gebhart/patrepeval huggingface dataset:
Myeloid-Derived Suppressor Cells Promote Cross-Tolerance in B-Cell Lymphoma by Expanding Regulatory T Cells (2008)

Tumor-induced T-cell tolerance is a major mechanism that facilitates tumor progression and limits the efficacy of immune therapeutic interventions. Regulatory T cells (Treg) play a central role in the induction of tolerance to tumor antigens, yet the precise mechanisms regulating its induction in vivo remain to be elucidated. Using the A20 B-cell lymphoma model, here we identify myeloid-derived suppressor cells (MDSC) as the tolerogenic antigen presenting cells capable of antigen uptake and presentation to tumor-specific Tregs. MDSC-mediated Treg induction requires arginase but is transforming growth factor-beta independent. In vitro and in vivo inhibition of MDSC function, respectively, with NOHA or sildenafil abrogates Treg proliferation and tumor-induced tolerance in antigen-specific T cells. These findings establish a role for MDSCs in antigen-specific tolerance induction through preferential antigen uptake mediating the recruitment and expansion of Tregs. Furthermore, therapeutic interventions, such as in vivo phosphodiesterase 5-inhibition, which effectively abrogate the immunosuppressive role of MDSCs and reduce Treg numbers, may play a critical role in delaying and/or reversing tolerance induction.
Organization of the Cores of the Mammalian Pyruvate Dehydrogenase Complex Formed by E2 and E2 Plus the E3-binding Protein and Their Capacities to Bind the E1 and E3 Components (2004)

The subunits of the dihydrolipoyl acetyltransferase (E2) component of mammalian pyruvate dehydrogenase complex can form a 60-mer via association of the C-terminal I domain of E2 at the vertices of a dodecahedron. Exterior to this inner core structure, E2 has a pyruvate dehydrogenase component (E1)-binding domain followed by two lipoyl domains, all connected by mobile linker regions. The assembled core structure of mammalian pyruvate dehydrogenase complex also includes the dihydrolipoyl dehydrogenase (E3)-binding protein (E3BP) that binds the I domain of E2 by its C-terminal I' domain. E3BP similarly has linker regions connecting an E3-binding domain and a lipoyl domain. The composition of E2.E3BP was thought to be 60 E2 plus approximately 12 E3BP. We have prepared homogenous human components. E2 and E2.E3BP have s(20,w) values of 36 S and 31.8 S, respectively. Equilibrium sedimentation and small angle x-ray scattering studies indicate that E2.E3BP has lower total mass than E2, and small angle x-ray scattering showed that E3 binds to E2.E3BP outside the central dodecahedron. In the presence of saturating levels of E1, E2 bound approximately 60 E1 and maximally sedimented 64.4 +/- 1.5 S faster than E2, whereas E1-saturated E2.E3BP maximally sedimented 49.5 +/- 1.4 S faster than E2.E3BP. Based on the impact on sedimentation rates by bound E1, we estimate fewer E1 (approximately 12) were bound by E2.E3BP than by E2. The findings of a smaller E2.E3BP mass and a lower capacity to bind E1 support the smaller E3BP substituting for E2 subunits rather than adding to the 60-mer. We describe a substitution model in which 12 I' domains of E3BP replace 12 I domains of E2 by forming 6 dimer edges that are symmetrically located in the dodecahedron structure. Twelve E3 dimers were bound per E248.E3BP12 mass, which is consistent with this model.
Occlusion Reasoning for Temporal Interpolation using Optical Flow (2009)

We present an optical-flow-based algorithm to smoothly interpolate between two images. We reason about the depth ordering of objects, and show how bidirectional flow can be used to reduce holes in the estimated flow at the interpolated time and perform occlusion reasoning. We develop a purely pixel-wise algorithm and then add spatial regularization. We evaluate our algorithm on the interpolation set of the Middlebury flow benchmark.
Application of cutaneous microdialysis to evaluate metronidazole and its main metabolite concentrations in the skin after a single oral dose (2003)

Use of cutaneous microdialysis technique permits the characterization of true systemic drug disposition, for optimizing drug treatment strategies.
Inducible nitric oxide synthase and inflammation (1998)

Nitric oxide (NO), derived from L-arginine (L-Arg) by the enzyme nitric oxide synthase (NOS), is involved in acute and chronic inflammatory events. In view of the complexity associated with the inflammatory response, the dissection of possible mechanisms by which NO modulates this response will be profitable in designing novel and more efficacious NOS inhibitors. In this review we describe the consequences associated with the induction of inducible nitric oxide synthase (iNOS) and its therapeutic implications.
Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions (1996)

Methane is oxidized to methanol by the enzyme methane mono-oxygenase (MMO) in methanotrophic bacteria. In previous work, this multicomponent enzyme system has been extensively characterized at the biochemical and molecular level. Copper ions have been shown to irreversibly inhibit MMO activity in vivo and in vitro, but the effect of copper ions on transcription of the genes encoding the soluble (cytoplasmic) MMO (sMMO) has not previously been investigated. To examine more closely the regulation of bacterial methane oxidation and to determine the role of copper in this process, we have investigated transcriptional regulation of the sMMO gene cluster in the methanotrophic bacterium Methylococcus capsulatus (Bath). Using Northern blot analysis and primer extension experiments, it was shown that the six ORFs of the sMMO gene cluster are organized as an operon and the transcripts produced upon expression of this operon have been identified. The synthesis of these transcripts was under control of a single copper-regulated promoter, which is as yet not precisely defined.
Crystal Splitting in the Growth of Bi2S3 (2006)

Bi2S3 nanostructures with a sheaflike morphology are obtained via reaction of bismuth acetate-oleic acid complex with elemental sulfur in 1-octadecence. These structures may form by the splitting crystal growth mechanism, which is known to account for the morphology some mineral crystals assume in nature. By control of the synthetic parameters, different shapes are obtained, analogous to those which have been observed to occur by crystal splitting in minerals. These new and complex Bi2S3 nanostructures are characterized by transmission and scanning electron microscopy, and electron and X-ray diffraction.
Assessment of Blood Coagulation Under Various Flow Conditions With Ultrasound Backscattering (2007)

Several in vitro studies have employed ultrasonic techniques to detect varying properties of coagulating blood under static or stirred conditions. Most of those studies mainly addressed on the development and feasibility of modalities and however were not fully considering the effect of blood flow. To better elucidate this issue, ultrasonic backscattering were measured from the coagulating porcine blood circulated in a mock flow loop with various steady laminar flows at mean shear rates from 10 to 100 s(-1). A 3 ml of 0.5 M CaCl2 solution for inducing blood coagulation was added to that of 30 ml blood circulated in the conduit. For each measurement carried out with a 10-MHz transducer, backscattered signals digitized at 100-MHz sampling frequency were acquired for a total of 20 min at temporal resolution of 50 A-lines per s. The integrated backscatter (IB) was calculated for assessing backscattering properties of coagulating blood. The results show that blood coagulation tended to be increased corresponding to the addition of CaCl2 solution: the IB was increased approximately 6.1 +/- 0.6 (mean +/- standard deviation), 5.4 +/- 0.9, and 4.5 +/- 1.2 dB at 310 +/- 62, 420 +/- 88, and 610 +/- 102 s associated with mean shear rates of 10, 40, and 100 s(-1), respectively. The rate of increasing IB for evaluating the growth of clot was estimated to be 0.075 +/- 0.017, 0.052 +/- 0.027, and 0.038 +/- 0.012 delta dB delta s(-1) corresponding to the increase of mean shear rates. These results consistently demonstrate that higher shear rate tends to prolong the duration for the flowing blood to be coagulated and to decrease the rate of IB. Moreover, the laminar flow was changed to turbulent flow during that the blood was clotting discerned by spatial variations of ultrasound backscattering in the conduit. All these results validate that ultrasound backscattering is feasible to be utilized for detecting and assessing blood coagulation under dynamic conditions.
Magnetic behaviour of a hybrid polymer obtained from ethyl acrylate and the magnetic cluster Mn12O12(acrylate)16 (2004)

The magnetic properties of polymers prepared by polymerization of the magnetic cluster Mn12O12(acrylate)16 with various portions of ethyl acrylate as co-monomer are reported. According to SAXS studies, the clusters are homogeneously distributed in the polymer. Ac susceptibility measurements show superparamagnet-like behaviour of the cluster-crosslinked polymers with relaxation following an Arrhenius law with τ0 = 4–8 × 10−8 s and an energy barrier in the range 45–65 K.
Uptake pharmacokinetics of the Fentanyl Oralet® in children scheduled for central venous access removal: implications for the timing of initiating painful procedures (2002)

The wide and flat concentration versus time profile may allow flexibility in the timing of a painful procedure following Fentanyl Oralet administration. However, the variability of the time to peak concentration makes it difficult to suggest a minimum interval between Fentanyl Oralet consumption and the start of a painful procedure.
Covalently attached graft polymer monolayer on organic polymeric substrate via confined surface inhibition reaction (2007)

Abstract A grafting technique was proposed for the preparation of polymer monolayer on polymeric substrate. On the basis of our recent work on polymer‐supported inhibitor (PSI), hydroquinone (HQ) was first implanted onto polypropylene (PP) surface through UV‐initiated grafting. The resulting immobilized HQ was used as PSI for the thermal‐induced free radical polymerization (FRP) of acrylic acid (AA). The inhibition mechanism was similar to that of free HQ molecule, that is, polymer chain‐carrying radical or peroxy radical could be deactivated by abstracting hydrogen atom from hydroxyl group of immobilized HQ, and the resulting oxyradical (semiquinone radical) combined with another active chain free radical. According to this mechanism, a devised redox initiator consisting of sodium hydrogen sulfite and ammonium persulfate was used to initiate FRP of AA in water at low temperature (50 °C). High crystalline biaxial oriented PP film with HQ immobilized was deliberately laid in this system as a radical trap to capture poly(acrylic acid) (PAA) short chain radical. Through X‐ray photoelectron spectra (XPS) analysis it was found that the atom ratio of C HQ (carbon in HQ) to C COOH (carbon in COOH) decreased with prolonging polymerization time and became stable after about 30 min. The formed PAA short chain on the surface showed a distribution of monolayer, and the saturated thickness was calculated as 5–7 Å. The degree of polymerization of graft chain in PAA monolayer was estimated as 15–20 through three different models. Relating to surface coverage being 100% in ideal densely packed PAA monolayer, real monolayer surface coverage in such reaction system was estimated as 12.3–18.5%. This method was expected to give us a general approach for constructing kinds of graft polymer monolayer on polymeric substrate, because the involved chemistry was only common inhibition reaction between immobilized inhibitor (HQ) and FRP system in solution (herein redox initiating system of AA). We named this grafting chemistry as confined surface inhibition reaction. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 745–755, 2007
A new force sensor incorporating force-feedback control for interfacial force microscopy (1991)

A new interfacial-force microscope capable of measuring the forces between two surfaces over the entire range of surface separations, up to contact, is described. The design is centered around a differential-capacitance displacement sensor where the common capacitor plate is supported by torsion bars. A force-feedback control system is incorporated which balances the interfacial forces at the sensor, maintaining the common capacitor plate at its rest position. This control therefore eliminates the instability or ‘‘jumping’’ which occurs with conventional cantilever-based force sensors when the attractive force gradient between the fixed sample and sensor exceeds the mechanical stiffness of the cantilever. The operating characteristics of the sensor and its ability to measure interfacial forces using the feedback control at surface separations smaller than this instability point are demonstrated.
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy (2012)

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
Real-time control of Internet based teleoperation with force reflection (2002)

The use of the Internet is no longer limited to the transmission of data. In the past few years many successful attempts have been made to use the Internet as a command transmission media; through which control can be sent to remote systems and feedback can be obtained. But with this media come several limitations: delay, lost packets and disconnection. All of these limitations may cause instability in the system especially if the system loop is closed. All the previous work addressing these problems assumed several conditions; for example, time delay is constant or has an upper bound, control is not in real-time. A new real-time control approach is presented that deals with these limitations without any assumptions made regarding delay. The approach is based on event-based control, which was implemented on a mobile robot over the Internet. The commands sent to the robot are velocity and the feedback is force based on the environment. It will be shown that this approach results in a stable system. In addition, a new force feedback generation method is used.
Hemopexin joins transferrin as representative members of a distinct class of receptor-mediated endocytic transport systems. (1990)

Receptor-mediated transport of heme by hemopexin in vivo and in vitro results in catabolism of heme but not the protein, suggesting that intact apohemopexin recycles from cells. However, until now, the intracellular transport of hemopexin by receptor-mediated endocytosis remained to be established. Biochemical studies on cultured human HepG2 and mouse Hepa hepatoma cells demonstrate that hemopexin is transported to an intracellular location and, after endocytosis, is subsequently returned intact to the medium. During incubation at 37 degrees C, hemopexin accumulated intracellularly for ca. 15 min before reaching a plateau while surface binding was saturated by 5 min. No internalization of ligand took place during incubation at 4 degrees C. These and other data suggest that hemopexin receptors recycle, and furthermore, incubation with monensin significantly inhibits the amount of cell associated of heme-[125I]hemopexin during short-term incubation at 37 degrees C, consistent with a block in receptor recycling. Ammonium chloride and methylamine were less inhibitory. Electron microscopic autoradiography of heme-[125I]hemopexin showed the presence of hemopexin in vesicles of the classical pathway of endocytosis in human HepG2 hepatoma cells, confirming the internalization of hemopexin. Colloidal gold-conjugated hemopexin and electron microscopy showed that hemopexin bound to receptors at 4 degrees C is distributed initially over the entire cell surface, including microvilli and coated pits. After incubation at 37 degrees C, hemopexin-gold is located intracellularly in coated vesicles and then in small endosomes and multivesicular bodies. Colocalization of hemopexin and transferrin intracellularly was shown in two ways. Radioiodinated hemopexin was observed in the same subcellular compartment as horseradish peroxidase conjugates of transferrin using the diaminobenzidine-induced density shift assay. In addition, colloidal gold derivatives of heme-hemopexin and diferric transferrin were found together in coated pits, coated vesicles, endosomes and multivesicular bodies. Therefore, hemopexin and transferrin act by a similar receptor-mediated mechanism in which the transport protein recycles after endocytosis from the cell to undergo further rounds of intracellular transport.
Ionic regulation of sea urchin sperm motility, metabolism and fertilizing capacity. (1986)

In order to pursue the significance of the ionic regulation of sea urchin sperm behaviour, alterations in the cation composition of sea water were tested for their effects on sperm fertilizing capacity. Nearly all changes which resulted in lowered sperm intracellular pH, including lowered sea-water pH, inclusion of the divalent ion chelator EGTA, addition of dithiothreitol, or removal of sea-water Na+, enhanced sperm viability for periods of up to a week. These conditions caused decreased cell motility and elevated ATP concentrations, and prevented the acrosome reaction. Conversely, changes which increased the intracellular pH, decreased sperm ATP concentrations, or induced the acrosome reaction, reduced sperm viability. A single medium, high sea-water K+ concentrations (greater than 100 mM), provided an exception to these general trends. At elevated K+ concentrations sperm were quiescent but became completely infertile. These data show that sperm fertilizing capacity is generally extended by maintenance of the sperm in an inactive state, and the results suggest that decreased cellular energy levels contribute to decreased fertility.
Permeability of Membranes to the Müllerian-Inhibiting Substance Synthesized by the Human Fetal Testisin Vitro: A Clue to its Biochemical Nature (1972)

The ability of the human fetal testis to inhibit the müllerian duct of the 14½-day-old fetal rat, in organ culture has been already reported. In this study, membranes were inserted between the human fetal testis and its target-organ. Müllerian inhibition proceeded normally when the rat reproductive tract was separated from the human fetal testis by the vitelline membrane of a hen's egg, thus proving that direct contact between the two organs is not necessary to the activity of the müllerian-inhibiting substance. In contrast, no inhibition of the müllerian duct took place when this structure was separated from the fetal testis by Visking cellulose, a membrane permeable to molecules under 15.000 of molecular weight. Control experiments showed that 16½-day-old androgen-dependent wolffian ducts are maintained when separated from rat fetal testes by this same membrane. Our data indicate that the müllerian-inhibiting substance is not a steroid in free form. They are compatible with the hypothesis that the müllerian-inhibiting activity is supported by a macromolecule.
Csk homologous kinase inhibits CXCL12-CXCR4 signaling in neuroblastoma (2008)

Neuroblastoma is the second most common pediatric malignancy. The clinical course of this disease ranges from spontaneous regression and good survival to highly malignant therapy-resistant tumors. There is a continuous need for genetic and biologic markers for the diverse clinical phenotypes observed in neuroblastoma patients. One of the known markers in neuroblastoma is expression of the CXCR4 chemokine receptor. CXCR4 expression correlates with high-stage disease, and the autocrine stimulation of CXCR4 by its ligand (CXCL12) was shown to be necessary for the survival of some neuroblastoma cells in vitro. However, the mechanisms responsible for activation of the CXCL12-CXCR4 autocrine pathway in neuroblastoma remain uncertain. Our previous findings suggest that Csk homologous kinase (CHK) is a physiological inhibitor of CXCR4 expression. Since CHK is highly expressed in neurons, we evaluated changes in CHK expression in human neuroblastoma. CHK protein expression was below detectable levels based on Western blot analyses in 13 out of 16 human neuroblastoma cell lines and in 6 out of 16 primary neuroblastoma tissues. When CHK expression was restored in IMR32 neuroblastoma cells by retrovirus-mediated cDNA transfer, diminished CXCR4 mRNA and protein levels were observed, as assessed by RT-PCR and flow cytometry analyses, respectively. Furthermore, exogenous expression of CHK markedly suppressed the mRNA levels and secretion of the CXCL12 chemokine from IMR32 cells as well as inhibited the growth rate of these cells. Taken together, our data strongly suggest that CHK is capable of inhibiting the CXCL12-CXCR4 pathway in neuroblastoma.
Surface Antigens as Virulence Factors in Infection with Bacteroides fragilis (1979)

Organisms of the genus Bacteroides represent the major group of obligate anaerobes involved in human infections. Bacteroides usually cause either bacteremia or localized abscesses. Of the numerous species of Bacteroides, Bacteroides fragilis is the single most frequent clinical isolate. B. fragilis and Bacteroides melaninogenicus have chemically incomplete lipopolysaccharides as compared with the lipopolysaccharides (endotoxins) of aerobic bacteria, and the lipopolysaccharides of Bacteroides lack the biologic potency characteristic of endotoxin. This inactivity may account for the very infrequent occurrence of disseminated intravascular coagulation or purpura that can accompany sepsis due to these organisms. Furthermore, strains of B. fragilis have an immunologically common capsular polysaccharide. In an animal model of intraabdominal sepsis, the encapsulated strains caused abscesses when given without other organisms, but abscess formation from unencapsulated strains of Bacteroides generally required the administration of a synergistic aerobe. The abscesses caused by encapsulated strains were shown to be directly attributable to the capsular polysaccharide, which is an important virulence factor of this organism. Patients or experimental animals infected with B. fragilis develop antibodies to the capsular polysaccharide, and these antibodies can be detected in a radioactive antigen-binding assay.