gebhart/patrepeval huggingface dataset:
Oenococcus oeni, a species born and moulded in wine: a critical review of the stress impacts of wine and the physiological responses (2020)

Oenococcus oeni is a lactic acid bacterium highly adapted to the stressful environment of wine, and is widely used as an industrial starter culture to conduct malolactic fermentation (MLF), the conversion of L-malate to L-lactate. Some cold-climate wine regions still produce wines which prove too stressful for the application of a starter culture, resulting in sluggish or stuck MLFs which compromise the quality and stability of the wine. The literature on the three primary stress factors, low pH, ethanol and SO2, is reviewed as well as their toxic mechanisms; possible interactions between the stress factors are also discussed. In particular, the toxic mechanisms of SO2, an extremely inhibitory compound, are poorly understood. in vitro studies as well as in vivo studies in other prokaryotes point to numerous mechanisms which could have widespread impacts on the cell envelope, proteins and DNA in O. oeni. We also review the responses of O. oeni to these stress factors and offer a simplified model of events which cultures inoculated into particularly stressful wines may experience. Although significant advances have been made in our understanding of the stress responses in recent years, many fundamental aspects still require study.
ChemInform Abstract: Synthesis of Biaryl Compounds Through Three‐Component Assembly: Ambidentate Effect of the tert‐Butyldimethylsilyl Group for Regioselective Diels—Alder and Hiyama Coupling Reactions. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Glycemic effectiveness and medication adherence with fixed-dose combination or coadministered dual therapy of antihyperglycemic regimens: a meta-analysis (2012)

In a meta-analysis, use of FDCs with antihyperglycemic agents was associated with lower HbA(1c) and higher MPR values compared to CDT use in patients with type 2 diabetes.
[(1,2,3,4,5-η)-1,2,3,4,5-Pentamethyl-2,4-cyclopentadien-1-yl]-[(4a,5,6,7,7a-η)-4-(1-pyrrolidinyl)-5H-cyclopenta[1,2-b]]pyridin-5-yl]iron (2010)

[217459-11-5] C22H28FeN2 (MW 376.90) InChI = 1/C12H13N2.C10H15.Fe/c1-2-9-14(8-1)12-6-7-13-11-5-3-4-10(11)12;1-6-7(2)9(4)10(5)8(6)3;/h3-7H,1-2,8-9H2;1-5H3; InChIKey = VEYBLEBWZYYQAE-UHFFFAOYAY (chiral catalyst for the O-to-C rearrangement of O-acylated enolates, the kinetic resolution of primary amines, and the dynamic kinetic resolution/ring opening of azlactones) Physical Data: mp 165–172 °C. Solubility: soluble in t-amyl alcohol, chlorinated, aromatic, and ethereal solvents. Form Supplied in: burgundy crystals. Handling, Storage, and Precautions: can be handled in air; best if stored under nitrogen.
Decarboxylation of alpha-ketoglutarate coupled to collagen proline hydroxylase. (1968)

Mutations are important because they provide raw material for evolution. Some types of mutations occur more often than others, and the strength of such mutational bias varies across species. It is not clear how this variation arises. We ...Biased mutation spectra are pervasive, with wide variation in the magnitude of mutational biases that influence genome evolution and adaptation. How do such diverse biases evolve? Our experiments show that changing the mutation spectrum allows populations ...
Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production (2020)

Summary Nitrogen‐fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen‐activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress‐induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well‐known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti . SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK , showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP‐tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP‐tagged SIMK led to increase of biomass in above‐ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.
Virulence of South African isolates of Haemophilus paragallinarum. Part 3: experimentally produced NAD-independent isolate. (2002)

A NAD-dependent isolate 46 (C-3) of Haemophilus paragallinarum, which was previously demonstrated to be of high virulence, was transformed to NAD independence using a plasmid isolated from a naturally occurring NAD-independent isolate of H. paragallinarum. The transformation was performed by two different methods and the identity of all of the isolates, before and after transformation was confirmed using a H. paragallinarum-specific PCR test. The transformed NAD-independent serovar C-3 isolate and the wild-type serovar C-3 isolate were used to experimentally infect vaccinated layer chickens. It was shown that the transformation to NAD independence significantly altered the virulence of the serovar C-3 isolate that was used in the transformation experiment. The mechanisms responsible for a decrease in virulence are not clear, but may be related to the pathology of the transformed isolate in the sinus of the chickens.
Computer Simulation of Vinyl Polymer Tacticity (1995)

170. Statistical description of stereoregularity illustrated through the use of a computer program that uses Bernoullian statistics to simulate the relative handedness of successive monomer units along a polymer chain.
GaAs Transmission Photocathode Grown by MBE (1980)

Negative-electron-affinity (NEA) GaAs/GaP photocathodes have been grown by MBE for the first time. The surfaces of GaAs emitters are atomically smooth. The compositionally graded interface layer GaAsP produced by infer-diffusion at the GaAs/GaP interface has played an important role for a high photoemissive quantum yield and for the spectral response curves of photoemission from the thin GaAs layers.
A Novel Class of secA Alleles That Exert a Signal-Sequence-Dependent Effect on Protein Export in Escherichia coli (2002)

The murine plasminogen activator inhibitor 2 (PAI2) signal sequence inefficiently promotes the export of E. coli alkaline phosphatase (AP). High-level expression of PAI2::AP chimeric proteins from the arabinose P(BAD) promoter is toxic and confers an Ara(S) phenotype. Most Ara(R) suppressors map to secA, as determined by sequencing 21 independent alleles. Mutations occur throughout the gene, including both nucleotide binding domains (NBDI and NBDII) and the putative signal sequence binding domain (SSBD). Using malE and phoA signal sequence mutants, we showed that the vast majority of these secA suppressors exhibit weak Sec phenotypes. Eight of these secA mutations were further characterized in detail. Phenotypically, these eight suppressors can be divided into three groups, each localized to one domain of SecA. Most mutations allow near-normal levels of wild-type preprotein export, but they enhance the secretion defect conferred by signal sequence mutations. Interestingly, one group exerts a selective effect on the export of PAI2::AP when compared to that of AP. In conclusion, this novel class of secA mutations, selected as suppressors of a toxic signal sequence, differs from the classical secA (prlD) mutations, selected as suppressors of defective signal sequences, although both types of mutations affect signal sequence recognition.
Calculations of giant magnetoimpedance and of ferromagnetic resonance response are rigorously equivalent (1996)

It is simply demonstrated that the giant magnetoimpedance (GMI) response of a plate or ribbon is rigorously equivalent to the response of the same sample in ferromagnetic resonance (FMR) experiment. Thus, all of the solutions for FMR response behavior of metals may be applied to the description of GMI. For situations which have not been studied before, the methods which have been developed over the past 40 years for theoretical description of FMR in metals may be applied to predict the GMI behavior.
Interface structure and luminescence properties of epitaxial PbSe films on InAs(111)A (2021)

Epitaxial heterostructures of narrow-gap IV-VI and III-V semiconductors offer a platform for new electronics and mid-infrared photonics. Stark dissimilarities in the bonding and the crystal structure between the rocksalt IV–VIs and the zincblende III–Vs, however, mandate the development of nucleation and growth protocols to reliably prepare high-quality heterostructures. In this work, we demonstrate a route to single crystal (111)-oriented PbSe epitaxial films on nearly lattice-matched InAs (111)A templates. Without this technique, the high-energy heterovalent interface readily produces two populations of PbSe grains that are rotated 180° in-plane with respect to each other, separated by rotational twin boundaries. We find that a high-temperature surface treatment with the PbSe flux extinguishes one of these interfacial stackings, resulting in single-crystalline films with interfaces that are mediated by a monolayer of distorted PbSe. While very thin PbSe-on-InAs films do not emit light, hinting toward a type-III band alignment, we see strong room temperature photoluminescence from a 1.5 μm thick film with a minority carrier lifetime of 20 ns at low-excitation conditions and bimolecular recombination at high excitation conditions, respectively, even with threading dislocation densities exceeding 108 cm−2. We also note near-complete strain relaxation in these films despite large thermal expansion mismatch to the substrate, with dislocations gliding to relieve strain even at cryogenic temperatures. These results bring to light the exceptional properties of IV-VI semiconductors and the new IV-VI/III-V interfaces for a range of applications in optoelectronics.
Some challenges in making accurate and reproducible measurements of minority carrier lifetime in high-quality Si wafers (2014)

Measurement of the minority carrier lifetime (τ) of high-quality wafers (having bulk minority carrier lifetime, τ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> > few milliseconds) requires surface passivation with very low surface recombination velocity, typically <; 1cm/s. Furthermore, for mapping large (e.g., 156 x156 mm) wafers, the passivation must also be stable and uniform over the entire wafer surfaces. These are very demanding requirements and it is a common experience that they are very difficult to achieve. Yet, they are necessary for performing defect analyses of the current N-type wafers. To understand the problems associated with these measurements, we have studied effect of wafer preparation (cleaning procedures, handling) and the passivation characteristics (stability, sensitivity to light, thickness of the passivation medium required for stable passivation) for many commonly used passivation media-iodine-ethanol (IE), quinhydrone-methanol (QHM), aluminum oxide (Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ), amorphous-silicon (a-Si), and silicon dioxide (SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ). Here, we will discuss main factors that influence the accuracy and repeatability of lifetime measurements.
Assessing the quality and trustworthiness of citizen science data (2012)

SUMMARY The Internet, Web 2.0 and Social Networking technologies are enabling citizens to actively participate in ‘citizen science’ projects by contributing data to scientific programmes via the Web. However, the limited training, knowledge and expertise of contributors can lead to poor quality, misleading or even malicious data being submitted. Subsequently, the scientific community often perceive citizen science data as not worthy of being used in serious scientific research—which in turn, leads to poor retention rates for volunteers. In this paper, we describe a technological framework that combines data quality improvements and trust metrics to enhance the reliability of citizen science data. We describe how online social trust models can provide a simple and effective mechanism for measuring the trustworthiness of community‐generated data. We also describe filtering services that remove unreliable or untrusted data and enable scientists to confidently reuse citizen science data. The resulting software services are evaluated in the context of the CoralWatch project—a citizen science project that uses volunteers to collect comprehensive data on coral reef health. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Imidazole-modified deferasirox encapsulated polymeric micelles as pH-responsive iron-chelating nanocarrier for cancer chemotherapy (2017)

Modified deferasirox encapsulated polymeric micelles demonstrate pH-responsive and ON–OFF release behavior to deplete the iron level in cancer cells. The cellular iron deficiency is a novel strategy for cancer treatment.
Nonlinear control of transcription through enhancer–promoter interactions (2022)

Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)<sup>1-4</sup>. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.
A high resolution mirror-based digitally controlled optical beam shaper (2004)

A novel digitally controlled programmable optical beam shaper is proposed using a two-dimensional small tilt micromirror device. The optical intensity profile at any spatial positions can be independently modified by using the macropixel concept incorporated with the binary pulsewidth modulation.
Discovery of novel inducers of cellular differentiation using HL-60 promyelocytic cells. (2001)

Non-physiological inducers of terminal differentiation have been used as novel therapies for the prevention and therapy of cancer. We have used cultured HL-60 promyelocytic cells to monitor differentiation, proliferation and cell death events as induced by a large set of extracts derived from plants. Screening of more than 1400 extracts led to the discovery of 34 with potent activity (ED50 <8 mg/ml). Bioassay-guided fractionation led to the isolation of zapotin and 2',5,6-trimethoxyflavone as active principles from Casimiroa edulis, dibenzyltrisulfide and 2-[(phenylmethyl)dithio]ethanol as active principles from Petiveria alliacea, and desmethylrocaglamide from Aglaia ponapensis. Zapotin demonstrated the most favorable biological profile in that induction of differentiation correlated with proliferation arrest, and a lack of cytotoxicity. We conclude that the HL-60 cell model is a useful system for the discovery of novel pharmacophores with potential to suppress the process of carcinogenesis, and that flavonoids may be especially useful in this capacity.
Performance of genotypic tropism testing on proviral DNA in clinical practice: results from the DIVA study group. (2012)

There was high concordance in the genotypic tropism prediction based on proviral DNA among different virological centers throughout Italy. Our results are in line with other European studies, and support the use of genotypic tropism testing on proviral DNA in patients with suppressed plasma HIV-1 RNA candidate to CCR5-antagonist treatment.
Crystallization and crystallographic analysis of anArabidopsisnuclear proteinaceous RNase P (2015)

RNase P activity is ubiquitous and involves the 5' maturation of precursor tRNAs. For a long time, it was thought that all RNases P were ribonucleoproteic enzymes. However, the characterization of RNase P in human mitochondria and in plants revealed a novel kind of RNase P composed of protein only, called PRORP for `proteinaceous RNase P'. Whereas in human mitochondria PRORP has two partners that are required for RNase P activity, PRORP proteins are active as single-subunit enzymes in plants. Three paralogues of PRORP are found in Arabidopsis thaliana. PRORP1 is responsible for RNase P in mitochondria and chloroplasts, while PRORP2 and PRORP3 are nuclear enzymes. Here, the purification and crystallization of the Arabidopsis PRORP2 protein are reported. Optimization of the initial crystallization conditions led to crystals that diffracted to 3 Å resolution.
Adaptive filtering in the frequency domain (1978)

Adaptive filtering in the frequency domain can be accomplished by Fourier transformation of the input signal and independent weighting of the contents of each frequency bin. The frequency-domain filter performs similarly to a conventional adaptive transversal filter but promises a significant reduction in computation when the number of weights equals or exceeds 16.
WITHDRAWN: Impact of Gravitation on Identification of Gaseous Pollutant Source (2014)

The Publisher regrets that this article is an accidental duplication of an article that has already been published in CJA, 26/2 (2013) 261-268, http://dx.doi.org/10.1016/j.cja.2013.02.002. The duplicate article has therefore been withdrawn.
Use of the Chick Embryo for Pharmacological Screening of Retinoids (1988)

Retinoic acid and some selected analogs were tested to evaluate their effect on skin morphogenesis and toxicity in the chick embryo. Retinoids dissolved in dimethyl sulfoxide were injected at doses varying from 10 pmol to 10 mumol into the amniotic cavity of 10-day-old chick embryos (n = 20). At 16 days of incubation, the eggs were opened to record the number of dead embryos and the number of embryos presenting club-shaped feathers. A lethal embryotoxic dose (LED50d16) which, at 16 days of incubation, provokes the death of 50% of the embryos and an effective dose (ED50) which induces production of club-shaped feathers in 50% of surviving embryos were then calculated using log-probit analysis. Retinoids could be classified according to their ED50. For example, arotinoid Ro 13-7410 appears approximately 1,000 times more active than all transretinoic acid. However, the analogs which are more active are also more toxic. The assay described in the present study appears to be a simple and useful model for the screening of retinoids.
Sulfolipid in Arabidopsis thaliana (1999)

Das Sulfolipid Sulfoquinovosyldiacylglycerin wird in nahezu allen photosynthetischen sowie in einigen wenigen nichtphotosynthetischen Organismen gefunden. Bisher wurde die Biosynthese und Funktion dieses außergewöhnlichen Lipids hauptsächlich in Bakterien studiert. Im Rahmen dieser Arbeit wird die Modellpflanze Arabidopsis thaliana als Untersuchungsobjekt eingeführt. Ein Teil der Arbeit befaßt sich mit der Biosynthese von Sulfolipid, wobei vor allem die Reaktion, die zur Bildung der Sulfoquinovose-Kopfgruppe führt, untersucht wird. In einem molekularbiologisch/genetischen Ansatz wird das SQD1-Gen von Arabidopsis rekombinant exprimiert und aufgereinigt. Das Protein konnte mit Hilfe eines Homologiemodells charakterisiert und biochemisch untersucht werden. So wurde NAD+ als Cofaktor und UDP-Glucose als Substrat von SQD1 identifiziert. Mit der Kristallisation des SQD1-Proteins und der sich daraus ergebenden Kristallstruktur konnten die Ergebnisse des Homologiemodells und der biochemischen Charakterisierung bestätigt werden. Die Resultate wurden in einem Vorschlag für den SQD1-Reaktionsmechanismus zusammengefaßt. In dem zweiten Teil der Arbeit konnte ein Beitrag zum Verständnis der Regulation und der Funktion von Sulfolipid in Arabidopsis geleistet werden. Es konnte eine drastische Änderung der Lipidkomposition unter Phosphatmangel festgestellt werden, einhergehend mit einem deutlichen Anstieg auf SQD1 mRNA- und SQD1-Protein. Zur weiteren Untersuchung der Funktion von Sulfolipid wurde die pho1 Mutante herangezogen. Die physiologischen Untersuchungen dieser pho1 Mutante im Vergleich zum Wildtyp ergaben, daß sie trotz deutlich veränderter Lipidzusammensetzung keine Unterschiede in der Lichtanpassung aufweist. Diese Beobachtungen lassen einerseits darauf schließen, daß die Substitution eines Thylakoidlipides durch ein anderes Lipid eine weitverbreitete Strategie der Pflanze ist, um die Funktionsfähigkeit der photosynthetischen Membran zu gewährleisten. Andererseits wird gezeigt, daß offensichtlich ein gewisser Anteil anionischer Lipide für diese Funktionsfähigkeit nötig ist. Unter Phosphatmangel ist Sulfolipid der geeignete Substituent für das anionische Phospholipid Phosphatidylglycerin.