gebhart/patrepeval huggingface dataset:
Nanostructured Pluronic hydrogels as bioinks for 3D bioprinting (2015)

Bioprinting is an emerging technology in the field of tissue engineering as it allows the precise positioning of biologically relevant materials in 3D, which more resembles the native tissue in our body than current homogenous, bulk approaches. There is however a lack of materials to be used with this technology and materials such as the block copolymer Pluronic have good printing properties but do not allow long-term cell culture. Here we present an approach called nanostructuring to increase the biocompatibility of Pluronic gels at printable concentrations. By mixing acrylated with unmodified Pluronic F127 it was possible to maintain the excellent printing properties of Pluronic and to create stable gels via UV crosslinking. By subsequent elution of the unmodified Pluronic from the crosslinked network we were able to increase the cell viability of encapsulated chondrocytes at day 14 from 62% for a pure acrylated Pluronic hydrogel to 86% for a nanostructured hydrogel. The mixed Pluronic gels also showed good printability when cells where included in the bioink. The nanostructured gels were, with a compressive modulus of 1.42 kPa, mechanically weak, but we were able to increase the mechanical properties by the addition of methacrylated hyaluronic acid. Our nanostructuring approach enables Pluronic hydrogels to have the desired set of properties in all stages of the bioprinting process.
Effects of Structural Distortions on Photonic Band-gap Fibers (2007)

A scanning electron micrograph of a photonic band-gap fiber profile is analyzed using a finite element method. It is shown that structural distortions have significant impacts on fiber properties such as bandwidth and tunneling loss.
Characterization of Human Immunodeficiency Virus Type 1 Monomeric and Trimeric gp120 Glycoproteins Stabilized in the CD4-Bound State: Antigenicity, Biophysics, and Immunogenicity (2007)

The human immunodeficiency virus type 1 exterior gp120 envelope glycoprotein is highly flexible, and this flexibility may contribute to the inability of monomeric gp120 immunogens to elicit broadly neutralizing antibodies. We previously showed that an S375W modification of a critical interfacial cavity central to the primary receptor binding site, the Phe43 cavity, stabilizes gp120 into the CD4-bound state. However, the immunological effects of this cavity-altering replacement were never tested. Subsequently, we screened other mutations that, along with the S375W alteration, might further stabilize the CD4-bound state. Here, we define a selected second cavity-altering replacement, T257S, and analyze the double mutations in several gp120 envelope glycoprotein contexts. The gp120 glycoproteins with the T257S-plus-S375W double mutation (T257S+S375W) have a superior antigenic profile compared to the originally identified single S375W replacement in terms of enhanced recognition by the broadly neutralizing CD4 binding-site antibody b12. Isothermal titration calorimetry measuring the entropy of the gp120 interaction with CD4 indicated that the double mutant was also stabilized into the CD4-bound state, with increasing relative fixation between core, full-length monomeric, and full-length trimeric versions of gp120. A significant increase in gp120 affinity for CD4 was also observed for the cavity-filling mutants relative to wild-type gp120. The most conformationally constrained T257S+S375W trimeric gp120 proteins were selected for immunogenicity analysis in rabbits and displayed a trend of improvement relative to their wild-type counterparts in terms of eliciting neutralizing antibodies. Together, the results suggest that conformational stabilization may improve the ability of gp120 to elicit neutralizing antibodies.
p53 functions as a cell cycle control protein in osteosarcomas. (1990)

Mutations in the p53 gene have been associated with a wide range of human tumors, including osteosarcomas. Although it has been shown that wild-type p53 can block the ability of E1a and ras to cotransform primary rodent cells, it is poorly understood why inactivation of the p53 gene is important for tumor formation. We show that overexpression of the gene encoding wild-type p53 blocks the growth of osteosarcoma cells. The growth arrest was determined to be due to an inability of the transfected cells to progress into S phase. This suggests that the role of the p53 gene as an antioncogene may be in controlling the cell cycle in a fashion analogous to the check-point control genes in Saccharomyces cerevisiae.
Explanation-Based Neural Network Learning for Robot Control (1992)

How can artificial neural nets generalize better from fewer examples? In order to generalize successfully, neural network learning methods typically require large training data sets. We introduce a neural network learning method that generalizes rationally from many fewer data points, relying instead on prior knowledge encoded in previously learned neural networks. For example, in robot control learning tasks reported here, previously learned networks that model the effects of robot actions are used to guide subsequent learning of robot control functions. For each observed training example of the target function (e.g. the robot control policy), the learner explains the observed example in terms of its prior knowledge, then analyzes this explanation to infer additional information about the shape, or slope, of the target function. This shape knowledge is used to bias generalization when learning the target function. Results are presented applying this approach to a simulated robot task ...
The Nuclear Membrane (1992)

The nuclear membrane forms a major barrier within the cell, permitting levels of regulation not found in prokaryotes. The dynamics and diverse functions of the nuclear membrane and its associated structures are considered in this review. The role of the nuclear pore complex in selective transport across the nuclear membrane has been studied to a considerable degree; however, many crucial questions remain. Components of a signal transduction mechanism are associated with the nucleus, suggesting that nuclear functions may be influenced directly by this system. The involvement of the heat shock cognate protein Hsc70 in nuclear protein import is discussed, and a specific signal-presentation role for this protein is proposed.
Noncharged amino acid residues at the solvent‐exposed positions in the middle and at the C terminus of the α‐helix have the same helical propensity (2003)

It was established previously that helical propensities of different amino acid residues in the middle of alpha-helix in peptides and in proteins are very similar. The statistical analysis of the protein helices from the known three-dimensional structures shows no difference in the frequency of noncharged residues in the middle and at the C terminus. Yet, experimental studies show distinctive differences for the helical propensities of noncharged residues in the middle and in the C terminus in model peptides. Is this a general effect, and is it applicable to protein helices or is it specific to the model alanine-based peptides? To answer this question, the effects of substitutions at positions 28 (middle residue) and 32 (C2 position at the C terminus) of the alpha-helix of ubiquitin on the stability of this protein are measured by using differential scanning calorimetry. The two data sets produce similar values for intrinsic helix propensity, leading to a conclusion that noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. This conclusion is further supported with an excellent correlation between the helix propensity scale obtained for the two positions in ubiquitin with the experimental helix propensity scale established previously and with the statistical distribution of the residues in protein helices.
A Microporous Lanthanide-Organic Framework (1999)

Stable zeolite-like microporosity, even in the absence of guest molecules, is exhibited by a lanthanide-benzenedicarboxylate (BDC) framework, which was synthesized by the copolymerization of Tb(III) and 1,4-benzenedicarboxylic acid. The open Tb-BDC framework adopts an expanded PtS network structure (see diagram; Tb: open circles; C: full circles; lines connecting Tb to C represent O atoms, and those connecting C atoms are benzene rings) and is capable of reversible gas and liquid sorption.
In vitro Culture of Dirofilaria immitis Third- and Fourth-Stage Larvae under Defined Conditions (1987)

The objective of the present study was to define culture conditions under which larval Dirofilaria immitis would molt, grow, and survive. Third-stage larvae (L3) survived for over 3 wk with a molt rate of up to 95% in a variety of media supplemented with fetal calf serum. Bovine albumin, added to several media at concentrations of 10-30 mg/ml, also proved to be an effective culture supplement for the induction of molting and for supporting larval survival. Two gas phases were tested, 5% CO2/95% N2 and 5% CO2/air; no differences were noted in larval development based on gas phase. Larvae, maintained in media with FCS or albumin for 48 hr, were capable of completing the molting process and growing in length in unsupplemented media. If the temperature at which cultures were maintained was changed from 37 C to 27 C, L3 did not molt but did survive for several weeks. Two factors required for larval D. immitis molting and growth have been identified, temperature of approximately 37 C and the presence of albumin in the culture medium. The defined culture system developed for D. immitis L3 may provide a source for collection of excretory-secretory antigens, which could prove useful in immunodiagnosis or immunoprophylaxis as well as provide a means of studying the process and requirements of filarial larval molting.
Characterization of a Palmitoyl-Acyl Carrier Protein Thioesterase (FatB1) in Cotton (1999)

The relatively high level of palmitic acid (22 mol%) in cotton seeds may be due in part to a palmitoyl-acyl carrier protein (ACP) thioesterase (PATE), which prefers C16:0-ACP as its substrate. In embryo extracts, PATE activity was highest at the maximum rate of reserve accumulation (oil and protein), occurring about 30-35 d post anthesis. Thioesterase activity toward oleoyl-ACP was relatively similar at all developmental stages examined, but was considerably lower than the PATE activity. In developing seeds and in cotyledons and hypocotyls of seedlings, the PATE activity predominated. A cotton PATE cDNA clone isolated by screening a cDNA library with a heterologous Arabidopsis FatB1 probe has a 1.7-kb insert sequence with an open reading frame of 410 amino acids, lacking codons for the three N-terminal amino acids. The predicted amino acid sequence of the cotton PATE preprotein has a characteristic stromal-targeting domain and a 63% identity to the Arabidopsis long-chain acyl ACP-thioesterase FatB1 sequence. Alkaline blot hybridization of cotton genomic DNA with the Arabidopsis FatB1 probe suggested the presence of at least two FatB1 thioesterase genes in cotton. Relative cotton FatB1 transcript abundance was compared by RT-PCR and slot blot analysis in total RNA extracts from embryos, seedlings and leaves of mature plants. The cotton FatB1 mRNA apparently was expressed in all tissues but paralleled the profiles of PATE enzyme activity and seed oil accumulation in embryos.
Studies on Pyrimidine-Annelated Heterocycles; 8.1Intramolecular Cycloaddition of Thiophene and Nitrile Oxide or Nitrone Groups Bonded to 1,3-Dimethyluracils (1988)

1,3-Dimethyluracils having a nitrile oxide moiety or a nitronomethyl group at C-5 and an N-aryl-2-thienylmethylamino group at C-6 undergo an intramolecular cycloaddition reaction to give novel uracil-fused heterocycles.
Presentation of prostate tumor antigens by dendritic cells stimulates T‐cell proliferation and cytotoxicity (1996)

Dendritic cells (DCs) are “professional” antigen-presenting cells capable of stimulating T-cell proliferation and cytotoxicity when loaded with and presenting specific antigens, including tumor antigens. We demonstrated the stimulation of an autologous cytotoxic T-cell response elicited by DC loaded with autologous tumor cell lysate derived from primary prostate tumor. A candidate tumor antigen is prostate-specific membrane antigen (PSMA), which is overexpressed in prostate cancer patients. We identified a HLA-A2 motif in PSMA, isolated patient DC, loaded peptide into DC, and stimulated autologous T cells to proliferate. The ability to use DC for presentation of either tumor or peptide antigen in an HLA-restricted fashion in order to stimulate T-cell proliferation and cytotoxicity demonstrates the potential of this technology for development of a prostate cancer vaccine. © 1996 Wiley-Liss, Inc.
Structures of the austalides A–E, five noval toxic metabolites from Aspergillus ustus (1981)

The structures of austalides A–E, five new mycotoxins isolated from cultures of Aspergillus ustus, are based on the X-ray crystallographic study of austalide A, chemical derivatization, and correlation of their 13C and 1H n.m.r spectral data.
Surface-associated proteins ofStaphylococcus aureus:Their possible roles in virulence (1994)

A class of proteins that are associated with the cell surface of Gram-positive bacteria has been recognised. Common structural features which are implicated in the proper secretion and attachment of these proteins to the cell surface occur in the C-termini. N-terminal domains interact with the host by binding to soluble host proteins, to matrix proteins or to host cells. They probably have important roles in pathogenicity by allowing bacteria to avoid host defences and by acting as adhesins. Four such proteins of Staphylococcus aureus have been characterised: protein A (immunoglobulin binding protein), fibronectin binding proteins, collagen binding protein and the fibrinogen binding protein (clumping factor). Site-specific mutants are being used to define their roles in pathogenesis in in vitro and in vivo models of adherence and infection.
Herpes keratitis in the absence of anterograde transport of virus from sensory ganglia to the cornea (2005)

Herpes stromal keratitis is an immunopathologic disease in the corneal stroma leading to scarring, opacity, and blindness, and it is an important problem in common corneal surgeries. Paradoxically, virus antigens are largely focused in the epithelial layer of the cornea and not in the stromal layer, and viral antigens are eliminated before stromal inflammation develops. It is not clear what drives inflammation, whether viral antigens are necessary, or how viral antigens reach the stroma. It has been proposed that herpes simplex virus (HSV) travels from the corneal epithelium to sensory ganglia then returns to the stroma to cause disease. However, there is also evidence of HSV DNA and infectious virus persistent in corneas, and HSV can be transmitted to transplant recipients. To determine whether HSV resident in the cornea could cause herpes stromal keratitis, we constructed an HSV US9- mutant that had diminished capacity to move in neuronal axons. US9- HSV replicated and spread normally in the mouse corneal epithelium and to the trigeminal ganglia. However, US9- HSV was unable to return from ganglia to the cornea and failed to cause periocular skin disease, which requires zosteriform spread from neurons. Nevertheless, US9- HSV caused keratitis. Therefore, herpes keratitis can occur without anterograde transport from ganglia to the cornea, probably mediated by virus persistent in the cornea.
An Investigation of Spinel‐Related and Orthorhombic LiMnO2 Cathodes for Rechargeable Lithium Batteries (1994)

Cathode materials that have been synthesized by reduction of lithium-manganese-oxide and manganese-oxide precursors with hydrogen at 300 to 350°C and with carbon at 600°C have been evaluated in rechargeable lithium cells. The cathodes which initially have a composition close to LiMnO₂ contain structures related to the lithiated-spinel phase Li₂[Mn₂]0₄ and/or orthorhombic LiMnO₂. The orthorhombic LiMnO₂ component transforms gradually to a spinel structure on cycling. These cathodes are significantly more tolerant to repeated lithium insertion and extraction, when cycled over both the 4 and 3 V regions, than a standard Liₓ[Mn₂]0₄ spinel electrode (0 < x < 2).
Uplink channel capacity of space-division-multiple-access schemes (1998)

The signal-to-noise ratio (SNR) and signal bandwidth have been viewed as the dominant factors determining the channel capacity. In wireless communications, the channel capacity can be increased for a given SNR and a given spectral region, by exploiting the spatial diversity provided by the use of multiple antennas and transceivers at a base station. We calculate the channel capacity enhancement of a so-called space-division-multiple-access (SDMA) system and investigate its dependence with respect to different decoding schemes, terminal positions, and receiver numbers. Inner and outer capacity boundaries for joint decoding and independent decoding are presented, along with physical explanations as to how these boundaries can be achieved. We show that exploitation of the spatial diversity not only increases the overall achievable rates of both joint and independent decoding, but also closes the gap between their corresponding capacity regions, thus bringing the performance of the low-cost independent decoding scheme close to that of the optimal joint decoding. Practical issues of optimum projection and power control are also addressed.
Salmon Calcitonin in the Treatment of Post Herpetic Neuralgia (2006)

A 78-year-old man with severe chronic obstructive pulmonary disease presented to our pain medicine clinic for treatment of post herpetic neuralgia. Pharmacotherapy with tricyclic antidepressants, anticonvulsants, tramadol and traditional analgesics had failed, primarily due to adverse drug effects, particularly sedation, dizziness and nausea. Consequently, intravenous salmon calcitonin was administered, based on evidence of efficacy in the treatment of other neuropathic pain syndromes and its relatively benign side-effects profile. The patient reported immediate and sustained improvement in his post herpetic neuralgia for over two months, without adverse effects from the calcitonin therapy.
Blocking IL-21 signaling ameliorates xenogeneic GVHD induced by human lymphocytes (2011)

In rodent graft-versus-host disease (GVHD) models, anti-IL-21 neutralizing mAb treatment ameliorates lethality and is associated with decreases in Th1 cytokine production and gastrointestinal tract injury. GVHD prevention was dependent on the in vivo generation of donor-inducible regulatory T cells (Tregs). To determine whether the IL-21 pathway might be targeted for GVHD prevention, skin and colon samples obtained from patients with no GVHD or grade 2 to 4 GVHD were analyzed for IL-21 protein expression. By immunohistochemistry staining, IL-21 protein-producing cells were present in all gastrointestinal tract samples and 54% of skin samples obtained from GVHD patients but not GVHD-free controls. In a human xenogeneic GVHD model, human IL-21-secreting cells were present in the colon of GVHD recipients and were associated with elevated serum IL-21 levels. A neutralizing anti-human IL-21 mAb given prophylactically significantly reduced GVHD-associated weight loss and mortality, resulting in a concomitant increase in Tregs and a decrease in T cells secreting IFN-γ or granzyme B. Based on these findings, anti-IL-21 mAb could be considered for GVHD prevention in the clinic.
Location-aware computing: a neural network model for determining location in wireless LANs (2002)

The strengths of the RF signals arriving from more access points in a wireless LANs are related to the position of the mobile terminal and can be used to derive the location of the user. In a heterogeneous environment, e.g. inside a building or in a variegated urban geometry, the received power is a very complex function of the distance, the geometry, the materials. The complexity of the inverse problem (to derive the position from the signals) and the lack of complete information, motivate to consider flexible models based on a network of functions (neural networks). Specifying the value of the free parameters of the model requires a supervised learning strategy that starts from a set of labeled examples to construct a model that will then generalize in an appropriate manner when confronted with new data, not present in the training set. The advantage of the method is that it does not require ad-hoc infrastructure in addition to the wireless LAN, while the flexible modeling and learning capabilities of neural networks achieve lower errors in determining the position, are amenable to incremental improvements, and do not require the detailed knowledge of the access point locations and of the building characteristics. A user needs only a map of the working space and a small number of identified locations to train a system, as evidenced by the experimental results presented.
IN VITRO EFFECTS OF NALOXONE ON T-LYMPHOCYTE-DEPENDENT ANTIBACTERIAL ACTIVITY IN HEPATITIS C VIRUS (HCV) INFECTED PATIENTS AND IN INFLAMMATORY BOWEL DISEASE (IBD) PATIENTS (2001)

Naloxone acts as an opioid antagonist, displacing opioid drugs from cellular receptors. Among opioid substances, beta-endorphins are able to bind to several cell receptors, even including those expressed by immune cells. In this respect, evidence has been provided that in the course of viral infections, as well as in patients with ulcerative colitis high levels of beta-endorphins are detectable. Here, peripheral blood lymphocytes (PBL) from 21 HCV infected patients and 14 patients with IBD, respectively, were incubated with Naloxone and Naloxone + Ca2+ in order to evaluate a putative modulation of PBL-mediated antibacterial activity. In fact, previous studies have demonstrated a reduction of this T-cell activity in HCV and IBD patients. In general terms, the above treatment led to a recovery of the depressed antibacterial activity. In some cases, increase in T lymphocyte function was obtained with Naloxone alone, while in other cases the combination Naloxone + Ca2+ gave rise to a restorative effect. Of note, in some instances, lymphocytes were unresponsive to pharmacological modulation. The overall results suggest that beta-endorphins may down modulate T-cell antibacterial response in HCV and in IBD patients by saturating peripheral receptors on immune cells. Therefore, it is likely that Naloxone and/or Naloxone + Ca2+ may displace opioid drugs, thus antagonizing their effects.
The glypican family of heparan sulfate proteoglycans: major cell-surface proteoglycans of the developing nervous system. (1996)

The glypican family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans comprises four vertebrate members, glypican, cerebroglycan, OCI-5, and K-glypican, and the Drosophila protein, daily. These molecules share highly conserved protein structural features that sharply distinguish them from the syndecans, the other major class of cell surface heparan sulfate proteoglycans. All members of the glypican family are expressed in the developing nervous system, with one member (cerebroglycan) being restricted to that tissue. In the developing rodent brain, glypican and cerebroglycan--which appear to be the most abundant family members in that tissue--are expressed mainly by neurons, and both are strongly localized to axons. In the case of cerebroglycan, expression is limited to axons at or about the time they are extending toward their targets. Although the functions of the vertebrate members of this family are not known, in Drosophila, the effects of mutations in the daily gene suggest a role for members of the glypican family in regulating cell cycle progression during the transition of neural cells from proliferation to neuronal differentiation. It is likely that proteoglycans of the glypican family also play other important roles in neural development.