gebhart/patrepeval huggingface dataset:
Transendothelial migration enhances integrin-dependent human neutrophil chemokinesis (2006)

Transendothelial migration of neutrophils induces phenotypic changes that influence the interactions of neutrophils with extravascular tissue components. To assess the influence of transmigration on neutrophil chemokinetic motility, we used polyethylene glycol hydrogels covalently modified with specific peptide sequences relevant to extracellular matrix proteins. We evaluated fMLP-stimulated human neutrophil motility on peptides Arg-Gly-Asp-Ser (RGDS) and TMKIIPFNRTLIGG (P2), alone and in combination. RGDS is a bioactive sequence found in a number of proteins, and P2 is a membrane-activated complex-1 (Mac-1) ligand located in the gamma-chain of the fibrinogen protein. We evaluated, via video microscopy, cell motility by measuring cell displacement from origin and total accumulated distance traveled and then calculated average velocity. Results indicate that although adhesion and shape change were supported by hydrogels containing RGD alone, motility was not. Mac-1-dependent motility was supported on hydrogels containing P2 alone. Motility was enhanced through combined presentation of RGD and P2, engaging Mac-1, alpha(V)beta(3), and beta(1) integrins. Naïve neutrophil motility on combined peptide substrates was dependent on Mac-1, and alpha(4)beta(1) while alpha(6)beta(1) contributed to speed and linear movement. Transmigrated neutrophil motility was dependent on alpha(v)beta(3) and alpha(5)beta(1), and alpha(4)beta(1), alpha(6)beta(1), and Mac-1 contributed to speed and linear motion. Together, the data demonstrate that efficient neutrophil migration, dependent on multi-integrin interaction, is enhanced after transendothelial migration.
Potentiation by specific short-chain fatty acids of differentiation and apoptosis in human colonic carcinoma cell lines. (1994)

The architecture of normal colonic mucosa suggest that terminally differentiated epithelial cells near the top of the crypt are extruded into the colonic lumen. Morphological studies have identified apoptotic cells among the differentiated phenotypes near the crypt-lumen interface, suggesting a link between pathways of differentiation, apoptosis, and cellular shedding. We studied these processes in HT29 and SW620 cells and found that compared to adherent cells, those cells which were shed during standard, uninduced culture conditions exhibited nonrandom DNA fragmentation characteristic of apoptosis. Moreover, these apoptotic cells, which accumulate in the media, exhibited a more differentiated phenotype. Because short-chain fatty acids (SCFAs) are natural effectors of colonic cell differentiation in vivo, we investigated the specificity of three 4-carbon atom SCFAs on potentiating differentiation and apoptosis, and thus accumulation of shed cells in the conditioned media, in these colonic carcinoma cell lines. Whereas the unbranched SCFA butyrate induced a more differentiated phenotype and enhanced apoptosis, two derivatives of butyrate, branched isobutyric acid and a nonmetabolizable fluorine-substituted analogue, heptafluorobutyric acid, were ineffective in inducing either differentiation or apoptosis. Thus, potentiated differentiation and apoptosis in colonic carcinoma cells were linked to SCFA structure and, most likely, utilization.
1077 (2012)

Introduction: We have been providing extracorporeal life support (ECLS) since 1993 for adults, and 2000 for children. Percutaneous cannulation (PC) is performed by intensivists with surgical backup. Except for rapid deployment, the approach includes the pre-insertion ultrasound (U/S) to assess vessel size, fluoroscopy (FL) to image guidewire placement, and as of 2005 the use of ultrasound to guide vascular access and cannula insertion. The objective of this study was to review our percutaneous cannulation experience. Methods: Patients were identified by query of the ELSO Registry. Hospital records were reviewed to obtain cannulation data. Major complications were the inability to complete cannulation, major vessel injury, major hemorrhage, and death. Results: A total of 185 PCs in 90 patients were attempted. 82 patients had respiratory support, 4 had cardiac support and 4 had ECPR. PC of each patient was performed by one or two of four intensivists. 19 were pediatric (age 1 to 16), with the remaining 71 adults. Of the pediatric patients, 12 were dual lumen (DL) venovenous (VV), 6 were two-site VV, and 1 was three-site venovenoarterial (VVA). Of the adult patients, 11 were DL VV, 43 were two-site VV, 12 were VV, and 5 were VVA. Pre-insertion U/S was performed in 83 patients (92%), FU guidance in 76 patients (84%), and U/S -guided insertion in 56 patients (62%). Cannulation was successful in all but two patients (98%). In the first case cannulation was attempted for severe respiratory failure. Without U/S guidance, a right IJ attempt resulted in a major laceration of the vein not amenable to surgical repair. The patient died before other sites could be accessed. In the second case a 12 y/o patient underwent IJ cannulation without imaging during CPR following cardiac arrest. After cannulation, air returned from the cannula, and resuscitation attempts were not successful. Autopsy revealed perforation of the right atrium, with the cause of cardiac arrest identified as staphylococcal myocarditis. Conclusions: PC for ECLS can be performed successfully with a low complication rate by intensivists. The use of U/S combined with FU may afford an index of safety and appear to be key factors in our experience.
Artificial three-dimensional niches deconstruct pancreas development <i>in vitro</i> (2013)

In the context of a cellular therapy for diabetes, methods for pancreatic progenitor expansion and subsequent differentiation into insulin-producing beta cells would be extremely valuable. Here we establish three-dimensional culture conditions in Matrigel that enable the efficient expansion of dissociated mouse embryonic pancreatic progenitors. By manipulating the medium composition we generate either hollow spheres, which are mainly composed of pancreatic progenitors, or complex organoids that spontaneously undergo pancreatic morphogenesis and differentiation. The in vitro maintenance and expansion of pancreatic progenitors require active Notch and FGF signaling, thus recapitulating in vivo niche signaling interactions. Our experiments reveal new aspects of pancreas development, such as a community effect by which small groups of cells better maintain progenitor properties and expand more efficiently than isolated cells, as well as the requirement for three-dimensionality. Finally, growth conditions in chemically defined biomaterials pave the way for testing the biophysical and biochemical properties of the niche that sustains pancreatic progenitors.
Experimental Tumor Metastasis: Characteristics and Organ Specificity (1978)

Journal Article Experimental Tumor Metastasis: Characteristics and Organ Specificity Get access Garth L. Nicolson Garth L. Nicolson Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 28, Issue 7, July 1978, Pages 441–447, https://doi.org/10.2307/1307226 Published: 01 July 1978 Article history Accepted: 11 April 1978 Published: 01 July 1978
Mechanism of Action of a Distal NF-κB-Dependent Enhancer (2006)

The monocyte chemoattractant protein 1 gene (MCP-1) is regulated by TNF through an NF-kappaB-dependent distal enhancer and an Sp1-dependent promoter-proximal regulatory region. In the silent state, only the distal regulatory region is accessible to transcription factors. Upon activation by tumor necrosis factor, NF-kappaB binds to the distal regulatory region and recruits CBP and p300. CBP and p300 recruitment led to specific histone modifications that ultimately enabled the binding of Sp1 to the proximal regulatory region. During this process, a direct interaction between the distal and proximal regulatory regions occurred. Sp1, NF-kappaB, CBP, and p300 were required for this interaction. CBP/p300-mediated histone modifications enhanced the binding of the coactivator CARM1 to the distal regulatory region. CARM1, which is necessary for MCP-1 expression, was not required for distal-proximal region interactions, suggesting that it plays a later downstream activation event. The results describe a model in which the separation of the distal enhancer from the promoter-proximal region allows for two independent chromatin states to exist, preventing inappropriate gene activation at the promoter while at the same time allowing rapid induction through the distal regulatory region.
Reliability-Based Inspection Protocols for Mast-Arm Sign Support Structures (2016)

There have been numerous examples of poor in-service performance of welded, tube-to-transverse plate connections within mast-arm sign support structures in the last several decades. A considerable amount of research has been devoted to identifying structural response characteristics of these sign support systems and identifying how these connections may be repaired, retrofitted, or designed to facilitate longer service lives. Little attention has been given to using a systematic reliability-based approach to assess the probability of fatigue-induced crack initiation for in-service structures. The present research effort focuses on quantifying sources of uncertainty and formulating a reliability-based approach for prescribing inspection intervals corresponding to user-specified levels of probability of fatigue-induced crack initiation. The results indicate that implementation of reliability-based assessment procedures can be used to assign inspection intervals based on this probability, and the engineering community can use the results to establish inspection intervals that better align inspection needs with limited fiscal and human resources.
Multimodal user interfaces in the Open Agent Architecture (1997)

The design and development of the Open Agent Architecture (OAA)l system has focused on providing access to agentbased applications through an intelligent, cooperative, distributed, and multimodal agent-based user interfaces. The current multimodal interface supports a mix of spoken language, handwriting and gesture, and is adaptable to the user's preferences, resources and environment.
Immuno-affinity purification of specific antibodies against vasoactive intestinal polypeptide(VIP) on VIP (1-10)-linked polydimethylacrylamide resin. (1989)

A novel method for immuno-affinity purification of specific antibodies against amino-terminal (N-terminal) porcine vasoactive intestinal polypeptide (p-VIP) was developed. The antiserum VP (No. 6203) elicited by p-VIP-immunoglobulin G (IgG) conjugate was heterogenous and reacted not only with the N-terminal fragments of p-VIP but also with carboxy-terminal (C-terminal) fragments. To obtain specific antibodies against the N-terminal fragment of p-VIP, antiserum VP was purified by column chromatography on N-terminal decapeptide (p-VIP 1-10)-linked polydimethylacrylamide resin. The antibody thus obtained was highly specific to the N-terminal sequence of p-VIP and hardly reacted with the C-terminal fragments of VIP in enzyme-linked immunosorbent assay.
Energy Management Strategies for Plug-In Hybrid Electric Vehicles (2007)

<div class="htmlview paragraph">Plug-in hybrid electric vehicles (PHEVs) differ from hybrid vehicles (HEVs) with their ability to use off-board electricity generation to recharge their energy storage systems. In addition to possessing charge-sustaining HEV operation capability, PHEVs use the stored electrical energy during a charge-depleting operating period to displace a significant amount of petroleum consumption. The particular operating strategy employed during the charge-depleting mode will significantly influence the component attributes and the value of the PHEV technology. This paper summarizes three potential energy management strategies, and compares the implications of selecting one strategy over another in the context of the aggressiveness and distance of the duty cycle over which the vehicle will likely operate.</div>
Perforation Peritonitis and the Developing World (2014)

Background. Perforation peritonitis is the one of the commonest emergency encountered by surgeons. The aim of this paper is to provide an overview of the spectrum of perforation peritonitis managed in a single unit of a tertiary care hospital in Delhi. Methods. A retrospective study was carried out between May 2010 and June 2013 in a single unit of the department of Surgery, Lok Nayak Hospital, Delhi. It included 400 patients of perforation peritonitis (diffuse or localized) who were studied retrospectively in terms of cause, site of perforation, surgical treatment, complications, and mortality. Only those patients who underwent exploratory laparotomy for management of perforation peritonitis were included. Results. The commonest cause of perforation peritonitis included 179 cases of peptic ulcer disease (150 duodenal ulcers and 29 gastric ulcers) followed by appendicitis (74 cases), typhoid fever (48 cases), tuberculosis (40 cases), and trauma (31). The overall mortality was 7%. Conclusions. Perforation peritonitis in India has a different spectrum as compared to the western countries. Peptic ulcer perforation, perforating appendicitis, typhoid, and tubercular perforations are the major causes of gastrointestinal perforations. Early surgical intervention under the cover of broad spectrum antibiotics preceded by adequate aggressive resuscitation and correction of electrolyte imbalances is imperative for good outcomes minimizing morbidity and mortality.
The B&W mPower&trade; Scalable, Practical Nuclear Reactor Design (2012)

The Babcock & Wilcox Company launched an aggressive program in 2008 to develop a scalable nuclear reactor using its unique history of over 50 years of continuous reactor engineering and manufacturing. The B&W mPower™ reactor design is a passively safe advanced light water reactor (ALWR) with a below-ground containment structure. This optimized ALWR represents true generation III+ nuclear technology that B&W believes can be certified, manufactured, and operated within today’s existing U.S. regulatory, industrial supply chain, and utility operational infrastructure.The mPower reactor takes a competitive approach to plant operations and emphasizes safety and compliance with the EPRI Utilities Requirements Document (URD), incorporating decades of lessons learned from the operating fleet. The design’s scalability, ease of transport, and independence from water rights for secondary heat rejection make it well suited for deployment in a wide range of applications, including incremental additions to the base load, load-following conditions, and industrial applications. The mPower reactor is also a viable solution to retrofit aging conventional power plants, leveraging the existing plant siting and transmission system.
Immunophenotypic analysis of human articular chondrocytes: Changes in surface markers associated with cell expansion in monolayer culture (2004)

Cartilage tissue engineering relies on in vitro expansion of primary chondrocytes. Monolayer is the chosen culture model for chondrocyte expansion because in this system the proliferative capacity of chondrocytes is substantially higher compared to non-adherent systems. However, human articular chondrocytes (HACs) cultured as monolayers undergo changes in phenotype and gene expression known as "dedifferentiation." To gain a better understanding of the cellular mechanisms involved in the dedifferentiation process, our research focused on the characterization of the surface molecule phenotype of HACs in monolayer culture. Adult HACs were isolated by enzymatic digestion of cartilage samples obtained post-mortem. HACs cultured in monolayer for different time periods were analyzed by flow cytometry for the expression of cell surface markers with a panel of 52 antibodies. Our results show that HACs express surface molecules belonging to different categories: integrins and other adhesion molecules (CD49a, CD49b, CD49c, CD49e, CD49f, CD51/61, CD54, CD106, CD166, CD58, CD44), tetraspanins (CD9, CD63, CD81, CD82, CD151), receptors (CD105, CD119, CD130, CD140a, CD221, CD95, CD120a, CD71, CD14), ectoenzymes (CD10, CD26), and other surface molecules (CD90, CD99). Moreover, differential expression of certain markers in monolayer culture was identified. Up-regulation of markers on HACs regarded as distinctive for mesenchymal stem cells (CD10, CD90, CD105, CD166) during monolayer culture suggested that dedifferentiation leads to reversion to a primitive phenotype. This study contributes to the definition of HAC phenotype, and provides new potential markers to characterize chondrocyte differentiation stage in the context of tissue engineering applications.
Synthesis of Organoboron Compounds via the Transition Metal-Catalyzed Addition and Coupling Reaction of (Alkoxo)diborons. (1999)

Transition metal-catalyzed additions and cross-coupling reactions of the metal-metal compounds have attracted considerable attention as direct routes to prepare various organometallic compounds. Although the corresponding reactions of boron compounds had not yet been well developed, we recently reported the first platinum (0) -catalyzed addition reaction of bis (pinacolato) diboron (1 d) to either terminal or internal alkynes to give cis-bis (boryl) alkenes. The addition of 1 d to 1, 3-dienes and alkenes with platinum (0) complexes afforded a new access to the cis-1, 4-bis (boryl) butene and bis- (boryl) alkane derivatives. The palladium (0) -catalyzed cross-coupling reactions of 1 d with aryl halides or triflates, and allyl chlorides or acetates gave the corresponding aryl- and allylboronates in high yields, which provides the first one-step procedure for organoboronic esters from organic electrophiles. Since (alkoxo) diborons are thermally stable and easily handled in air, the reagent can be useful as boron nucleophiles for cross-coupling reactions with organic halides. The mechanisms and the synthetic applications of those reactions are discussed.
Recent Advances in <i>N</i>‐Protection for Amino Sugar Synthesis (1997)

Abstract Recent synthetic efforts in the construction of oligosaccharides, glycoproteins, glycolipids and other glycoconjugates containing a variety of 2‐amino‐2‐deoxy sugars have led to the development of new methods for nitrogen protection. These new nitrogen‐protecting groups have been removed from substrates using mild and often chemoselective conditions. In this microreview, the preparation, present uses, and deprotection of amino sugar derivatives employing these new agents are described. Applications of phthalimides with electron‐withdrawing groups including the tetrachlorophthaloyl (TCP), dichlorophthaloyl (DCPhth), dithiasuccinoyl (Dts), N ‐pent‐4‐enoyl and N,N ‐diacetyl functionalities are discussed.
Surface Coating with a Thermoresponsive Copolymer for the Culture and Non‐Enzymatic Recovery of Mouse Embryonic Stem Cells (2009)

A thermoresponsive substrate based on a triblock copolymer, poly(N-isopropylacrylamide)-block-poly[(R)-3-hydroxybutyrate]-block-poly(N-isopropylacrylamide) (PNIPAAm-PHB-PNIPAAm), co-coated with gelatin, was developed for the culture and non-enzymatic recovery of mouse embryonic stem cells. After culture, the cells could be detached by cooling at 4 degrees C for 20 min without trypsin digestion. The embryonic stem cells remained undifferentiated after culture on the gelatin/copolymer-coated surfaces, similar to standard culture techniques. Overall, the triblock copolymer coating was superior to the PNIPAAm homopolymer coating in terms of supporting better cell growth, being more stable, presenting a more homogeneous surface coating, and maintaining pluripotency of the embryonic stem cells.
Complex effects of phenylarsine oxide in T cells. Induction of tyrosine phosphorylation and calcium mobilization independent of CD45 expression. (1993)

The effects of phenylarsine oxide, a phosphotyrosine phosphatase inhibitor, on early signal transduction events in human T cells were studied. Simultaneous stimulation of T cells with anti-CD3 monoclonal antibody and phenylarsine oxide prevented increased tyrosine phosphorylation of phospholipase C gamma 1. In contrast, treatment of resting T cells with phenylarsine oxide alone resulted in increased tyrosine phosphorylation of a number of other intracellular substrates. Further, phenylarsine oxide was able to cause an immediate disruption of signal transduction in T cells after anti-CD3 stimulation, as measured by a return of intracellular calcium concentration and inositol 1,4,5-trisphosphate production to base-line levels. Surprisingly, in view of the inhibitory effects of phenylarsine oxide on T cell receptor signal transduction, treatment of T cells with phenylarsine oxide alone caused a dose-dependent increase in intracellular-free calcium concentration that was not accompanied with detectable increases in inositol 1,4,5-trisphosphate production. The phenylarsine oxide-induced increase in free calcium had distinct kinetics from antigen receptor-activated calcium mobilization and was derived from both intracellular sources and increased plasma membrane calcium permeability. This effect was independent of the CD45 transmembrane tyrosine phosphatase. Phenylarsine oxide thus has complex effects on signal transduction in T cells that suggests multiple intracellular targets, and these should be considered in the interpretation of experiments using this agent to study cellular kinase and phosphatase interactions. Finally, the effects of phenylarsine oxide on cellular calcium homeostasis may provide a mechanism of action for the therapeutic and/or toxic effects of arsenicals used for various forms of chemotherapy.
Versatile live attenuated SARS-CoV-2 vaccine platform applicable to variants induces protective immunity (2021)

SUMMARY Live attenuated vaccines are generally highly effective. Here, we aimed to develop one against SARS-CoV-2, based on the identification of three types of temperature-sensitive (TS) strains with mutations in nonstructural proteins (nsp), impaired proliferation at 37-39°C, and the capacity to induce protective immunity in Syrian hamsters. To develop a live-attenuated vaccine, we generated a virus that combined all these TS-associated mutations (rTS-all), which showed a robust TS phenotype in vitro and high attenuation in vivo . The vaccine induced an effective cross-reactive immune response and protected hamsters against homologous or heterologous viral challenges. Importantly, rTS-all rarely reverted to the wild-type phenotype. By combining these mutations with an Omicron spike protein to construct a recombinant virus, protection against the Omicron strain was obtained. We show that immediate and effective live-attenuated vaccine candidates against SARS-CoV-2 variants may be developed using rTS-all as a backbone to incorporate the spike protein of the variants.