gebhart/patrepeval huggingface dataset:
Three-Dimensional Differentiation of Embryonic Stem Cells into Islet-like Insulin-Producing Clusters (2009)

The production of mature pancreatic cells that function similarly to primary islets is the premise of cell therapy for diabetes. Here, we describe a novel approach to generating more mature insulin-producing cells from embryonic stem (ES) cells. A three-dimensional (3D) ES cell pancreatic differentiation system was developed and used to direct the ES cell differentiation into glucose-responsive, insulin-secreting cells. Using mouse ES cells as a model, we demonstrate that more mature insulin-producing cells can be generated from ES cells in 3D cultures. The 3D differentiated pancreatic endocrine cells can assemble into an islet-like tissue structure that displays greater similarities in phenotype and gene expression profile to adult mouse pancreatic islets, that is, with beta cells in the core and non-beta cells forming the mantel, leading to a significant improvement of the maturity of the insulin-producing cells. Our findings show that nearly 50-60% of the cells in 3D formed cell clusters express insulin. More importantly, those cells exhibit a high level of glucose-responsive insulin and C-peptide syntheses and release. A high level of expression of glucose transporter-2 was also detected in these cells. Compared to two-dimensional ES cell-derived insulin-producing cells, the insulin release from 3D ES cell-derived insulin-producing cells showed a nearly fivefold (p<0.05) increase when exposed to a high glucose (27.7 mM) medium. This 3D culture model provides an excellent system to study pancreatic endocrine morphogenesis and tissue organization. This study also demonstrates the feasibility of producing clinically relevant beta cells from ES cells in a 3D environment.
Hematopoietic cytokines: Similarities and differences in the structures, with implications for receptor binding (1993)

Crystal and NMR structures of helical cytokines--interleukin-4 (IL-4), granulocyte-macrophage colony-stimulating factor (GM-CSF), and interleukin-2 (IL-2)--have been compared. Root mean square deviations in the C alpha coordinates for the conserved regions of the helices were 1-2 A between different cytokines, about twice the differences observed for independently determined crystal and solution structures of IL-4. Considerable similarity in amino acid sequence in the areas expected to interact with the receptors was detected, and the available mutagenesis data for these cytokines were correlated with structure conservation. Models of cytokine-receptor interactions were postulated for IL-4 based on its structure as well as on the published structure of human growth hormone interacting with its receptors (de Vos, A.M., Ultsch, M., & Kossiakoff, A.A., 1992, Science 255, 306-312). Patches of positively charged residues on the surfaces of helices C and D of IL-4 may be responsible for the interactions with the negatively charged residues found in the complementary parts of the IL-4 receptors.
The Human Capsaicin Model of Allodynia and Hyperalgesia (1998)

Intradermal and topical application of capsaicin have been used to study mechanisms of mechanical allodynia (MA) and pinprick hyperalgesia (PPH) and the efficacy of drugs in relieving these symptoms. However, it is associated with significant inter- and intra-subject variability. In order to improve the model's sensitivity, we examined several potential sources of variability of capsaicin-evoked MA and PPH in healthy volunteers, including skin temperature fluctuations, method (intradermal vs. topical) and site (volar forearm vs. foot dorsum) of administration. In study I, 12 subjects received, in a 6-session, randomized, crossover trial, 1) 250 micrograms of intradermal (ID) CAP to the volar forearm with skin temperature fixed at 36 degrees C (36 ID). 2) 250 micrograms ID CAP with varying skin temperature (VT ID), or 3) 250 microliters of l% CAP patch placed on the skin at 36 degrees C. The resulting MA and PPH areas observed with each method were measured. In study II, a 4-session, randomized crossover trial, 12 subjects were given 100 micrograms ID CAP in the volar forearm or foot dorsum and subsequent areas of MA and PPH recorded. In study I, 5/12 subjects had small MA areas (< or = 5 cm2) and one subject had small PPH areas in at least 4/6 sessions. The most consistent intra-subject responses were seen with the 36 ID method. Correlation coefficients for the two sessions using the same method of administration were: MA; 36 ID r = 0.83, VT ID = 0.19. Topical r = 0.81; PPH: 36 ID r = 0.93; VT ID r = 0.38, Topical r = 0.78. In study II, 4/12 subjects had little MA for both forearm and foot though all subjects developed PPH. However, greater intra-subject consistency (MA: foot: r = 0.84; arm: r = 0.49; PPH: r = 0.87; r = 0.39) and significantly larger areas of MA (15.8 +/- 4.2 vs 9.1 +/- 2.5, p < 0.05) were seen with the foot. (PPH: foot: 28.9 +/- 6.7; arm: 21.6 +/- 4.2, NS). Large variability exists among subjects receiving CAP, with some developing minimal MA. However, these subjects may be screened out prior to entry, increasing the sensitivity of the model, which may be further improved by clamping the skin temperature.
Production of Sepiapterin in Escherichia coli by Coexpression of Cyanobacterial GTP Cyclohydrolase I and Human 6-Pyruvoyltetrahydropterin Synthase (2002)

Synechocystis sp. strain PCC 6803 GTP cyclohydrolase I and human 6-pyruvoyltetrahydropterin synthase were coexpressed in Escherichia coli. The E. coli transformant produced sepiapterin, which was identified by high-performance liquid chromatography and enzymatically converted to dihydrobiopterin by sepiapterin reductase. Aldose reductase, another indispensable enzyme for sepiapterin production, may be endogenous in E. coli.
Pair-cat codes: autonomous error-correction with low-order nonlinearity (2019)

Abstract We introduce a driven-dissipative two-mode bosonic system whose reservoir causes simultaneous loss of two photons in each mode and whose steady states are superpositions of pair-coherent/Barut-Girardello coherent states. We show how quantum information encoded in a steady-state subspace of this system is exponentially immune to phase drifts (cavity dephasing) in both modes. Additionally, it is possible to protect information from arbitrary photon loss in either (but not simultaneously both) of the modes by continuously monitoring the difference between the expected photon numbers of the logical states. Despite employing more resources, the two-mode scheme enjoys two advantages over its one-mode cat-qubit counterpart with regards to implementation using current circuit QED technology. First, monitoring the photon number difference can be done without turning off the currently implementable dissipative stabilizing process. Second, a lower average photon number per mode is required to enjoy a level of protection at least as good as that of the cat-codes. We discuss circuit QED proposals to stabilize the code states, perform gates, and protect against photon loss via either active syndrome measurement or an autonomous procedure. We introduce quasiprobability distributions allowing us to represent two-mode states of fixed photon number difference in a two-dimensional complex plane, instead of the full four-dimensional two-mode phase space. The two-mode codes are generalized to multiple modes in an extension of the stabilizer formalism to non-diagonalizable stabilizers. The M -mode codes can protect against either arbitrary photon losses in up to M − 1 modes or arbitrary losses and gains in any one mode.
Inflammatory Bowel Disease (2002)

Clinical experience has suggested that Crohn's disease and ulcerative colitis constitute distinct, if not discrete, entities. However, whether these conditions are fundamentally different or are part of a mechanistic continuum is a question with both conceptual and practical implications for management. This review summarizes current understanding of the mechanisms underlying the major forms of inflammatory bowel disease and discusses approaches to therapy.
Differential expression of Ia molecules by human monocytes. (1984)

Human immune response genes can be divided into three distinct loci, each of which codes for three distinct families of Ia molecules: HLA-SB, HLA-DC, and HLA-DR. The tissue distribution and function of only one of these Ia molecules, HLA-DR, has been thoroughly studied. Using monoclonal antibodies, we examined the display of HLA-DR and HLA-DC molecules by adherent, human peripheral blood monocytes. The results of these studies demonstrate that although all human peripheral blood monocytes display easily detectable HLA-DR molecules, only 50% display easily detectable HLA-DC molecules. Separation of peripheral blood monocytes into HLA-DC+ and HLA-DC- cells demonstrates that each population displays an equivalent density of HLA-DR molecules. Therefore, on the basis of differences in their display of these two Ia molecules, adherent peripheral blood monocytes can be divided into two broad populations: HLA-DR+, HLA-DC+, and HLA-DR+, HLA-DC-. Despite the dis-coordinate display of these Ia antigens, the expression of both HLA-DR and HLA-DC can be regulated by a common signal, gamma interferon (IFN-gamma). Incubation of monocytes for 96 h in autologous serum leads to a marked decrease in the expression of both HLA-DR and HLA-DC. Addition of recombinant IFN-gamma to the cultures leads to reexpression of both HLA-DR and HLA-DC to levels comparable to those seen in fresh monocytes. In addition, although IFN-gamma does not modulate all monocyte surface markers, it can be demonstrated to modulate expression of one marker, MAC 120, in a manner similar to that observed for Ia antigens. These studies demonstrate that among human peripheral blood monocytes, the distribution of the Ia molecule, HLA-DC, is not coordinate with that of HLA-DR, although both respond to the same regulatory signal.
A Decade of Silicone Hydrogel Development (2013)

Since the initial launch of silicone hydrogel lenses, there has been a considerable broadening in the range of available commercial material properties. The very mobile silicon-oxygen bonds convey distinctive surface and mechanical properties on silicone hydrogels, in which advantages of enhanced oxygen permeability, reduced protein deposition, and modest frictional interaction are balanced by increased lipid and elastic response. There are now some 15 silicone hydrogel material variants available to practitioners; arguably, the changes that have taken place have been strongly influenced by feedback based on clinical experience. Water content is one of the most influential properties, and the decade has seen a progressive rise from lotrafilcon-A (24%) to efrofilcon-A (74%). Moduli have decreased over the same period from 1.4 to 0.3 MPa, but not solely as a result of changes in water content. Surface properties do not correlate directly with water content, and ingenious approaches have been used to achieve desirable improvements (e.g., greater lubricity and lower contact angle hysteresis). This is demonstrated by comparing the hysteresis value of the earliest (lotrafilcon-A, >40°) and most recent (delefilcon-A, <10°) coated silicone hydrogels. Although wettability is important, it is not of itself a good predictor of ocular response because this involves a much wider range of physicochemical and biochemical factors. The interference of the lens with ocular dynamics is complex leading separately to tissue-material interactions involving anterior and posterior lens surfaces. The biochemical consequences of these interactions may hold the key to a greater understanding of ocular incompatibility and end of day discomfort.
Aminoacylases (1994)

Aminoacylases catalyze the hydrolysis of N-acyl-L-amino acids to give fatty acids and amino acids as products. It has been proposed that aminoacylases may participate in the catabolism of terminal N-acylpeptides or in the salvage of N-acetylated amino acids. The aminoacylases play a role in xenobiotic detoxication and bioactivation and are important in the interorgan processing of xenobiotic-derived amino acid conjugates. Aminoacylases participate in conjugation-dependent toxicity—for example, mercapturates may serve to deliver nephrotoxic cysteine S-conjugates to the kidney. In this mechanism, mercapturates delivered via the circulation to the kidney may be taken up by the probenecid-sensitive anion transport system located on the basolateral surface of renal proximaltubular cells. Although aminoacylase activity is found in many tissues, this chapter focuses largely on renal aminoacylases, which are the only aminoacylases that have been linked to xenobiotic bioactivation reactions.
Ribosome Display: A Technology for Selecting and Evolving Proteins from Large Libraries (2010)

The selection and concomitant affinity maturation of proteins to bind to user-defined target molecules have become a key technology in biochemical research, diagnostics, and therapy. One of the most potent selection technologies for such applications is ribosome display. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation. Ribosome display has been used successfully for the selection of antibody fragments and other binding proteins, such as Designed Ankyrin Repeat Proteins (DARPins).
Fludarabine modulates composition and function of the T cell pool in patients with chronic lymphocytic leukaemia (2010)

The combination of cytotoxic treatment with strategies for immune activation represents an attractive strategy for tumour therapy. Following reduction of high tumour burden by effective cytotoxic agents, two major immune-stimulating approaches are being pursued. First, innate immunity can be activated by monoclonal antibodies triggering antibody-dependent cellular cytotoxicity. Second, tumour-specific T cell responses can be generated by immunization of patients with peptides derived from tumour antigens and infused in soluble form or loaded onto dendritic cells. The choice of cytotoxic agents for such combinatory regimens is crucial since most substances such as fludarabine are considered immunosuppressive while others such as cyclophosphamide can have immunostimulatory activity. We tested in this study whether fludarabine and/or cyclophosphamide, which represent a very effective treatment regimen for chronic lymphocytic leukaemia, would interfere with a therapeutic strategy of T cell activation. Analysis of peripheral blood samples from patients prior and during fludarabine/cyclophosphamide therapy revealed rapid and sustained reduction of tumour cells but also of CD4(+) and CD8(+) T cells. This correlated with a significant cytotoxic activity of fludarabine/cyclophosphamide on T cells in vitro. Unexpectedly, T cells surviving fludarabine/cyclophosphamide treatment in vitro had a more mature phenotype, while fludarabine-treated T cells were significantly more responsive to mitogenic stimulation than their untreated counterparts and showed a shift towards T(H)1 cytokine secretion. In conclusion, fludarabine/cyclophosphamide therapy though inducing significant and relevant T cell depletion seems to generate a micromilieu suitable for subsequent T cell activation.
The Interleukin-17 Gene of Herpesvirus Saimiri (1998)

In comparison to wild-type herpesvirus saimiri, viral interleukin-17 gene knockout mutants have unaltered behavior regarding viral replication, T-cell transformation in vitro, and pathogenicity in cottontop tamarins. Thus, this gene is not required for T-cell lymphoma induction but may contribute to apathogenic viral persistence in the natural host, the squirrel monkey.
Efficient transfer of receptor-associated protein (RAP) across the blood-brain barrier (2004)

We have sought to identify a high-capacity transport system that mediates transcytosis of proteins from the blood to the brain. The 39 kDa receptor-associated protein (RAP) functions as a specialized endoplasmic reticulum chaperone assisting in the folding and trafficking of members of the low-density lipoprotein (LDL) receptor family. RAP efficiently binds to these receptors and antagonizes binding of other ligands. Previous studies have shown that two large members of the LDL receptor family, LDL receptor-related protein 1 (LRP1) and LDL receptor-related protein 2 (LRP2 or megalin), possess the ability to mediate transcytosis of ligands across the brain capillary endothelium. Here, we tested whether blood-borne RAP crosses the blood-brain barrier (BBB) by LRP1- or megalin-mediated transport by studying the pharmacokinetics of [125I]-RAP transport into the brain in intact mice and across cell monolayers in vitro. Our results show that [125I]-RAP is relatively stable in blood for 30 minutes and has a mean influx constant of 0.62+/-0.08 microl/g-minute from blood to brain. In situ brain perfusion in blood-free buffer shows that transport of [125I]-RAP across the BBB is a saturable process. Capillary depletion of brain homogenates indicates that 70% of [125I]-RAP is localized in the parenchyma rather than in the vasculature of the brain. Results of transport in stably transfected MDCK cells are consistent with the hypothesis that megalin mediates most of the apical-to-basolateral transport across polarized epithelial cells. The inhibition of [125I]-RAP influx by excess RAP and the involvement of megalin indicate the presence of a saturable transport system at the BBB. The higher permeability of RAP compared with that of melanotransferrin and transferrin show that the LRP receptor is a high capacity transport system. These studies suggest that RAP may provide a novel means of protein-based drug delivery to the brain.
Mitigation of Layered to Spinel Conversion of a Li-Rich Layered Metal Oxide Cathode Material for Li-Ion Batteries (2013)

We have prepared the Li-rich layered NMC composite cathode material of the composition 0.3Li2MnO30.7LiMn0.33Ni0.33Co0.33O2, (NMC) with 5 wt% Na doping. The latter material with composition of 0.3Li2MnO3.0.7Li0.97Na0.03Mn0.33Ni0.33Co0.33O2, synthesized as 200–300 nm size particles, was compared to its counterpart without Na. The discharge rate capability of the Li-rich NMC was greatly improved at both room temperature and 50°C with the Na doping. The Na doped material exhibited significantly higher conductivity than its un-doped analog as evidenced by dc electronic conductivity data and impedance of Li cells. Charge/discharge cycling results of Li cells at 50°C indicated that the voltage decay of Li-rich NMC accompanied by a layer to spinel structural conversion was mitigated with Na doping. XRD analysis revealed that ionic exchange of Na occurs upon contact of the cathode material with the electrolyte and produces a volume expansion of the crystal lattice which triggers a favorable metal (probably Ni) migration to Li depleted regions during oxidation of Li2MnO3 in the first cycle. XANES data showed that Na doped NMC has better Ni reduction efficiency to provide higher rate capability. EXAFS data supported this conclusion by showing that in the case of Na doped NMC, the structure has larger crystal cage allowing for better metal migration into the Li depleted regions located in the layered unit cell of C2/m space group. XANES of Mn K-edge supported by pre-edge analysis also revealed that during charging of the electrode, the Na doped NMC was oxidized to a higher Mn valence state compared to its undoped counterpart.
From Self-Assembled Monolayers to Coatings: Advances in the Synthesis and Nanobio Applications of Polymer Brushes (2015)

In this review, we describe the latest advances in synthesis, characterization, and applications of polymer brushes. Synthetic advances towards well-defined polymer brushes, which meet criteria such as: (i) Efficient and fast grafting, (ii) Applicability on a wide range of substrates; and (iii) Precise control of surface initiator concentration and hence, chain density are discussed. On the characterization end advances in methods for the determination of relevant physical parameters such as surface initiator concentration and grafting density are discussed. The impact of these advances specifically in emerging fields of nano- and bio-technology where interfacial properties such as surface energies are controlled to create nanopatterned polymer brushes and their implications in mediating with biological systems is discussed.
α-Hydroxybutyrate Is an Early Biomarker of Insulin Resistance and Glucose Intolerance in a Nondiabetic Population (2010)

alpha-hydroxybutyrate is an early marker for both insulin resistance and impaired glucose regulation. The underlying biochemical mechanisms may involve increased lipid oxidation and oxidative stress.
Impaired Genome Maintenance Suppresses the Growth Hormone–Insulin-Like Growth Factor 1 Axis in Mice with Cockayne Syndrome (2006)

Cockayne syndrome (CS) is a photosensitive, DNA repair disorder associated with progeria that is caused by a defect in the transcription-coupled repair subpathway of nucleotide excision repair (NER). Here, complete inactivation of NER in Csb(m/m)/Xpa(-/-) mutants causes a phenotype that reliably mimics the human progeroid CS syndrome. Newborn Csb(m/m)/Xpa(-/-) mice display attenuated growth, progressive neurological dysfunction, retinal degeneration, cachexia, kyphosis, and die before weaning. Mouse liver transcriptome analysis and several physiological endpoints revealed systemic suppression of the growth hormone/insulin-like growth factor 1 (GH/IGF1) somatotroph axis and oxidative metabolism, increased antioxidant responses, and hypoglycemia together with hepatic glycogen and fat accumulation. Broad genome-wide parallels between Csb(m/m)/Xpa(-/-) and naturally aged mouse liver transcriptomes suggested that these changes are intrinsic to natural ageing and the DNA repair-deficient mice. Importantly, wild-type mice exposed to a low dose of chronic genotoxic stress recapitulated this response, thereby pointing to a novel link between genome instability and the age-related decline of the somatotroph axis.
The Design and Enzyme-Bound Crystal Structure of Indoline Based Peptidomimetic Inhibitors of Hepatitis C Virus NS3 Protease (2004)

The design of a series of peptidomimetic inhibitors of the hepatitis C virus NS3 protease is described. These inhibitors feature an indoline-2-carboxamide as a novel heterocyclic replacement for the P3 amino acid residue and N-terminal capping group of tripeptide based inhibitors. The crystal structure of the ternary NS3/NS4A/inhibitor complex for the most active molecule in this series highlights its suitability as an N-terminal capping group of a dipeptide inhibitor of the NS3 protease.
Comparative Effects of Basic Fibroblast Growth Factor and Vascular Endothelial Growth Factor on Coronary Collateral Development and the Arterial Response to Injury (1996)

Short-term treatment with bFGF enhanced collateral development without increasing neointimal accumulation at sites of vascular injury. Although VEGF did not increase collateral development as administered in this study, it significantly exacerbated neointimal accumulation. These data provide support for the clinical investigation of bFGF in selected patients with ischemic heart disease.