gebhart/patrepeval huggingface dataset:
Retargeted clostridial endopeptidases: Inhibition of nociceptive neurotransmitter release in vitro, and antinociceptive activity in in vivo models of pain (2004)

Clostridial neurotoxins potently and specifically inhibit neurotransmitter release in defined cell types. Previously reported data have demonstrated that the catalytically active LH(N) endopeptidase fragment of botulinum neurotoxin type A (termed LH(N)/A) can be retargeted to a range of cell types in vitro to lead to inhibition of secretion of a range of transmitters. Here, we report the synthesis of endopeptidase conjugates with in vitro selectivity for nociceptive afferents compared to spinal neurons. Chemical conjugates prepared between Erythrina cristagalli lectin and LH(N)/A are assessed in vitro and in in vivo models of pain. Chemical conjugates prepared between E. cristagalli lectin and either natively sourced LH(N)/A, or recombinant LH(N)/A purified from Escherichia coli are assessed, and equivalence of the recombinant material is demonstrated. The duration of action of inhibition of neurotransmitter release by the conjugate in vitro is also assessed and is comparable to that observed with Clostridium botulinum neurotoxin. Selectivity of targeting and therapeutic potential have been confirmed by in vivo electrophysiology studies. Furthermore, the analgesic properties of the conjugate have been assessed in in vivo models of pain and extended duration effects observed. These data provide proof of principle for the concept of retargeted clostridial endopeptidases as novel analgesics.
Integration of Germanium-on-Insulator and Silicon MOSFETs on a Silicon Substrate (2006)

The monolithic integration of germanium-on-insulator (GeOI) p-MOSFETs with silicon n-MOSFETs on a silicon substrate is demonstrated. The GeOI p-MOSFETs are fabricated on the oxide for silicon device isolation based on the newly developed rapid-melt-growth method. CMOS inverters consisting of the silicon n-MOSFET and GeOI p-MOSFET were obtained, and the measured results show that the processing of high-performance GeOI devices is compatible with bulk-silicon technology
The development of Honda humanoid robot (2002)

In this paper, we present the mechanism, system configuration, basic control algorithm and integrated functions of the Honda humanoid robot. Like its human counterpart, this robot has the ability to move forward and backward, sideways to the right or the left, as well as diagonally. In addition, the robot can turn in any direction, walk up and down stairs continuously. Furthermore, due to its unique posture stability control, the robot is able to maintain its balance despite unexpected complications such as uneven ground surfaces. As a part of its integrated functions, this robot is able to move on a planned path autonomously and to perform simple operations via wireless teleoperation.
Hyper‐interleukin (IL)‐6‐naemia in haemophagocytic lymphohistiocytosis (1996)

Clinical features in patients with haemophagocytic lymphohistiocytosis (HLH) have been demonstrated to be characterized by hypercytokinaemia. Previously, we reported the impact of high serum levels of interferon (IFN)-gamma and soluble IL-2 receptor (sIL-2R) on patient outcome; however, it was not known if serum levels of interleukin (IL)-6 also could be a prognostic factor. In a study during the active phase of disease in 25 cases of HLH in children and young adults (median age 3 years, range 0.1-23 years), we noted 12 cases which showed serum IL-6 > 100 (normal < 4.0) pg/ml. Five of these cases showed hyper-IL-6-naemia alone without hyper-IFN-gamma-naemia (group A) whereas seven cases showed both hyper-IL-6- and IFN-gamma-naemia (group B). Patient outcome did not differ between the patients with IL-6 > 100 pg/ml and those with IL-6 < 100 pg/ml, suggesting that high serum concentrations of IL-6 alone do not necessarily indicate poor prognosis in patients with HLH. Among the cases with hyper-IL-6-naemia ( > 100 pg/ml), underlying disorders causing haemophagocytosis were found to be different between groups A and B.
Host binding proteins and bacterial adhesion: ecology and binding model (1988)

Defining the involvement of specific recognition and (or) adhesion molecules in the precise association formed between cells of an organism during development or between bacteria and specific host tissues has become a focus of extensive research. The possibility that the same molecules responsible for cellular adhesion in the host may also play a major role in determining host–bacterial interactions is now becoming more evident. The following review looks at the interaction of a group of host binding proteins, including lectins, fibronectin, and laminin, with respect to their specific association with bacteria. This information is dealt with both from the perspective of the ecology of the host and its autochthonous and pathogenic bacterial populations, as well as in terms of the difficulties in defining the nature of ligand associations even in the more simplified bacterial–host interaction.
Uterine eosinophils and reproductive performance in interleukin 5-deficient mice (2000)

Interleukin 5 is expressed in type 2 T lymphocytes and has a key role in driving the differentiation, recruitment and activation of eosinophils. Mice with a null mutation in the interleukin 5 gene (IL-5 -/- mice) have altered type 2 immune responses and severely depleted eosinophil populations. In the present study, the effect of interleukin 5 deficiency on the abundant population of eosinophils present in the female reproductive tract was investigated, and the reproductive performance in C57Bl/6 IL-5 -/- mice was measured. Endometrial eosinophils, detected on the basis of their endogenous peroxidase activity, were reduced in number by four-sevenfold during the oestrous cycle and in early pregnancy in IL-5 -/- mice. Eosinophils present in the cervix and decidual tissues at the time of parturition were similarly diminished. The temporal fluctuations in eosinophil recruitment and localization within these tissues were otherwise unchanged, indicating that interleukin 5 is not a necessary chemotactic agent in the female reproductive tract. Oestrous cycles were moderately greater in duration in IL-5 -/- mice (mean +/- SD = 5.6 +/- 1.0 days in IL-5 -/- mice versus 5.0 +/- 0.8 days in IL-5 +/+ mice), owing to an extended period in oestrus (2.7 +/- 0.9 days per cycle in IL-5 -/- mice versus 1.8 +/- 0.7 in IL-5 +/+ mice). The interval between placing females with males and the finding of copulatory plugs was reduced significantly in interleukin 5-deficient mice. Implantation rates and subsequent fetal development were comparable in IL-5 -/- and IL-5 +/+ mice, irrespective of whether pregnancies were sired by syngeneic (C57Bl/6) or allogeneic (CBA or Balb/c) males, apart from a 10% increase in placental size and a 6.5% decrease in placental&ratio;fetal ratio seen on day 17 in pregnancies sired by CBA males. Parturition and post-partum uterine repair were not compromised in interleukin 5-deficient mice, as judged by the length of gestation, and the outcomes of pregnancies initiated at post-partum oestrus. The birth weights and growth trajectories of pups were significantly influenced by interleukin 5 status, with small but significant increases in the weights of IL-5 -/- pups, particularly C57Bl/6 and CBA F(1) animals, remaining evident until adulthood. These data are consistent with the view that eosinophils have a role in endometrial tissue remodelling associated with the oestrous cycle, but indicate that the events of pregnancy and parturition proceed quite normally in the absence of maternal and fetal interleukin 5. However, strain-dependent effects of interleukin 5 deficiency on placental growth and function and subsequent weight gain in the newborn indicate that this cytokine may act through the maternal or fetal immune axis to exert subtle influences on reproductive outcome.
“Macromolecular crowding”: thermodynamic consequences for protein-protein interactions within the T4 DNA replication complex. (1990)

In vitro biochemical assays are typically performed using very dilute solutions of macromolecular components. On the other hand, total intracellular concentrations of macromolecular solutes are very high, resulting in an in vivo environment that is significantly "volume-occupied." In vitro studies with the DNA replication proteins of bacteriophage T4 have revealed anomalously weak binding of T4 gene 45 protein to the rest of the replication complex. We have used inert macromolecular solutes to mimic typical intracellular solution conditions of high volume occupancy to investigate the effects of "macromolecular crowding" on the binding equilibria involved in the assembly of the T4 polymerase accessory proteins complex. The same approach was also used to study the assembly of this complex with T4 DNA polymerase (gene 43 protein) and T4 single-stranded DNA binding protein (gene 32 protein) to form the five protein "holoenzyme". We find that the apparent association constant (Ka) of gene 45 for gene 44/62 proteins in forming both the accessory protein complex and the holoenzyme increases markedly (from approximately 7 x 10(6) to approximately 3.5 x 10(8) M-1) as a consequence of adding polymers such as polyethylene glycol and dextran. Although the processivity of the polymerase alone is not directly effected by the addition of such polymers to the solution, macromolecular crowding does significantly stabilize the holoenzyme and thus indirectly increases the observed processivity of the holoenzyme complex. The use of macromolecular crowding to increase the stability of multienzyme complexes in general is discussed, as is the relevance of these results to DNA replication in vivo.
Two genetically and molecularly distinct functions involved in early neurogenesis reside within the Enhancer of split locus of Drosophila melanogaster. (1991)

Molecular correlation of the genetic aspects of the function of the neurogenic gene Enhancer of split [E(spl)] has previously been hampered by the densely transcribed nature of the chromosomal region within which it resides. We present data indicating that two distinct molecular species contribute to E(spl) function. Analysis of new E(spl) alleles has allowed us to define two complementing functions within the locus. Subsequent phenotypic analysis of different E(spl) deficiencies combined with P element-transformed constructs has demonstrated that these two functions correspond to: (1) a family of helix-loop-helix (HLH) protein-encoding genes and (2) the single copy gene E(spl) m9/10, whose product shares homology with G-protein beta subunits. The zygotically active E(spl) HLH genes can, at least partially, substitute for one another's functions and their total copy number determines the activity of the locus. E(spl) m9/10 acts synergistically with the E(spl) HLH genes and other neurogenic genes in the process of neurogenesis. The maternal component of E(spl) m9/10 has the most pronounced effect in neurogenesis, while its zygotic component is predominantly required during postembryonic development. The lethality of trans-heterozygotes of null E(spl) deficiency alleles with a strong Delta point mutation is a result of the concomitant reduction in activity of both E(spl) HLH and m9/10 functions. Immunocytochemical localization of the E(spl) m9/10 protein has revealed that it is a ubiquitously distributed nuclear component in embryonic, larval and imaginal tissues.
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria (2005)

The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box.
Fast Training of Support Vector Machines Using Sequential Minimal Optimization (1998)

This chapter describes a new algorithm for training Support Vector Machines: Sequential Minimal Optimization, or SMO. Training a Support Vector Machine (SVM) requires the solution of a very large quadratic programming (QP) optimization problem. SMO breaks this large QP problem into a series of smallest possible QP problems. These small QP problems are solved analytically, which avoids using a time-consuming numerical QP optimization as an inner loop. The amount of memory required for SMO is linear in the training set size, which allows SMO to handle very large training sets. Because large matrix computation is avoided, SMO scales somewhere between linear and quadratic in the training set size for various test problems, while a standard projected conjugate gradient (PCG) chunking algorithm scales somewhere between linear and cubic in the training set size. SMO's computation time is dominated by SVM evaluation, hence SMO is fastest for linear SVMs and sparse data sets. For the MNIST database, SMO is as fast as PCG chunking; while for the UCI Adult database and linear SVMs, SMO can be more than 1000 times faster than the PCG chunking algorithm.
Vaccination for Neuroprotection in the Mouse Optic Nerve: Implications for Optic Neuropathies (2001)

T-cell autoimmunity to myelin basic protein was recently shown to be neuroprotective in injured rat optic nerves. In the present study, using the mouse optic nerve, we examined whether active immunization rather than passive transfer of T-cells can be beneficial in protecting retinal ganglion cells (RGCs) from post-traumatic death. Before severe crush injury of the optic nerve, SJL/J and C3H.SW mice were actively immunized with encephalitogenic or nonencephalitogenic peptides of proteolipid protein (PLP) or myelin oligodendrocyte glycoprotein (MOG), respectively. At different times after the injury, the numbers of surviving RGCs in both strains immunized with the nonencephalitogenic peptides pPLP 190-209 or pMOG 1-22 were significantly higher than in injured controls treated with the non-self-antigen ovalbumin or with a peptide derived from beta-amyloid, a non-myelin-associated protein. Immunization with the encephalitogenic myelin peptide pPLP 139-151 was beneficial only when the disease it induced, experimental autoimmune encephalomyelitis, was mild. The results of this study show that survival of RGCs after axonal injury can be enhanced by vaccination with an appropriate self-antigen. Furthermore, the use of nonencephalitogenic myelin peptides for immunization apparently allows neuroprotection without incurring the risk of an autoimmune disease. Application of these findings might lead to a promising new approach for treating optic neuropathies such as glaucoma.
An Injectable, Calcium Responsive Composite Hydrogel for the Treatment of Acute Spinal Cord Injury (2014)

Immediately following spinal cord injury, further injury can occur through several secondary injury cascades. As a consequence of cell lysis, an increase in extracellular Ca(2+) results in additional neuronal loss by inducing apoptosis. Thus, hydrogels that reduce extracellular Ca(2+) concentration may reduce secondary injury severity. The goal of this study was to develop composite hydrogels consisting of alginate, chitosan, and genipin that interact with extracellular Ca(2+) to enable in situ gelation while maintaining an elastic modulus similar to native spinal cord (∼1000 Pa). It was hypothesized that incorporation of genipin and chitosan would regulate hydrogel electrostatic characteristics and influence hydrogel porosity, degradation, and astrocyte behavior. Hydrogel composition was varied to create hydrogels with statistically similar mechanical properties (∼1000 Pa) that demonstrated tunable charge characteristics (6-fold range in free amine concentration) and degradation rate (complete degradation between 7 and 28 days; some blends persist after 28 days). Hydrogels demonstrate high sensitivity to Ca(2+) concentration, as a 1 mM change during fabrication induced a significant change in elastic modulus. Additionally, hydrogels incubated in a Ca(2+)-containing solution exhibited an increased linear viscoelastic limit (LVE) and an increased elastic modulus above the LVE limit in a time dependent manner. An extension of the LVE limit implies a change in hydrogel cross-linking structure. Attachment assays demonstrated that addition of chitosan/genipin to alginate hydrogels induced up to a 4-fold increase in the number of attached astrocytes and facilitated astrocyte clustering on the hydrogel surface in a composition dependent manner. Furthermore, Western blots demonstrated tunable glial fibrillary acid protein (GFAP) expression in astrocytes cultured on hydrogel blends, with some hydrogel compositions demonstrating no significant increase in GFAP expression compared to astrocytes cultured on glass. Thus, alginate/chitosan/genipin hydrogel composites show promise as scaffolds that regulate astrocyte behavior and for the prevention of Ca(2+)-related secondary neuron damage during acute SCI.
Rheological Properties of Nonfat Yogurt Stabilized Using Lactobacillus delbrueckii ssp. bulgaricus Producing Exopolysaccharide or Using Commercial Stabilizer Systems (1997)

Properties of yogurts made using three strains of Lactobacillus delbrueckii ssp. bulgaricus that produce exopolysaccharide or made with a nonproducing strain, with and without addition of commercial stabilizer blends, were compared. A simple test, developed to measure the extensibility of yogurts, was able to discriminate yogurt made with exopolysaccharide-producing strains from yogurt made with the nonproducing strain and to discriminate among yogurts made with different exopolysaccharide-producing strains. The force required to penetrate the surface of yogurt made with exopolysaccharide-producing strains was less than that needed for yogurts made with the nonproducing strain. Yogurt made with exopolysaccharide-producing strains exhibited less shear thinning than products made with the nonproducing strain. Storage and loss moduli decreased monotonically as strain exceeded 5% for yogurts made using the nonproducing strain. Both moduli decreased monotonically between 5 and 10% strain for yogurt made with the exopolysaccharide-producing strains but exhibited an inflection in the slope between 10 and 100% strain. These data are consistent with a mechanism for shear-induced structural degradation of yogurt made using exopolysaccharide-producing strains in which polymer associated with the casein network prevents disruption of portions of the network.
Myeloid‐derived suppressor cell activation by combined LPS and IFN‐γ treatment impairs DC development (2009)

Myeloid-derived suppressor cells (MDSC) and DC are major controllers of immune responses against tumors or infections. However, it remains unclear how DC development and MDSC suppressor activity both generated from myeloid precursor cells are regulated. Here, we show that the combined treatment of BM-derived MDSC with LPS plus IFN-gamma inhibited the DC development but enhanced MDSC functions, such as NO release and T-cell suppression. This was not observed by the single treatments in vitro. In the spleens of healthy mice, we identified two Gr-1(low)CD11b(high)Ly-6C(high)SSC(low)Mo-MDSC and Gr-1(high)CD11b(low)PMN-MDSC populations with suppressive potential, whereas Gr-1(high)CD11b(high) neutrophils and Gr-1(low)CD11b(high)SSC(low) eosinophils were not suppressive. Injections of LPS plus IFN-gamma expanded these populations within the spleen but not LN leading to the block of the proliferation of CD8(+) T cells. At the same time, their capacity to develop into DC was impaired. Together, our data suggest that spleens of healthy mice contain two subsets of MDSC with suppressive potential. A two-signal-program through combined LPS and IFN-gamma treatment expands and fully activates MDSC in vitro and in vivo.
A Stability Control by Active Angle Control of Front-Wheel in a Vehicle System (2008)

Side-slip angle information is required for stabilizing a vehicle. Conventional stability control methods assume that side-slip angle information can be obtained directly from a sensor. However, this is difficult to do in a normal car because an expensive sensor is needed to realize these methods. In this paper, a strategy for stability control based on the estimated side-slip is proposed. First, a novel linear observer that can make the estimated error small compared with the conventional linear observer is designed. Second, the yaw rate following the controller is constructed. To implement this control system in an actual vehicle system, a steering angle controller is designed. Finally, to confirm the effectiveness of the proposed control system, numerical simulation is implemented with the consideration of a gust of wind and vehicle modeling error. Also, running a vehicle experiment on the road is shown.
Early detection of ovarian cancer (2011)

Primary care physicians are recognizing the symptoms of ovarian cancer and ordering the appropriate diagnostic tests. On the basis of the diverse behavior of epithelial cancers, the goal of screening technology should shift from diagnosing early stage to diagnosing low‐volume disease.
Non-ideality of aqueous solutions of polyethylene glycol: consequences for its use as a macromolecular crystallizing agent in vapor-diffusion experiments (1995)

Microisopiestic measurements of the concentrations of polyethylene glycol (PEG 8000) paired with the salts sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been made in a sitting-drop arrangement with PEG in the droplet and salt in the reservoir. Resulting graphs of the concentrations of PEG and salt that are equivalent with respect to the vapor pressure of water are non-linear, do not intersect their origins, and demonstrate that relatively low (mM) salt concentrations are equivalent to relatively high PEG concentrations. The consequences of each of these observations for macromolecular crystallization by the vapor-diffusion technique when PEG is employed as the crystallizing agent are discussed.
Specificity determinants for the AMP‐activated protein kinase and its plant homologue analysed using synthetic peptides (1993)

Inspection of sequences around sites phosphorylated by the AMP-activated protein kinase (AMP-PK), and homologous sequences from other species, indicates conserved features. There are hydrophobic residues (M, V, L, I) at P-5 and P+4, and at least one basic residue (R, K, H) at P-2, P-3 or P-4. The importance of these residues has been established for AMP-PK and its putative plant homologue using a series of synthetic peptides. These results confirm the functional similarity of the animal and plant kinases, and suggest that the required motif for recognition of substrate by either kinase is M/V/L/I-(R/K/H,X,X)-X-S/T-X-X-X-M/V/L/I.