gebhart/patrepeval huggingface dataset:
Eubacterium (2015)

Abstract Eu.bac.te'ri.um. Gr. pref. eu ‐ good‐, well‐, beneficial (not as opposed to pseudo‐); Gr. neut. dim. n. bakterion a small rod; N.L. neut. n. Eubacterium beneficial bacterium. Uniform or pleomorphic nonspore‐forming , Gram‐stain‐positive rods . Nonmotile or motile. Obligately anaerobic. Chemoorganotrophs , saccharoclastic or nonsaccharoclastic. Usually produce mixtures of organic acids from carbohydrates or peptone, often including large amounts of butyric, acetic, or formic acids . Do not produce: DNA G + C content ( mol %): 47 (T m ). Type species : Eubacterium limosum (Eggerth 1935) Prévot 1938, 295 AL ( Bacteroides limosus Eggerth 1935; Butyribacterium rerrgeri Barker and Haas 1944, 303). Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Eubacterium is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Eubacteriaceae / Eubacterium The genus Eubacterium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Eubacterium (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Eubacteriales / f__Eubacteriaceae / g__Eubacterium * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods (2018)

Virus-like particles (VLPs) have been used as nanocarriers to display foreign epitopes and/or deliver small molecules in the detection and treatment of various diseases. This application relies on genetic modification, self-assembly, and cysteine conjugation to fulfill the tumor-targeting application of recombinant VLPs. Compared with genetic modification alone, chemical conjugation of foreign peptides to VLPs offers a significant advantage because it allows a variety of entities, such as synthetic peptides or oligosaccharides, to be conjugated to the surface of VLPs in a modulated and flexible manner without alteration of the VLP assembly. Here, we demonstrate how to use the hepatitis E virus nanoparticle (HEVNP), a modularized theranostic capsule, as a multifunctional delivery carrier. Functions of HEVNPs include tissue-targeting, imaging, and therapeutic delivery. Based on the well-established structural research of HEVNP, the structurally independent and surface-exposed residues were selected for cysteine replacement as conjugation sites for maleimide-linked chemical groups via thiol-selective linkages. One particular cysteine-modified HEVNP (a Cys replacement of the asparagine at 573 aa (HEVNP-573C)) was conjugated to a breast cancer cell-specific ligand, LXY30 and labeled with near-infrared (NIR) fluorescence dye (Cy5.5), rendering the tumor-targeted HEVNPs as effective diagnostic capsules (LXY30-HEVNP-Cy5.5). Similar engineering strategies can be employed with other macromolecular complexes with well-known atomic structures to explore potential applications in theranostic delivery.
Systemic release of osteoprotegerin during oxaliplatin-containing induction chemotherapy and favorable systemic outcome of sequential radiotherapy in rectal cancer (2016)

In colorectal cancer, immune effectors may be determinative for disease outcome. Following curatively intended combined-modality therapy in locally advanced rectal cancer metastatic disease still remains a dominant cause of failure. Here, we investigated whether circulating immune factors might correlate with outcome. An antibody array was applied to assay changes of approximately 500 proteins in serial serum samples collected from patients during oxaliplatin-containing induction chemotherapy and sequential chemoradiotherapy before final pelvic surgery. Array data was analyzed by the Significance Analysis of Microarrays software and indicated significant alterations in serum osteoprotegerin (TNFRSF11B) during the treatment course, which were confirmed by osteoprotegerin measures using a single-parameter immunoassay. Patients experiencing increase in circulating osteoprotegerin during the chemotherapy had significantly better 5-year progression-free survival than those without increase (78% versus 48%; P = 0.009 by log-rank test). Hence, systemic release of this soluble tumor necrosis factor decoy receptor following the induction phase of neoadjuvant therapy was associated with favorable long-term outcome in patients given curatively intended chemoradiotherapy and surgery but with metastatic disease as the main adverse event. This finding suggests that osteoprotegerin may mediate or reflect systemic anti-tumor immunity invoked by combined-modality therapy in locally advanced rectal cancer.
Physico-Chemical Characteristics of Pomegranate Harvested in Yamanashi Prefecture in Japan (2016)

To elucidate the physico-chemical properties of the juice and the fruit as a whole for pomegranates harvested in the Yamanashi prefecture in Japan compared to that of the imported ones, following analysis were conducted. ① On average, the domestic fruit weight was approximately 150g per fruit, while the aril and juice ratios to the fruit weight were about 60% and 42%, respectively. The juice ratio to the aril weight was approximately 70%. These ratios were lower than those calculated for the imported fruit (approximately 400g per fruit), and not dependent on the fruit size. ② The brix measurement of pomegranate juice from domestic fruit was 17 and the sugar was glucose and fructose, while both ratios were nearly equivalent, it was slightly high in fructose. The same results were obtained for imported fruits. Titratable acidity in the imported fruit was much higher than that in the domestic fruit, which mainly composed of 0.7% oxalic acid. However the organic acid content in the imported fruit was 1.5% citric acid with a small amount of malic acid. ③ The dominant free-amino acids in the juices listed in order of high to low concentration were glutamine, glutamic acid, aspartic acid and serine. There were no significant differences between the juices from domestic And the imported fruit. Small quantities of sarcosine were detected in both juices. ④ Total polyphenol content in the juices was approximately 100mg% and 200mg% in the domestic and imported fruit, respectively. The HPLC analysis of the polyphenol revealed that punicalin and punicalagin were detected in the juices from the domestic fruit and not the imported fruit.
Natural Killer Cell Receptor Signaling Pathway in Mammals (2005)

NK (natural killer) cells are large granular lymphocytes of the innate immune system. They are widespread throughout the body, being present in both lymphoid organs and nonlymphoid peripheral tissues. NK cells are involved in direct innate immune reactions against viruses, bacteria, parasites, and other triggers of pathology, such as malignant transformation, all of which cause stress in affected cells. Importantly, NK cells also link the innate and adaptive immune responses, contributing to the initiation of adaptive immune responses. NK cell responses are mediated through two major effector functions, the direct cytolysis of target cells and the production of cytokines and chemokines. We focus here on how recognition events are integrated to trigger distinct and graded effector functions.
Structure analysis of a soluble polysiloxane-block-polyimide and kinetic analysis of the solution imidization of the relevant polyamic acid (1998)

A series of polysiloxane-block-polyimides were synthesized by solution imidization of the polyamic acids derived from the combination of 3,3′,4,4′-diphenylsulfonetetracarboxylic dianhydride (DSDA), 2,2-bis[4-(4-aminophenoxy)phenyl]propane (BAPP), and diamino(polysiloxane) (PSX (Mw = 750)) in N-methyl-2-pyrrolidone (NMP). Their structures were analyzed by 1H-, 13C-, and 29Si-NMR spectra as well as by IR spectroscopy. The solid-state NMR spectrum was also measured to determine the spin–lattice relaxation time of the copolyimides. The observed relaxation times of both aromatic and polysiloxane segments were similar in the copolyimides having 10–30 wt % of PSX, while those in the copolyimide with 50 wt % of PSX was significantly different. This may be attributed to the morphology change due to the increase in PSX composition in the polymer backbone. The reduced viscosity of the copolyimides could be controlled by changing the monomer ratio in the feed or by adding an end-capping reagent such as phthalic anhydride into the polymerization system. The kinetic study of the solution imidization revealed that the imidization reaction obeyed second-order kinetics. The activation energy calculated for this imidization was 99.2 kJ/mol, being similar to that for the imidization of the DSDA-based aromatic polyimides. © 1998 John Wiley & Sons, Inc. J. Polym. Sci. A Polym. Chem. 36: 2237–2245, 1998
Time and Frequency Domain Investigations on Ultrafast Photoreaction Dynamics of Photoactive Yellow Protein (PYP) (2004)

Low frequency vibrations of the native PYP and related systems in solution have been investigated in "time" (fs fluorescence up-conversion) and "frequency" (resonance Raman) domains to elucidate their role in ultrafast photoisomerization reaction dynamics of PYP. Tentative assignments of the oscillatory components to particular vibrations are proposed supported by normal mode calculations based on DFT and ab initio MO methods. It is concluded that the out-of-plane skeleton bending mode of the chromophore, γ16, is responsible for the observed oscillations in native and all mutant PYPs (f1 ∼ 135 cm-1), while in-plane ν'42 and ν'43 modes are probably responsible for oscillations observed in the PYP analogue with locked chromophore. A dynamic model called "trigger mode mediated guidance" has been proposed to explain in simple terms the ultrafast primary process initiating PYP's photocycle. Furthermore, first successful fluorescence dynamics experiments on PYP single crystals with femtosecond time resolution are presented and discussed.
Delivering MicroRNA‐137 to the Brain via Nanoparticles (2022)

Genetic mutations of microRNA‐137 (miR‐137) are strongly associated with symptoms of schizophrenia. Elevated miR‐137 impairs neuronal, dendritic, and synaptic development. Additionally, miR‐137 regulates multiple key mRNA transcripts that are critical for cognitive and sensory processing, and that are common genes dysregulated in schizophrenia. However, there remains a major barrier to treatment of schizophrenia due to the lack of targeted delivery of effective therapeutics to the brain. Encapsulating miR‐137 in nanoparticles offers a drug delivery system that can pass the blood‐brain‐barrier, allowing miR‐137 to have effects in the brain. We hypothesize that inhibiting endogenous levels of miR‐137, with the antisense sequence (anti‐miR‐137), may improve neurobiological and behavioral deficits as a result of miR‐137 overexpression. We encapsulated miR‐137 in nanoparticles and analyzed the size, polydispersity index, zeta potential, uptake efficiency, cargo delivery, and toxicity of miR‐137 loaded nanoparticles after treatment in cell culture. Results indicate nanoparticles are nontoxic delivery vehicles and are easily incorporated into cells. Additionally, the miR‐137 cargo is released from the nanoparticles and is detected as elevated miR‐137 levels. Following in vitro studies, we will test the most efficient delivery method to deliver nanoparticles to the brain in vivo by florescent labeling and ex vivo nanoparticle tracking. Delivering therapeutic RNAs to the brain will improve targeted drug delivery systems for central nervous system disorders.
Vaccine Potential of Attenuated Mutants ofCorynebacterium pseudotuberculosisin Sheep (1998)

Corynebacterium pseudotuberculosis, a gram-positive facultative intracellular bacterial pathogen, is the etiological agent of the economically important disease caseous lymphadenitis (CLA) in both sheep and goats. Attenuated mutants of C. pseudotuberculosis have the potential to act as novel vaccines against CLA and as veterinary vaccine vectors. In this report, we have assessed the virulence of both aroQ and pld mutants of C. pseudotuberculosis in sheep and concurrently their capacity to act as vaccines against homologous challenge. The results suggest that aroQ mutants of C. pseudotuberculosis are attenuated with regard to both lymph node persistence and vaccination site reactogenicity. Immunologically, aroQ mutants failed to elicit detectable specific gamma interferon (IFN-gamma)-secreting lymphocytes and induced low levels of antibodies to C. pseudotuberculosis culture supernatant antigens. Following subcutaneous vaccination, the immune responses induced by aroQ mutants did not protect sheep from infection with the wild-type strain but did appear to reduce the clinical severity of disease resulting from challenge. Conversely, an attenuated C. pseudotuberculosis strain expressing an enzymatically inactive phospholipase D exotoxin, when used as a vaccine, elicited a protective immune response. Protection appeared to correlate with in vivo persistence of the vaccine strain, the induction of IFN-gamma-secreting lymphocytes, and relatively high levels of antibodies to culture supernatant antigens. The results suggest that aroQ mutants of C. pseudotuberculosis may be overly attenuated for use as a CLA vaccines or as vaccine vectors.
Hierarchical attribute-based encryption for fine-grained access control in cloud storage services (2010)

Cloud computing, as an emerging computing paradigm, enables users to remotely store their data into a cloud so as to enjoy scalable services on-demand. Especially for small and medium-sized enterprises with limited budgets, they can achieve cost savings and productivity enhancements by using cloud-based services to manage projects, to make collaborations, and the like. However, allowing cloud service providers (CSPs), which are not in the same trusted domains as enterprise users, to take care of confidential data, may raise potential security and privacy issues. To keep the sensitive user data confidential against untrusted CSPs, a natural way is to apply cryptographic approaches, by disclosing decryption keys only to authorized users. However, when enterprise users outsource confidential data for sharing on cloud servers, the adopted encryption system should not only support fine-grained access control, but also provide high performance, full delegation, and scalability, so as to best serve the needs of accessing data anytime and anywhere, delegating within enterprises, and achieving a dynamic set of users. In this paper, we propose a scheme to help enterprises to efficiently share confidential data on cloud servers. We achieve this goal by first combining the hierarchical identity-based encryption (HIBE) system and the ciphertext-policy attribute-based encryption (CP-ABE) system, and then making a performance-expressivity tradeoff, finally applying proxy re-encryption and lazy re-encryption to our scheme.
Elastic scattering of 179.3 MeV antiprotons by deuterium (1988)

Bruge, G; Garreta, D; Birien, P; Catz, H; Chaumeaux, A; Janouin, S; Legrand, Dominique; Lemaire, M C; Mayer, B; Pain, J; Perrot, F; Aslanides, Elie; Bing, O; Drake, D M; Peng, J C; Berrada, M; Bocquet, J P; Monnand, E; Mougey, J; Perrin, P; Lichtenstadt, J; Yavin, A I
Vertical adiabatic taper for efficient in-coupling in nano-interferometric waveguide biosensors (2017)

Summary form only given. Despite the intense developments in the field of integrated optics, there is still a need of a compact, easy and cost-effective solution for light in-coupling in integrated photonic optical waveguides for biosensing, which are designed to be single use devices in clinical environments. The majority of current solutions are based on grating couplers fabricated with e-beam lithography, which increases the device cost [1]. For example, in the case of our bimodal waveguide interferometric biosensor [2], gratings require tapers of up to 2000 μm to guide the light towards the waveguide entrance.We propose instead an adiabatic vertical two-stage taper (see Figure 1a), which can be fabricated using standard lithography techniques at wafer level by slightly modifying our current fabrication process. The taper is compact enough (~1200 μm) while offering theoretical coupling efficiencies up to 72% with an input area of 10 μm x 6 μm instead of the actual 3 μm x 0.15 μm, facilitating the coupling process. Vertical adiabatic tapers have been previously proposed in the short IR range but its fabrication at wafer level and its integration into a photonic visible biosensor have not been yet reported [3,4].
On the fast multipole method applications for inverse problems (2012)

A novel inverse Fast Multipole Method (FMM) application for imaging applications is presented. The idea is based on the multipole expansion of the integral equations relating the scattered fields and equivalent currents. This kind of expansion allows an easy inversion of the FMM operators, resulting in a forward solution of the inverse problem, i.e. without matrix inversion or cost function minimization. 3D application examples are presented, highlighting the achieved inverse FMM speed-up with respect to previous inverse source-based problem for geometry reconstruction.
Detection and characterization of monoclonal antibodies specific to IgE receptors on human lymphocytes by flow cytometry. (1985)

BALB/c mice were immunized with human lymphoblastoid cells (RPMI 8866 cells) expressing surface receptors for IgE (Fc epsilon R). Spleen cells from animals displaying high titres of anti-Fc epsilon R antibodies were fused with HGPRT-deficient NSI myeloma cells. Anti-Fc epsilon R antibodies were identified by a flow cytometric assay based on their ability to block the binding of IgE-coated fluorescent latex particles to Fc epsilon R-positive cells. Fourteen monoclonal hybridoma cell lines secreting antibody of the required specificity were amplified in tissue culture and then grown in the peritoneal cavity of BALB/c mice in order to obtain ascitic fluids with high antibody titres. The specificity of each monoclonal antibody (Mab) to lymphocyte Fc epsilon R was shown by the following observations: (i) the intact monoclonal antibody molecule or, in some cases, its F(ab')2 fragments blocked the binding of IgE to several Fc epsilon R(+) cell lines different from that employed for the initial immunization; (ii) the Mab bound directly to all the Fc epsilon R(+) cell lines tested, but not to several Fc epsilon R(-) cells as determined by indirect immunofluorescence; (iii) the binding of Mab to Fc epsilon R(+) cells was selectively blocked by IgE, but not by the other classes of Ig; and (iv) Mab had no effect on the binding of IgG to Fc gamma R on normal human peripheral blood mononuclear cells (PBMC).
Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis (2009)

Escherichia coli ribosomal protein S1 is required for the translation initiation of messenger RNAs, in particular when their Shine-Dalgarno sequence is degenerated. Closely related forms of the protein, composed of the same number of domains (six), are found in all Gram-negative bacteria. More distant proteins, generally formed of fewer domains, have been identified, by sequence similarities, in Gram-positive bacteria and are also termed 'S1 proteins'. However in the absence of functional information, it is generally difficult to ascertain their relationship with Gram-negative S1. In this article, we report the solution structure of the fourth and sixth domains of the E. coli protein S1 and show that it is possible to characterize their beta-barrel by a consensus sequence that allows a precise identification of all domains in Gram-negative and Gram-positive S1 proteins. In addition, we show that it is possible to discriminate between five domain types corresponding to the domains 1, 2, 3, 4-5 and 6 of E. coli S1 on the basis of their sequence. This enabled us to identify the nature of the domains present in Gram-positive proteins and, subsequently, to probe the filiations between all forms of S1.
Relay Selection, Link Scheduling, and Rate Allocation in Dual-Hop Buffer-Aided Networks with Statistical Delay Constraints (2015)

This work considers the relay selection and resource allocation problem (i.e., link scheduling, and rate allocation) for multi-source, multi-relay dual-hop wireless networks. The relays employ buffers to store the received data from the sources for future transmissions. End-to-end (E2E) delay of each traffic flow originated from a source or a relay is constrained in terms of maximum allowable delay-outage probability. To solve this problem, we first study the resource allocation problem to maximize the constant supportable arrival rate of a non-prioritized source under minimum rate requirements of the prioritized sources and relays for a given relay selection solution. Then, the optimal relay selection can be determined to support the largest rate of the non-prioritized source among all possible relay selection solutions. We derive the resource allocation solutions using asymptotic delay analysis and convex optimization techniques. We also develop an online allocation algorithm which does not require the knowledge of the fading statistics by using stochastic approximation theory. Numerical results are presented to demonstrate the usefulness of the proposed resource allocation design for relay selection under different delay and rate constraint regimes.
Prevalence and predictors of severe menopause symptoms among HIV-positive and -negative Nigerian women (2017)

We compared the prevalence of menopause symptoms between women living with HIV to their HIV-negative peers and determined predictors of severe menopause symptoms in Jos, Nigeria. This descriptive cross-sectional study included 714 women aged 40-80 years. We compared prevalence and severity of menopause symptoms using the menopause rating scale (MRS). Logistic regression analysis was used to determine the predictors of severe symptoms. Six-hundred and seven (85.0%) were HIV-positive, with a mean duration of infection of 5.6 ± 2.7 years. The mean age of the cohort was 46 ± 5 years. The most prevalent menopause symptoms were hot flushes (67.2%), joint and muscle discomfort (66.2%), physical/mental exhaustion (65.3%), heart discomfort (60.4%), and anxiety (56.4%). The median MRS score was higher for HIV-positive compared to HIV-negative women (p = 0.01). Factors associated with severe menopause symptoms included HIV-positive status (aOR: 3.01, 95% CI: 1.20-7.54) and history of cigarette smoking (aOR: 4.18, 95% CI: 1.31-13.26). Being married (aOR: 0.49, 95% CI: 0.32-0.77), premenopausal (aOR: 0.60, 95% CI: 0.39-0.94), and self-reporting good quality of life (aOR: 0.62. 95% CI: 0.39-0.98) were protective against severe menopause symptoms. We found HIV infection, cigarette smoking, quality of life, and stage of the menopause transition to be associated with severe menopause symptoms. As HIV-positive populations are aging, additional attention should be given to the reproductive health of these women.