gebhart/patrepeval huggingface dataset:
Outer Membrane Vesicles Prime and Activate Macrophage Inflammasomes and Cytokine Secretion In Vitro and In Vivo (2017)

Outer membrane vesicles (OMVs) are proteoliposomes blebbed from the surface of Gram-negative bacteria. Chronic periodontitis is associated with an increase in subgingival plaque of Gram-negative bacteria, <i>Porphyromonas gingivalis, Treponema denticola</i>, and <i>Tannerella forsythia</i>. In this study, we investigated the immune-modulatory effects of <i>P. gingivalis, T. denticola</i>, and <i>T. forsythia</i> OMVs on monocytes and differentiated macrophages. All of the bacterial OMVs were phagocytosed by monocytes, M(naïve) and M(IFNγ) macrophages in a dose-dependent manner. They also induced NF-κB activation and increased TNFα, IL-8, and IL-1β cytokine secretion. <i>P. gingivalis</i> OMVs were also found to induce anti-inflammatory IL-10 secretion. Although unprimed monocytes and macrophages were resistant to OMV-induced cell death, lipopolysaccharide or OMV priming resulted in a significantly reduced cell viability. <i>P. gingivalis, T. denticola</i>, and <i>T. forsythia</i> OMVs all activated inflammasome complexes, as monitored by IL-1β secretion and ASC speck formation. ASC was critical for OMV-induced inflammasome formation, while AIM2-/- and Caspase-1-/- cells had significantly reduced inflammasome formation and NLRP3-/- cells exhibited a slight reduction. OMVs were also found to provide both priming and activation of the inflammasome complex. High-resolution microscopy and flow cytometry showed that <i>P. gingivalis</i> OMVs primed and activated macrophage inflammasomes <i>in vivo</i> with 80% of macrophages exhibiting inflammasome complex formation. In conclusion, periodontal pathogen OMVs were found to have significant immunomodulatory effects upon monocytes and macrophages and should therefore influence pro-inflammatory host responses associated with disease.
Separation technologies: Marketing factors (1991)

The chemical and petroleum industries consume approximately 5.8 quads per year of energy. Within these industries, 43% of the energy is used by separation processes to recover and purify products. With 40,000 distillation columns in operation, distillation is used to make 95% of all separations in these two industries. Although separations are identified which are amenable to advanced separation technologies (that make distillation more energy-efficient), they are not implemented because of commercial barriers. The focus of this work was on barriers which can by overcome by implementing advanced separation-related technologies. Barriers were screened and prioritized, and Return On Investment (ROI) was calculated for each project designed to overcome a high priority barrier. Economic analyses were based on specific separations such as ethylene-ethane, propylene-propane, ethyl benzene-styrene, and ethanol-water. These separations were selected because they consume significant amounts of energy for separation. Thus, conclusions are based on a limited number of case studies; an approach necessary to complete this project within a reasonable time frame. Recommended projects are discussed and summarized.
Automatic Generation of Virtual Lumbar Motion Segments for Population-Based Simulation of Lumbar Spine Biomechanics (2010)

Computational modeling of the spine has become a viable option for evaluating new implants and procedures. Most models described in the literature, however, represent only a single subject and neglect the normal variation that exists among specimens. A probabilistic simulation comprised of virtual specimens representing a broad population of subjects can address this limitation and be used to evaluate implants or procedures pre-clinically. Challenges exist to applying probabilistic modeling techniques to biologic systems, and perhaps the greatest is parameterization of the anatomy to capture normal variation in shape from specimen to specimen. It’s also critical to implement soft tissues in a robust, automated manner that produces representative biomechanics. The purpose of our research is to overcome these challenges and develop a probabilistic framework to perform population-based studies of lumbar spine biomechanics. This paper describes our results to date for the automated generation of virtual lumbar motion segments.
Genomic and antigenic differences between the European and African/Australian clusters of Mycoplasma mycoides subsp. mycoides SC The GenBank accession numbers for the nucleotide sequences determined in this work are: AF165134 for the 3·4 kb HindIII fragment from M. mycoides subsp. mycoides SC strain L2; AF165135 for the analogous locus in strain Afadé (containing lppB and IS1634); and AF1651136 for the DNA segment containing lppB[MmymyLC] and ORF6[MmymyLC] from M. mycoides subsp. mycoides LC strain Y-goat. (2000)

Mycoplasma mycoides subsp. mycoides small-colony type (SC), the aetiological agent of contagious bovine pleuropneumonia (CBPP), can be grouped into two major, epidemiologically distinct, clusters. One cluster contains strains isolated from different European countries since 1980 and a second cluster contains African and Australian strains collected over the last 50 years. Genetic analysis of representative strains from the two clusters revealed a genomic segment of 8.84 kb, located close to a copy of IS1296, which is present in all strains of the African cluster but lacking in all strains of the European cluster. This segment contains a copy of IS1634, a gene for a potential lipoprotein, IppB, open reading frames encoding a putative surface-located membrane protein and a hypothetical proline-rich membrane protein, and two open reading frames showing similarity to putative ABC transporters. The product of the IppB gene, lipoprotein B (LppB), has an apparent molecular mass of 70 kDa and was shown to be surface located. It is detected with monospecific antibodies in all strains of the African cluster tested, but not in European-cluster strains. DNA sequence analysis of the splicing site at which European strains differ from African-cluster strains by the lack of the 8.84 kb segment showed that the European cluster has arisen by deletion from a strain of the African cluster. Hence, M. mycoides subsp. mycoides SC strains isolated in different European countries from the newly reemerging outbreaks of CBPP, which occurred after the eradication of the epizootic in Europe in the middle of the 20th century, represent a phylogenetically newer cluster that has been derived from a strain of the older cluster of M. mycoides subsp. mycoides SC which is still endemic on the African continent.
Performance and Reliability Planning for SCN of the Automatically Switched Optical Networks (2004)

The restoration performance and reliability of connections depend on that of the signaling communications network (SCN) in the automatically switched optical network.This paper analyzes the performance,transmission delay and reliability of the SCN and gets some important factors which affect the performance and reliability of the routing and signaling.Then,a planning scheme for the performance of the SCN based restoration time of the connection and a planning scheme for the reliability of the SCN based on single link-fault no-failure restoration are addressed.The planning scheme for the performance enables estimation of the restoration time for connection.The planning scheme for the reliability solves the issue of no-failure restoration on single link-fault and improves the efficiency of the broadcasting of routing information.
The FoxM1 Transcription Factor Is Required to Maintain Pancreatic β-Cell Mass (2006)

The FoxM1 transcription factor is highly expressed in proliferating cells and activates several cell cycle genes, although its requirement appears to be limited to certain tissue types. Embryonic hepatoblast-specific inactivation of Foxm1 results in a dramatic reduction in liver outgrowth and subsequent late gestation lethality, whereas inactivation of Foxm1 in adult liver impairs regeneration after partial hepatectomy. These results prompted us to examine whether FoxM1 functions similarly in embryonic outgrowth of the pancreas and beta-cell proliferation in the adult. We found that FoxM1 is highly expressed in embryonic and neonatal endocrine cells, when many of these cells are proliferating. Using a Cre-lox strategy, we generated mice in which Foxm1 was inactivated throughout the developing pancreatic endoderm by embryonic d 15.5 (Foxm1(Deltapanc)). Mice lacking Foxm1 in their entire pancreas were born with normal pancreatic and beta-cell mass; however, they displayed a gradual decline in beta-cell mass with age. Failure of postnatal beta-cell mass expansion resulted in impaired islet function by 6 wk of age and overt diabetes by 9 wk. The decline in beta-cell mass in Foxm1(Deltapanc) animals is due to a dramatic decrease in postnatal beta-cell replication and a corresponding increase in nuclear localization of the cyclin-dependent kinase inhibitor, p27(Kip1), a known target of FoxM1 inhibition. We conclude that Foxm1 is essential to maintain normal beta-cell mass and regulate postnatal beta-cell turnover. These results suggest that mechanisms regulating embryonic beta-cell proliferation differ from those used postnatally to maintain the differentiated cell population.
Micellar Catalysis for Ruthenium(II)‐Catalyzed C−H Arylation: Weak‐Coordination‐Enabled C−H Activation in H<sub>2</sub>O (2019)

Chemoselective C-H arylations were accomplished through micellar catalysis by a versatile single-component ruthenium catalyst. The strategy provided expedient access to C-H-arylated ferrocenes with wide functional-group tolerance and ample scope through weak chelation assistance. The sustainability of the C-H arylation was demonstrated by outstanding atom-economy and recycling studies. Detailed computational studies provided support for a facile C-H activation through thioketone assistance.
Detrimental effect of antiepileptic drugs dose in pediatric children with epilepsy in Saudi Arabia (2021)

This study aims to evaluate the effect of dose titration for different oral antiepileptic medications among children with epilepsy in Riyadh, Saudi Arabia.A single-center prospective pilot, cohort study was undertaken at a tertiary hospital in Riyadh, Saudi Arabia. All medical records of pediatric patients below the age of 14 years of age who has been newly diagnosed with epilepsy by attending a medical specialist or on a new epileptic treatment plans were enrolled in the study.A total of 76 epileptic patients were screened for 3 months' period and 48 patients were included in this study. Out of the 48 patients, 31 patients followed the regular practice in the titration processes and 17 patients were in the British national formulary (BNF) guideline. Fifteen children who were on monotherapy of levetiracetam were in regular practice guideline experienced poor seizure control with a recorded number of seizure incidence (n = 10). The patient in regular practice guidelines using a combination therapy of phenytoin and levetiracetam were experiencing some behavioral disturbance and sedation effect. Seventeen patients followed in the BNF guideline who were on levetiracetam were experienced less adverse effect (n = 2) with no behavioral changes.The group who followed the regular practice found having a greater incidence of documented adverse effects compared to the patients following the BNF guideline. The titrating antiepileptic medication has a detrimental effect on the pediatric population as observed in this study.
Basic Science for the Clinician 36 (2006)

One of the miracles of immunology is tolerance, the ability of the immune system to differentiate self from nonself and leave the former alone. Autoreactive thymocytes (the cells that would otherwise differentiate into mature autoaggressive T cells) are deleted from the emerging immunologic repertoire within the thymus; only a very small proportion of thymocytes survive the thymus--perhaps 2% to 5% emerge to become mature T cells in the periphery, the rest dying to assure tolerance. This apparent wastage somehow works to the benefit of the developing animal and if the process works, all goes well for the maturing immune system. In some autoimmune syndromes, autoreactive thymocytes are not eliminated within the thymus by either clonal deletion or activation-induced cell death; these then emerge to wreak their havoc. However, how does this deletion happen? Recent research from a number of groups has (incredibly!) identified expression of nonthymic, nonlymphoid proteins within the thymus (casting of the "immunologic shadow of self"), and this is under the control of a single protein: AIRE (autoimmune regulator). By allowing autoreactive thymocytes to encounter a broad spectrum of proteins from extrathymic organs, aire allows deletion of these cells and the maintenance of tolerance. The absence of aire leads to autoimmune polyendocrinopathy, proof that aire is the center of an amazing "filtering" system. These and other molecular mechanisms underlying tolerance are explored in this and the next paper in this series.
Dysplasia Capitis Femoris und ihre Beziehung zur Hüftkopfnekrose (Morbus Perthes) (2008)

Fifty-five patients totaling 98 hips afflicted by Dysplasia Capitis Femoris (DFC), monitored between 1960 and 1983, were analyzed. Mean follow-up: 8 years and 4 months (minimum 2 years, maximum 22 years and 2 months). Forty-three (78%) patients were males; fourteen (25%) were females. Non displayed any alteration in other osteoarticular segments. In 24 of the 98 affected hips it was possible to determine the exact radiological age appearance of the Epiphyseal Nucleus. Thirty-seven of the 55 patients had moderate signs and symptoms which were of short evolution. According to presence or absence of necrotic signs of the femoral epiphysis, two types of lesions were classified: Type 1: Pure Dysplasia Capitis Femoris (88 hips). Type 2: Dysplasia Capitis Femoris with unequivocal signs of necrosis (10 hips). Upon review of the 98 diseased hips, 80 (81.63%) had been fully repaired, while 18 (18.37%) were in reparatory stage. From the 80 fully healed hips, 56 were normal; 18 exhibited a Spherical Coxa Magna and 6 had a non-spherical epiphysis. As treatment concerns, patients with D.C.F. Type 1-A or Type 1-B only require observation and periodical control in addition to moderate restrictions in physical activities upon presence of symptomatic pain that is transitional. Patients with D.C.F. Type 2 must be treated as a classic case of Perthes Disease. Finally, a hypothesis of their etiopathogenis and its relationship to Perthes Disease is brought forth.
Transition Dipoles from 1D and 2D Infrared Spectroscopy Help Reveal the Secondary Structures of Proteins: Application to Amyloids (2015)

Transition dipoles are an underutilized quantity for probing molecular structures. The transition dipole strengths in an extended system like a protein are modulated by the couplings and thus probe the structures. Here we measure the absolute transition dipole strengths of human and rat amylin in their solution, aggregated, membrane, and micelleular bound forms, using a combination of 1D and 2D infrared spectroscopy. We find that the vibrational modes of amyloid fibers made of human amylin can extend across as many as 12 amino acids, reflecting very ordered β-sheets in the most carefully prepared samples. Rat amylin has FTIR spectra that are nearly identical in solution, micelles, and membranes. We show that the transition dipoles of rat amylin are much larger when bound to micelles and membranes than when in solution, consistent with rat amylin adopting an α-helical structure. We interpret the transition dipole strengths as experimental measurements of the inverse participation ratio often calculated in theoretical studies. The structure of aggregating and membrane-bound proteins can be difficult to identify with existing techniques, especially during kinetics. These results demonstrate how absolute transition dipoles measured via our 1D/2D spectroscopy method can provide important structural information.
Nano‐Scale Design of TiAl Alloys Based on β‐Phase Decomposition (2006)

Abstract Phase decomposition and ordering reactions in β/B2‐phase containing TiAl alloys were utilized to establish a novel, previously unreported, type of laminate microstructure. The characteristic constituent of this microstructure are laths with a nanometer‐scale substructure that are comprised of several stable and metastable phases. Microstructural control can be achieved by conventional thermomechanical processing and leads to a structurally and chemically very homogeneous material with excellent mechanical properties. The physical metallurgy of this novel type of alloy has been assessed by transmission electron microscope investigations and mechanical testing.
Connecting different worlds - Technology abstraction for reliability-aware design and Test (2014)

The rapid shrinking of device geometries in the nanometer regime requires new technology-aware design methodologies. These must be able to evaluate the resilience of the circuit throughout all System on Chip (SoC) abstraction levels. To successfully guide design decisions at the system level, reliability models, which abstract technology information, are required to identify those parts of the system where additional protection in the form of hardware or software coun-termeasures is most effective. Interfaces such as the presented Resilience Articulation Point (RAP) or the Reliability Interchange Information Format (RIIF) are required to enable EDA-assisted analysis and propagation of reliability information. The models are discussed from different perspectives, such as design and test.
Supplementary Figure 1 from Biallelic Mutations in &lt;i&gt;BRCA1&lt;/i&gt; Cause a New Fanconi Anemia Subtype (2023)

&lt;p&gt;Supplementary Figure 1. BRCA1 mutations lead to impaired MMC induced DNA damage signaling.&lt;/p&gt;
A 1.5V Current-Mode Operational Amplifier Using Level Shifter Technique (2006)

A low-voltage and low-power consumption of current-mode operational amplifier designed with level shifter technique is presented. This simple integrator is built up with only 9 typical MOSFETs and 2 bias current sources. To minimize the influence of common-mode signal and noise to the signal processing, the differential structure is applied. As the result of simulation, it has been confirmed that the proposed circuit works as integrator in the frequency range 0-1.6MHz at 1.5V supply voltage and consumed DC power at maximum 8.85muW with 1.2mum double-poly CMOS process
Effects of the complete removal of basic amino acid residues from the signal peptide on secretion of lipoprotein in Escherichia coli. (1983)

We have examined the importance of the positively charged NH2 terminus of the major outer membrane lipoprotein precursor, prolipoprotein, in the early steps of secretion in Escherichia coli. For this purpose, we have generated three mutants using oligonucleotide-directed mutagenesis in which the charge at the NH2-terminal region was changed from +2 to +1, 0, and -2. The results indicate that the synthesis of prolipoprotein is facilitated by the presence of a positively charged NH2 terminus. In addition, the translocation of prolipoprotein across the cytoplasmic membrane does not absolutely require any basic amino acids at its NH2 terminus. However, the presence of a net negatively charged NH2 terminus causes an initial cytoplasmic accumulation of prolipoprotein which is slowly, post-translationally translocated across the cytoplasmic membrane at a rate which is dependent on the number of positive charges present in this region. The analysis of these mutants clearly demonstrates the importance of the NH2 terminus of the lipoprotein signal peptide in initiating the secretion of this protein in E. coli.
Mapping the homotypic binding sites in CD31 and the role of CD31 adhesion in the formation of interendothelial cell contacts. (1995)

CD31 is a member of the immunoglobulin superfamily consisting of six Ig-related domains. It is constitutively expressed by platelets, monocytes, and some lymphocytes, but at tenfold higher levels on vascular endothelial cells. CD31 has both homotypic and heterotypic adhesive properties. We have mapped the homotypic binding sites using a deletion series of CD31-Fc chimeras and a panel of anti-CD31 monoclonal antibodies. An extensive surface of CD31 is involved in homotypic binding with domains 2 and 3 and domains 5 and 6 playing key roles. A model consistent with the experimental data is that CD31 on one cell binds to CD31 on an apposing cell in an antiparallel interdigitating mode requiring full alignment of the six domains of each molecule. In addition to establishing intercellular homotypic contacts. CD31 binding leads to augmented adhesion via beta 1 integrins. The positive cooperation between CD31 and beta 1 integrins can occur in heterologous primate cells (COS cells). The interaction is specific to both CD31 and beta 1 integrins. Neither intercellular adhesion molecule-1 (ICAM-1)/leukocyte function-associated antigen-1 (LCAM-1) nor neural cell adhesion molecule (NCAM)/NCAM adhesion leads to recruitment of beta 1 integrin adhesion pathways. Establishment of CD31 contacts have effects on the growth and morphology of endothelial cells. CD31(D1-D6)Fc inhibits the growth of endothelial cells in culture. In addition, papain fragments of anti-CD31 antibodies (Fab fragments) disrupt interendothelial contact formation and monolayer integrity when intercellular contacts are being formed. The same reagents are without effect once these contacts have been established, suggesting that CD31-CD31 interactions are critically important only in the initial phases of intercellular adhesion.
Measurement of Capacitance Using Spread Spectrum Time Domain Reflectometry (SSTDR) and Dictionary Matching (2020)

In this paper, we present a method for estimating capacitances with SSTDR and a dictionary matching algorithm. We simulate a dictionary of simulated SSTDR reflections for a range of capacitances, based on parameters of the transmitted SSTDR signal, the SSTDR signal generator, and the transmission line. The measured SSTDR reflection data is compared with each simulated reflection through cross-correlation, and the estimated capacitance is found from the highest correlation. We validate this method with experiments on capacitors ranging from 1pF to 450pF using a 12 MHz SSTDR. The dictionary matching algorithm estimated the capacitor values within 4% to 20% in the capacitance range of 100pF to 400pF.