gebhart/patrepeval huggingface dataset:
Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species (2021)

Abstract Harnessing the plant microbiome has the potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses, while also relieving economic and environmental costs of crop production. While previous studies have gained valuable insights into the underlying genetics facilitating plant-fungal interactions, these have largely been skewed towards certain fungal clades (e.g. arbuscular mycorrhizal fungi). Several different phyla of fungi have been shown to positively impact plant growth rates, including Mortierellaceae fungi. However, the extent of the plant growth promotion (PGP) phenotype(s), their underlying mechanism(s), and the impact of bacterial endosymbionts on fungal-plant interactions remain poorly understood for Mortierellaceae. In this study, we focused on the symbiosis between soil fungus Linnemannia elongata (Mortierellaceae) and Arabidopsis thaliana (Brassicaceae), as both organisms have high-quality reference genomes and transcriptomes available, and their lifestyles and growth requirements are conducive to research conditions. Further, L. elongata can host bacterial endosymbionts related to Mollicutes and Burkholderia . The role of these endobacteria on facilitating fungal-plant associations, including potentially further promoting plant growth, remains completely unexplored. We measured Arabidopsis aerial growth at early and late life stages, seed production, and used mRNA sequencing to characterize differentially expressed plant genes in response to fungal inoculation with and without bacterial endosymbionts. We found that L. elongata improved aerial plant growth, seed mass and altered the plant transcriptome, including the upregulation of genes involved in plant hormones and “response to oxidative stress”, “defense response to bacterium”, and “defense response to fungus”. Furthermore, the expression of genes in certain phytohormone biosynthetic pathways were found to be modified in plants treated with L. elongata . Notably, the presence of Mollicutes - or Burkholderia -related endosymbionts in Linnemannia did not impact the expression of genes in Arabidopsis or overall growth rates.
Effects of chloroquine and cytochalasin B on the infection of cells by Sindbis virus and vesicular stomatitis virus (1981)

The effects of cytochalasin B and chloroquine on the process of endocytosis of Sindbis virus particles and polystyrene spheres were determined by electron microscopy. The effects of these agents on the process of infection (attachment, penetration, and uncoating) of BHK-21 cells by Sindbis virus and vesicular stomatitis virus were also determined. Cytochalasin B completely blocked ingestion of Sindbis virus particles or latex spheres by BHK cells but had no effect on the ability of Sindbis virus or vesicular stomatitis virus to infect or replicate in BHK cells. Chloroquine did not inhibit the ingestion of either latex spheres or virus particles but greatly reduced the yields of virus produced. These data suggest that endocytosis is not essential for the infection of cultured cells by Sindbis virus or vesicular stomatitis virus.
Combined parallel and agent-based methods in distributed logistics networks (2026)

Globalization and collaborative cooperation are key words for modern logistics management. Companies become “global players”, which have to react quickly to changing market conditions and which have additionally to cope with an intensive competition and an increase in flexibility. One possibility to face the increasing requirements of flexibility and reactivity to the market is the cooperation with formerly competing service providers in order to jointly offer a broad range of services. These services will be organized and managed in supply-nets. In those the independent cooperation partners can separately accept orders and under certain economic conditions can also pass these on to other partners against commission payments for sub-contracting. Thereby both partners would profit from the collaborative transport disposition because company-specific, economically unprofitable orders do not have to be rejected but instead can be profitably passed on. This paper examines approaches for the technical realization of network formations of independent service providers.
Structural Bayesian Models of Conditionals (2004)

In the past decade the traditional falsificationist view of hypothesis-testing tasks, such as Wason’s selection task, has become criticized from a Bayesian perspective. In this report a normative extension of Oaksford’s and Chater’s (1994, 1998) influential Bayesian theory is proposed, that not only takes quantitative but also qualitative (structural) knowledge into account. In an experiment it is shown that humans appear to be sensitive to both the quantitative and the qualitative preconditions of the proposed normative models.
Cutting Edge: B-1 Cells Are Deficient in Lck: Defective B Cell Receptor Signal Transduction in B-1 Cells Occurs in the Absence of Elevated Lck Expression (2005)

B-1 cells constitute a unique B cell subset that is primarily responsible for producing nonimmune Ig. This natural Ig acts as a principal line of defense against infection. A key feature of B-1 cells is the failure of BCR-triggered signal transduction. Recently, defective BCR signaling in B-1 cells has been attributed to elevated expression of the canonical T cell src kinase, Lck. In the present study, we re-examined Lck expression in normal B-1 cells. We found that B-1 cells expressed less Lck at both the protein and RNA levels than did B-2 cells. The same B-1 cells manifested defective BCR-mediated induction of IKKbeta phosphorylation, IkappaBalpha degradation, and intracellular Ca(2+) mobilization. Thus, the failure of BCR signaling in B-1 cells does not relate to subset-specific elevation of Lck.
Observation of fretting fatigue cracks by micro-computed-tomography using ultrabright synchrotron radiation (2009)

Micro computed-tomography (&mu;CT) using ultrabright synchrotron radiation was applied to observe the shape of fretting fatigue cracks in a titanium alloy. Three dimensional shape and coalescence of fretting fatigue cracks could be observed, and the shapes of the cracks obtained by the imaging agreed well with that obtained by the stereogram analysis of fracture surface using scanning electron microscopy. Transition of crack propagation mode inside specimen in fretting fatigue also could be observed nondestructively.
Improved many-to-one sweeping (2005)

This paper presents PMOST, the polymorphic many-to-one sweep tool. Through its polymorphic design it is able to project nodes quickly and with high quality through ‘modular’ node projection schemes. PMOST currently employs two different node projection schemes: Faceted and BoundaryError node projectors. Implementation details are presented for both of these methods. The proposed many-to-one sweep tool was compared to existing software with respect to speed and element quality. Performance testing using PMOST showed that the Faceted node projection scheme was the most efficient while the BoundaryError method produced less element distortion while approximating the efficiency of the Faceted scheme. We also demonstrate improved performance with respect to both element quality and algorithm efficiency when compared to other existing node projection methods. Published in 2005 by John Wiley & Sons, Ltd.
[Research status of dental titanium casting in China]. (2005)

钛及钛合金具有优异的生物相容性、良好的耐腐蚀性,比强度高,抗疲劳性强,无磁性,对人体组织无过敏,特别适合制作义齿支架和种植体上部结构.是一种有广阔应用前景的口腔生物材料,被很多学者认为是 21 世纪口腔修复的主要金属材料.由于钛及钛合金在高温下化学性能十分活泼,几乎能与所有的耐火材料及氧、氢、氮等气体发生化学反应,导致钛的熔炼浇注工艺和造型工艺发展缓慢.上世纪 80 年代初,日本、德国、美国、意大利等国家才开始使用钛制作的口腔修复体.我国也于 90 年代开始钛制修复体的研究,并在钛铸造包埋料、钛铸造工艺、钛的激光焊接、钛表面烤瓷等方面取得了较好的成果.目前,钛及钛合金在口腔修复中应用的加工工艺有:计算机辅助设计与辅助制作(CAD-CAM)加工,电火花蚀刻,钛铸造,超塑成型等.其中钛铸造工艺最适合口腔修复体的制作且应用最广泛。
Table S2 from Systemic LRG1 Expression in Melanoma is Associated with Disease Progression and Recurrence (2023)

&lt;p&gt;Table S2 shows the patient characteristics OpACIN-neo&lt;/p&gt;
TLR7 Is Critical for Anti-Viral Humoral Immunity to EV71 Infection in the Spinal Cord (2021)

Enterovirus 71 (EV71) is a positive single-stranded RNA (ssRNA) virus from the enterovirus genus of <i>Picornaviridae</i> family and causes diseases ranged from the mild disease of hand, foot and mouth disease (HFMD) to the severe disease of neurological involvement in young children. TLR7 is an intracellular pattern recognition receptor (PRR) recognizing viral ssRNA. In this study, we investigated the role of TLR7 in EV71 infection in mouse pups (10-12 days old) and found that wild-type (WT) and TLR7 knock-out (TLR7KO) mice infected with EV71 showed similar limb paralysis at the onset and peak of the disease, comparable loss of motor neurons, and similar levels of antiviral molecules in the spinal cord. These results suggest that TLR7 is not the absolute PRR for EV71 in the spinal cord. Interestingly, TLR7KO mice infected with EV71 exhibited significantly delayed recovery from limb paralysis compared with WT mice. TLR7KO mice infected with EV71 showed significantly decreased levels of IgM and IgG2, important antibodies for antiviral humoral immunity. Furthermore, TLR7KO mice infected with EV71 showed a decrease of germinal center B cells in the spleen compared with WT mice. Altogether, our study suggests that TLR7 plays a critical role in anti-viral humoral immunity rather than in being a PRR in the spinal cord during EV71 infection in young mice.
Urinary urobilinogen determined by a mercuric chloride procedure. (1981)

In this quantitative assay, urinary urobilinogen is oxidized to urobilin with iodate in an acid medium, the pH is adjusted to 6 with sodium acetate, and the mixture is reacted with alcoholic HgCl2 solution, extracted with CHCl3, the measured spectrophotometrically at 513 nm. The artificial standards of previous methods have been replaced with crystalline stercobilin IX (commercially available), a urobilin closely related to the urinary urobilins. The reproducibility of the method, as assessed from 10 replicates of a single urine specimen to which urobilinogen was added, gave a coefficient of variation of 3.9%. Analytical recovery of urobilinogen added to urines was 90.4% (SD 14.5%). Bilirubin, biliverdin, mesobilirubin, coproporphyrin I, uroporphyrin I, and porphobilinogen do not interfere.
Nonsolvent Application of Ionic Liquids: Organo-Catalysis by 1-Alkyl-3-methylimidazolium Cation Based Room-Temperature Ionic Liquids for Chemoselective N-tert-Butyloxycarbonylation of Amines and the Influence of the C-2 Hydrogen on Catalytic Efficiency (2011)

1-Alkyl-3-methylimidazolium cation based ionic liquids efficiently catalyze N-tert-butyloxycarbonylation of amines with excellent chemoselectivity. The catalytic role of the ionic liquid is envisaged as "electrophilic activation" of di-tert-butyl dicarbonate (Boc(2)O) through bifurcated hydrogen bond formation with the C-2 hydrogen of the 1-alkyl-3-methylimidazolium cation and has been supported by a downfield shift of the imidazolium C-2 hydrogen of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][NTf(2)]) from δ 8.39 to 8.66 in the presence of Boc(2)O in the (1)H NMR and a drastic reduction of the catalytic efficiency with 1-butyl-2,3-dimethylimidazolium ionic liquids that are devoid of the C-2 hydrogen. The differential time required for reaction with aromatic and aliphatic amines has offered means for selective N-t-Boc formation during inter and intramolecular competitions. Preferential N-t-Boc formation with secondary aliphatic amine has been achieved in the presence of primary aliphatic amine. Comparison of the catalytic efficiency for N-t-Boc formation with a common substrate revealed that [bmim][NTf(2)] is superior to the reported Lewis acid catalysts.
Molecular identification of the active ninja retrotransposon and the inactive aurora element in Drosophila simulans and D. melanogaster. (1998)

How transposable elements evolve is a key facet in understanding of spontaneous mutation and genomic rearrangements in various organisms. One of the best ways to approach this question is to study a newly evolved transposable element whose presence is restricted to a specific population or strain. The retrotransposons ninja and aurora may provide insights into the process of their evolution, because of their contrasting characteristics, even though they show high sequence identity. The ninja retrotransposon was found in a Drosophila simulans strain in high copy number and is potent in transposition. On the other hand, aurora elements are distributed widely among the species belonging to the Drosophila melanogaster species complex, but are immobile at least in D. melanogaster. In order to distinguish the two closely resembled retrotransposons by molecular means, we determined and compared DNA sequence of the elements, and identified characteristic internal deletions and nucleotide substitutions in 5'-long terminal repeats (LTR). Analyses of the structure of ninja homologs and LTR sequences amplified from both genomic and cloned DNA revealed that the actively transposable ninja elements were present only in D. simulans strains, but inactive aurora elements exist in both D. melanogaster and D. simulans.
Broadband Microwave Frequency Conversion Based on an Integrated Optical Micro-Comb Source (2019)

We report a broadband microwave frequency converter based on a coherent Kerr optical micro-comb generated by an integrated micro-ring resonator. The coherent micro-comb displays features that are consistent with soliton crystal dynamics with a free spectral range of 48.9 GHz. We use this to demonstrate a high-performance millimeter-wave local oscillator for microwave frequency conversion. We experimentally verify the microwave performance up to 40 GHz, achieving a ratio of -6.8 dB between output radio frequency power and intermediate frequency power and a spurious suppression ratio of >43.5 dB. The experimental results show good agreement with theory and verify the effectiveness of microwave frequency converters based on coherent optical micro-combs, with the ability to achieve reduced size, complexity, and potential cost.
Improved sinterability and microwave dielectric properties of [Zn 0.5 Ti 0.5 ] 3+ ‐doped ZnAl 2 O 4 spinel solid solution (2019)

Abstract Low‐permittivity ZnAl 2‐ x (Zn 0.5 Ti 0.5 ) x O 4 ceramics were synthesized via conventional solid‐state reaction method. A pure ZnAl 2 O 4 solid‐state solution with an Fd‐3m space group was achieved at x ≤ 0.1. Results showed that partial substitution of [Zn 0.5 Ti 0.5 ] 3+ for Al 3+ effectively lowered the sintering temperature of the ZnAl 2 O 4 ceramics and remarkably increased the quality factor ( Q × f ) values. Optimum microwave dielectric properties ( ε r = 9.1, Q × f = 115,800 GHz and τ f = −78 ppm/°C) were obtained in the sample with x = 0.1 sintered at 1400°C in oxygen atmosphere for 10 h. The temperature used for the sample was approximately 250°C lower than the sintering temperature of conventional ZnAl 2 O 4 ceramics.
Development of a New Method for Synthesis of Tandem Hairpin Pyrrole–Imidazole Polyamide Probes Targeting Human Telomeres (2013)

Pyrrole–imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. To visualize telomeres specifically, tandem hairpin PI polyamides conjugated with a fluorescent dye have been synthesized, but the study of telomeres using these PI polyamides has not been reported because of difficulties synthesizing these tandem hairpin PI polyamides. To synthesize tandem hairpin PI polyamides more easily, we have developed new PI polyamide fragments and have used them as units in Fmoc solid-phase peptide synthesis. Using this new method, we synthesized four fluorescent polyamide probes for the human telomeric repeat TTAGGG, and we examined the binding affinities and specificities of the tandem hairpin PI polyamides, the UV–vis absorption and fluorescence spectra of the fluorescent polyamide probes, and telomere staining in mouse MC12 and human HeLa cells. The polyamides synthesized using the new method successfully targeted to human and mouse telomeres under mild conditions and allow easier labeling of telomeres in the cells while maintaining the telomere structure. Using the fluorescent polyamides, we demonstrated that the telomere length at a single telomere level is related to the abundance of TRF1 protein, a shelterin complex component in the telomere.
Ergotamine Abuse: Results of Ergotamine Discontinuation, With Special Reference To the Plasma Concentrations (1982)

Twenty-three patients suffering from continuous headache linked with habitual daily use of ergotamine tartrate were studied. Their headaches were classified clinically, and possible side effects of ergotamine medication, plasma levels of ergotamine, and occurrence of withdrawal symptoms after discontinuation of drug abuse were recorded. Seventeen of the patients were clinically diagnosed as suffering from “ergotamine headache”, and seven of them complained of coldness in the extremities. Plasma ergotamine levels were measured by using a radioimmunoassay. In almost half of the patients the 1 h plasma levels after the daily dose were below the detection limit of the procedure (0.12 ng/ml). The duration and severity of the withdrawal symptoms did not correlate with the doses and plasma levels of ergotamine. In only 4 of the 21 patients who were followed up for 3 to 6 months did headache symptoms not improve after ergotamine withdrawal. The results indicate that even small (0.5-1.0 mg/day) doses of ergotamine tartrate taken regularly may cause continuous headache symptoms and withdrawal symptoms after discontinuation.
Architecture of RNA Polymerase II and Implications for the Transcription Mechanism (2000)

A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.
Fluorescent Bithiophene Chromophores: Synthesis and Application in CD Exciton Chirality Studies (1997)

Bithiophene chromophores were synthesized and used to derivatize NH2 and OH groups in aminocyclohexane, (IR, 2R)diaminocyclohexane, (lR, 2R)-trans-l,2-cyclohexanediol and methyl Lacosamidine for their application in the exciton chirality method.Schiff base, ester and amide derivatives were generated in good yields and were found to exhibit exciton-split CD curves.Besides their absorption at long wavelengths (red-shifted) in the visible range, the bithiophene derivatives showed fluorescence and solvatochromic properties.
A second autologous transplant may be efficacious in selected patients with Hodgkin's lymphoma relapsing after a previous autograft (2007)

Treatment options for patients who relapse following autologous transplantation for Hodgkin's lymphoma are limited. There are anecdotal reports of lengthy remissions following second autologous procedures, although treatment-related toxicity can be significant. We report a single centre experience of second autologous transplant performed in seven highly selected patients, who relapsed following initial high-dose therapy. They were all young and had slow tempo disease, which was still sensitive to conventional dose chemotherapy. All received BEAM conditioning for the first transplant, and six of the seven received BEAM for the second. All six of these patients regenerated successfully and with no delay, the final patient dying during the procedure following alternative conditioning. Only one case of presumed carmustine-related pneumonitis was seen, which responded rapidly to corticosteroid therapy. Four patients have subsequently relapsed, of whom three have died at 29, 33, and 38 months postprocedure. One is alive with active disease at 68 months, and the final two are alive and in continuing complete remission at 104 and 68 months.
Review on Mechanical Support and Cell-Based Therapies for the Prevention and Recovery of the Failed Fontan-Kreutzer Circulation (2021)

Though the current staged surgical strategy for palliation of single ventricle heart disease, culminating in a Fontan circulation, has increased short-term survival, mounting evidence has shown that the single ventricle, especially a morphologic right ventricle (RV), is inadequate for long-term circulatory support. In addition to high rates of ventricular failure, high central venous pressures (CVP) lead to liver fibrosis or cirrhosis, lymphatic dysfunction, kidney failure, and other comorbidities. In this review, we discuss the complications seen with Fontan physiology, including causes of ventricular and multi-organ failure. We then evaluate the clinical use, results, and limitations of long-term mechanical assist devices intended to reduce RV work and high CVP, as well as biological therapies for failed Fontan circulations. Finally, we discuss experimental tissue engineering solutions designed to prevent Fontan circulation failure and evaluate knowledge gaps and needed technology development to realize a more robust single ventricle therapy.
A Heterogeneous Silica‐Supported Scandium/Ionic Liquid Catalyst System for Organic Reactions in Water (2006)

Several carbon–carbon bond-forming reactions are catalyzed by a silica-supported scandium triflate catalyst combined with an ionic liquid. The combination of these two components creates a hydrophobic reaction environment in water (see scheme; blue: water, yellow: substrate, orange: ionic liquid). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z603070_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Software-Hardware Codesign for Efficient Neural Network Acceleration (2017)

Designers making deep learning computing more efficient cannot rely solely on hardware. Incorporating software-optimization techniques such as model compression leads to significant power savings and performance improvement. This article provides an overview of DeePhi's technology flow, including compression, compilation, and hardware acceleration. Two accelerators, named Aristotle and Descartes, are designed to achieve extremely high energy efficiency for both client and datacenter applications with convolutional neural network and recurrent neural network, respectively.