X-ray scattering (SAXS) with a spatial resolution in the 10 &mu;m range allows determining the size and orientation of the constituents on the nanometer scale with reasonable precision. So far, only some dental materials, i.e. the fiber reinforced posts exhibit anisotropic properties related to the micrometer-size glass fibers. Dental fillings, composed of nanostructures oriented similar to the natural hard tissues of teeth, however, do not exist at all. The current X-ray-based investigations of extracted human teeth provide evidence for oriented micro- and nanostructures in dentin and enamel. These fundamental quantitative findings result in profound knowledge to develop biologically inspired dental fillings with superior resistance to thermal and mechanical shocks.
Core-based lipid nanoparticles as a nanoplatform for delivery of near-infrared fluorescent imaging agents. (2014)

Pyropheophorbide a (Pyro) is a near-infrared (NIR) fluorescent dye and photosensitizer with high quantum yield that makes the dye suitable for tumor treatment both as an imaging and therapy agent. We have designed and synthesized a series of a Pyro-based NIR probes, based on the conjugation of Pyro with lipids. The nature of our probes requires the use of a lipophilic carrier to deliver the probes to cancer cell membranes. To address this, we have utilized lipid-based nanoparticles (LNPs) consisting of PEGylated lipids, which form the nanoparticle shell, and a lipid core. To endow the LNPs with targeting properties, nitrilotriacetic acid (NTA) lipids were included in the composition that enables the non-covalent attachment of His-tag targeting proteins preserving their functional activity. We found that the nature of the core molecules influence the nanoparticle size, shelf-life and stability at physiological temperature. Two different Pyro-lipid conjugates were loaded either into the core or shell of the LNPs. The conjugates revealed differential ability to be accumulated in the cell membrane of the target cells with time. Thus, the modular organization of the core-shell LNPs allows facile adjustment of their composition with goal to fine tuning the nanoparticle properties for in vivo application.
Soluble CD23 in Human Immunodeficiency Virus Type 1 Infected Patients (1993)

The level of sCD23 produced in the course of human immunodeficiency virus (HIV) infection was measured in patients grouped according to the Centers for Disease Control by using an immunoradiometric assay. Soluble CD23 was evaluated in supernatants of peripheral blood mononuclear cell (PBMC) (10(6) cells/ml) stimulated by phytohemagglutinin (PHA). Compared with healthy controls (m +/- S.D. = 1.0 +/- 0.34 U/ml, n = 7), higher values were observed in some of the patients of group II (asymptomatic) (m +/- S.D. = 2 +/- 1.33, n = 9) and some of the patients of group IV (AIDS) (m +/- S.D. = 1.3 +/- 1.40, n = 8). Those results prompted us to compare the plasma levels of sCD23 in group II and group IV HIV-infected patients and in healthy individuals. Soluble CD23 plasma levels in healthy patients (n = 42) ranged from 0 to 1.5 U/ml (m +/- S.D. = 0.9 +/- 0.33), in group II patients (n = 17) from 0 to 3 U/ml (m +/- S.D. = 0.92 +/- 0.83) and in group IV patients (n = 73) from 0 to 2.9 U/ml (m +/- S.D. = 1.15 +/- 0.71). The differences between the patients and the healthy individuals were not statistically significant but individual sCD23 values higher than 2 U/ml were obtained in 6% of the group II patients and 16.7% of the group IV patients. Increased values of sCD23 were obtained in plasma from patients with secondary infectious diseases (groups IV-Cl and IV-C2) and from patients without secondary infectious diseases (group II, group IV-A and group IV-B).(ABSTRACT TRUNCATED AT 250 WORDS)
Obstructed Surface States as the Descriptor for Predicting Catalytic Active Sites in Inorganic Crystalline Materials (Adv. Mater. 26/2022) (2022)

Catalytic Active Sites In article number 2201328, Guowei Li, B. Andrei Bernevig, Claudia Felser, and co-workers propose a descriptor to predicate the position of catalytic active sites fast and precisely. By a simple checking of the space group and the position of obstructed surface states for the given obstructed insulators, high-performance catalysts can be predicated.
Human Autoantibodies Against C1q: Lack of Cross‐Reactivity with the Collectins Mannan‐Binding Protein, Lung Surfactant Protein A and Bovine Conglutinin (1996)

The collectins, a group of humoral C-type lectins, have globular and collagen-like regions and share structural features with the complement protein C1q. The question was asked if autoantibodies to the collagen-like region of C1q (anti-C1qCLR) might cross-react with collectins, such as mannan-binding protein (MBP), lung surfactant protein A (SP-A) and bovine conglutinin (BK). Anti-C1qCLR antibodies of the systemic lupus erythematosus (SLE) type and anti-C1qCLR antibodies of the hypocomplementemic urticarial vasculitis syndrome (HUVS) type were investigated. Cross-absorption and elution experiments combined with antibody detection by enzyme-linked immunosorbent assay (ELISA) and immunoblot analysis gave no evidence of cross-reactive anti-C1qCLR antibodies. However, one serum with HUVS type anti-C1qCLR antibodies contained anti-MBP antibodies that were cross-reactive with SP-A. Judging from results of ELISA inhibition experiments and immunoblot analysis, four SLE sera contained antibodies to native BK, while two sera with HUVS type anti-C1qCLR antibodies contained antibodies to epitopes of denatured BK. This might imply that autoimmunity to collagen-like structures is not restricted to C1qCLR in HUVS and HUVS/SLE overlap syndromes.
Characterization of CD4+ T cells expressing an elevated interferon-stimulated gene signature in SLE patients (2016)

Abstract The type I interferon (IFN) signaling pathway plays a key role in Systemic Lupus Erythematosus (SLE) pathology, and a majority of patients display elevated expression levels of interferon-stimulated genes (ISGs) in the peripheral blood. However, it is unclear which immune cells are responding to IFN to drive disease pathology. We compared the ISG signatures of cell types sorted from peripheral blood of IFNβ-treated relapsing-remitting multiple sclerosis (RRMS) patients with those of SLE patients. While systemic IFNβ treatment stimulated ISG expression in the monocytes and neutrophils of RRMS patients, the ISG signature in SLE patients was primarily detected in CD4+ T and B cells. This suggests these cells may be exposed to higher levels of IFN in microenvironments of inflammation within SLE patients, such as upon interaction with APC presenting SLE antigens. We hypothesize that a subset of primarily antigen-specific CD4+ T cells expand and express ISGs during SLE disease activity, and that these cells and their signature pathways can serve as disease biomarkers and therapeutic targets. To examine ISG expression by CD4+ T cells in SLE, we compared the expression of several ISG-correlated surface markers between high- and low-IFN score patients and healthy controls. Subsets of CD4+ T cells in high-IFN score patients expressed elevated levels of PD1, CD66a, and OX40, while the majority of cells expressed a similar level as cells in healthy controls. This suggests that only a small subset of CD4+ T cells is activated by localized IFN sources and is involved in SLE pathology. We have further characterized PD1+, OX40+ CD66a+, and SLE-specific memory CD4+ T cells by RNAseq and flow cytometry.