gebhart/patrepeval huggingface dataset:
Growth differentiation factor 15 is a promising diagnostic and prognostic biomarker in colorectal cancer (2016)

Although various studies have demonstrated that growth differentiation factor 15 (GDF15) might be a potential diagnostic and prognostic marker in colorectal cancer (CRC) patients, the results are inconsistent and the statistical power of individual studies is also insufficient. An original study was conducted to explore the diagnostic and prognostic value of serum GDF15 in CRC patients. We also conducted a meta-analysis study which aimed to summarize the diagnostic and prognostic performance of serum GDF15 in CRC. We searched PubMed and ISI Web of Knowledge up to 1 November 2014 for eligible studies. In order to explore the diagnostic performance of GDF15, standardized mean difference (SMD) and their 95% confidence intervals (CI) were estimated and receiver-operating characteristic (ROC) curves were constructed. For prognostic meta-analysis, study-specific hazard ratios (HRs) of serum GDF15 for survival were summarized. A total of eight studies were included in the meta-analyses. Our results revealed that serum GDF15 levels in CRC patients were higher than those in healthy controls (SMD = 1.08, 95% CI: 0.56-1.59, P < 0.001). For discriminating CRC from healthy controls, the AUC of GDF15 was 0.816 (95% CI: 0.792-0.838). The sensitivity and specificity were 58.9% (95% CI: 55.0-62.8) and 92.08% (95% CI: 89.2-94.4), respectively, when a cut-off value of 1099 pg/ml was established. Besides, higher GDF15 expression level was associated with worse overall survival for CRC patients (pooled HR = 2.09, 95% CI: 1.47-2.96). In conclusion, the present meta-analysis suggests that serum GDF15 may be a useful diagnostic and prognostic biomarker for CRC.
High efficiency InGaAs solar cells on Si by InP layer transfer (2007)

In P ∕ Si substrates were fabricated through wafer bonding and helium-induced exfoliation of InP, and InGaAs solar cells lattice matched to bulk InP were grown on these substrates using metal-organic chemical-vapor deposition. The photovoltaic characteristics of the InGaAs cells fabricated on the wafer-bonded InP∕Si substrates were comparable to those synthesized on commercially available epiready InP substrates, thus providing a demonstration of wafer-bonded InP∕Si substrates as an alternative to bulk InP substrates for solar cell applications.
Oxidation of Guanine in DNA by Ru(phen)<sub>2</sub>(dppz)<sup>3+</sup> Using the Flash-Quench Technique (1997)

A flash-quench method has been developed to probe oxidative damage to DNA. A photoexcited Ru(II) intercalator is quenched in DNA by a weakly bound, electron-transfer quencher to generate Ru(III), a powerful ground-state oxidant. Once generated, Δ-Ru(phen)2(dppz)3+ bound to poly(dG-dC) rapidly oxidizes guanine within the DNA duplex. Transient absorption spectroscopy indicates rapid formation of the neutral guanine radical within the DNA duplex. Permanent damage resulting from the flash-quench experiment is monitored by gel electrophoresis of synthetic oligonucleotide duplexes. Oxidative damage, visualized by treatment with piperidine, occurs selectively at the 5‘-G of 5‘-GG-3‘ sites and at the 5‘- and central G of 5‘-GGG-3‘ triplets; enzymatic digestion in the absence of piperidine treatment shows formation of 8-oxo-2‘-deoxyguanosine with Ru(NH3)63+ as quencher. The yield of base damage is, furthermore, modulated by the choice of electron-transfer quencher. Quantum yields for damage vary in the order Ru(NH3)63+ < methyl viologen2+ < Co(NH3)5Cl2+ and correlate with the instability of the reduced quencher. The flash-quench method, combining spectroscopy and product analysis, offers a novel and tunable approach to explore electron transfer chemistry on double helical DNA.
Targeting the epidermal growth factor receptor in breast cancer cell lines with a recombinant ligand fusion toxin (DAB389EGF). (2006)

Breast cancer cell lines expressing intermediate to high levels of EGF-R are sensitive to low concentrations of DAB389EGF. This activity requires intact receptor binding and diphtheria toxin domains. DAB389EGF offers promise as a new therapeutic strategy for solid tumors such as breast cancer that overexpress EGF-R.
Effects of serotonin 5‐HT1A agonist in advanced Parkinson's disease (2005)

Intermittent stimulation of striatal dopaminergic receptors seems to contribute to motor dysfunction in advanced Parkinson's disease (PD). With severe dopaminergic denervation, exogenous levodopa is largely decarboxylated to dopamine in serotonergic terminals. If 5-HT1A autoreceptors regulate dopamine as well as serotonin release, in parkinsonian patients inhibition of striatal serotonergic neuron firing might help maintain more physiological intrasynaptic dopamine concentrations and thus ameliorate motor fluctuations and dyskinesias. To evaluate this hypothesis, effects of a selective 5-HT1A agonist, sarizotan, given orally at 2 and 5 mg twice daily to 18 relatively advanced parkinsonian patients, were compared with baseline placebo function during a 3-week, double-blind, placebo-controlled, proof-of-concept study. Sarizotan alone or with intravenous levodopa had no effect on parkinsonian severity. But at safe and tolerable doses, sarizotan coadministration reduced levodopa-induced dyskinesias and prolonged its antiparkinsonian response (P < or = 0.05). Under the conditions of this study, our findings suggest that 5-HT1A receptor stimulation in levodopa-treated parkinsonian patients can modulate striatal dopaminergic function and that 5-HT1A agonists may be useful as levodopa adjuvants in the treatment of PD.
Development of Low-Cost Satellite Communications System for Helicopters and General Aviation (1994)

In this paper, the development of low-cost satellite communications (SATCOM) system for helicopters and General Aviation (GA) aircrafts is described. System design and standards analysis have been conducted to meet the low-cost, light-weight, small-size and low-power system requirements for helicopters and GA aircraft environments. Other specific issues investigated include coding schemes, spatial diversity, and antenna arraying techniques. Coding schemes employing Channel State Information (CSI) and inverleaving have been studied in order to mitigate severe banking angle fading and the periodic RF signal blockage due to the helicopter rotor blades. In addition, space diversity and antenna arraying techniques have been investigated to further reduce the fading effects and increase the link margin.
Multiple origins of XY female mice ( <i>genus Akodon</i> ): phylogenetic and chromosomal evidence (2000)

Despite the diversity in sex determination across organisms, theory predicts that the evolution of XY females is rare in mammals due to fitness consequences associated with infertility or the loss of YY zygotes. We investigated this hypothesis from a phylogenetic perspective by examining the inter- and intraspecific distribution of Y chromosomes in males and females (XY females) in South American field mice (Akodon). We found that XY females occurred at appreciable frequencies (10-66%) in at least eight Akodon species, raising the possibility that this system of sex determination has arisen multiple times independently. To determine the number of origins of XY females in Akodon, we constructed a molecular phylogeny of 16 species of Akodon based on mitochondrial DNA control region sequences. Both parsimony and maximum-likelihood reconstruction of ancestral states suggest that multiple steps (gains or losses of XY females) best explain the evolution of XY females, but do not clearly differentiate between single and multiple origins. We then directly compared functional and non-functional Y chromosomes in six species by Southern blot analysis. We found that male and female Y chromosome restriction fragment length polymorphism patterns were identical within species, but always differed between species, providing evidence that XY females arose at least six times within the Akodon lineage. To our knowledge, this pattern in Akodon is the first documentation of a novel sex-determining system arising multiple times within a tight clade of mammals. In addition, this system provides a clear test of the accuracy of phylogenetic methods to reconstruct ancestral states.
The Effects of Plant Transposable Element Insertion on Transcription Initiation and RNA Processing (1990)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
<i>PAX-6</i>IN DEVELOPMENT AND EVOLUTION (1997)

Pax-6 is a member of the Pax gene class and encodes a protein containing a paired domain and a homeodomain. The molecular characterization of Pax-6 genes from species of different animal phyla and the analysis of Pax-6 function in the developing eyes and central nervous system of vertebrates, Drosophila melanogaster, and Caenorhabditis elegans suggest that Pax-6 homologues share conserved functions. In this review, we present recent data on the structural and functional characterization of Pax-6 homologues from species of different animal phyla. We discuss the implications of these findings for our understanding of the development and evolution of eyes and nervous systems.
Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing (2012)

The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.
Convolutional Social Pooling for Vehicle Trajectory Prediction (2018)

Forecasting the motion of surrounding vehicles is a critical ability for an autonomous vehicle deployed in complex traffic. Motion of all vehicles in a scene is governed by the traffic context, i.e., the motion and relative spatial configuration of neighboring vehicles. In this paper we propose an LSTM encoder-decoder model that uses convolutional social pooling as an improvement to social pooling layers for robustly learning interdependencies in vehicle motion. Additionally, our model outputs a multi-modal predictive distribution over future trajectories based on maneuver classes. We evaluate our model using the publicly available NGSIM US-101 and I-80 datasets. Our results show improvement over the state of the art in terms of RMS values of prediction error and negative log-likelihoods of true future trajectories under the model's predictive distribution. We also present a qualitative analysis of the model's predicted distributions for various traffic scenarios.
Venlafaxine in depressed outpatients. (1991)

Venlafaxine is a structurally novel compound with a biochemical and pharmacological profile suggesting antidepressant properties. We report the results of a Phase II, double-blind, placebo-controlled clinical trial assessing the efficacy and safety of venlafaxine in a sample of 93 depressed outpatients. Venlafaxine doses of 25 mg t.i.d., 75 mg t.i.d., and 125 mg t.i.d. were compared to placebo. Patients receiving venlafaxine showed a significantly greater improvement in their mood symptoms compared to those receiving placebo. Venlafaxine was well tolerated and the most common side effect was nausea. There was some evidence to suggest that venlafaxine may have antidepressant activity within the first 2 weeks of treatment.
Options and Efficiency (1976)

This paper argues that in an uncertain world options written on existing assets can improve efficiency by permitting an expansion of the contingencies that are covered by the market. The two major results obtained are, first, that complex contracts can be "built up" as portfolios of simple options and, second, that there exists a single portfolio of the assets, the efficient fund, on which all options can be written with no loss of efficiency.
Dynamically Cross-Linked Polydimethylsiloxane Networks with Ambient-Temperature Self-Healing (2015)

Dynamically cross-linked polymer networks have promising potential to serve as self-healing materials, but this is often limited to occur at elevated temperature. We overcome this limitation by refinement of an earlier approach to synthesize dynamically cross-linked polydimethylsiloxane networks such to show stress relaxation and self-healing at room temperature on short time scales, which we probe by oscillatory shear rheology and piercing experiments. Our studies reveal a direct correlation between the amount of anionic groups in the polymer networks and their stress-relaxation and self-healing rates, allowing these materials to be designed in a rational fashion.
Iodinated fatty acids as probes for myristate processing and function. Incorporation into pp60v-src. (1993)

The myristyl group makes a critical contribution to the processing, trafficking, and function of myristylated proteins. A series of [omega-125I]iodo-fatty acids was synthesized in order to elucidate the myristyl group's contribution to the membrane association of pp60v-src, the transforming protein of Rous sarcoma virus. In vitro translation of v-src mRNA was employed to monitor incorporation of myristyl analogs into pp60v-src polypeptide. 12-Iodododecanoic, 13-iodotridecanoic, and 14-iodotetradecanoic acids were selectively incorporated in vitro into pp60v-src. One-dimensional peptide analysis confirmed that the analogs were attached to the N terminus of pp60v-src. Upon addition of membranes, the Src proteins modified by these analogs bound to membranes at levels comparable with or slightly less than the myristyl parent. Myristyl analogs were also shown to be incorporated into pp60v-src in vivo. Fractionation of [omega-125I]iodo-fatty acid labeled cells showed that 12-iododecanoic acid, 13-iodotridecanoic acid, and 14-iodotetradecanoic acid modified pp60v-src associated preferentially with the membrane fractions. These results demonstrate that fatty acyl groups one carbon longer or shorter than myristate can be accommodated within the membrane binding site for pp60v-src and illustrate the utility of in vitro systems for predicting analog behavior in vivo. We anticipate that iodinated fatty acids can be used as tools to aid in clarifying the role of the fatty acid in a variety of myristylated molecules.
Failure of 2-deoxy-D-glucose and 5-thio-D-glucose to kill hypoxic cells of two murine tumors. (1983)

We have administered the glycolysis inhibitors 2-deoxy-D-glucose and 5-thio-D-glucose to C3H/HeJ mice bearing KHT or 16/C transplantable tumors to seek evidence for hypoxic cell toxicity in vivo. The drugs were given (a) with or without insulin, (b) as large single doses or as multiple hourly injections, and (c) alone or immediately after the tumors had received radiation to kill most of the aerobic cell population. Tumor response was assessed by growth delay or by lung colony assay. Limiting toxicity of 2-deoxy-D-glucose and 5-thio-D-glucose was neurological, leading to seizures and/or death, and this toxicity was increased by insulin. The drugs had at most minimal effects on the growth of either untreated or irradiated tumors at maximal tolerated doses. Despite the known selective toxicity of these glucose analogues for hypoxic cells in tissue culture, we have found them to be ineffective in killing hypoxic cells of two murine tumors.
Characterization of photoaffinity labeling of benzodiazepine binding sites. (1981)

The specific photoaffinity labeling of membrane-bound and detergent-solubilized benzodiazepine binding sites has been investigated using UV irradiated [3H] flunitrazepam as a photochemical probe. The time course and the regional and pharmacological specificity of the photolabeling reaction has been determined for "brain-specific" benzodiazepine binding sites; "peripheral-type" binding sites treated in an identical manner were not specifically labeled. Comparison of the number of sites labeled and blocked by [3H]flunitrazepam photolabeling of detergent-solubilized preparations indicated that about one site was blocked and unavailable for reversible binding for each site photolabeled. In contrast, when membrane-bound sites were photolabeled, about four sites were inactivated for each site photolabeled. Examination of photolabeled binding sites from various brain regions including cortex, striatum, and hippocampus using sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave only a single labeled band of apparent Mr = 48,000.
Acoustofluidics 7: The acoustic radiation force on small particles (2012)

In this paper, Part 7 of the thematic tutorial series "Acoustofluidics-exploiting ultrasonic standing waves, forces and acoustic streaming in microfluidic systems for cell and particle manipulation", we present the theory of the acoustic radiation force; a second-order, time-averaged effect responsible for the acoustophoretic motion of suspended, micrometre-sized particles in an ultrasound field.
Change in Body Weight and Longevity (1992)

Both body weight loss and weight gain are associated with significantly increased mortality from all causes and from coronary heart disease but not from cancer.
The Syntheses of 16a‘-<i>homo-</i>Leurosidine and 16a‘-<i>homo-</i>Vinblastine. Generation of Atropisomers (2001)

The synthesis of 16a'-homo-leurosidine was achieved through enantioselective generation of a ring D'-seco-precursor 33 (without requirement of a chiral auxiliary). Its cyclization provided the N(b')-quaternary salt 35 with a configuration corresponding to the atropisomeric form 8a rather than 8b of the target product. On debenzylation, the amine 8a was obtained and found not to isomerize thermally to the anticipated atropisomer 8b (in contrast to its lower homologue, with its formation of natural leurosidine). However, on protonation, a 1:1 mixture of atropisomers of 16a'-homo-leurosidine was obtained. A synthesis of 16a'-homo-vinblastine provided two atropisomers 5a and 5b for the free base at equilibrium (1:2.3 at room temperature in CDCl(3)), with a shift to the major conformer 5b with increasing solvent acidity or decreasing temperature. The synthesis was achieved through a stereoselective inversion of the tertiary hydroxyl function in the enantioselectively generated C-20' progenitor 39.
ChemInform Abstract: AMMOXIDATION OF ACROLEIN ON CATALYST OF IRON‐BISMUTH‐PHOSPHORUS MIXED OXIDE SYSTEM (1976)

Abstract Die Oxidation von Acrolein (I) in Gegenwart von Ammoniak in einem Festbettreaktor bei Temperaturen zwischen 3 l0 und 380°C liefert Acrylnitril (II), Acetonitril (III) und Kohlendioxid.
Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. (1989)

We determined the fidelity of avian myeloblastosis virus and Moloney murine leukemia virus reverse transcriptases (RTs) during DNA synthesis in vitro using the M13mp2 lacZ alpha gene as a mutational target. Both RTs commit an error approximately once for every 30,000 nucleotides polymerized. DNA sequence analysis of mutants generated in a forward mutation assay capable of detecting many types of errors demonstrated that avian myeloblastosis virus RT produced a variety of different mutations. The majority (58%) were single-base substitutions; all of which resulted from the misincorporation of either dAMP or dGMP. Minus-one frameshifts were also common, composing about 30% of the mutations. In addition to single-base events, eight mutants contained sequence changes involving from 2 to 59 bases. The frequency of these mutants suggests that, at least during DNA synthesis in vitro, RTs also commit errors by mechanisms other than classical base miscoding and misalignment. We examined the ability of RTs to synthesize DNA from a mismatched primer terminus at a sequence where the mismatched base was complementary to the next base in the template. Unlike cellular DNA polymerases which polymerize from the mismatched template-primer, RTs preferred to polymerize from a rearranged template-primer containing a matched terminal base pair and an unpaired base in the template strand. The unusual preference for this substrate suggests that the interactions between RTs and the template-primer are different from those of cellular DNA polymerases. The overall error rate of RT in vitro is sufficient to account for the estimated mutation rate of these viruses.
Recombinant Squalene Synthase. Synthesis of Non-Head-to-Tail Isoprenoids in the Absence of NADPH (2002)

Squalene synthase (SQase) catalyzes two consecutive reactions in sterol biosynthesis. The first is the condensation of two molecules of farnesyl diphosphate (FPP) to form a cyclopropylcarbinyl intermediate, presqualene diphosphate (PSPP). The subsequent conversion of PSPP to squalene (SQ) involves an extensive rearrangement of the carbon skeleton and a NADPH-dependent reduction. Incubation of a truncated soluble form of recombinant yeast SQase with FPP in buffer lacking NADPH gave (1R,2R,3R)-PSPP. As the incubation continued, SQase catalyzed the subsequent conversion of PSPP to a mixture of triterpenes. Two of the major products, (Z)-dehydrosqualene (DSQ) and (R)-12-hydroxysqualene (HSQ), have the same 1'-1 linkage between the farnesyl units from FPP that is found in squalene. The other major product, (10S,13S)-10-hydroxybotryococcene (HBO), has a 1'-3 linkage between the farnesyl units. Small quantities of (S)-HSQ and (10R,13S)-HBO were also formed. Three additional triterpenes, the allylic isomers of HSQ and HBO, and an unidentified alcohol were produced in minor amounts. A methyl ether corresponding to HSQ was detected when methanol was present in the incubation buffer. These compounds are the expected "solvolysis" products from PSPP. They provide strong support for mechanisms that propose cyclopropylcarbinyl cations as intermediates in the SQase-catalyzed rearrangement of PSPP to SQ and unambiguously demonstrate that the catalytic machinery of SQase is capable of synthesizing a variety of irregular isoprenoids.
Color Tunability and Electrochemiluminescence of Silver Nanoclusters (2009)

Colorful clusters: Silver nanoclusters consisting of only a few atoms exhibit large chemical-environment-responsive shifts of their optical absorption and emission bands, that is, large solvatochromism (see picture). The photophysical characteristics and electrochemiluminescence of the Ag clusters give them remarkable advantages over larger nanoparticles in applications such as molecular sensing.
Work rhythms (2002)

We examined records of minute-by-minute computer activity coupled with information about the location of the activity, online calendar appointments, and e-mail activity. We present a number of visualizations of the data that exhibit meaningful patterns in users' activities. We demonstrate how the patterns vary between individuals and within individuals according to time of day, location, and day of the week. Some patterns augment the schedule information found in people's online calendars. We discuss applications for group coordination (especially across time zones) plus opportunities for future research. In light of the popularity of instant messaging, this research identifies some of the benefits and privacy risks associated with the uses of online presence and awareness information.