gebhart/patrepeval huggingface dataset:
An Old Yellow Enzyme Gene Controls the Branch Point between <i>Aspergillus fumigatus</i> and <i>Claviceps purpurea</i> Ergot Alkaloid Pathways (2010)

Ergot fungi in the genus Claviceps and several related fungal groups in the family Clavicipitaceae produce toxic ergot alkaloids. These fungi produce a variety of ergot alkaloids, including clavines as well as lysergic acid derivatives. Ergot alkaloids are also produced by the distantly related, opportunistic human pathogen Aspergillus fumigatus. However, this fungus produces festuclavine and fumigaclavines A, B, and C, which collectively differ from clavines of clavicipitaceous fungi in saturation of the last assembled of four rings in the ergoline ring structure. The two lineages are hypothesized to share early steps of the ergot alkaloid pathway before diverging at some point after the synthesis of the tricyclic intermediate chanoclavine-I. Disruption of easA, a gene predicted to encode a flavin-dependent oxidoreductase of the old yellow enzyme class, in A. fumigatus led to accumulation of chanoclavine-I and chanoclavine-I-aldehyde. Complementation of the A. fumigatus easA mutant with a wild-type allele from the same fungus restored the wild-type profile of ergot alkaloids. These data demonstrate that the product of A. fumigatus easA is required for incorporation of chanoclavine-I-aldehyde into more-complex ergot alkaloids, presumably by reducing the double bond conjugated to the aldehyde group, thus facilitating ring closure. Augmentation of the A. fumigatus easA mutant with a homologue of easA from Claviceps purpurea resulted in accumulation of ergot alkaloids typical of clavicipitaceous fungi (agroclavine, setoclavine, and its diastereoisomer isosetoclavine). These data indicate that functional differences in the easA-encoded old yellow enzymes of A. fumigatus and C. purpurea result in divergence of their respective ergot alkaloid pathways.
Measurement and interpolation uncertainties in rainfall maps from cellular communication networks (2015)

Abstract. Accurate measurements of rainfall are important in many hydrological and meteorological applications, for instance, flash-flood early-warning systems, hydraulic structures design, irrigation, weather forecasting, and climate modelling. Whenever possible, link networks measure and store the received power of the electromagnetic signal at regular intervals. The decrease in power can be converted to rainfall intensity, and is largely due to the attenuation by raindrops along the link paths. Such an alternative technique fulfils the continuous effort to obtain measurements of rainfall in time and space at higher resolutions, especially in places where traditional rain gauge networks are scarce or poorly maintained. Rainfall maps from microwave link networks have recently been introduced at country-wide scales. Despite their potential in rainfall estimation at high spatiotemporal resolutions, the uncertainties present in rainfall maps from link networks are not yet fully comprehended. The aim of this work is to identify and quantify the sources of uncertainty present in interpolated rainfall maps from link rainfall depths. In order to disentangle these sources of uncertainty, we classified them into two categories: (1) those associated with the individual microwave link measurements, i.e. the errors involved in link rainfall retrievals, such as wet antenna attenuation, sampling interval of measurements, wet/dry period classification, dry weather baseline attenuation, quantization of the received power, drop size distribution (DSD), and multi-path propagation; and (2) those associated with mapping, i.e. the combined effect of the interpolation methodology and the spatial density of link measurements. We computed ~ 3500 rainfall maps from real and simulated link rainfall depths for 12 days for the land surface of the Netherlands. Simulated link rainfall depths refer to path-averaged rainfall depths obtained from radar data. The ~ 3500 real and simulated rainfall maps were compared against quality-controlled gauge-adjusted radar rainfall fields (assumed to be the ground truth). Thus, we were able to not only identify and quantify the sources of uncertainty in such rainfall maps, but also test the actual and optimal performance of one commercial microwave network from one of the cellular providers in the Netherlands. Errors in microwave link measurements were found to be the source that contributes most to the overall uncertainty.
Early classification of multivariate temporal observations by extraction of interpretable shapelets (2012)

Early classification of time series is beneficial for biomedical informatics problems such including, but not limited to, disease change detection. Early classification can be of tremendous help by identifying the onset of a disease before it has time to fully take hold. In addition, extracting patterns from the original time series helps domain experts to gain insights into the classification results. This problem has been studied recently using time series segments called shapelets. In this paper, we present a method, which we call Multivariate Shapelets Detection (MSD), that allows for early and patient-specific classification of multivariate time series. The method extracts time series patterns, called multivariate shapelets, from all dimensions of the time series that distinctly manifest the target class locally. The time series were classified by searching for the earliest closest patterns. The proposed early classification method for multivariate time series has been evaluated on eight gene expression datasets from viral infection and drug response studies in humans. In our experiments, the MSD method outperformed the baseline methods, achieving highly accurate classification by using as little as 40%-64% of the time series. The obtained results provide evidence that using conventional classification methods on short time series is not as accurate as using the proposed methods specialized for early classification. For the early classification task, we proposed a method called Multivariate Shapelets Detection (MSD), which extracts patterns from all dimensions of the time series. We showed that the MSD method can classify the time series early by using as little as 40%-64% of the time series’ length.
Colibactin: understanding an elusive gut bacterial genotoxin (2015)

This highlight provides an overview of recent progress towards elucidating the structure, biosynthesis, and mode of action of colibactin, a genotoxic secondary metabolite synthesized by human gut bacteria. While isolating colibactin has been problematic, efforts to characterize its biosynthesis have provided critical information that has led to a rapid increase in our knowledge of this metabolite's structure and function. Major questions and gaps remain however, and the broader lessons learned from studying colibactin underscore central challenges to be faced in the genomics era of natural product research and in efforts to understand the human microbiome.
Genetics of Growth Habit and Development of New Coleus (Solenostemon scutellarioides (L.) Codd) Varieties with Trailing Habit and Bright Color (2008)

A high level of genetic variability for growth habit types is observed in tetraploid, cultivated coleus (Solenostemon scutellarioides (L.) Codd). Very few cultivars with trailing habit exist, and those that are available generally have dark green or purple foliage color. Coleus with trailing growth habit is desirable as it increases its utility for use in hanging baskets, mixed containers, and as ground cover. There is a lack of published information on the genetic mechanism controlling growth habit and the development of new trailing types with orange colors. Two commercial cultivars, "Red Trailing Queen" (RQ) with trailing habit and "Sedona" (S) with upright stature, were selfed and crossed (RQ x S) to produce self and F(1) populations. F(2) populations were produced by selfing plants in the F(1) population. For each population analyzed, growth habit was rated on a visual 1-5 phenotypic scale, where 1 = upright, 2 = semi-upright, 3 = prostrate, 4 = semitrailing, and 5 = trailing. Genotypes were assigned to each phenotype, assuming that upright was dominant to trailing. In this study, growth habit was observed to be controlled by a single gene (U) with additive effects, with upright growth habit designated with a UUUU genotype and trailing growth habit designated with a uuuu genotype. In addition, foliage color was rated on a visual 1-5 phenotypic scale, and purple foliage color was found to be dominant to yellow-orange color. Several new coleus selections with trailing growth habit and orange foliage color were successfully developed.
Performance measurement for improved working-capital management (2002)

A new strain of chickens (mPNU) that segregates a severely deleted rDNA cluster was studied. Individuals heterozygous (+/p<sup>2</sup> ) and homozygous (p<sup>2</sup> /p<sup>2</sup> ) for the deletion were found to have 56 and 27%, respectively, of the normal complement of rRNA genes (290 copies/cell). Morphogenesis, cellular rRNA levels, and nucleolar sizes, were investigated and compared in normal +/+, +/p<sup>2</sup> , and p<sup>2</sup> /p<sup>2</sup> embryos. Cellular rRNA contents were similar among the three genotypes at stage X, but subsequently during gastrulation, p<sup>2</sup> /p<sup>2</sup> levels were reduced to 56% and eventually to 43% of +/+. Viability and morphogenesis were normal in p<sup>2</sup> /p<sup>2</sup> embryos until the initial primitive streak stage of gastrulation. However, further development was abnormal and characterized by disrupted axis formation. In +/+ and +/p<sup>2</sup> embryos, rRNA levels and nucleolar sizes increased during early development; however, the profile of these increases differed temporally and quantitatively between the genotypes. The +/p<sup>2</sup> embryos, at the full streak stage of gastrulation, exhibited reduced rRNA levels and nucleolar sizes (80% of +/+), yet the +/p<sup>2</sup> embryos developed normally. These studies establish a minimum copy number requirement lower than previously demonstrated, that is, a rDNA genotype with only 56% of the normal gene complement (∼160 genes) is compatible with early embryonic viability. Also, a rRNA threshold was detected: rRNA levels that were 56% of +/+ failed to support normal gastrulation; however, even under the circumstance of reduced rRNA levels (43% of control), some aspects of gastrulation apparently continue (cell migration and invagination). The teratogenic development of p<sup>2</sup> /p<sup>2</sup> embryos is a biological consequence unique from that found in other metazoan models of rDNA-deficiency, and will be useful as a model to investigate mechanisms of vertebrate gastrulation and axis formation.
Messaging capabilities of V2I networks (2018)

Modern Intelligent Transport Systems' (ITS) are based on data acquisition and exchange of information between different devices (fixed or mobile). The communication requirements are very severe due to a multitude of signal propagation issues that may occur: interferences, reflection, refraction, diffraction, Doppler frequency shifts and so on. Therefore, it results that the messaging capability of wireless vehicular networks is limited. On the other hand, increased number of information sources (based also on the fast development of Internet of Things (IoT) solutions) arise new challenges for information collection, processing and distribution. Another aspect that must be considered is data security, especially for vehicular cooperative safety applications. This adds up several bits/bytes to the message hence diminishing useful information that may be transmitted. From these we may conclude that is critical to analyze and develop proper communication solutions for vehicular, both for critical and non-critical applications. Considering this, the present paper aims to investigate specific, non-critical ITS applications that are the most suitable for different short-range communications technologies, with an emphasis on the Bluetooth and ZigBee applicability in vehicular communications of V2I type.
Immunogenicity, Safety, and Tolerability of Bivalent rLP2086 Meningococcal Group B Vaccine Administered Concomitantly With Diphtheria, Tetanus, and Acellular Pertussis and Inactivated Poliomyelitis Vaccines to Healthy Adolescents (2016)

Immune responses to DTaP/IPV administered with bivalent rLP2086 to adolescents were noninferior to DTaP/IPV administered alone. Bivalent rLP2086 was well tolerated and elicited substantial and broad bactericidal responses to diverse MnB strains in a high proportion of recipients after 2 vaccinations, and these responses were further enhanced after 3 vaccinations.ClinicalTrials.gov identifier NCT01323270.
Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells (2018)

Poor prognoses remain the most challenging aspect of hepatocellular carcinoma (HCC) therapy. Consequently, alternative therapeutics are essential to control HCC. This study investigated the anticancer effects of safranal against HCC using in vitro, in silico, and network analyses. Cell cycle and immunoblot analyses of key regulators of cell cycle, DNA damage repair and apoptosis demonstrated unique safranal-mediated cell cycle arrest at G2/M phase at 6 and 12 h, and at S-phase at 24 h, and a pronounced effect on DNA damage machinery. Safranal also showed pro-apoptotic effect through activation of both intrinsic and extrinsic initiator caspases; indicating ER stress-mediated apoptosis. Gene set enrichment analysis provided consistent findings where UPR is among the top terms of up-regulated genes in response to safranal treatment. Thus, proteins involved in ER stress were regulated through safranal treatment to induce UPR in HepG2 cells.
Multiphoton Intrapulse Interference 3:  Probing Microscopic Chemical Environments (2003)

Phase modulation, through its influence on the probability of two-photon excitation at specific frequencies, is used to probe a molecule's microscopic chemical environment. The spectral phase required is designed according to the principles of multiphoton intrapulse interference. We show experimental results where phase modulation of 20 fs pulses from a titanium sapphire laser oscillator controls the intensity of two-photon induced fluorescence from the pH-sensitive dye 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) in solution. We show that the dependence of fluorescence yield on the phase can be utilized as a means of distinguishing molecules in different environments. Consequently, this method can be used to achieve selective multiphoton microscopy. To illustrate this capability, we show images where phase modulation was used to selectively excite HPTS in acidic or basic microscopic regions.
Overlap subtype of chronic graft-versus-host disease is associated with an adverse prognosis, functional impairment, and inferior patient-reported outcomes: a Chronic Graft-versus-Host Disease Consortium study (2011)

These findings suggest that the presence of acute features in patients with chronic graft-versus-host disease is a marker of adverse prognosis, greater functional impairment, and higher symptom burden.
Silylated Melamine and Cyanuric Acid as Precursors for Imprinted and Hybrid Silica Materials with Molecular Recognition Properties (2009)

Two monotrialkoxysilylated compounds that consist of complementary fragments of melamine (M) and cyanuric acid (CA) have been synthesised. The molecular recognition properties of the M and CA fragments through complementary hydrogen bonds (DAD and ADA; D=donor, A=acceptor) are the key factor used to direct the formation of hybrid silica materials by using a sol-gel process. These materials were synthesised following two methods: First, an organo-bridged silsesquioxane was obtained by the hydrolysis of the two complementary monotrialkoxysilylated melamine and cyanuric acid derivatives, with fluoride ions as a catalyst. The hydrogen-bonding interactions between the two organic fragments are responsible for the formation of the bridging unit. The transcription of the assembly into the hybrid material was characterised and evidenced by solid-state NMR (29Si, 13C) and FTIR spectroscopic experiments. Second, the molecular recognition was exploited to synthesise an imprinted hybrid silica. This material was prepared by co-condensation of tetraethyl orthosilicate (TEOS) with the monosilylated cyanuric acid derivative (CA) templated by nonsilylated melamine. The melamine template was completely removed by treating the solid material with hydrochloric acid. The reintroduction of the template was performed by treating the resulting material with an aqueous suspension of melamine. These steps were monitored and analysed by several techniques, such as solid-state NMR (29Si, 13C) and FTIR spectroscopic analysis and nitrogen adsorption-desorption isotherms.
Differential Time-Series CCD Photometry of BL Camelopardalis (1999)

Differential time-series observations of BL Camelopardalis classified as a double mode SX Phoenicis type variable were secured with a charge coupled device. The observed photometric data was reduced using the IRAF Package and the differential magnitudes were obtained through aperture photometry. The periods of BL Cam were analyzed with the Generalized Least-Square Method by Vanicek (1971) and the Fourier Decomposition Method. It was found that the first and second period of BL Cam were 0.0391 day and 0.0317 day respectively which lead the period ratio of P1/P0 = 0.81. This period ratio is much different from 0.78 determined by other investigators and also much more larger than that of other double-mode SX Phe type variables. In addition, this period ratio is much different from the value expected from the relation between the metallicity and period ratio. From these results, it can be confirmed that BL Cam is the most extreme case among all double-mode SX Phe type variables.
Using Convolutional Networks and Satellite Imagery to Identify Patterns in Urban Environments at a Large Scale (2017)

Urban planning applications (energy audits, investment, etc.) require an understanding of built infrastructure and its environment, i.e., both low-level, physical features (amount of vegetation, building area and geometry etc.), as well as higher-level concepts such as land use classes (which encode expert understanding of socio-economic end uses). This kind of data is expensive and labor-intensive to obtain, which limits its availability (particularly in developing countries). We analyze patterns in land use in urban neighborhoods using large-scale satellite imagery data (which is available worldwide from third-party providers) and state-of-the-art computer vision techniques based on deep convolutional neural networks. For supervision, given the limited availability of standard benchmarks for remote-sensing data, we obtain ground truth land use class labels carefully sampled from open-source surveys, in particular the Urban Atlas land classification dataset of $20$ land use classes across $~300$ European cities. We use this data to train and compare deep architectures which have recently shown good performance on standard computer vision tasks (image classification and segmentation), including on geospatial data. Furthermore, we show that the deep representations extracted from satellite imagery of urban environments can be used to compare neighborhoods across several cities. We make our dataset available for other machine learning researchers to use for remote-sensing applications.
Autoxidation of Ferrous Ion Complexes: A Method for the Generation of Hydroxyl Radicals (1998)

The kinetics of the production of hydroxyl radicals during the autoxidation of ferrous ion complexes at pH 7.4 was investigated using the fluorescent probe coumarin-3-carboxylic acid. Polyphosphates (tri- and tetrapolyphosphate and their adenosine derivatives), citrate, and acetic derivatives of ethyleneamine ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTPA), triethylenetetraminehexaacetic acid (TTHA), ethylenediamine-(N,N')-diacetic acid (EDDA) and nitrilotriacetic acid (NTA) were used as iron chelators. Production of hydroxyl radical in these chemical systems was compared with that by radiation to determine the equivalent doses of radiation that produced equal amounts of .OH. The amount of .OH formed during ferrous ion autoxidation is determined by the concentration of the complex, its structure and the radical scavenging by the chelator molecule. Production of .OH for homologous ethylenamine acetates increases with increased complex stability: NTA < EDDA < TTHA < EDTA < DTPA. The radiation dose equivalence for 0.1 mM complexes increased from 5 Gy for NTA to 25 Gy for DTPA. The radiation dose equivalence for polyphosphates was 15 Gy for tripolyphosphate and 32 Gy for tetrapolyphosphate. The dose equivalences for adenosine phosphates are lower, 5 Gy for ATP and 10 Gy for adenosine tetraphosphate, due to intramolecular .OH scavenging. The rate of generation of .OH shows an inverse correlation with the charge of the ferrous ion complex, varying from 2 cGy/s for DTPA to 1.2 Gy/s for EDTA. The data presented indicate the usefulness of autoxidation of ferrous ion complexes for generation of .OH in chemical systems. The ability to control the amount and the rate of production of .OH may prove useful for examining the cytotoxic effects of .OH generated in biological systems.
Nuclear magnetic resonance studies of domain growth in the late stage of phase separation of a binary liquid mixture (1995)

The domain growth processes occurring during the gravity-dominated regime of the phase separation of a cyclohexane/aniline critical mixture, following a temperature quench in the unstable region below the temperature-composition coexistence curve, were investigated with high-resolution 1H NMR. Diffusive exchange of cyclohexane molecules between a small volume fraction of immiscible droplets and the surrounding fluid with a different cyclohexane concentration leads to a domain-size dependent 1H NMR cyclohexane chemical shift in the continuous phase. In this case, the equations of motion for the transverse magnetization density reduce to a first-order exchange between two immiscible phases with rate coefficients depending on the droplet size and the transport process across the liquid–liquid interface. Application of this model to the data yields a power law for the growing droplets, R(t)=Atφ, where R is a typical domain size, with the growth exponent φ=0.30±0.01 and the amplitude A≂0.9×10−6 ms−φ. These values are in close agreement with previous visualization studies on the same binary mixture [F. Cau and S. Lacelle, Phys. Rev. E 47, 1429 (1993)]. The results also confirm the presence of a new domain growth regime involving Brownian coagulation and sedimentation in the very late stage of the phase separation processes of binary liquid mixtures. A strong linear composition dependence of the 1H NMR cyclohexane chemical shift in one-phase cyclohexane/aniline mixtures was interpreted on the basis of solvent shift effects induced by intermolecular interactions and susceptibility effects. In each phase of the two-phase equilibrium mixture, inhomogeneous line broadening, arising from the magnetic susceptibility discontinuity at the interface between phases, is also investigated.