gebhart/patrepeval huggingface dataset:
Generation and characterisation of stable ethanol-tolerant mutants of Saccharomyces cerevisiae (2009)

Saccharomyces spp. are widely used for ethanologenic fermentations, however yeast metabolic rate and viability decrease as ethanol accumulates during fermentation, compromising ethanol yield. Improving ethanol tolerance in yeast should, therefore, reduce the impact of ethanol toxicity on fermentation performance. The purpose of the current work was to generate and characterise ethanol-tolerant yeast mutants by subjecting mutagenised and non-mutagenised populations of Saccharomyces cerevisiae W303-1A to adaptive evolution using ethanol stress as a selection pressure. Mutants CM1 (chemically mutagenised) and SM1 (spontaneous) had increased acclimation and growth rates when cultivated in sub-lethal ethanol concentrations, and their survivability in lethal ethanol concentrations was considerably improved compared with the parent strain. The mutants utilised glucose at a higher rate than the parent in the presence of ethanol and an initial glucose concentration of 20 g l(-1). At a glucose concentration of 100 g l(-1), SM1 had the highest glucose utilisation rate in the presence or absence of ethanol. The mutants produced substantially more glycerol than the parent and, although acetate was only detectable in ethanol-stressed cultures, both mutants produced more acetate than the parent. It is suggested that the increased ethanol tolerance of the mutants is due to their elevated glycerol production rates and the potential of this to increase the ratio of oxidised and reduced forms of nicotinamide adenine dinucleotide (NAD(+)/NADH) in an ethanol-compromised cell, stimulating glycolytic activity.
Distance Distortion: A Comparison of Real World and Computer Animated Environments (2002)

The overall goal of this study was to examine the effectiveness of computer animated spaces within the context of design professions, with particular attention to potential distortions of perceived distance that such animations might produce. Three questions were addressed: 1| Do observers accurately perceive the magnitude of distance represented in animated displays? 2) Does the manner in which animated space is divided affect the magnitudes of the distances perceived? 3) Are there differences between male and female observers in such accuracy? Participants were 61 undergraduate psychology students at Washington State University. Computer animations provided participants seven “virtual walks” through computer generated corridors, some of which were divided into segments by open portals or doors. Following each virtual walk, participants were led to a nearby corridor and asked to walk a distance they perceived to be equal to the virtual walk they had just experienced at the computer. Analysis of variance, with a posteriori Fisher LSD tests, showed that computer represented distances were consistently underestimated by both males and females, with females underestimating the distances to a significantly greater degree than males. The presence or number of segments present in the animated spaces had no significant effect on distance estimates. These findings suggest that there may be important limitations in the extent to which computer animations represent distance for observers of both sexes, and that these limitations may be even more pronounced for females than for males. The manner in which the virtual spaces were segmented did not exert a consistent influence on the perception of distance; however, the manner in which virtual spaces are divided and the kind of visual features that are used to indicate such divisions merits further study.
Robust Diffusion-Weighted Imaging with Deep Learning-Based DW PROPELLER Reconstruction (2023)

Compared to DW-EPI, DW PROPELLER is less sensitive to susceptibility, chemical shift, and motion, and thus shows better image quality in areas, such as skull base, head-neck and pelvis. However, the SNR and in-plane resolution of DW PROPELLER images are often inferior to DW-EPI and often requires a longer scan time to compensate for this. In this work, we evaluated a deep-learning reconstruction method to improve the SNR of in-plane resolution of DW PROPELLER images without increasing acquisition time.
Porcine innate and adaptative immune responses to influenza and coronavirus infections (2005)

International audience
Fiber-coupled microsphere laser (2000)

We demonstrate a 1.5‐µm-wavelength fiber laser formed by placement of glass microsphere resonators along a fiber taper. The fiber taper serves the dual purpose of transporting optical pump power into the spheres and extracting the resulting laser emission. A highly doped erbium:ytterbium phosphate glass was used to form microsphere resonant cavities with large gain at 1.5 µm. Laser threshold pump powers of 60 µW and fiber-coupled output powers as high as 3 µW with single-mode operation were obtained. A bisphere laser system consisting of two microspheres attached to a single fiber taper is also demonstrated.
Wild food plants and wild edible fungi of Heihe valley (Qinling Mountains, Shaanxi, central China): herbophilia and indifference to fruits and mushrooms (2012)

&lt;p&gt;The aim of the study was to investigate knowledge and use of wild food plants and fungi in Han (i.e. Chinese) nationality villages in central China, including famine plants used in the respondents' childhood. A valley adjacent to the extremely species-rich temperate forest vegetation of the Taibai Nature Reserve was chosen. Eighty-two people from 5 villages took part in the study. Altogether, 159 wild food plant species and 13 fungi folk taxa were mentioned by informants. The mean number of freelisted wild foods was very high (24.8; median – 21.5). An average respondent listed many species of wild vegetables (mean – 17, me- dian – 14.5), a few wild fruits (mean – 5.9 and median – 6) and very few fungi (mean – 1.9, median – 1), which they had eaten.&lt;/p&gt; &lt;p&gt;Over 50% of respondents mentioned gathering the young shoots or leaves of &lt;em&gt;Celastrus orbiculatus&lt;/em&gt;, &lt;em&gt;Staphylea bumalda &lt;/em&gt;and &lt;em&gt;S. holocapra&lt;/em&gt;, &lt;em&gt;Caryopteris divaricata&lt;/em&gt;, &lt;em&gt;Helwingia japonica&lt;/em&gt;, &lt;em&gt;P&lt;/em&gt;&lt;em&gt;teridium aquilinum&lt;/em&gt;, &lt;em&gt;Pimpinella &lt;/em&gt;sp., &lt;em&gt;Amaranthus &lt;/em&gt;spp., &lt;em&gt;Matteucia struthiopteris&lt;/em&gt;, &lt;em&gt;Allium &lt;/em&gt;spp., &lt;em&gt;Cardamine macrophylla &lt;/em&gt;and &lt;em&gt;Chenopodium album&lt;/em&gt;. Only one species of fruits (&lt;em&gt;Schisandra sphenanthera&lt;/em&gt;) and none of the mushrooms were mentioned by over half of the respondents. Although very diverse, it can be noted that the use of wild vegetables has decreased compared to the second half of the 20th century, as informants listed several plants which they had stopped using (e.g. &lt;em&gt;Abelia engleriana&lt;/em&gt;) due to the availability of cultivated vegetables and other foodstuffs. On the other hand, the collection of the most well-known wild vegetables is maintained by selling them to tourists visiting agritourist farms, and restaurants.&lt;/p&gt;
Indistinguishable near-infrared single photons from an individual organic molecule (2010)

By using the zero-phonon line emission of an individual organic molecule, we realized a source of indistinguishable single photons in the near infrared. A Hong-Ou-Mandel interference experiment is performed and a two-photon coalescence probability higher than $50%$ at 2 K is obtained. The contribution of the temperature-dependent dephasing processes to the two-photon interference contrast is studied. We show that the molecule delivers nearly ideal indistinguishable single photons at the lowest temperatures when the dephasing is nearly lifetime limited. This source is used to generate postselected polarization-entangled photon pairs as a test bench for applications in quantum information.
Flavouring agents in pharmaceutical formulations. (1988)

This paper deals with the various aspects of commonly used flavouring agents for the preparation of medicaments.
Androgen Receptor Function in Prostate Cancer Progression (2007)

Despite initially encouraging response to hormone therapy, prostate tumors finally develop a resistant phenotype and progress to a life-threatening disease. Critically involved in the mechanisms of therapy resistance and tumor progression is the androgen receptor, the central mediator of the proliferation and survival effects of androgens, and the target of endocrine therapy. There is mounting evidence that alteration of androgen signaling and function enables tumor cells to survive and adapt to hormone deprivation, resulting in autonomous activation of growth-promoting downstream targets. Changes include increased expression, gain of function mutations, activation of ligand-independent stimulation mechanisms, and altered expression of and interaction with co-modulatory proteins. A profound understanding of the pivotal changes underlying prostate cancer progression will be the key to the development of more efficient hormone therapy and novel treatment strategies for prostate cancer patients.
Synthesis of β-Amino Diaryldienones Using the Mannich Reaction (2019)

The Mannich reaction has been used for decades to prepare many pharmaceutically important molecules. Here, using a "double-Mannich-β-elimination" synthetic sequence, we report the synthesis and the characterization details of a novel class of β-amino diaryldienones with prominent antiprostate cancer activity. Through these studies, we correct an erroneous structure in the current literature, present a discussion of the stereochemical outcome of a new reaction, and probe the mechanism(s) of byproduct formation through isotopic studies.
Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease (2019)

Transposable Elements (TEs) are mobile genetic elements whose sequences constitute nearly half of the human genome. Each TE copy can be present in hundreds to thousands of locations within the genome, complicating the genetic and genomic studies of these highly repetitive sequences. The recent development of better tools for evaluating TE derived sequences in genomic studies has enabled an increasing appreciation for the contribution of TEs to human development and disease. While some TEs have contributed novel and beneficial host functions, this review will summarize the evidence for detrimental TE activity in neurodegenerative disorders. Much of the evidence for pathogenicity implicates endogenous retroviruses (ERVs), a subset of TEs that entered the genome by retroviral infections of germline cells in our evolutionary ancestors and have since been passed down as a substantial fraction of the human genome. Human specific ERVs (HERVs) represent some of the youngest ERVs in the genome, and thus are presumed to retain greater function and resultant pathogenic potential.
Surface ligands engineering of semiconductor quantum dots for chemosensory and biological applications (2017)

Featuring size-tunable electrical and optical properties, semiconductor quantum dots (QDs) are appealing intensive interests in developing ingenious luminescent materials for chemosensory and biological applications. The surface modification of QDs with functional ligands not only fine-tunes the physiochemical properties and fluorescence emission behaviors, but also induces the designated interplay between analytes and probes for special determination. In this review, the fundamental principles guiding the rational design of high-efficiency luminescent sensors with surface engineering are overviewed. The state-of-the-art applications of QDs-based probes are highlighted for the sensing of molecular substrates and ionic species as well as various biological applications, with the inherent recognition mechanisms elaborated for representative cases. The challenge and future research direction in this emerging and promising research field are also discussed.
Identification of DEAD-box RNA Helicase 6 (DDX6) as a Cellular Modulator of Vascular Endothelial Growth Factor Expression under Hypoxia* (2013)

Vascular endothelial growth factor A (VEGF) is a crucial proangiogenic factor, which regulates blood vessel supply under physiologic and pathologic conditions. The VEGF mRNA 5'-untranslated region (5'-UTR) bears internal ribosome entry sites (IRES), which confer sustained VEGF mRNA translation under hypoxia when 5'-cap-dependent mRNA translation is inhibited. VEGF IRES-mediated initiation of translation requires the modulated interaction of trans-acting factors. To identify trans-acting factors that control VEGF mRNA translation under hypoxic conditions we established an in vitro translation system based on human adenocarcinoma cells (MCF-7). Cytoplasmic extracts of MCF-7 cells grown under hypoxia (1% oxygen) recapitulate VEGF IRES-mediated reporter mRNA translation. Employing the VEGF mRNA 5'-UTR and 3'-UTR in an RNA affinity approach we isolated interacting proteins from translational active MCF-7 extract prepared from cells grown under normoxia or hypoxia. Interestingly, mass spectrometry analysis identified the DEAD-box RNA helicase 6 (DDX6) that interacts with the VEGF mRNA 5'-UTR. Recombinant DDX6 inhibits VEGF IRES-mediated translation in normoxic MCF-7 extract. Under hypoxia the level of DDX6 declines, and its interaction with VEGF mRNA is diminished in vivo. Depletion of DDX6 by RNAi further promotes VEGF expression in MCF-7 cells. Increased secretion of VEGF from DDX6 knockdown cells positively affects vascular tube formation of human umbilical vein endothelial cells (HUVEC) in vitro. Our results indicate that the decrease of DDX6 under hypoxia contributes to the activation of VEGF expression and promotes its proangiogenic function.
N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae (2020)

Extreme overproduction of gratuitous proteins can overload cellular protein production resources, leading to growth defects, a phenomenon known as the protein burden/cost effect. Genetic screening in the budding yeast Saccharomyces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect, but individual characterization thereof has yet to be delineated. We found that deletion of the YJL175W ORF yielded an N-terminal deletion of Swi3, a subunit of the SWI/SNF chromatin remodeling complex, and partial loss of function of Swi3. The deletion mutant showed a reduction in transcription of genes encoding highly expressed, secreted proteins and an overall reduction in translation. Mutations in the chromatin remodeling complex could thus mitigate the protein burden effect, likely by reallocating residual cellular resources used to overproduce proteins. This cellular state might also be related to cancer cells, as they frequently harbor mutations in the SWI/SNF complex.
GaInAsP/InP waveguide dual core spot size converter for optical fiber (2011)

A dual core spot size converter was developed for reducing a coupling loss between an optical fiber and a III-V compound semiconductor optical waveguide. It can be fabricated without a crystal regrowth process.
1438-P: Diabetes after Cardiac Transplant with Low-Dose Everolimus and Tacrolimus (2023)

Background: Although modern immunosuppressants improve survival post-transplant, they are associated with long-term metabolic complications, such as post-transplant diabetes mellitus (PTDM). Calcineurin inhibitor-sparing regimens using everolimus attenuate some complications such as left ventricular hypertrophy. However, the metabolic effects of everolimus following transplant are less clear. Aims: To compare incidence of diabetes in heart transplant recipients exposed to low-dose everolimus and tacrolimus versus standard-dose tacrolimus. Methods: Post-hoc analysis in participants of a randomised open-label clinical trial of low-dose everolimus and tacrolimus versus standard-dose tacrolimus in heart transplant recipients. Results: There were 39 participants in the trial, mean follow up was 6.4 ± 1.5 years. There was a high rate of pre-existing diabetes (26%) and newly-diagnosed PTDM (36%) during follow-up (Figure 1). Half the patients who developed PTDM in the everolimus-tacrolimus group (n=4/8) ceased diabetes medications during follow-up, which was not observed in patients on standard tacrolimus (n=0/6). Conclusion: This study suggests that treatment with everolimus may improve PTDM outcomes relative to treatment with standard doses of calcineurin inhibitor. These findings should be further studied in prospective randomised trials. Disclosure L.M.Raven: None. C.A.Muir: None. J.Pouliopoulos: None. P.S.Macdonald: Advisory Panel; AstraZeneca, Boehringer Ingelheim Inc., Other Relationship; Novartis. A.Jabbour: None. J.Greenfield: None.
Effect of UV irradiation on stabilization of collagen (2011)

Collagen is the main protein of connective tissue. It has great tensile strength, and is the main component of ligaments and tendons. It is responsible for skin elasticity, and its degradation leads to wrinkles that accompany aging. Sunlight has a profound effect on the skin causing premature skin aging, skin cancer, and a host of skin changes. Exposure to ultraviolet light, UVA or UVB, from sunlight accounts for 90% of the symptoms of premature skin aging. In this paper, effect of UV irradiation on collagen stabilization was investigated. UV irradiation will promote speed of collagen fibrillogenesis and lead to lower fibril organization level. Electrophoresis analysis and circular dichroism measurement was performed to study the relationship between collagen structure changes and UV irradiation time. At last, FTIR spectroscopy was used to investigate the main absorption bands of collagen and given the detail structure changes of collagen during UV irradiation.
Functional and Structural Imaging of Retinal Tissue with Spatio-Temporal Optical Coherence Tomography (STOC-T) (2022)

We report on a novel human retina imaging system based on Spatio-Temporal Optical Coherence Tomography (STOC-T). We present structural images and spatially-resolve functional responses of the retinal tissue to white light stimulation.
Effect of lactic acid bacteria probiotic culture treatment timing onSalmonella Enteritidis in neonatal broilers (2010)

In the present study, a series of experiments were conducted to evaluate the ability of a combination of 3 ATCC lactobacilli (LAB3) or a commercially available probiotic culture (PROB) to reduce Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) in broiler chicks. Additionally, we varied the timing of PROB administration in relationship to Salmonella challenge and determined the influence on recovery of enteric Salmonella. In experiments 1 to 3, chicks were randomly assigned to treatment groups and were then challenged via oral gavage with Salmonella Enteritidis. Chicks were treated 1 h after Salmonella Enteritidis challenge with LAB3 or PROB. Twenty-four hours posttreatment, cecal tonsils were collected for recovery of enteric Salmonella. In experiments 4 to 7, day-of-hatch chicks were randomly assigned to treatment groups and were then treated with PROB via oral gavage and placed into pens. Chicks were challenged with Salmonella Enteritidis 24 h after treatment via oral gavage. At 24 h after Salmonella Enteritidis challenge, cecal tonsils were collected and recovery of enteric Salmonella was determined. In experiments 8 to 10, 1-d-old chicks were randomly assigned to treatment groups and were then challenged via oral gavage with Salmonella Enteritidis and placed into pens. Chicks were treated 24 h after challenge with PROB via oral gavage. Twenty-four hours post PROB treatment, cecal tonsils were collected and enriched as described above. It was found that PROB significantly reduced cecal Salmonella Enteritidis recovery 24 h after treatment as compared with controls or LAB3-treated chicks in experiments 1 to 3 (P<0.05). Administration of PROB 24 h before Salmonella Enteritidis challenge significantly reduced recovery of Salmonella Enteritidis in 2 out of 4 experiments and no reduction in cecal Salmonella Enteritidis was observed when chicks were challenged with Salmonella Enteritidis and treated 24 h later with PROB. These data demonstrate that PROB more effectively reduced Salmonella Enteritidis than LAB3, and the timing of PROB treatment affects Salmonella Enteritidis-associated reductions.
Modification of Brain Aging and Neurodegenerative Disorders by Genes, Diet, and Behavior (2002)

Multiple molecular, cellular, structural, and functional changes occur in the brain during aging. Neural cells may respond to these changes adaptively, or they may succumb to neurodegenerative cascades that result in disorders such as Alzheimer's and Parkinson's diseases. Multiple mechanisms are employed to maintain the integrity of nerve cell circuits and to facilitate responses to environmental demands and promote recovery of function after injury. The mechanisms include production of neurotrophic factors and cytokines, expression of various cell survival-promoting proteins (e.g., protein chaperones, antioxidant enzymes, Bcl-2 and inhibitor of apoptosis proteins), preservation of genomic integrity by telomerase and DNA repair proteins, and mobilization of neural stem cells to replace damaged neurons and glia. The aging process challenges such neuroprotective and neurorestorative mechanisms. Genetic and environmental factors superimposed upon the aging process can determine whether brain aging is successful or unsuccessful. Mutations in genes that cause inherited forms of Alzheimer's disease (amyloid precursor protein and presenilins), Parkinson's disease (alpha-synuclein and Parkin), and trinucleotide repeat disorders (huntingtin, androgen receptor, ataxin, and others) overwhelm endogenous neuroprotective mechanisms; other genes, such as those encoding apolipoprotein E(4), have more subtle effects on brain aging. On the other hand, neuroprotective mechanisms can be bolstered by dietary (caloric restriction and folate and antioxidant supplementation) and behavioral (intellectual and physical activities) modifications. At the cellular and molecular levels, successful brain aging can be facilitated by activating a hormesis response in which neurons increase production of neurotrophic factors and stress proteins. Neural stem cells that reside in the adult brain are also responsive to environmental demands and appear capable of replacing lost or dysfunctional neurons and glial cells, perhaps even in the aging brain. The recent application of modern methods of molecular and cellular biology to the problem of brain aging is revealing a remarkable capacity within brain cells for adaptation to aging and resistance to disease.
Effect of Polymer−Metal Complexation on the Phase Transition of Thermoreversible Copolymer Gels (1999)

We have investigated the effect of transition metal complexation on the swelling behavior in water of a new terpolymer gel made from N-tert-butylacrylamide (N-t-BAm) as the hydrophobic monomer, 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) as the hydrophilic monomer, and N,N‘-methylenebisacrylamide (BisAm) as the cross-linker. At a critical balance of hydrophilicity and hydrophobicity, the terpolymer exhibited a sharp volume transition at 15 °C. A shift in the transition temperature of the terpolymer was observed after complexation with trace metal ions. Electron paramagnetic resonance spectroscopy (EPR) suggested a tetrahedral structure for the complexes. We propose that the shift in volume transition temperature of the gel is due to subtle changes in the hydrophilic−hydrophobic balance resulting from the complexation of hydrophilic −SO3H groups of the gel with trace amounts of the metal ions.
Polymerase chain reaction—technology and applications (1991)

E. Hagelberg, K. M. Sullivan, G. Tully, R. Hopgood, D. Lingard, P. Gill and A. D. B. Malcolm, Anal. Proc., 1991, 28, 152 DOI: 10.1039/AP9912800152