gebhart/patrepeval huggingface dataset:
Mitotic DNA damage response: Polo-like Kinase-1 is dephosphorylated through ATM-Chk1 pathway (2010)

DNA damage during the cell division cycle can activate ATM/ATR and their downstream kinases that are involved in the checkpoint pathway, and cell growth is halted until damage is repaired. As a result of DNA damage induced in mitotic cells by doxorubicin treatment, cells accumulate in a G2-like phase, not in mitosis. Under these conditions, two mitosis-specific kinases, Cdk1 and Plk1, are inhibited by inhibitory phosphorylation and dephosphorylation, respectively. G2-specific phosphorylation of Cdc25 was increased during incubation after mitotic DNA damage. Inhibition of Plk1 through dephosphorylation was dependent on ATM/Chk1 activity. Depleted expression of ATM and Chk1 was achieved using small hairpin RNA (shRNA) plasmid constructs. In this condition, damaged mitotic cells did not accumulated in a G2-like stage, and entered into G1 phase without delay. Protein phosphatase 2A was responsible for dephosphorylation of mitotic Plk1 in response to DNA damage. In knockdown of PP2A catalytic subunits, Plk1 was not dephosphorylated, but rather degraded in response to DNA damage, and cells did not accumulate in G2-like phase. The effect of ATM/Chk1 inhibition was counteracted by overexpression of PP2A, indicated that PP2A may function as a downstream target of ATM/Chk1 at a mitotic DNA damage checkpoint, or may have a dominant effect on ATM/Chk1 function at this checkpoint. Finally, we have shown that negative regulation of Plk1 by dephosphorylation is important to cell accumulation in G2-like phase at the mitotic DNA damage checkpoint, and that this ATM/Chk1/PP2A pathway independent on p53 is a novel mechanism of cellular response to mitotic DNA damage.
Mutation of Glutamate 199 of the Human C5a Receptor Defines a Binding Site for Ligand Distinct from the Receptor N Terminus (1995)

C5a, a potent chemoattractant for monocytes, neutrophils, and other leukocytes, binds to a cell surface receptor of the seven-transmembrane superfamily. Here we report the effects of substituting Gln for Glu199 of the human C5a receptor (hC5aR) expressed in a model cell system for chemoattractant receptor signaling, the rat basophilic leukemia cell line RBL-2H3. Both the binding affinity for hC5a and the EC50 for subsequent cellular signals are reduced 5-10-fold by this substitution. A peptide mimic of the C terminus of C5a also binds to, and activates, hC5aR. The response to this peptide is reduced in cells bearing mutated hC5aR, indicating that the mutation affects interactions with the C terminus of hC5a. The C-terminal peptide contains only two basic residues, a Lys and an Arg (assumed to be analogous to Lys68 and Arg74 of hC5a), which could act as counter-ions for Glu199 of the receptor. If the counter-ion on hC5a was Arg74, then it would be expected that intact hC5a and hC5a des-Arg74 would have identical affinities and potencies when interacting with mutant hC5aR. It was found, however, that the binding affinity and potency (for receptor signaling events) of hC5a des-Arg74 was always lower than for intact hC5a. Furthermore, the equivalent C-terminal peptide to hC5a des-Arg74 (i.e. lacking the C-terminal Arg) could partially activate the wild type but not the mutant receptor, whereas the converse peptide, containing Arg but containing Met instead of Lys, had equal potencies for both wild type and mutant receptors. Taken together these data indicate that Glu199 of hC5aR is not involved in an interaction with Arg74 of hC5a, but may interact with Lys68 of hC5a. Mutation of Glu199 defines a second ligand binding site on hC5aR, distinct from the previously characterized site on the receptor N terminus. Unlike the N-terminal binding site, this second site is associated not just with the interaction with hC5a, but also with receptor activation.
Cyclosporine effects on isolated membranes, proximal tubule cells, and interstitium of the kidney. (1988)

The pathogenesis of renal cell injury is a complex interplay among derangements in subcellular membrane function and mediators of injurious processes. Plasma and subcellular membrane injury and the resulting membrane dysfunction appear especially important. As detailed previously in this report, Cs, an extremely lipophilic compound, has the ability to bind to renal brush border membranes, interact with mitochondrial membranes resulting in multiple sites of dysfunction, and accumulate in high concentrations in renal proximal tubule cells. In spite of these interactions, Cs could not be shown to be directly toxic in vitro to proximal tubule cells. Thus, from these experiments, it is difficult to conclude that Cs-induced acute renal failure observed in vivo is due to a direct tubular toxic effect, even though Cs has the capability to interact with critical renal membranes at low concentrations. The majority of present evidence, therefore, does not suggest a toxic effect of Cs on renal epithelial cells. Instead, the acute effect of Cs to produce a decline in renal excretory function appears to be due to a fall in renal blood flow. On the other hand, the chronic effect of Cs to produce a decline in renal excretory function appears to be due to an effect of this agent to induce interstitial fibrosis. In this regard, recent findings summarized in this report demonstrate that Cs produces (over ten days) a higher than normal collagen content, as measured by hydroxyproline levels, in the kidney. In addition, this increase in collagen content with Cs treatment was associated with a significant increase in proliferation of cells in the renal interstitium, as determined by 3H-thymidine incorporation into DNA. This increase in DNA incorporation after Cs was not observed in other organs, including liver, spleen, or heart. Histologic assessment of these proliferating cells revealed them to be mononuclear. Cell surface markers also demonstrated an increase in LCA positive cells in the renal interstitium. These results, therefore, suggest a readily demonstrable effect of Cs on the renal interstitium. The relationship between Cs dosage and interstitial cell proliferation as well as the relationship between Cs-induced renal perfusion alterations and this interstitial proliferative process mandates further investigation.
Communication in the Presence of Noise (1949)

A method is developed for representing any communication system geometrically. Messages and the corresponding signals are points in two "function spaces," and the modulation process is a mapping of one space into the other. Using this representation, a number of results in communication theory are deduced concerning expansion and compression of bandwidth and the threshold effect. Formulas are found for the maxmum rate of transmission of binary digits over a system when the signal is perturbed by various types of noise. Some of the properties of "ideal" systems which transmit at this maxmum rate are discussed. The equivalent number of binary digits per second for certain information sources is calculated.
Determining Motion Parameters for Scenes with Translation and Rotation (1984)

A study of methods that determine the rotation parameters of a camera moving through synthetic and real scenes is conducted. Algorithms that combine ideas of Jain and Prazdny, using hypothesizeand-verify paradigm, are developed to find translational and rotational parameters. An argument is made for using hypothesized motion parameters rather than relaxation labeling to find correspondence. Some work with real scenes shows the difficulties introduced by noise, the lack of resolution, and the need for better low-level techniques.
Atom Transfer Radical Polymerization Using Multidentate Amine Ligands Supported on Soluble Hyperbranched Polyglycidol (2004)

Abstract Summary: Controlled polymerization of styrene in toluene was achieved by atom transfer radical polymerization (ATRP) using hyperbranched polyglycidol‐supported multidentate amine ligands/Cu I Br catalyst systems. These catalyst systems with nanoscopic dimensions were more active than the corresponding low‐molecular‐weight ligands. The controlled/living nature of the polymerization is supported by linear first order plots (ln[M] o /[M] versus time) and a linear increase of $\overline M _{\rm n}$ versus conversion as well as low polydispersity. Similar controlled polymerization of methyl methacrylate was possible in acetonitrile. Up to 97% of total copper used for polymerization could be removed from the polymer by simple precipitation in methanol and filtration. Molecular weight characteristics for styrene polymerization using PG‐triamine as a ligand. magnified image Molecular weight characteristics for styrene polymerization using PG‐triamine as a ligand.
A novel KIF5B‐ALK variant in nonsmall cell lung cancer (2011)

The discovery of the novel KIF5B-ALK variant further consolidated the role of aberrant ALK signaling in lung carcinogenesis.
233 Development of a Measuring System of Elastic Constants Using a Three-Dimensional Resonance Method (2000)

This paper describes a novel measuring system of elastic constants using a three-dimensional resonance method which can determine the elastic constants of several materials including ceramics and metals with elastic anisotropy. The system is composed of three modules: (1) measurement of resonant frequencies of cylindrical or rectangular parallelepiped small specimens, (2) numerical calculation of the specimen's resonant frequency, (3) control of these two modules and determination of the elastic constants. These modules are linked with feed back connections. To identify the vibration modes between measured and calculated resonant frequencies, a graphical user interface and a visualization tool for examining the vibration mode of the specimen were developed. Using this system, the turn-around time of determination of the elastic constants was much improved.
Phosphorylated Insulin-Like Growth Factor-I/Insulin Receptor Is Present in All Breast Cancer Subtypes and Is Related to Poor Survival (2008)

Drugs that target the insulin-like growth factor-I receptor (IGF-IR) and/or insulin receptor (IR) are currently under investigation for a variety of malignancies including breast cancer. Although we have previously reported that IGF-IR expression in primary breast tumors is common, the activation status of this receptor has not been examined in relation to survival. Phosphorylated IGF-IR/IR (P-IGF-IR/IR) and its downstream signaling partner phospho-S6 (P-S6) were evaluated immunohistochemically in tumor tissue microarrays representing 438 cases of invasive breast cancer. P-IGF-IR/IR (n = 114; P = 0.046) and total levels of IR (n = 122; P = 0.009) were indicative of poor survival, whereas total IGF-IR (n = 112; P = 0.304) was not. P-IGF-IR/IR and P-S6 were coordinately expressed in primary breast tumors (likelihood ratio, 11.57; P = 6.70 x 10(-4)). Importantly, P-IGF-IR/IR was detected in all breast cancer subtypes (luminal, 48.1%; triple negative, 41.9%; and HER2, 64.3%). In vitro, the IGF-IR/IR inhibitor BMS-536924 decreased phospho-RSK and P-S6, and significantly suppressed the growth of breast cancer cell lines MCF-7, SUM149, and AU565 representing the luminal, triple negative, and HER2 subtypes, respectively, in monolayer and soft agar. BMS-536924 also inhibited growth in tamoxifen resistant MCF-7 Tam-R cells while having little effect on immortalized normal breast epithelial cells. Thus, we can determine which patients have the activated receptor and provide evidence that P-IGF-IR/IR is a prognostic factor for breast cancer. Beyond this, P-IGF-IR/IR could be a predictive marker for response to IGF-IR and/or IR-targeted therapies, as these inhibitors may be of benefit in all breast cancer subtypes including those with acquired resistance to tamoxifen.
Transgenic Mice Overexpressing Peroxiredoxin 6 Show Increased Resistance to Lung Injury in Hyperoxia (2006)

Peroxiredoxin 6 (Prd x 6) is a novel peroxidase enzyme that is expressed at a high level in the lung. We tested the hypothesis that transgenic (Tg) mice overexpressing Prd x 6 would exhibit increased resistance to hyperoxia-induced lung injury. Wild-type and Tg mice were exposed to 100% O(2) and evaluated for survival, lung histopathology, total protein, and nucleated cells in bronchoalveolar lavage fluid (BALF), and oxidation of lung protein and lipids. Prd x 6 protein expression and enzyme activity were approximately 3-fold higher in Tg lungs compared with wild-type. Tg mice survived longer during exposure to 100% O(2) (LT(50) 104+/-2.8 h in Tg versus 88.9+/-1.1 h for wild-type). Lung wet/dry weight ratio and total protein and nucleated cell count in lung lavage fluid were significantly greater in wild-type mice at 72 and 96 h of hyperoxia compared with Tg mice. At 96 h of hyperoxia, Tg mice had less epithelial cell necrosis, perivascular edema, and inflammatory cell recruitment by light microscopy, and lower TBARS and protein carbonyls in lung homogenate (P<0.05). These results show that Tg mice have increased defense against lung injury in hyperoxia, providing evidence that Prd x 6 functions as a lung antioxidant enzyme.
Heterotic effects in triploid watermelon hybrids (2005)

Twelve experimental triploid hybrids were evaluated to estimate heterotic effectsfor some pIam andfruit traits in triploid watermelon (Citrullus lanatus).Tiffany, a triploid hybrid was I/sed as standard cultivar.The experiment in a randomized block design was carried out in three replications at the Experimental Station of Embrapa Semi-Árido in Petrolina, state of Pernambuco.Thefollowing traits were evaluated: earliness, prolificacy, main stem length, fruit weight, soluble solid content, rind thickness,flesh color, and hollow heart disorder.All evaluated traits presented significant variability among the hybrids.Mid-parent heterosis effects were found as well as the standard cultivar ranging from negative to positive values attaining up to 300% prolificacy in some cases.The tetraploid lines should be improvedfor several traits in order to produce earlier triploid hybrids with more compact plants andfruits without the hollowheart disorder.
Transneuronal tracing of diverse CNS circuits by Cre-mediated induction of wheat germ agglutinin in transgenic mice (2002)

Systems neuroscience addresses the complex circuits made by populations of neurons in the CNS and the cooperative function of these neurons. Improved approaches to the neuroanatomical analysis of CNS circuits are thus of great interest. In fact, significant advances in tract-tracing methods have recently been made by using transgenic mice that express transneuronal lectin tracers under the control of neuron-specific promoters. The utility of those animals, however, is limited to the CNS circuit influenced by the particular promoter. Here, we describe a new transgenic mouse that can be used for transneuronal tracing analysis of circuits in any region of the brain or spinal cord. The transgene in these mice results in expression of LacZ in neurons throughout the CNS. Excision of the LacZ gene by Cre-mediated recombination initiates expression of the lectin, wheat germ agglutinin (WGA). To illustrate the diverse uses of these ZW (LacZ-WGA) mice, we triggered WGA expression either by crossing the mice with two Cre-expressing transgenic mouse lines or by microinjecting a Cre-expressing adeno-associated virus into the cerebellum or cerebral cortex. Both approaches resulted in extensive WGA expression in the cell bodies and dendrites of neurons in which the recombination event occurred, as well as anterograde and transneuronal transport of the lectin to second and third order neurons. Because the lectin can be induced in developing and adult animals, and in all regions of the brain and spinal cord, these ZW may prove extremely valuable for numerous studies of CNS circuit analysis.
[Current possibilities of reconstruction of the lower jaw in bony defects following tumor resection. Animal experiments and clinical results]. (1982)

The animal experimental methods as well as the clinical application in patients and histological results of a new reconstruction plate for use in bridging defects in the lower jaw are discussed. The principles of fixation of the plate with hollow titanium powder sprayed screws and a titanium mesh for stabilising the autologous cancellous bone are also given. Resection was carried out in irradiated and non-irradiated mandibles of dogs. The direct contact between the surface of the screw and the bone as well as proliferation of bone into the hollow screw are demonstrated by light and scanning electron microscope studies. New methods for the evaluation of the interface between implant and bone are described.
Ddsign of a backcap system for remote control of hydraulic valves (1994)

Backcap is an electric remote control system for the operation of directional flow control valves. This paper presents a new type of basckcap system which is characterized by its simple construction. The backcap is essentially a hydraulic cylinder of which the piston is connected to a spool of hydraulic valve and controlled by input current. An inherent feedback is imposed on its mechanism so that no artificial noe is needed. Characteristics of the backcap is verified by stability analysis, transient motion and steady state positioning for step inputs. Design parameter analyses have been executer by some analytical approaches and computer simulations, which lead to their optimal valves. These results contributed to an effective new backcap system and its design strategy.
Effect of Lignocellulose-Derived Inhibitors on Growth of and Ethanol Production by Growth-Arrested Corynebacterium glutamicum R (2007)

In cellulosic ethanol production, pretreatment of a biomass to facilitate enzymatic hydrolysis inevitably yields fermentation inhibitors such as organic acids, furans, and phenols. With representative inhibitors included in the medium at various concentrations, individually or in various combinations, ethanol production by Corynebacterium glutamicum R under growth-arrested conditions was investigated. In the presence of various inhibitors, the 62 to 100% ethanol productivity retained by the C. glutamicum R-dependent method far exceeded that retained by previously reported methods.
Influenza B and C Virus NEP (NS2) Proteins Possess Nuclear Export Activities (2001)

Nucleocytoplasmic transport of viral ribonucleoproteins (vRNPs) is an essential aspect of the replication cycle for influenza A, B, and C viruses. These viruses replicate and transcribe their genomes in the nuclei of infected cells. During the late stages of infection, vRNPs must be exported from the nucleus to the cytoplasm prior to transport to viral assembly sites on the cellular plasma membrane. Previously, we demonstrated that the influenza A virus nuclear export protein (NEP, formerly referred to as the NS2 protein) mediates the export of vRNPs. In this report, we suggest that for influenza B and C viruses the nuclear export function is also performed by the orthologous NEP proteins (formerly referred to as the NS2 protein). The influenza virus B and C NEP proteins interact in the yeast two-hybrid assay with a subset of nucleoporins and with the Crm1 nuclear export factor and can functionally replace the effector domain from the human immunodeficiency virus type 1 Rev protein. We established a plasmid transfection system for the generation of virus-like particles (VLPs) in which a functional viral RNA-like chloramphenicol acetyltransferase (CAT) gene is delivered to a new cell. VLPs generated in the absence of the influenza B virus NEP protein were unable to transfer the viral RNA-like CAT gene to a new cell. From these data, we suggest that the nuclear export of the influenza B and C vRNPs are mediated through interaction between NEP proteins and the cellular nucleocytoplasmic export machinery.
Conserved residue clustering and protein structure prediction (2003)

Protein residues that are critical for structure and function are expected to be conserved throughout evolution. Here, we investigate the extent to which these conserved residues are clustered in three-dimensional protein structures. In 92% of the proteins in a data set of 79 proteins, the most conserved positions in multiple sequence alignments are significantly more clustered than randomly selected sets of positions. The comparison to random subsets is not necessarily appropriate, however, because the signal could be the result of differences in the amino acid composition of sets of conserved residues compared to random subsets (hydrophobic residues tend to be close together in the protein core), or differences in sequence separation of the residues in the different sets. In order to overcome these limits, we compare the degree of clustering of the conserved positions on the native structure and on alternative conformations generated by the de novo structure prediction method Rosetta. For 65% of the 79 proteins, the conserved residues are significantly more clustered in the native structure than in the alternative conformations, indicating that the clustering of conserved residues in protein structures goes beyond that expected purely from sequence locality and composition effects. The differences in the spatial distribution of conserved residues can be utilized in de novo protein structure prediction: We find that for 79% of the proteins, selection of the Rosetta generated conformations with the greatest clustering of the conserved residues significantly enriches the fraction of close-to-native structures.
Carbon dioxide (CO2) as sustainable feedstock for polyurethane production (2013)

A dream comes true: tailor-made polyethercarbonate polyols are synthesised from propylene oxide and CO2. Molecular weight and functionality of these polyethercarbonate polyols are controlled by the use of an appropriate alcohol starter enabling innovative applications as a polymer building block. Interestingly, the properties of the polyethercarbonate polyols can be adjusted in a wide range by tuning CO2 content and architecture. The feasibility of using such tailored polyethercarbonate polyols in the production of polyurethanes is demonstrated as a prime example for a novel CO2 utilization with industrial potential.
Current induced periodic ferroelectric domain structures in LiNbO3 applied for efficient nonlinear optical frequency mixing (1985)

Periodic laminar ferroelectric domain superstructures in chromium-doped LiNbO3 have been grown by modulating the bias current during Czochralski growth. Periodic domain patterns stacked along the y axis with domain thicknesses as low as 8 μm have been prepared. The alternating sign of the effective nonlinear optical (nlo) coefficient enables efficient frequency mixing independent of the constraints of birefringence. This is demonstrated by realizing frequency doubling of 1.06-μm YAG : Nd laser radiation using the largest nlo coefficient, d33. For domain thicknesses equal to an odd multiple of the coherence length, d=(2m+1)lc, the second harmonic intensity varies as the square of the domain number. For the optimum case, d=lc, an improvement of the nlo efficiency, as compared to the 90° phase-matched process, by the factor [(2/π)d33/d31]2=15 is inferred.