gebhart/patrepeval huggingface dataset:
Defects in d -Alanyl-Lipoteichoic Acid Synthesis in Streptococcus mutans Results in Acid Sensitivity (2000)

In the cariogenic organism, Streptococcus mutans, low pH induces an acid tolerance response (ATR). To identify acid-regulated proteins comprising the ATR, transposon mutagenesis with the thermosensitive plasmid pGh9:ISS1 was used to produce clones that were able to grow at neutral pH, but not in medium at pH 5.0. Sequence analysis of one mutant (IS1A) indicated that transposition had created a 6.3-kb deletion, one end of which was in dltB of the dlt operon encoding four proteins (DltA-DltD) involved in the synthesis of D-alanyl-lipoteichoic acid. Inactivation of the dltC gene, encoding the D-alanyl carrier protein (Dcp), resulted in the generation of the acid-sensitive mutant, BH97LC. Compared to the wild-type strain, LT11, the mutant exhibited a threefold-longer doubling time and a 33% lower growth yield. In addition, it was unable to initiate growth below pH 6.5 and unadapted cells were unable to survive a 3-h exposure in medium buffered at pH 3.5, while a pH of 3.0 was required to kill the wild type in the same time period. Also, induction of the ATR in BH97LC, as measured by the number of survivors at a pH killing unadapted cells, was 3 to 4 orders of magnitude lower than that exhibited by the wild type. While the LTA of both strains contained a similar average number of glycerolphosphate residues, permeabilized cells of BH97LC did not incorporate D-[(14)C]alanine into this amphiphile. This defect was correlated with the deficiency of Dcp. Chemical analysis of the LTA purified from the mutant confirmed the absence of D-alanine-esters. Electron micrographs showed that BH97LC is characterized by unequal polar caps and is devoid of a fibrous extracellular matrix present on the surface of the wild-type cells. Proton permeability assays revealed that the mutant was more permeable to protons than the wild type. This observation suggests a mechanism for the loss of the characteristic acid tolerance response in S. mutans.
Towards a fiber-based strategy to prevent bacteria-mucus interactions in enterotoxingenic Escherichia coli infections? (2020)

International audience
Diterpenes from the Roots of Euphorbia kansui and Their in Vitro Effects on the Cell Division of Xenopus (2) (2003)

Four new ingenane-type diterpenes, 3-O-(2,3-dimethylbutanoyl)-13-O-dodecanoyl-20-O-acetylingenol (1), 3-O-(2,3-dimethylbutanoyl)-13-O-dodecanoyl-20-deoxyingenol (2), 3-O-(2E,4Z-decadienoyl)-20-deoxyingenol (3), and 3-O-(2E,4E-decadienoyl)-20-deoxyingenol (4), two new jatrophane-type diterpenes, kansuinins D (9) and E (10), and four known ingenane-type diterpenes were isolated from the root of Euphorbia kansui. Their structures were elucidated by spectroscopic and chemical analysis, and individual Xenopus cells at the blastular stage were cultured with the diterpenes to test for biological activity. 20-Deoxyingenol diterpenes 3 and 4 induced the greatest cell cleavage arrest (0.5 micro g/ml of each compound resulted in >75% cleavage arrest), but cell cleavage inhibitory activity became weak when C-16 had an acyl residue. In contrast, the jatrophane diterpene kansuinin D (9) showed no activity.
Clinical Implications of Genetic Admixture in Hispanic Puerto Ricans: Impact on the Pharmacogenetics of CYP2C19 and PON1 (2012)

Clinical Implications of Genetic Admixture in Hispanic Puerto Ricans: Impact on the Pharmacogenetics of CYP2C19 and PON1
DIGITAL IMAGING ANALYSIS - A NEW METHOD FOR EVALUATION OF POTATO AFTER-COOKING DARKENING (2003)

ISHS XXVI International Horticultural Congress: Potatoes, Healthy Food for Humanity: International Developments in Breeding, Production, Protection and Utilization DIGITAL IMAGING ANALYSIS - A NEW METHOD FOR EVALUATION OF POTATO AFTER-COOKING DARKENING
Kausalattributionen von körperlichen Beschwerden bei somatoformen Störungen (2007)

Zusammenfassung. Es wird angenommen, dass Patienten mit somatoformen Störungen überwiegend organmedizinisch-biologische Ursachen für ihre Beschwerden verantwortlich machen - und dass diese Attributionen an der Aufrechterhaltung der Störung beteiligt sind. Bislang wurden die Kausalattributionen nur selten und überwiegend mit Bestätigungsmethoden an somatoformen Störungen untersucht. Ziele der Studie waren die Identifikation der spontanen Ursachenzuschreibungen und der Prädiktoren des Attributionsstils bei Patienten mit somatoformen Störungen - sowie die Überprüfung der Auswirkung der Kausalattributionen auf den Therapieverlauf. Insgesamt wurden 79 Patienten einer psychosomatischen Klinik mit somatoformen Störungen aufgenommen. Im Rahmen eines Interviews zur Erfassung der Kausalattributionen (KAUSOM) wurden die subjektiven Ursachen für die Körperbeschwerden offen erfragt und anschließend durch eine Stichprobe externer Rater (n = 51) in somatische vs. psychische Ursachen kategorisiert. Zusätzlich wurden Angaben zu der somatoformen Symptomatik (SOMS), Krankheitsängsten (WI), katastrophisierenden Kognitionen (FKG) und Depressionssymptomatik (BDI) vor und nach der Therapie erhoben. Schrittweise multiple Regressionsanalysen ergaben das Geschlecht, die Anzahl der somatoformen Symptome und die Depressivität als Prädiktoren des Attributionsstils. In der Folge der verhaltensmedizinischen Therapie verbesserte sich die Symptomatik insgesamt, ohne dass der Attributionsstil den Verlauf der somatoformen Symptomatik, der Krankheitsangst und der Depressivität beeinflusste. Modellkonform zeigte sich ein Überwiegen der somatischen Kausalattributionen. Jedoch wurden häufig auch psychosoziale Ursachen für die Beschwerden genannt, insbesondere bei ausgeprägterer Depressivität. Die generelle Annahme, dass somatoformen Störungen mit organmedizinisch-biologischen Kausalattributionen verbunden sind, erscheint nicht voll zutreffend. Auch präjudizieren somatische Kausalattributionen nicht zwangsläufig einen negativen Behandlungsverlauf.
ChemInform Abstract: Functionalization of Indazoles by Means of Transition Metal‐Catalyzed Cross‐Coupling Reactions (2016)

Abstract Review: 101 refs.
[A 13-week subchronic oral toxicity study of Perilla extracts in F344 rats]. (1999)

A 13-week subchronic oral toxicity study of Perilla extracts in drinking water containing 0%, 2.5%, 5% and 10% extracts was performed in both sexes of F344 rats. Rats were randomly divided into 4 groups each consisting of 10 males and 10 females. No animals died during the period of administration. There were no treatment-related changes in body weight gain or in hematological or blood biochemistry values. Nor were any treatment-related histopathological changes observed in the highest dose group. These findings indicate that ingestion of 10% Perilla extracts in drinking water for 13-week does not cause any toxicological changes in rats.
Simultaneous Evaluation of Fission Cross Sections of Uranium and Plutonium Isotopes for JENDL-3.3 (2000)

A simultaneous evaluation of the fission cross sections of 233U, 235U, 238U, 239Pu, 240Pu and 241Pu was carried out for the evaluated nuclear data library JENDL-3.3. A least-squares method was applied to selected absolute and relative measurements on the fission cross sections. Covariance matrices of the experimental data were constructed from the uncertainty information reported in the references. The fission cross sections obtained were compared with the JENDL-3.2 and ENDF/B-VI evaluations. It was found from the comparison that the present results are not so different from those in JENDL-3.2, except for the fission cross sections of 233U and the cross sections above 15MeV, and give smaller X2 value than the JENDL-3.2 cross sections. The averaged fission cross sections of 233U, 238U, and 239Pu relative to that of 235U were calculated for a neutron spectrum produced by 9Be (d,xn) reaction. It was confirmed that the calculated cross-section ratios are in good agreement with the experimental data.
Preferential oxygenation of 4-cycloalkylideneoxazol-5(4H)-ones: synthesis of N-acylcycloalk-1-enecarboxamides (1993)

The addition of oxygen, in the presence of base, to 4-cycloalkylideneoxazol-5(4H)-ones led to new substituted N-acylcycloalkenecarboxamides in high yield, via base-catalysed isomerisation, oxygenation and subsequent fragmentation of a hydro- or endo-peroxide intermediate.
Novel Insights on Obligate Symbiont Lifestyle and Adaptation to Chemosynthetic Environment as Revealed by the Giant Tubeworm Genome (2021)

The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole-genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here, we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulfur metabolism, detoxification, antioxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establish that the trophosome is a multifunctional organ marked by intracellular digestion of endosymbionts, storage of excretory products, and hematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbor highly expressed genes involved with cell cycle, programed cell death, and immunity indicating a high cell turnover and defense mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whereas it simultaneously provides new insights into the development, whole organism functions, and evolution in the giant tubeworm.
MARS: Motion-Augmented RGB Stream for Action Recognition (2019)

Most state-of-the-art methods for action recognition consist of a two-stream architecture with 3D convolutions: an appearance stream for RGB frames and a motion stream for optical flow frames. Although combining flow with RGB improves the performance, the cost of computing accurate optical flow is high, and increases action recognition latency. This limits the usage of two-stream approaches in real-world applications requiring low latency. In this paper, we introduce two learning approaches to train a standard 3D CNN, operating on RGB frames, that mimics the motion stream, and as a result avoids flow computation at test time. First, by minimizing a feature-based loss compared to the Flow stream, we show that the network reproduces the motion stream with high fidelity. Second, to leverage both appearance and motion information effectively, we train with a linear combination of the feature-based loss and the standard cross-entropy loss for action recognition. We denote the stream trained using this combined loss as Motion-Augmented RGB Stream (MARS). As a single stream, MARS performs better than RGB or Flow alone, for instance with 72.7% accuracy on Kinetics compared to 72.0% and 65.6% with RGB and Flow streams respectively.
Periods for nineteen RR Lyrae variables in NGC 1851 (1978)

Periods, light curves, mean B magnitudes, and positions are presented for 12 previously known and seven recently discovered RR Lyrae variables in the southern globular cluster NGC 1851. From the periods and shapes of the light curves, it is concluded that five of these stars are type RR<SUB>c</SUB> variables, while the remaining 14 are of type RR<SUB>ab.</SUB> The mean magnitudes of all but two of the variables are found to be very similar to one another, which implies probable cluster membership. A distance modulus of 15.3 mag is obtained for NGC 1851, and the mean period of the RR<SUB>ab</SUB> variables is determined to be 0.573 day, indicating an Oosterhoff type I system. The ratio of the number of RR<SUB>c</SUB> to RR<SUB>ab</SUB> variables is shown to equal 0.36, which suggests that NGC 1851 remains in approximately the same position relative to the other Oosterhoff type I systems.
A DNA Fragment Containing the Upstream Activator Sequence Determines Nucleosome Positioning of the Transcriptionally Repressed PHO5 Gene of Saccharomyces cerevisiae (1986)

The functional relationship of nucleosome positioning and gene expression is not known. Using high-copy plasmids, containing the yeast phosphate-repressible acid phosphatase gene (PHO5) and the TRP1/ARS1 vector system, I have determined the nucleosomal structure of the 5' region of the PHO5 gene and demonstrated that the nucleosomal positioning of this region is independent of orientation or position in the various plasmid constructions utilized. However, deletion of a 278-base pair BamHI-ClaI fragment from the 5'-flanking sequences of the PHO5 gene causes the nucleosome positioning to become dependent on orientation or position in the plasmids tested. Use of PHO5-CYC1-lACZ fusions have demonstrated that this DNA fragment contains the sequences responsible for the transcriptional regulation of the PHO5 gene in response to the level of phosphate in the growth media. The nucleosome positioning in the 5' region of PHO5 may be determined by an interaction with the sequences or machinery responsible for transcriptional regulation of the gene.
Inhibition of Human Immunodeficiency Virus Type 1 Integration by Diketo Derivatives (2002)

A series of diketo derivatives was found to inhibit human immunodeficiency virus type 1 (HIV-1) integrase activity. Only L-708,906 inhibited the replication of HIV-1(III(B)) (50% effective concentration, 12 micro M), HIV-1 clinical strains, HIV-1 strains resistant to reverse transcriptase or fusion inhibitors, HIV-2 (ROD strain) and simian immunodeficiency virus (MAC(251)). The combinations of L-708,906 with zidovudine, nevirapine, or nelfinavir proved to be subsynergistic. In cell culture, addition of L-708,906 could be postponed for 7 h after infection, a moment coinciding with HIV integration. Inhibition of integration in cell culture was confirmed by quantitative Alu-PCR.
SiO2/SiN membranes as MEMS Pirani gauges for wide pressure measurement range (2019)

Thanks to an original surface microfabrication process, large membranes suspended 1 micron above a substrate have been elaborated. A membrane with a wide heat exchange area and such a small gap allows the gauge to be sensitive in the high vacuum regime, and ensures a broader pressure range of measurement. By optimizing the membrane and beam sizes, this paper shows that one can combine different membranes to design a packaged sensor with a wide sensitive pressure range (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> Pa) and a very low power consumption (maximum 115 microwatt in this paper). These results allow the design of a fully integrated sensor, based on a unique technology, that can be integrated for in-situ pressure measurements in vacuum applications.
An Investigator's Journey in Cardiology (1992)

SUMMING up 60 years in academic medicine, in hospital wards, and in research laboratories is a difficult task: memories and impressions converge and the resonance from past events continually changes. How is one to judge one's past? Many would rate it by honors received, societies elected to, or fortune amassed. I judge my life by the degree of happiness I have received from my work, from my music, and from my family. I have been fortunate in having all my life done what I love most: pursuing the science of medicine and creating music. These have formed the anchor that has given my life stability and a continuous sense of value. <h3>Student Years in Europe</h3> From the beginning of medical school I was interested in science and felt that the purely clinical side was only half the coin, for without a strong emphasis on science, medicine would become stagnant. But
Magnetic Domains and Twin Microstructure of Single Crystal Ni–Mn–Ga Exhibiting Magnetic Shape Memory Effect (2015)

Magnetic domains structure of a Ni–Mn–Ga single crystal was analyzed using a magneto-optical indicator film (MOIF), magnetic force microscopy (MFM), and scanning electron microscopy (SEM) (Lorenz contrast). Thanks to magnetically induced reorientation, the different configurations of magnetic domains can be obtained in the same place of the crystal. MOIF gives the overall domain configuration, while MFM shows the details of the structure revealing the domain branching. The magnetic domain structure in the vicinity of the mobile single twin boundary of Type II was observed by SEM and related to the complex twin structure of the martensite obtained from the calculation.
Fine epitope mapping of monoclonal antibodies to the NH2‐terminal part of von Willebrand factor (vWF) by using recombinant and synthetic peptides: interest for the localization of the factor VIII binding domain (1994)

Two different approaches were used in order to define the epitope of three monoclonal antibodies (MoAbs) against the NH2-terminal part of the mature subunit of von Willebrand factor (vWF) which contains its factor VIII (FVIII) binding site. First, a vWF cDNA fragment library using the bacteriophage lambda gt11 expression vector was screened with radiolabelled MoAbs. The epitope of each MoAb was defined, following sequence analysis, by the overlapping DNA sequence of immunoreactive clones. MoAb 32B12, a potent inhibitor of FVIII/vWF interaction, binds within the Glu35-Ile81 sequence of vWF subunit. MoAb 14A12, a non-inhibitory antibody, recognizes a sequence within Thr141-Val220. MoAb 31H3, a partial inhibitory antibody, gives no positive clone. In the second method, a panel of 24 synthetic pentadecapeptides corresponding to the first NH2-terminal 105 amino acid residues was used to block the binding of inhibitor MoAbs to immobilized vWF in an ELISA system. The localization of MoAb 32B12 epitope was confirmed and restricted to the Met51-Ala60 sequence. The MoAb 31H3 binding to vWF is inhibited by two synthetic peptides with the overlapping sequence Cys66-Gly76. All these data confirm that the FVIII binding site of vWF is not limited to the binding area (Thr78-Thr96) of the previously described MoAbs inhibiting FVIII/vWF interaction but is composed of several key sequences.
Integrating hundred's of products through one architecture - the industrial IT architecture (2003)

During the last few years, software product line engineering has gained significant interest as a way for creating software products faster and cheaper. But what architecture is needed to integrate huge amounts of products from different product lines? The paper describes such an architecture and its support processes and tools. Through cases it is illustrated how the architecture is used to integrate new and old products in such diverse integration projects as vessel motion control, airport baggage handling systems, pulp and paper and oil and gas, in a very large organization. However, in a large organization it is a challenge to make everyone follow an architecture. Steps taken to ensure global architectural consistency are presented. It is concluded that a single architecture can be used to unify development in a huge organization where the distributed development practices otherwise may prohibit integration of various products.
Cooperative Multicomponent Self‐Assembly of Nucleic Acid Structures for the Activation of DNAzyme Cascades: A Paradigm for DNA Sensors and Aptasensors (2009)

The activation of a DNAzyme cascade by the cooperative self-assembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1. The resulting supramolecular nucleic acid structure includes the Mg(2+)-dependent DNAzyme that cleaves the ribonucleobase site of 4. The cleavage of the quasi-circular DNA 4 results in the fragmentation of the supramolecular structure and the release of two horseradish peroxidase (HRP) mimicking units that were incorporated in the blocked quasi-circular DNA 4. The HRP-mimicking DNAzyme catalyzed the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS(2-)) by H(2)O(2) to ABTS(*-), and the product provided the colorimetric readout signal for the analyzed DNA. The method enabled the analysis of DNA with a detection limit of 1 x 10(-12) M. Similarly, an analogous DNAzyme cascade was activated by the low-molecular-weight substrates, adenosine triphosphate (ATP) or cocaine. This was induced by the self-assembly of nucleic acids that included fragments of the respective aptamers and the Mg(2+)-dependent DNAzyme. Furthermore, nucleic acids consisting of fragments of the aptamers against ATP or cocaine and fragments of the HRP-mimicking DNAzyme self-assemble, in the presence of the respective substrates, to the active DNAzyme structure that catalyzes the oxidation of ABTS(2-) by H(2)O(2) to form the colored product ABTS(*-). The resulting product provided the readout signal for the recognition events. The cooperative interaction in the formation of the supramolecular nucleic acid assemblies and the activation of the DNAzymes are discussed.
Anastomotic Leaks after Bowel Resection: What Does Peer Review Teach Us about the Relationship to Postoperative Mortality? (2008)

The variability in leak rate by surgeons doing similar operations suggests that many leaks may be preventable. But death after a leak is most often a surrogate for a critically ill patient and was infrequently the actual cause of death.
Effects of fishing rope strength on the severity of large whale entanglements (2015)

Entanglement in fixed fishing gear affects whales worldwide. In the United States, deaths of North Atlantic right (Eubalaena glacialis) and humpback whales (Megaptera novaeangliae) have exceeded management limits for decades. We examined live and dead whales entangled in fishing gear along the U.S. East Coast and the Canadian Maritimes from 1994 to 2010. We recorded whale species, age, and injury severity and determined rope polymer type, breaking strength, and diameter of the fishing gear. For the 132 retrieved ropes from 70 cases, tested breaking strength range was 0.80-39.63 kN (kiloNewtons) and the mean was 11.64 kN (SD 8.29), which is 26% lower than strength at manufacture (range 2.89-53.38 kN, mean = 15.70 kN [9.89]). Median rope diameter was 9.5 mm. Right and humpback whales were found in ropes with significantly stronger breaking strengths at time of manufacture than minke whales (Balaenoptera acuturostrata) (19.30, 17.13, and 10.47 mean kN, respectively). Adult right whales were found in stronger ropes (mean 34.09 kN) than juvenile right whales (mean 15.33 kN) and than all humpback whale age classes (mean 17.37 kN). For right whales, severity of injuries increased since the mid 1980s, possibly due to changes in rope manufacturing in the mid 1990s that resulted in production of stronger ropes at the same diameter. Our results suggest that broad adoption of ropes with breaking strengths of ≤ 7.56 kN (≤ 1700 lbsf) could reduce the number of life-threatening entanglements for large whales by at least 72%, and yet could provide sufficient strength to withstand the routine forces involved in many fishing operations. A reduction of this magnitude would achieve nearly all the mitigation legally required for U.S. stocks of North Atlantic right and humpback whales. Ropes with reduced breaking strength should be developed and tested to determine the feasibility of their use in a variety of fisheries.