gebhart/patrepeval huggingface dataset:
Comprehensive Probiogenomics Analysis of the Commensal Escherichia Coli CEC15 as a Potential Probiotic Strain (2023)

Abstract Background: Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico , in vitro , and in vivo analyses, comparing it to the reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. Results: CEC15 mitigates inflammation, reinforces intestinal barrier and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). The majority of predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and its intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis. Conclusions: These findings suggest that the CEC15 strain holds promise as a probiotic, capable of modulating the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly inflammatory bowel disease.
THE BENEFITS OF STATIC COMPLIANCE TESTING FOR SCA NEXT (2011)

The next generation of the Software Communications Architecture (SCA) specification (SCA Next) introduces several features that will affect the compliance certification process. Among the more significant and high-profile changes are the introduction of multiple supported platform models and support for both CORBA and non-CORBA transport layers. These features, which further abstract the specification away from a uniform hardware/software interface, make constructing an all-purpose dynamic testing platform more difficult. This suggests that a certification plan that relies more heavily on static testing might provide a more versatile and cost-effective approach. In this paper, we describe the benefits and implications of static compliance testing in the context of SCA Next. This includes a discussion of which requirements are and are not amenable to static testing, the complexity of defining and customizing tests, the expected performance and limitations of those tests, and a summary of our experiences from the development of R-Check™ SCA, our platform for static SCA 2.2.2 compliance testing.
Randomised double-blind placebo-controlled study of the effect of Lactobacillus paracasei NCC 2461 on skin reactivity (2013)

In recent decades, the prevalence of subjects with reactive skin has considerably increased in industrialised countries. 50% of women and 30% of men report cutaneous discomfort classified under reactive/sensitive skin. Several topical approaches have been proposed, in particular through improvement of galenic forms or protection of epidermal surface. We propose to act differently, deeply from inside the body via an innovative nutritional approach. To this purpose, Lactobacillus paracasei NCC 2461 (ST11) was selected because of its specific beneficial skin properties discovered in in vitro studies, i.e. diminution of neurogenic inflammation and promotion of the recovery of skin barrier function. We designed a randomised double-blind placebo-controlled clinical study with a two-month supplementation in two female treatment groups (n=32 per group). A capsaicin test was performed to monitor the time course of skin sensitivity. Moreover, transepidermal water loss was assessed to analyse the rate of skin barrier function recovery; dryness of the leg and roughness of the cheeks was investigated by a dermatologist as well as by self-assessment. The results of the present clinical trial show that oral supplementation with the probiotic decreases skin sensitivity and increases the rate of barrier function recovery. Thus, the data provide evidence that daily intake of ST11 could improve reactive skin condition.
Interventional cardiovascular procedures guided by real‐time MR imaging: An interactive interface using multiple slices, adaptive projection modes and live 3D renderings (2007)

Interactive features not available on standard clinical scanners enhance real-time MRI for guiding cardiovascular interventional procedures.
The Economics of Big Area Additive Manufacturing (2016)

Case studies on the economics of Additive Manufacturing (AM) suggest that processing time is the dominant cost in manufacturing. Most additive processes have similar performance metrics: small part sizes, low production rates and expensive feedstocks. Big Area Additive Manufacturing is based on transitioning polymer extrusion technology from a wire to a pellet feedstock. Utilizing pellets significantly increases deposition speed and lowers material cost by utilizing low cost injection molding feedstock. The use of carbon fiber reinforced polymers eliminates the need for a heated chamber, significantly reducing machine power requirements and size constraints. We hypothesize that the increase in productivity coupled with decrease in feedstock and energy costs will enable AM to become more competitive with conventional manufacturing processes for many applications. As a test case, we compare the cost of using traditional fused deposition modeling (FDM) with BAAM for additively manufacturing composite tooling.
Central Role of the Holliday Junction Helicase RuvAB in vlsE Recombination and Infectivity of Borrelia burgdorferi (2009)

Antigenic variation plays a vital role in the pathogenesis of many infectious bacteria and protozoa including Borrelia burgdorferi, the causative agent of Lyme disease. VlsE, a 35 kDa surface-exposed lipoprotein, undergoes antigenic variation during B. burgdorferi infection of mammalian hosts, and is believed to be a critical mechanism by which the spirochetes evade immune clearance. Random, segmental recombination between the expressed vlsE gene and adjacent vls silent cassettes generates a large number of different VlsE variants within the infected host. Although the occurrence and importance of vlsE sequence variation is well established, little is known about the biological mechanism of vlsE recombination. To identify factors important in antigenic variation and vlsE recombination, we screened transposon mutants of genes known to be involved in DNA recombination and repair for their effects on infectivity and vlsE recombination. Several mutants, including those in BB0023 (ruvA), BB0022 (ruvB), BB0797 (mutS), and BB0098 (mutS-II), showed reduced infectivity in immunocompetent C3H/HeN mice. Mutants in ruvA and ruvB exhibited greatly reduced rates of vlsE recombination in C3H/HeN mice, as determined by restriction fragment polymorphism (RFLP) screening and DNA sequence analysis. In severe combined immunodeficiency (C3H/scid) mice, the ruvA mutant retained full infectivity; however, all recovered clones retained the 'parental' vlsE sequence, consistent with low rates of vlsE recombination. These results suggest that the reduced infectivity of ruvA and ruvB mutants is the result of ineffective vlsE recombination and underscores the important role that vlsE recombination plays in immune evasion. Based on functional studies in other organisms, the RuvAB complex of B. burgdorferi may promote branch migration of Holliday junctions during vlsE recombination. Our findings are consistent with those in the accompanying article by Dresser et al., and together these studies provide the first examples of trans-acting factors involved in vlsE recombination.
Conformational studies by nuclear magentic resonance—II: The effect of steric factors on hindered rotation in enamino aldehydes and ketones (1972)

Abstract Rotational barriers of the dimethylamino group in different enamino aldehydes and ketones have been applied for evaluation of their conformation. It has been maintained that repulsion between bulky substituents causes twisting of the molecule rather than planar deformations. Arguments for and against these alternative concepts based on the analysis of J HH and J ( 13 CH) coupling constants in different fragments of the molecule have been discussed.
The costs and benefits of screening for congenital hypothyroidism in Wisconsin (1984)

Abstract A comprehensive benefit‐cost analysis of the screening program to detect newborns with congenital hypothyroidism in Wisconsin is presented. Congenital hypothyroidism, if left undetected and untreated at an early age, can have serious irreversible effects on the growth and development of the brain. The monetary costs of the detection and treatment program for congenital hypothyroidism were compared with the projected benefits (avoided costs) that result from the prevention of the mental retardation associated with the disorder. Future costs and benefits were determined using a 4 per cent, 7 per cent, and 10 per cent rate of discount. Net benefits (benefits minus costs) for detecting and treating one individual with congenital hypothyroidism were approximately $98,200 ($141,700 ‐ $43,500) using the 7 per cent rate of discount. Net benefits for detecting the 13 individuals with congenital hypothyroidism in 1981–1982 totaled $1,277,000.
Cellular Regulation of Gamma Interferon Production: Lyt Phenotype of the Suppressor Cell (1982)

Suppressor cell activity for in vitro gamma interferon (IFNgamma) production can be induced in C57BL/6 mice with the T-cell mitogens staphylococcal enterotoxin A and concanavalin A. The suppressor cell lacked mitogen specificity in that injection of mice with either staphylococcal enterotoxin A or concanavalin A induced potent suppressor cell activity that inhibited the in vitro induction of IFNgamma by either mitogen. The suppressor cell is a T cell with a relatively high density of Thy 1 antigen. The IFNgamma-producing cell has a low density of Thy 1 and appears to have evolved from cells with a high density of Thy 1.2 or to have required such cells as helpers in the production of IFNgamma. Monoclonal anti-Lyt 2.2 antibody completely eliminated the suppressor cell activity, whereas anti-Lyt 1.2 partially, but significantly, reduced the suppressor cell activity. The suppressor cell, then, may be or may require a Lyt 1,2,3(+) cell with a relatively low density of the Lyt 1 antigen for activity. The Lyt phenotype of the IFNgamma- producing cells was examined for both virgin and suppressor cell populations. Treatment of cells with either anti-Lyt 1.2 or anti-Lyt 2.2 completely eliminated IFNgamma production in both virgin and suppressor cell cultures. Cocultivation of Lyt 1(+) and Lyt 2(+) cells in both virgin and suppressor cell cultures significantly restored the ability to produce IFNgamma when cells were stimulated with staphylococcal enterotoxin A. For the virgin cells, this seems to indicate clearly that both Lyt 1(+) and Lyt 2(+) cells are required for IFN production, but that Lyt 1,2,3(+) cells are not required. For the suppressor cell population this type of treatment resulted in IFNgamma production comparable to that of the virgin cell population. The treatment eliminated or depleted Lyt 1,2,3(+) cells from the suppressor cell population, thus providing additional evidence that a Lyt 1,2,3(+) cell is required for suppressor cell activity. Treatment of spleen cells with anti-Lyt antibodies at the time that they were involved in ongoing IFNgamma production showed that the IFNgamma-producing cell is Lyt 2(+). At least a 1:1 ratio of virgin to suppressor cells was required for optimal suppression of IFNgamma production by virgin spleen cells. This suggests that suppression involved cell-to-cell contact. Preliminary data showed that the suppressor cell activity could also be induced in in vitro cultures incubated with mitogen for 4 days. This is evidence that the suppressor cell is inducible and not necessarily recruited to the spleen from other lymphoid organs.
Myostatin: a modulator of skeletal-muscle stem cells (2005)

Myostatin, or GDF-8 (growth and differentiation factor-8), was first identified through sequence identity with members of the BMP (bone morphogenetic protein)/TGF-β (transforming growth factor-β) superfamily. The skeletal-muscle-specific expression pattern of myostatin suggested a role in muscle development. Mice with a targeted deletion of the myostatin gene exhibit a hypermuscular phenotype. In addition, inactivating mutations in the myostatin gene have been identified in ‘double muscled’ cattle breeds, such as the Belgian Blue and Piedmontese, as well as in a hypermuscular child. These findings define myostatin as a negative regulator of skeletal-muscle development. Myostatin binds with high affinity to the receptor serine threonine kinase ActRIIB (activin type IIB receptor), which initiates signalling through a smad2/3-dependent pathway. In an effort to validate myostatin as a therapeutic target in a post-embryonic setting, a neutralizing antibody was developed by screening for inhibition of myostatin binding to ActRIIB. Administration of this antimyostatin antibody to adult mice resulted in a significant increase in both muscle mass and functional strength. Importantly, similar results were obtained in a murine model of muscular dystrophy, the mdx mouse. Unlike the myostatin-deficient animals, which exhibit both muscle hypertrophy and hyperplasia, the antibody-treated mice demonstrate increased musculature through a hypertrophic mechanism. These results validate myostatin inhibition as a therapeutic approach to muscle wasting diseases such as muscular dystrophy, sarcopenic frailty of the elderly and amylotrophic lateral sclerosis.
The Write Stuff!: How to Prepare and Implement Unique Special Provisions (2019)

This presentation will help project managers and designers prepare the information required for department contracts with regard to the Standard Specifications and Special Provisions. We will share examples of both the right and wrong ways to present a Unique Special Provision, as well as what to avoid and questions to ask, in order to adhere to legal, moral, and ethical construction standards.
First Synthesis of meso‐Chlorinated Tetrabenzoporphyrins (2009)

Abstract meso ‐Chlorinated bicyclo[2.2.2]octadiene‐fused porphyrins 2 (Cl n TBCODPs; n = 1–4) have been synthesized by chlorination of the free base TBCODP‐H 2 ( 1 ‐H 2 ) using N ‐chlorosuccinimide (NCS). The chlorinated derivatives were easily separated by column chromatography on silica gel to give 2 ‐H 2 in good yields. This method for the chlorination of porphyrin using NCS is mild, safe, and economic compared with the established procedure for the meso ‐chlorination of porphyrins. We also discovered the unexpected meso ‐chlorination of the porphyrin with dichlorodicyanobenzoquinone (DDQ) by single‐electron transfer. Cl n TBCODPs 2 were converted into tetrabenzoporphyrins (Cl n TBPs) 3 in 100 % yields by retro‐Diels–Alder reaction. The derived compounds were characterized by NMR spectroscopy, UV/Vis spectrophotometry, cyclic voltammetry (CV), X‐ray crystallography, and organic field‐effect transistor (OFET) characteristics. The introduction of chlorine at the meso positions of the TBPs drastically changed their electronic and structural properties. The maxima of protonated Cl 4 TBP‐H 2 ( 3d ‐H 2 ; λ max = 494, 649, and 707 nm) were redshifted by around 50–65 nm relative to those of protonated TBP‐H 2 ( λ max = 431, 605, and 660 nm). The two Q‐band maxima of the Cl 4 TBP dication are similar to those of a tetraacenaphthoporphyrin dication ( λ max = 525, 646, and 702 nm), which has one of the most redshifted Q‐bands.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Efficient Catalysis of Polysiloxane Synthesis by Silicatein Requires Specific Hydroxy and Imidazole Functionalities (1999)

A protein isolated from a biosilica (shown schematically) catalyzes alkoxysilane polycondensation at neutral pH values and low temperatures. Replacement of either of two specific side chain functionalities (Ser-26 and His-165) significantly diminishes catalysis, supporting a reaction mechanism analogous to that of a well-known enzyme that is highly homologous to the silica protein. These results may be useful in the development of synthetic catalysts for environmentally benign synthesis of polysiloxanes.
0909 Development of method for estimating muscle activity with a conduction model of forearm (2010)

Development of method for estimating muscle
Review: femoral tunnel placement for PCL reconstruction in relation to the PCL fibre bundle attachments (2009)

Accurate placement of the femoral tunnel position is an important aspect of cruciate ligament reconstruction surgery. However, a wide range of positions have been described in the literature for the femoral tunnels for posterior cruciate ligament (PCL) reconstruction, and there is no consensus regarding the optimal placement. It was hypothesised that some of the prior studies used femoral PCL graft tunnels that were outside of the anatomical attachments. A systematic review and descriptive anatomical study in vitro were undertaken. Fifty articles that described PCL reconstruction since 1917 were reviewed; the description of the femoral tunnel placement was reproducible from only 20 of these. A right, distal femur was disarticulated and the PCL attachment was dissected; the centres of the anterolateral and posteromedial bundles were marked and confirmed to be close to the mean published data. The tunnel positions described in the 20 papers were also marked. The descriptions of 15 of the 20 anterolateral and 4 of the 5 posteromedial bundle tunnel centres were close (within +/-2 mm deep and +/-01:00 o'clock) to the anatomical centres of the bundle attachments. Other tunnels were placed either deeper or shallower than the anatomical attachments. The mean positions were: 7 mm from the articular cartilage at 1 o'clock for the anterolateral bundle, and 8 mm from the cartilage at 3 o'clock for the posteromedial bundle, in a right knee. It was concluded that it was not possible to replicate the tunnel positions used in most of the literature because of inadequate descriptions. Most of the usable descriptions of the anterolateral bundle position were close to the anatomical centre, but some tunnels were placed non-anatomically. A reproducible system for description of the femoral tunnel positions should be used.
Steady-state stability of synchronous generators as affected by regulators and governors (1955)

Voltage and power-angle regulation can be used to improve the steady-state stability of synchronous alternators, whereas speed governors and tie-line power controllers often introduce instability.In the paper, methods of determining the effects of voltage and angle regulation on the steady-state stability limit are discussed, and they are extended to allow for the control of the prime-mover torque by means of governors and power controllers. The machine analysis is based on the general equations for synchronous machines.A complete analysis of actual problems is rather tedious, and a differential analyser has been found most suitable for detailed investigations. Results, as obtained for typical alternators, are presented in the form of stability contour diagrams, which are very convenient for design purposes, since optimum control parameters can be read off directly.
Characterization of a novel iodinated ligand, IPMPP, for human dopamine D4 receptors expressed in CHO cells (1996)

A novel radioiodinated ligand with a high specific activity (2,200 Ci/mmol), 3-[4-(4-iodophenyl)piperazin-1-yl]methyl-1H-pyrrolo(2,3-b)pyridine ([125I]IPMPP), was successfully prepared. Binding characteristics of [125I]IPMPP were evaluated using human dopamine D4 (D4.2 variant) receptors expressed in Chinese hamster ovary (CHO) cells. Saturation analysis revealed high-affinity binding sites for [125I]IPMPP (Kd = 0.39 +/- 0.18 nM). The number of D4 receptors labeled with [125I]IPMPP at room temperature was four times higher than that labeled with [125I]S(-)5-OH-PIPAT, a radioiodinated agonist ligand (572 fmol/mg protein vs. 125 fmol/mg protein). A significant decrease in the number of binding sites was observed with [125I]S(-)5-OH-PIPAT when assays were carried out at a higher temperature (37 degrees C vs. 25 degrees C). In contrast to [125I]S(-)5-OH-PIPAT, [125I]IPMPP labeled more D4 sites at 37 degrees C. Neither magnesium ion nor guanylimidodiphosphate (Gpp(NH)p) affected [125I]IPMPP binding. These data support the conclusion that [125I]IPMPP is an antagonist ligand. The potency of various compounds, including clozapine, to inhibit [125I]IPMPP binding is consistent with the rank order measured with other radioligands for D4 receptors. In addition, measuring D4 receptor stimulation of [35S]GTPgammaS binding further demonstrated the antagonist property of IPMPP.
Polyurethane Dispersions with Peptide Corona: Facile Synthesis of Stimuli-Responsive Dispersions and Films (2015)

Peptide-polymer hybrid particles of submicron size yielding stimuli-responsive macroscopic films are presented. A thermoplastic polyurethane (PU) carrying polysiloxane and polyester soft segments serves as core material to obtain flexible, yet semicrystalline films with temperature-sensitivity. The synthesis is based on the high-sheer emulsification of isocyanate-terminated PU prepolymers, which in our model system purposefully lack any ability of colloidal self-stabilization. While emulsification in water leads to immediate coagulation, stable dispersions of polyurethane nanoparticles were formed in aqueous solutions of a hydrolyzed protein from wool. A comparison of dispersion and film properties to nonreactive, otherwise identical dispersions suggests covalent attachment of the peptide to the PU backbone. We show that the colloidal stability of the hybrid particles is completely governed by the peptide corona, and hence pH-triggered coagulation can be employed to induce particle deposition and film formation. Differential scanning calorimetry confirms partial crystallinity in the film and reveals strongly modified crystallization behavior due to the peptide.