gebhart/patrepeval huggingface dataset:
Transthyretin Stabilization by Iododiflunisal Promotes Amyloid-β Peptide Clearance, Decreases its Deposition, and Ameliorates Cognitive Deficits in an Alzheimer's Disease Mouse Model (2014)

Alzheimer's disease (AD) is the most common form of dementia and now represents 50-70% of total dementia cases. Over the last two decades, transthyretin (TTR) has been associated with AD and, very recently, a novel concept of TTR stability has been established in vitro as a key factor in TTR/amyloid-β (Aβ) interaction. Small compounds, TTR stabilizers (usually non-steroid anti-inflammatory drugs), bind to the thyroxine (T4) central binding channel, increasing TTR tetrameric stability and TTR/Aβ interaction. In this work, we evaluated in vivo the effects of one of the TTR stabilizers identified as improving TTR/Aβ interaction, iododiflunisal (IDIF), in Aβ deposition and other AD features, using AβPPswe/PS1A246E transgenic mice, either carrying two or just one copy of the TTR gene (AD/TTR+/+ or AD/TTR+/-, respectively), available and characterized in our laboratory. The results showed that IDIF administered orally bound TTR in plasma and stabilized the protein, as assessed by T4 displacement assays, and was able to enter the brain as revealed by mass spectrometry analysis of cerebrospinal fluid. TTR levels, both in plasma and cerebrospinal fluid, were not altered. In AD/TTR+/- mice, IDIF administration resulted not only in decreased brain Aβ levels and deposition but also in improved cognitive function associated with the AD-like neuropathology in this mouse model, although no improvements were detectable in the AD/TTR+/+ animals. Further, in AD/TTR+/- mice, Aβ levels were reduced in plasma suggesting TTR promoted Aβ clearance from the brain and from the periphery. Taken together, these results strengthen the importance of TTR stability in the design of therapeutic drugs, highlighting the capacity of IDIF to be used in AD treatment to prevent and to slow the progression of the disease.
New roles forcis-jasmone as an insect semiochemical and in plant defense (2000)

cis-jasmone, or (Z)-jasmone, is well known as a component of plant volatiles, and its release can be induced by damage, for example during insect herbivory. Using the olfactory system of the lettuce aphid to investigate volatiles from plants avoided by this insect, (Z)-jasmone was found to be electrophysiologically active and also to be repellent in laboratory choice tests. In field studies, repellency from traps was demonstrated for the damson-hop aphid, and with cereal aphids numbers were reduced in plots of winter wheat treated with (Z)-jasmone. In contrast, attractant activity was found in laboratory and wind tunnel tests for insects acting antagonistically to aphids, namely the seven-spot ladybird and an aphid parasitoid. When applied in the vapor phase to intact bean plants, (Z)-jasmone induced the production of volatile compounds, including the monoterpene (E)-beta-ocimene, which affect plant defense, for example by stimulating the activity of parasitic insects. These plants were more attractive to the aphid parasitoid in the wind tunnel when tested 48 h after exposure to (Z)-jasmone had ceased. This possible signaling role of (Z)-jasmone is qualitatively different from that of the biosynthetically related methyl jasmonate and gives a long-lasting effect after removal of the stimulus. Differential display was used to compare mRNA populations in bean leaves exposed to the vapor of (Z)-jasmone and methyl jasmonate. One differentially displayed fragment was cloned and shown by Northern blotting to be up-regulated in leaf tissue by (Z)-jasmone. This sequence was identified by homology as being derived from a gene encoding an alpha-tubulin isoform.
Coordinating multiple antenna cellular networks to achieve enormous spectral efficiency (2006)

Intercell interference limits the capacity of wireless networks. To mitigate this interference we explore coherently coordinated transmission (CCT) from multiple base stations to each user. To treat users fairly, we explore equal rate (ER) networks. We evaluate the downlink network efficiency of CCT as compared to serving each user with single base transmission (SBT) with a separate base uniquely assigned to each user. Efficiency of ER networks is measured as total network throughput relative to the number of network antennas at 10% user outage. Efficiency is compared relative to the baseline of single base transmission with power control, (ER-SBT), where base antenna transmissions are not coordinated and apart from power control and the assignment of 10% of the users to outage, nothing is done to mitigate interference. We control the transmit power of ER systems to maximise the common rate for ER-SBT, ER-CCT based on zero forcing, and ER-CCT employing dirty paper coding. We do so for (no. of transmit antennas per base, no. of receive antennas per user) equal to (1,1), (2,2) and (4,4). We observe that CCT mutes intercell interference enough, so that enormous spectral efficiency improvement associated with using multiple antennas in isolated communication links occurs as well for the base-to-user links in a cellular network.
Fluorene-based low band-gap copolymers for high performance photovoltaic devices (2004)

Low band-gap, soluble conjugated copolymers were synthesized from 9,9-dioctylfluorene and 4,7-di-2-thienyl-2,1,3-benzothiadiazole (PFO-DBT) and different composition ratios were used for the donor material in bulk heterojunction polymer photovoltaic cells (PVCs). In PVCs made with PFO-DBT:PCBM (methano-fullerene [6,6]-phenyl C61-butyric acid methyl ester) blends, the spectral response is extended up to 650 nm and the open-circuit voltage (Voc) is improved to 0.95 V. The energy conversion efficiency (ηe) in devices with optimized composition reaches 2.24% under an AM1.5 solar simulator (78.2 mW/cm2). In contrast to organic PVCs previously published, these PVCs retain high energy conversion efficiency at illumination up to 5 suns of AM1.5 spectral illumination. This feature allows high efficiency polymer PVC modules made in combination with a light concentrator.
MLH1, PMS1, and MSH2 Interactions During the Initiation of DNA Mismatch Repair in Yeast (1994)

The discovery that mutations in DNA mismatch repair genes can cause hereditary nonpolyposis colorectal cancer has stimulated interest in understanding the mechanism of DNA mismatch repair in eukaryotes. In the yeast Saccharomyces cerevisiae, DNA mismatch repair requires the MSH2, MLH1, and PMS1 proteins. Experiments revealed that the yeast MLH1 and PMS1 proteins physically associate, possibly forming a heterodimer, and that MLH1 and PMS1 act in concert to bind a MSH2-heteroduplex complex containing a G-T mismatch. Thus, MSH2, MLH1, and PMS1 are likely to form a ternary complex during the initiation of eukaryotic DNA mismatch repair.
Increased rigidity of the chiral centre of tocainide favours stereoselectivity and use‐dependent block of skeletal muscle Na+ channels enhancing the antimyotonic activity in vivo (2001)

1. Searching for the structural requirements improving the potency and the stereoselectivity of Na(+) channel blockers as antimyotonic agents, new derivatives of tocainide, in which the chiral carbon atom is constrained in a rigid alpha-proline or pyrrolo-imidazolic cycle, were synthesized as pure enantiomers. 2. Their ability to block Na(+) currents, elicited from -100 to -20 mV at 0.3 Hz (tonic block) and 2-10 Hz (use-dependent block) frequencies, was investigated in vitro on single fibres of frog semitendinosus muscle using the vaseline-gap voltage-clamp method. 3. The alpha-proline derivative, To5, was 5 and 21 fold more potent than tocainide in producing tonic and 10 Hz-use-dependent block, respectively. Compared to To5, the presence of one methyl group on the aminic (To6) or amidic (To7) nitrogen atom decreased use-dependence by 2- and 6-times, respectively. When methylene moieties were present on both nitrogen atoms (To8), both tonic and use-dependent block were reduced. 4. Contrarily to tocainide, all proline derivatives were stereoselective in relation to an increased rigidity. A further increase in the molecular rigidity as in pyrrolo-imidazolic derivatives markedly decreased the drug potency with respect to tocainide. 5. Antimyotonic activity, evaluated as the shortening of the time of righting reflexes of myotonic adr/adr mice upon acute drug in vivo administration was 3 fold more effective for R-To5 than for R-Tocainide. 6. Thus, constraining the chiral centre of tocainide in alpha-proline cycle leads to more potent and stereoselective use-dependent Na(+) channel blockers with improved therapeutic potential.
Homeostatic chemokines drive migration of malignant B cells in patients with non-Hodgkin lymphomas (2004)

This study investigated the role of several chemokines and their receptors on malignant B lymphocytes recovered from 13 patients with chronic lymphocytic leukemia (CLL), 9 with hairy cell leukemia (HCL), 5 with mantle cell lymphoma (MCL), 5 with marginal zone B-cell lymphoma (MZL), 6 with small lymphocytic lymphoma (SLL), and 5 with follicular cell lymphoma (FCL). Flow cytometry analysis demonstrated that CXCR4 and CXCR5 were expressed on all malignant and normal B cells. Considering CC receptors, CCR1 was expressed in 70% of patients with CLL and 40% of those with HCL but was lacking in patients with MCL, MZL, SLL, and normal B cells. CCR2 showed a heterogeneous pattern of expression. CCR3 was found in almost all patients with CLL and in the majority of those with HCL, whereas it was usually lacking in patients with MZL and SLL and in healthy subjects. CCR5 was expressed in patients with HCL and MCL. Migration assays showed that different chemokines, mainly CXCL12 and CXCL13, are able to trigger migration of malignant B lymphocytes. Some of these chemokines induce calcium mobilization. These data indicate that different patterns of chemokine receptor expression identify different malignant B-cell subsets and that these receptors are functional and might play a role in malignant B-cell circulation.
BiGGER: A new (soft) docking algorithm for predicting protein interactions (2000)

A new computationally efficient and automated "soft docking" algorithm is described to assist the prediction of the mode of binding between two proteins, using the three-dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works in two sequential steps: first, the complete 6-dimensional binding spaces of both molecules is systematically searched. A population of candidate protein-protein docked geometries is thus generated and selected on the basis of the geometric complementarity and amino acid pairwise affinities between the two molecular surfaces. Most of the conformational changes observed during protein association are treated in an implicit way and test results are equally satisfactory, regardless of starting from the bound or the unbound forms of known structures of the interacting proteins. In contrast to other methods, the entire molecular surfaces are searched during the simulation, using absolutely no additional information regarding the binding sites. In a second step, an interaction scoring function is used to rank the putative docked structures. The function incorporates interaction terms that are thought to be relevant to the stabilization of protein complexes. These include: geometric complementarity of the surfaces, explicit electrostatic interactions, desolvation energy, and pairwise propensities of the amino acid side chains to contact across the molecular interface. The relative functional contribution of each of these interaction terms to the global scoring function has been empirically adjusted through a neural network optimizer using a learning set of 25 protein-protein complexes of known crystallographic structures. In 22 out of 25 protein-protein complexes tested, near-native docked geometries were found with C(alpha) RMS deviations < or =4.0 A from the experimental structures, of which 14 were found within the 20 top ranking solutions. The program works on widely available personal computers and takes 2 to 8 hours of CPU time to run any of the docking tests herein presented. Finally, the value and limitations of the method for the study of macromolecular interactions, not yet revealed by experimental techniques, are discussed.
Team Cornell's Skynet: Robust perception and planning in an urban environment (2008)

Abstract Team Cornell's Skynet is an autonomous Chevrolet Tahoe built to compete in the 2007 DARPA Urban Challenge. Skynet consists of many unique subsystems, including actuation and power distribution designed in‐house, a tightly coupled attitude and position estimator, a novel obstacle detection and tracking system, a system for augmenting position estimates with vision‐based detection algorithms, a path planner based on physical vehicle constraints and a nonlinear optimization routine, and a state‐based reasoning agent for obeying traffic laws. This paper describes these subsystems in detail before discussing the system's overall performance in the National Qualifying Event and the Urban Challenge. Logged data recorded at the National Qualifying Event and the Urban Challenge are presented and used to analyze the system's performance. © 2008 Wiley Periodicals, Inc.
Porins in the Cell Wall of Mycobacterium tuberculosis (1999)

Lipid bilayer experiments indicated that the cell wall of Mycobacterium tuberculosis contains at least two different porins: (i) a cation-selective, heat-sensitive 0.7-nS channel which has a short-lived open state and is probably composed of 15-kDa subunits and (ii) a 3-nS, >60-kDa channel with a long-lived open state, resembling porins from fast-growing mycobacteria.
Softlithographie (1998)

Elastomere Stempel und Gußformen bieten die große Chance, die Nachteile der derzeit in der Erzeugung kleiner Strukturen führenden Photolithographie zu eliminieren. Bei den „Softlithographie”︁ genannten Verfahren werden keine aufwendigen Laborausrüstungen und hochenergetischen Strahlungen benötigt. Damit sind diese Techniken einfach, billig und auch für Molekülchemiker leicht zugänglich. Der derzeitige Entwicklungsstand auf diesem zukunftsweisenden Forschungsgebiet wird hier vorgestellt.
[Human cell transplantation]. (1988)

To summarize this review: it was written concerning human cell transplantations from various human organs based on already published historical reports. It was limited to only clinical cases for therapeutic treatment. Some of the methods in the article are commonly used, well-established methods found in everyday practice. Others are still in the experimental stages. I think we can try these, or even never methods for other cell groups in the near future.
Hygienic behaviour of honey bees and its application for control of brood diseases and varroa (1998)

AbstractPart I of this review summarized the initial research on hygienic behaviour of honey bees, Apis mellifera. This early work that concerned hygienic behaviour as a mechanism of resistance to American foulbrood (AFB) has been the foundation for all subsequent research on hygienic behaviour. In Part II, research on hygienic behaviour in relation to other bee diseases and to Varroa jacobsoni and in Apis species and subspecies is reviewed. In addition, techniques to screen bee colonies for the behaviour are detailed, and practical applications of breeding bees for hygienic behaviour are given. A section on neuroethology demonstrates how modern neurobiological techniques are being used to detect the reasons for differences in responses of hygienic and non-hygienic bees to abnormal brood.
[Proteases from Pseudomonas: immunologic comparison]. (1994)

We studied 5 strains of Pseudomonas fluorescens, its ability to produce proteolytic enzymes and the antigenic relatedness between P. fluorescens and P. aeruginosa proteases. Cells were grown in tryptic soy broth plus 2% skim milk powder, at 4 C during 5 days. All the proteases acted on gelatin, casein, and showed limited activity on congo redelastin. By zymograms in polyacrylamide gel (PAA), one enzyme responsible of whole enzymatic activity was shown. The extracellular protease of the strain P. fluorescens ATCC 17400 was purified by ammonium sulfate precipitation (60% saturation) and chromatography on DEAE cellulose with ionic strength gradient, and Sephadex G 100. A 181 fold increase in specific activity with a recovery of 21% was obtained. PAA-sodium dodecyl sulfate revealed a single band with a molecular weight of approximately 45,700 +/- 1,000 Daltons. P. fluorescens antiprotease rabbit serum showed by immunodiffusion (ID) and countercurrent immunoelectrophoresis (CIEF) identity pattern of reaction with the homology strains studied. Rabbit sera antielastase and anti-alkaline protease of P. aeruginosa did not exhibit by ID, CIEF and immunoblotting immunological reactivity with antigen (protease) from P. fluorescens; by enzyme linked immunosorbent assay (ELISA), P. aeruginosa antielastase rabbit serum showed a weak response with P. fluorescens protease. These preliminary observations showed analogy in enzymatic functions, such as specificity, between the enzymes produced by phylogenetically related species, but the immunological studies showed very little interspecific homology.
pH6 antigen (PsaA protein) of Yersinia pestis, a novel bacterial Fc-receptor (1996)

It was found that recombinant pH6 antigen (rPsaA protein) forming virulence-associated fimbriae on the surface of Yersinia pestis at pH 6.7 in host macrophage phagolysosomes or extracellularly in abscesses such as buboes, is a novel bacterial Fc-receptor. rPsaA protein displays reactivity with human IgG1, IgG2 and IgG3 subclasses but does not react with rabbit, mouse and sheep IgG.
Preclinical Studies in Support of Defibrotide for the Treatment of Multiple Myeloma and Other Neoplasias (2009)

Defibrotide's in vivo chemosensitizing properties and lack of direct in vitro activity against tumor cells suggest that it favorably modulates antitumor interactions between bone marrow stromal cells and endothelia in the tumor microenvironment. These data support clinical studies of defibrotide in combination with conventional and novel therapies to potentially improve patient outcome in multiple myeloma and other malignancies.
Chemical Activation of Cervical Cell Bodies: Effects on Responses to Colorectal Distension in Lumbosacral Spinal Cord of Rats (1999)

We have shown that stimulation of cardiopulmonary sympathetic afferent fibers activates relays in upper cervical segments to suppress activity of lumbosacral spinal cells. The purpose of this study was to determine if chemical excitation (glutamate) of upper cervical cell bodies changes the spontaneous activity and evoked responses of lumbosacral spinal cells to colorectal distension (CRD). Extracellular potentials were recorded in pentobarbital-anesthetized male rats. CRD (80 mmHg) was produced by inflating a balloon inserted in the descending colon and rectum. A total of 135 cells in the lumbosacral segments (L(6)-S(2)) were activated by CRD. Seventy-five percent (95/126) of tested cells received convergent somatic input from the scrotum, perianal region, hindlimb, and tail; 99/135 (73%) cells were excited or excited/inhibited by CRD; and 36 (27%) cells were inhibited or inhibited/excited by CRD. A glutamate (1 M) pledget placed on the surface of C(1)-C(2) segments decreased spontaneous activity and excitatory CRD responses of 33/56 cells and increased spontaneous activity of 13/19 cells inhibited by CRD. Glutamate applied to C(6)-C(7) segments decreased activity of 10/18 cells excited by CRD, and 9 of these also were inhibited by glutamate at C(1)-C(2) segments. Glutamate at C(6)-C(7) increased activity of 4/6 cells inhibited by CRD and excited by glutamate at C(1)-C(2) segments. After transection at rostral C(1) segment, glutamate at C(1)-C(2) still reduced excitatory responses of 7/10 cells. Further, inhibitory effects of C(6)-C(7) glutamate on excitatory responses to CRD still occurred after rostral C(1) transection but were abolished after a rostral C(6) transection in 4/4 cells. These data showed that C(1)-C(2) cells activated with glutamate primarily produced inhibition of evoked responses to visceral stimulation of lumbosacral spinal cells. Inhibition resulting from activation of cells in C(6)-C(7) segments required connections in the upper cervical segments. These results provide evidence that upper cervical cells integrate information that modulates activity of distant spinal neurons responding to visceral input.
HCV Genotype 3 Is Associated With an Increased Risk of Cirrhosis and Hepatocellular Cancer in a National Sample of U.S. Veterans With HCV (2014)

HCV genotype 3 is associated with a significantly increased risk of developing cirrhosis and HCC compared to HCV genotype 1. This association is independent of patients' age, diabetes, body mass index, or antiviral treatment.
Structural Studies on Anti-inflammatory Polysaccharides from <italic>Streptomyces fradiae</italic> (1974)

Two kinds of L-arabinans have been isolated from a broth of Streptomyces fradiae 3739 strain. Both of these arabinans, named P-1 and P-2, possess potential anti-carrageenin abscess activity. Chromatographic differences on TEAE-cellulose between P-1 and P-2 can be attributed to differences in the contents of D-galacturonic acid in these polysaccharides. From the results of various experiments, it is concluded that these L-arabinans have almost linear structures made up of 1→5 linked α-L-arabinofuranose units. D-Galacturonic acid was found to be linked to L-arabinose by an α-glycosidic linkage. The molecular weights of P-1 and P-2 were determined to be 9,800 and 4,700, respectively, by ultracentrifugal analyses. Periodate oxidation of these polysaccharides resulted in loss of biological activity.
Sinorhizobium meliloti Regulator MucR Couples Exopolysaccharide Synthesis and Motility (2008)

In order to enter symbiosis with its legume partner, Sinorhizobium meliloti requires regulatory systems for the appropriate responses to its environment. For example, motility is required for the chemotactic movement of bacteria toward the compounds released by its host, and exopolysaccharides (EPS) are required for bacterial attachment to the root or for invasion of the infection thread. Previous research has shown that ExoR/ExoS/ChvI as well as the ExpR/Sin quorum-sensing system inversely regulate both motility and EPS production, although the regulation mechanisms were unknown. We were able to attribute the ExpR-mediated regulation of motility to the ability of ExpR to bind a DNA sequence upstream of visN when activated by N-acyl-homoserine lactone. Furthermore, MucR, previously characterized as a regulator of EPS production, also affected motility. MucR inhibited expression of rem encoding an activator of motility gene expression and, consequently, the expression of Rem-regulated genes such as flaF and flgG. Binding of MucR to the rem promoter region was demonstrated and a sequence motif similar to the previously identified MucR binding consensus was identified within this region. The swarming ability of S. meliloti Rm2011 was shown to depend on a functional ExpR/Sin quorum-sensing system and the production of both flagella and EPS. Finally, we propose a model for the coordination of motility and EPS synthesis in S. meliloti.