gebhart/patrepeval huggingface dataset:
Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1 (2014)

Polyvalent vaccines use a mixture of Ags representing distinct pathogen strains to induce an immune response that is cross-reactive and protective. However, such approaches often have mixed results, and it is unclear how polyvalency alters the fine specificity of the Ab response and what those consequences might be for protection. In this article, we present a coarse-grain theoretical model of B cell affinity maturation during monovalent and polyvalent vaccinations that predicts the fine specificity and cross-reactivity of the Ab response. We stochastically simulate affinity maturation using a population dynamics approach in which the host B cell repertoire is represented explicitly, and individual B cell subpopulations undergo rounds of stimulation, mutation, and differentiation. Ags contain multiple epitopes and are present in subpopulations of distinct pathogen strains, each with varying degrees of cross-reactivity at the epitope level. This epitope- and strain-specific model of affinity maturation enables us to study the composition of the polyclonal response in granular detail and identify the mechanisms driving serum specificity and cross-reactivity. We applied this approach to predict the Ab response to a polyvalent vaccine based on the highly polymorphic malaria Ag apical membrane antigen-1. Our simulations show how polyvalent apical membrane Ag-1 vaccination alters the selection pressure during affinity maturation to favor cross-reactive B cells to both conserved and strain-specific epitopes and demonstrate how a polyvalent vaccine with a small number of strains and only moderate allelic coverage may be broadly neutralizing. Our findings suggest that altered fine specificity and enhanced cross-reactivity may be a universal feature of polyvalent vaccines.
Coloured zirconia (1994)

Abstract This paper deals with the growth of coloured zirconium oxide crystals, cubic stabilized with yttrium oxide. The host material–zirconia–is colourless. To generate colourations minor concentrations of 3d‐ and 4f‐elements are incorporated into the lattice. The resulting colours are dependent on the ions' valence and the local crystal symmetry. Both, the possibility to change the ions' valence by heat treatment, and the possibility to change the local crystal symmetry by alteration of the starting yttria concentration, are discussed in the following.
Suitability of laser drilling models containing melt eject mechanisms (2000)

A reliable model of the laser drilling process is potentially an important tool for operators of industrial laser drilling systems, allowing the effects of altering material and laser parameters to be studied without the need for extensive and costly, drilling trials. A number of models have been developed for laser drilling, but the reliability of their predictive capability depends on the specific drilling regime of the process (Le. whether material removal is predominately by vaporisation or by vaporisation and melt expulsion). Melt expulsion can account for up to 70% of the material removed, and occurs because the vapour ablation pressure inside the hole is large enough to expel the surrounding molten material from the hole. In this paper the predictions of analytical models with and without the melt ejection mechanism are compared with experimental measurements made using a free running Nd:YAG laser over a wide range of drilling conditions in aluminium and titanium. The importance of modelling the melt expulsion process is discussed. The models also consider the time dependence of the drilling pulse. The importance of modelling the time dependence of the drilling pulse for obtaining reliable model predictions is considered. The effect of the reactive nature of titanium is discussed as a possible source of discrepancy between the experimental measurements and the predictions of the models, which do not consider this effect.
Metal-diffused optical waveguides in LiNbO3 (1974)

Deposited films of transition metals (Ti, V, and Ni) have been diffused into LiNbO3 crystals to form low-loss TE and TM mode optical waveguides. Using Ti, single-mode low-loss waveguides which confine the guided light to within ∼1 μm of the surface have been constructed. The choice of diffusion parameters allows independent control of important waveguide parameters.
Optimisation of alignment materials for minimising residual retardation in in-plane switching liquid crystal display (2016)

The light leakage in a black state of in-plane switching (IPS) liquid crystal display (LCD) associated with rubbing process has been investigated. The mechanical rubbing process with a cloth caused orientation disorders in the liquid crystal directors and these partial orientation disorders result in residual retardations of the IPS LCD, causing the light leakages at the black state. In this study, we theoretically estimated how the light leakage is associated with the rubbing uniformity using 2 × 2 Jones matrix equation and also experimentally confirmed how it is associated with structural properties of the alignment layer. The light leakage was clearly reduced in the alignment layer with reduced crystallinity and flexibility.
Epigallocatechin-3-gallate suppresses pain-related and proinflammatory mediators in the subacromial bursa in rotator cuff tendinopathy. (2019)

Rotator cuff tendinopathy is one of the leading causes of shoulder pain. However, the mechanisms involved in the development of rotator cuff tendinopathy pain are not fully understood. In this study, we first examined the histological features of subacromial bursa from patients with rotator cuff tendinopathy who had symptoms of pain, and investigated the expression of pain mediators, proinflammatory cytokines, metalloproteinases, growth factors, and alarmins in diseased tendon and bursa tissue by real-time PCR, western blot, and/or immunohistochemistry/immunofluorescence staining. Then we investigated whether epigallocatechin-3-gallate (EGCG) could reduce the expression of pain mediators and proinflammatory cytokines in human primary bursa cells and explored the paracrine effect of these EGCG-treated bursa cells on tenocytes in vitro. Neovascularization and infiltration of immune cells including monocytes/macrophages and mast cells were observed in diseased bursa tissue. Bursa from patients with pain had higher mRNA expression of pain mediators and proinflammatory cytokines, compared to the rotator cuff tendon of the same patients, as well as the bursa from asymptomatic patients. EGCG treatment significantly suppressed the interleukin 1 beta (IL-1β)-induced elevation of mRNA expression of pain mediators, proinflammatory cytokines, and matrix metalloproteinases (MMPs) in bursa cells in vitro; conditioned medium from EGCG-treated bursa cells significantly reduced IL-1β-induced expression in human primary tenocytes. Our study suggests that the subacromial bursa might serve as a local source of pain mediators and proinflammatory cytokines in rotator cuff tendinopathy. Moreover, EGCG treatment by primarily targeting the subacromial bursa may be a potential strategy to relieve rotator cuff tendinopathy-related pain and symptoms.
Thermal Conductivity Enhancement of Metal-organic Frameworks Employing Mixed Valence Metal Doping Technique (2020)

Excellent adsorption properties of porous metal-organic frameworks (MOFs) render them highly potential adsorbent for adsorption heat pump applications. However, their thermal properties are not quite satisfactory. Aluminium fumarate is a bioavailable ligand-based metal-organic framework with promising water uptake capacity. In this study, aluminium fumarate was synthesized following a green synthesis route and was doped with Nickel and Cobalt material at 10% and 20% concentration to create a mixed-valence complex system. Their thermal diffusivity and thermal conductivity were studied at different compression (7 MPa, 17 MPa and 27 MPa) pressure over a temperature range of 30 °C to 110 °C. Metal doping enhances the thermal conductivity of the doped aluminium fumarate MOFs. Doping of cobalt has a greater effect compared to nickel and 20% cobalt doped aluminium fumarate shows the highest thermal conductivity at 7 MPa compression pressure.
Survival after a very low (< 5 × 106/l) CD4+ T-cell count in individuals infected with HIV (1997)

A CD4+ T-cell count of less than 5 x 10(6)/l did not necessarily mean imminent death, with a median survival after this count of just under 1 year. These results will enable clinicians to provide appropriate counselling for patients at this late stage and to plan terminal care.
Correlating Capacity Fading and Structural Changes in Li[sub 1+y]Mn[sub 2−y]O[sub 4−δ] Spinel Cathode Materials: A Systematic Study on the Effects of Li/Mn Ratio and Oxygen Deficiency (2001)

Several series of samples with the spinel structure were synthesized. These samples had different Li/Mn ratios (by varying the Li/Mn ratio used in starting materials) and various oxygen contents (by controlling synthesis conditions, including temperature, heat-treatment time, and purging gas during both the solid-state reaction and annealing). In systematic studies of charge-discharge cycling behavior and in situ X-ray diffraction (XRD) at room temperature, it was found that both the charge/discharge profile and the structural changes during cycling are closely related to the degree of oxygen deficiency created in the synthesis process. Their effects on the capacity fading are much more important than the Li/Mn ratio or other factors. A higher degree of oxygen deficiency is accompanied with a faster fading of capacity during cycling. In cells using spinel cathodes with an oxygen deficiency, the capacity fading during cycling occurs on both the 4.2 and 4.0 V plateaus. This behavior is quite different from that found in cathodes without an oxygen deficiency, where most of the capacity fading occurs on the 4.2 V plateau region only. Our in situ XRD results indicate clearly that the capacity fading on the 4.2 V plateau is related to the phase transition between the cubic II and cubic III structure, while the capacity fading on the 4.0 V plateau is related to the phase transition between the cubic I and cubic II spinel structures. The effects of oxygen deficiency on the structural phase transition of -type materials at temperatures around 10°C were also studied. It was found that this phase transition is closely related to the degree of oxygen deficiency of the material. In samples with no oxygen deficiency, this phase transition disappeared. © 2001 The Electrochemical Society. All rights reserved.
Pro: High dose of therapeutic plasma exchange—mind the gap! (2017)

'Mind the gap' is a recorded warning phrase used in the London Tube since 1969. The following article is meant to be a warning of an increasing knowing-doing gap in routine practice of therapeutic plasma exchange (TPE), a treatment method that is used more and more throughout the world. The American Society of Apheresis recommendations, including the most recent ones from 2016, suggest using a TPE volume of 1.0-1.5 times the actual calculated plasma volume of the patient. There are only a few exceptions to that rule, such as the recommnded exchange volume in vasculitis or mushroom poisoning. The published literature suggests that in routine clinical practice in many institutions in several countries the exchanged volume might in fact be lower than recommended by the guidelines. In the following article we argue for a high dose of exchanged plasma volume, yet sketch different scenarios on how this time-averaged high dose can be delivered in various ways depending on the underlying disease, refuting a one-size-fits-all strategy that might facilitate the procedure but may result in 'underpheresis' in many patients. Further, the objectives underlying the use of smaller exchange volumes, especially the gap between the cost of blood products and the reimbursement of TPE are discussed. Lastly, the knowing-guiding gap is described, which can only be overcome by collecting high-quality data and conducting prospective clinical trials in the field of TPE.
Changing interaction of compiler and architecture (1997)

Program optimizations that have been exclusively done by either the architecture or the compiler are now being done by both. This blurred distinction offers opportunities to optimize performance and redefine the compiler-architecture interface. We describe an optimization continuum with compile time and post run time as end points and show how different classes of optimizations fall within it. Most current commercial compilers are still at the compile-time end point, and only a few research efforts are venturing beyond it. As the gap between architecture and compiler closes, there are also attempts to completely redefine the architecture-compiler interface to increase both performance and architectural flexibility.
Transforming growth factor-beta1 in sarcoidosis (1998)

Transforming growth factor-beta (TGF-beta) is a cytokine that promotes extracellular matrix accumulation and inhibits matrix degradation. Although the natural course of sarcoidosis is usually favourable, granuloma healing in the lung may result in pulmonary fibrosis and respiratory impairment in some patients. In this study TGF-beta1 was evaluated in bronchoalveolar lavage (BAL) fluid and culture supernatants of alveolar macrophages (AM) from 73 patients with biopsy-proven sarcoidosis. Disease activity was defined when patients recently developed or increased symptoms (cough, dyspnoea, systemic symptoms) and/or demonstrated increasing opacities on chest radiography. Pulmonary function tests were performed in all patients including forced expiratory volume in one second (FEV1), forced vital capacity (FVC), total lung capacity (TLC) and the diffusing capacity of the lung for carbon monoxide (DL,CO). Fourteen patients with idiopathic pulmonary fibrosis (IPF) and 14 healthy subjects were investigated as a control group. Immunohistochemistry was used to evaluate the cell distribution of TGF-beta1 on lung specimens. TGF-beta1 levels in BAL and in AM supernatants were not different between sarcoidosis and healthy subjects, whereas they were markedly increased in IPF. However, the TGF-beta1 level was significantly increased in BAL fluid but not in AM supernatants from sarcoidosis with altered lung function, compared with patients with normal lung function. The TGF-beta1 level in BAL was increased in active sarcoidosis but this increased level was mainly related to the higher level observed in patients with altered lung function. TGF-beta1 levels in BAL correlated significantly with the lymphocyte percentage. TGF-beta1 staining assessed by immunohistochemistry was intense in epithelioid histiocytes comprising non-necrotizing granuloma and in bronchiolar epithelial cells, in hyperplastic type II pneumocytes and occasionally in AM. This study supports the hypothesis that overproduction of transforming growth factor-beta1 is associated with functional impairment in patients with pulmonary sarcoidosis.
MADIX Polymerization Follow-Up by Viscosity Sensing Using Love-Wave Devices (2006)

Love wave sensors are highly sensitive microacoustic devices which are especially suited for sensing in liquids due to the shear polarized wave. In this contribution, a Love-wave device is used to follow the xanthate-mediated controlled free radical homopolymerization (MADIX technology) of butyl acrylate and acrylic acid. During the polymerization, using an automated synthesis workstation, a sample of the solution is taken into the reactors and deposited on the Love-wave sensor. Velocity changes of the Love-wave due to the liquid properties (e.g. viscosity) allowed to determine in real time the component fractions (e.g. monomer and polymer fractions) and give indications about the advance of the polymerization.
Studies on cathepsin B in human articular cartilage (1978)

The thiol proteinase cathepsin B (EC 3.4.22.1), previously called cathepsin B1, was assayed in human articular cartilage by its hydrolysis of the synthetic substrate alpha-N-benzoyl-DL-arginine 2-naphthylamide. The enzyme was activated by cysteine and EDTA and completely inhibited by iodoacetamide and HgCl2. It was also partially inhibited by whole human serum. Human osteoarthrotic cartilage had increased activity when compared with normal cartilage. Cathepsin B activity of normal cartilage was age-related, being high in juveniles and declining to low values in adult and elderly individuals. Cathepsin D and cathepsin B both exhibited a zonal variation through the cartilage depth; the surface cells appeared to contain more activity than those close to the subchondral bone.
Liver, visceral and subcutaneous fat in men and women of South Asian and white European descent: a systematic review and meta-analysis of new and published data (2022)

There was no primary direct funding for undertaking the systematic review and meta-analysis.
Efficient O(N) recursive computation of the operational space inertia matrix (1993)

The operational space inertia matrix Lambda reflects the dynamic properties of a robot manipulator to its tip. In the control domain, it may be used to decouple force and/or motion control about the manipulator workspace axes. The matrix Lambda also plays an important role in the development of efficient algorithms for the dynamic simulation of closed-chain robotic mechanisms, such as multiple manipulator systems and walking machines. This paper presents the development of a recursive algorithm for computing the operational space inertia matrix (OSIM) that reduces the computational complexity to O(N). This algorithm, the inertia propagation method, is based on a single recursion that begins at the base of the manipulator and progresses out to the last link. Also applicable to redundant systems and mechanisms with multiple-degree-of-freedom joints, the inertia propagation method is the most efficient method known for computing Lambda for N>or=6. The numerical accuracy of the algorithm is discussed for a PUMA 560 robot with a fixed base.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preparation and Properties of CMC Gel (2007)

Novel elastic gel was obtained by immersing paste of sodium carboxymethylcellulose (CMC) in acid solution. The paste was prepared by mixing CMC and water at the concentration of 20%. Water absorption and mechanical strength of the resultant gel were evaluated after removing uncrosslinked CMC and acid. Combination of radiation crosslinking and the immersion in acid resulted precise molding and dimension stability of the gel. Maximum mechanical strength of the gel at 50% compression increased with acid concentration for the unirradiated and the irradiated samples at 5-20kGy. The gel prepared by irradiation at 5-lOkGy and the immersion did not cause rupture after 50% compression and was more than 100 times stronger than the radiation-crosslinked gel. The reason of the mechanical strength was attributed to crosslinks formed by the acid treatment The crosslinks by the irradiation had been referred to chemical bonds, whereas, those by acids were caused by hydrogen bonds, which was elucidated by FT-IR, ICP and TG-DTA measurements. Sodium in the carboxymethyl groups is replaced by hydrogen in the acid solution. The hydrogen bonds induced the decrease of CMC solubility in water and formed the elastic gel.
Zebrafish Vestigial Like Family Member 4b Is Required for Valvulogenesis Through Sequestration of Transcription Factor Myocyte Enhancer Factor 2c (2019)

A variety of cardiac transcription factors/cofactors, signaling pathways, and downstream structural genes integrate to form the regulatory hierarchies to ensure proper cardiogenesis in vertebrate. Major interaction proteins of the transcription cofactor vestigial like family member 4 (VGLL4) include myocyte enhancer factor 2 (MEF2) and TEA domain transcription factors (TEAD), both of which play important roles in embryonic cardiac development and in adulthood. In this study, we identified that the deficiency of zebrafish <i>vgll4b</i> paralog, a unique family member expressed in developing heart, led to an impaired valve development. Mechanistically, in <i>vgll4b</i> mutant embryos the disruption of Vgll4b-Mef2c complex, rather than that of Vgll4b-Tead complex, resulted in an aberrant expression of <i>krüppel-like factor 2a</i> (<i>klf2a</i>) in endocardium. Such misexpression of <i>klf2a</i> eventually evoked the valvulogenesis defects. Our findings suggest that zebrafish Vgll4b plays an important role in modulating the transcription activity of Mef2c on <i>klf2a</i> during valve development in a blood-flow-independent manner.
Control of light-dependent keto carotenoid biosynthesis inNostoc7120 by the transcription factor NtcA (2016)

In Nostoc PCC 7120, two different ketolases, CrtW and CrtO are involved in the formation of keto carotenoids from β-carotene. In contrast to other cyanobacteria, CrtW catalyzes the formation of monoketo echinenone whereas CrtO is the only enzyme for the synthesis of diketo canthaxanthin. This is the major photo protective carotenoid in this cyanobacterium. Under high-light conditions, basic canthaxanthin formation was transcriptionally up-regulated. Upon transfer to high light, the transcript levels of all investigated carotenogenic genes including those coding for phytoene synthase, phytoene desaturase and both ketolases were increased. These transcription changes proceeded via binding of the transcription factor NtcA to the promoter regions of the carotenogenic genes. The binding was absolutely dependent on the presence of reductants and oxo-glutarate. Light-stimulated transcript formation was inhibited by DCMU. Therefore, photosynthetic electron transport is proposed as the sensor for high-light and a changing redox state as a signal for NtcA binding.
Retrospective Analysis of Traumatic Dental Injuries in Saudi Children: An Institutional Study (2021)

Aim: This study aimed to analyse data from the records of the past five years of Saudi children seen in the dental trauma emergency clinic in College of Dentistry King Khalid University, Abha, Saudi Arabia. Materials and Methods: The current study was a cross-sectional observational analytic study. Our study includes the records of children having age groups of 2 to 12 years who visited the Department of Pediatric Dentistry in the College of Dentistry King Khalid University, from January 2015 to December 2019 as a result of pediatric TDI. Trauma records were obtained based on the Andreasen and Andreasen classification (1). The clinical Information regarding (i) Age, (ii) Sex, (iii) Most affected teeth, (iv) Cause of injury (falls, impact against a hard object or collisions, traffic accident, sport, and game accident, abuse), (v) Monthly distribution of trauma, (vi) Type of trauma (9), (vii) Time elapsed following injury, and (viii) Treatment was recorded. The data were entered and analyzed using the Statistical Package for the Social Sciences (SPSS 20). A P-value of less than 0.05 was considered to be statistically significant. Results: The dental trauma records of patients with an average age of 8 years, including 54 girls (40.9%) and 78 boys (59.1%), were evaluated. The most common cause of trauma was falling (61%). Enamel/ Dentin fracture was the most common type of dental hard tissue fracture around 53 (40.1%). In the category of periodontal tissue injuries, intrusive luxation injury (12.1%) was the most common. Conclusions: Our research disclosed that boys were exposed to more traumatic injuries, and the most crucial factor in traumatic injuries is falling. Therefore, teachers, pediatricians, parents, and children should be cautioned about probable dangers and emergency treatments for all age groups on dental trauma.