gebhart/patrepeval huggingface dataset:
Applied molecular genetics of fungi : symposium of the British Mycological Society, held at the University of Nottingham, April 1990 (1991)

Contributors Preface 1. Gene-transfer systems and vector development for filamentous fungi C. A. M. J. J. van den Hondel and P. J. Hunt 2. Strategies for cloning genes from filamentous fungi G. Turner 3. Novel methods of DNA transfer J. W. Watts and N. J. Stacey 4. Saccharomyces cerevisiae: a host for the production of foreign proteins J. E. Ogden 5. The molecular biology of Trichoderma reesei and its application to biotechnology M. Pentila, T. T. Teeri, H. Nevalainen and J. K. C. Knowles 6. Expression of heterologous genes in filamentous fungi R. W. Davies 7. Methylotrophic yeasts as gene expression systems R. A. Veale and P. E. Sudbery 8. Strain improvement of brewing yeast E. Hinchliffe 9. Identification of the Cephalosporium acremonium pbcAB gene using predictions from an evolutionary hypothesis P. L. Skatrud, J. Hoskins, M. B. Tobin, J. R. Miller, J. S. Wood, S. Kovacevic and S. W. Queener 10. Applications of genetically manipulated yeasts A. W. M. Strasser, Z. A. Janowicz, R. O. Roggenkamp, U. Dahlems, U. Weydemann, A. Merckelbach, G. Gellissen, R. J. Dohmen, M. Piontek, K. Melber and C. P. Hollenberg 11. Molecular biology of fungal plant pathogenicity R. P. Oliver, M. L. Farman, N. J. Talbot and M. T. McHale Index.
De-Elastisation: From Asynchronous Dataflows to Synchronous Circuits (2015)

Asynchronous VLSI programming provides a flexible abstract formalism for concurrent systems but the is an issue for industrial adoption. The asynchronous design paradigm provides `elasticity' enabling the system to tolerate delays in communication and computation but can impose a prohibitive communication overhead when applied at a fine-grained level. This paper proposes `De-elastisation' in a CAD flow for asynchronous dataflow networks to improve the circuits' performance and area. To preserve the architectural advantages of asynchronous design (e.g. short cycles), circuits are classified into blocking and non-blocking loops which the De-elastisation scheme relies upon. The technique is incorporated in the Teak CAD flow. Experimental results on substantial case studies show significant performance and area improvements. This work shows 3× improvement for the first category of circuits, suitable for iterative realisations and DSP-like architectures and 4× for the second category which are suitable for concurrent realisations.
Simultaneous light scattering-rheology measurements for studying stress induced phase transitions (2008)

There are a growing number of simultaneous rheological techniques that are of great interest for many applications. Simultaneous rheometry and small angle light scattering (SALS) is of particular interest for obtaining information on material structure, orientation, particle size and shape. A compact SALS setup for simultaneous measurements has been developed and integrated into a stress‐controlled rheometer. The laser source is positioned below a lower Peltier platen, which incorporates a small quartz window. The light beam is perpendicular to the surface of the Peltier platen. The beam passes through the quartz window, the sample and an upper quartz plate. As the beam is scattered by interactions with the electrons of objects within the sample, the pattern formed is collected by an optical assembly with collimator, redirected with a mirror away from the upper test fixture, and projected onto a 2D camera array. Quantitative measurements are possible by calibrating the setup with monodisperse micron size polystyrene beads. Two case studies are presented. The first study involves the use of SALS simultaneous with rheology to measure the onset of shear banding in a worm‐like micellar solution. A butterfly light scattering pattern that is a signature of shear banding is obtained, which indicates that the mechanism of shear banding in the fluid is due to shear‐induced phase separation. The second study tracks the kinetics of shear‐induced colloidal crystallization by large amplitude oscillatory shear using simultaneous rheology and SALS measurements of the crystal order parameter. This allows construction of a phase map for shear ordering and its dependence on oscillation frequency and amplitude.
ChemInform Abstract: Structure Elucidation of Restricticin, a Novel Antifungal Agent from Penicillium restrictum. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Abstract 4496: Cytokine-induced post-translational modifications of FOXA1 affect enhancer selection and estrogen signaling in breast cancer cells (2019)

The pioneer transcription factor FOXA1 is a critical determinant for estrogen receptor (ER) function in hormone-dependent breast cancers. Upon estrogen stimulation, liganded ER binds to poised enhancer regions across the genome that are demarcated by FOXA1 and histone modifications such as H3K4me1 and H3K27ac. In a recent publication, we show that proinflammatory signaling, caused by the cytokine TNFa, drives FOXA1 to latent enhancer binding sites to promote chromatin accessibility for subsequent ER binding upon estrogen ligation. These latent enhancers, activated by the combined treatment of estrogen and TNFa, induced the expression of a unique transcriptome with clinical significance. The effects of TNFa treatment on FOXA1 chromatin redistribution and subsequent gene expression occur within 40 minutes, which points to a rapid signaling cascade that culminates in either changes in FOXA1's posttranslational modifications (PTMs) or its binding partners. To understand how proinflammatory TNFa signaling can redirect FOXA1 to new sites across the genome, we started by characterizing the posttranslational modifications (PTMs) of FOXA1. We immunoprecipitated FOXA1 from MCF-7 breast cancer cells that were treated by E2, TNFa or E2+ TNFa, and then examined their posttranslational status using semi-quantitative and quantitative mass spectrometry approaches. Several phosphorylation sites and acetylation sites have been identified near the DNA binding domain of FOXA1, and acetylation of lysine 295 (K295) was found specifically enriched in TNFa treatment. To test if acetylation of FOXA1 at K295 changes its binding preference and genomic distribution, we used the programmable properties of CRISPR/Cas9 to create specific knockin mutations to mimic or prevent acetylation of K295 in MCF-7 cells. More specifically, we mutated K295 to glutamine (K295Q) to mimic acetylation and essentially “lock” FOXA1 into a permanently acetylated state and, for comparison, we created another cell line where K295 was mutated to arginine (K295R) to prevent acetylation of FOXA1. Our preliminary data shows changes in the genomic redistribution of FOXA1 in the knock-in cell lines resulting in altered gene expression programs. These data suggest that inflammation-based acetylation of FOXA1 can affect estrogen signaling pathways in breast cancer cells by altering the enhancer landscape of FOXA1 and consequently the estrogen receptor.Supported by a grant from the NIH/NCI (R00 CA204628) to H.L.FCitation Format: Shen Li, Raul Mendez-Giraldez, Joseph P. Garay, Kamila Wisniewska, Colby A. Tubbs, Charles M. Perou, Hector L. Franco. Cytokine-induced post-translational modifications of FOXA1 affect enhancer selection and estrogen signaling in breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4496.
Information Flow Control in Machine Learning through Modular Model Architecture (2023)

In today's machine learning (ML) models, any part of the training data can affect the model output. This lack of control for information flow from training data to model output is a major obstacle in training models on sensitive data when access control only allows individual users to access a subset of data. To enable secure machine learning for access-controlled data, we propose the notion of information flow control for machine learning, and develop an extension to the Transformer language model architecture that strictly adheres to the IFC definition we propose. Our architecture controls information flow by limiting the influence of training data from each security domain to a single expert module, and only enables a subset of experts at inference time based on the access control policy.The evaluation using large text and code datasets show that our proposed parametric IFC architecture has minimal (1.9%) performance overhead and can significantly improve model accuracy (by 38% for the text dataset, and between 44%--62% for the code datasets) by enabling training on access-controlled data.
Herpes simplex virus, cytomegalovirus and Epstein–Barr virus antibody titres in sera from schizophrenic patients (1986)

Serum antibody titres to herpes-simplex (HSV-1, 2), cytomegalovirus (CMV), and Epstein-Barr virus capsid antigen (EBV-VCA) were determined in 38 unrelated chronic schizophrenic patients, 11 nuclear families with at least 2 schizophrenic members, and 2 control groups. The distributions of antibody titres to herpes simplex and cytomegalovirus were similar among all groups. Patients had higher anti-EBV-VCA titres than non-hospitalized controls; however, hospital staff members in contact with the patients also had significantly higher antibody titres to EBV-VCA. Antibodies to EBV early antigen (EBV-EA) were also determined for 27 unrelated patients and 24 mental hospital employees. The schizophrenic patients had significantly higher antibody titres to EBV-EA than the hospital worker control group. These data do not support the hypothesis that herpes viruses are associated with the aetiology of schizophrenia. Although elevated anti-EBV early antigen titres may suggest persistent active EBV infection, it is unlikely to be related to the aetiology of the disorder, since discordance for EBV seropositivity was present among sibling pairs concordant for schizophrenia.
Safety and Efficacy of Minimally Interrupted Dabigatran vs Uninterrupted Warfarin Therapy in Adults Undergoing Atrial Fibrillation Catheter Ablation (2019)

umin.ac.jp Identifier: UMIN000013129.
GSDIM with quantum dots enables nanoscopy of cells with a webcam (2011)

We overcome the limiting role of native blinking kinetics and demonstrate superresolution fluorescence imaging of biological structures using bioconjugated CdSe/ZnS quantum dot markers. Spectral blueing in exciton emission enables temporal and spatial separation of blinking nanocrystal markers residing closer than the diffraction barrier. The high number of successively emitted photons enables ground state depletion microscopy followed by individual marker return (GSDIM) with a resolving power of the size of a single dot. We also show that nanoscale resolution has become possible using a simple webcam. EM CCD cameras are no longer required which now drastically simplifies far-field fluorescence nanoscopy in terms of the required hardware.
Segmentation of Medical Images using Three-dimensional Active Shape Models (2005)

Abstract. In this paper a fully automated segmentation system for the femur in the knee in Magnetic Resonance Images and the brain in Single Photon Emission Computed Tomography images is presented. To do this several data sets were first segmented manually. The resulting structures were represented by unorganised point clouds. With level set methods surfaces were fitted to these point clouds. The iterated closest point algorithm was then applied to establish correspondences between the different surfaces. Both surfaces and correspondences were used to build a three dimensional statistical shape model. The resulting model is then used to automatically segment structures in subsequent data sets through three dimensional Active Shape Models. The result of the segmentation is promising, but the quality of the segmentation is dependent on the initial guess. 1
Plant Stanol Esters Lower Serum Triacylglycerol Concentrations via a Reduced Hepatic VLDL‐1 Production (2009)

Plant stanol esters not only lower low density lipoprotein cholesterol but also have previously been shown to lower serum triacylglycerol (TAG) concentrations, especially in subjects with elevated TAG concentrations. To find a possible explanation, we explored changes in serum lipoprotein profiles, as measured with nuclear magnetic resonance. For this, serum samples from two parallel-designed controlled studies were evaluated before and 8 weeks after the consumption of plant stanol esters. In the first study, dyslipidemic metabolic syndrome subjects participated and in the second study normolipidemic subjects. In metabolic syndrome subjects, plant stanol esters lowered concentrations of large (>60 nm) and medium (35-60 nm) VLDL particles as compared to controls. In normolipidemic subjects, the serum concentration of large VLDL-1 particles was also lowered, although less pronounced. Based on these findings, we hypothesize that the effect of plant stanol esters on serum TAG concentrations origins from a lowered hepatic production of large TAG-rich VLDL-1 particles.
Thermoresponsive Terpolymeric Films Applicable for Osteoblastic Cell Growth and Noninvasive Cell Sheet Harvesting (2005)

A novel multifunctional linear block copolymer, poly(N-isopropylacrylamide-co-acrylic acid)-b-poly( L-lactic acid) (NAL), was synthesized to expand the concept of cell sheet engineering by using its thermoresponsive property and processibility. The chemical structure of synthesized NAL was confirmed by Fourier transform infrared spectroscopy, and its molar mass (103,500 g.mol(-1)) and molar mass distribution were determined by matrix-assisted laser desorption/ionization-time of flight mass spectroscopy. NAL copolymer was fabricated into thin films by spin-casting. Spin-cast NAL films displayed thermoresponsive properties as demonstrated by surface wettability and topology changes from relatively more hydrophobic (contact angle of 56 degrees) and rougher at 37 degrees C to relatively more hydrophilic (contact angle of 40 degrees) and smoother at 22 degrees C, as assessed by contact angle measurement and atomic force microscopy, respectively. Murine osteoblastic MC3T3-E1 cells displayed comparable adhesion but slower proliferation on NAL films than on poly(L-lactic acid) (PLLA) films and tissue culture polystyrene (TCPS). Within 9 days of cell culture, the highest alkaline phosphatase activity of MC3T3-E1 cells occurred later (on day 9) on NAL films than on PLLA films and TCPS (on day 6). A well-established MC3T3-E1 cell sheet was successfully detached from NAL films, in the absence of enzymes, within about 5 min by simply lowering the temperature from 37 degrees C to room temperature. NAL copolymer has potential for use in the controlled release of therapeutic agents while simultaneously supporting cell growth. In addition, it may be applicable for noninvasive two- or three-dimensional cell sheet harvesting.
What’s new in chronic pain pathophysiology (2020)

The understanding of pain pathophysiology is continuously evolving. Identifying underlying cellular and subcellular pathways helps create opportunities for targeted therapies that may prove to be effective interventions. This article is an update on four areas of developing knowledge as it pertains to clinical management of patients with pain: nerve growth factor antagonists, microglial modulation, AMP-activated protein kinase activators, and genetic pain factors. Each of these areas represents novel targets for targeted therapies to prevent, treat, and modify the disease course of acute, chronic, and neuropathic pain. Currently most pain management techniques do not target these pathways directly, but there is promising evidence to suggest that the field is advancing toward available therapies in the near future.
Cubature H<inf>∞</inf> information filter (2013)

This paper presents a state estimation algorithm referred to as a cubature H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> information filter (CH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> IF) for nonlinear systems. The proposed algorithm is developed from a cubature Kalman filter, an H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> filter and an extended information filter. The CH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> IF is a derivative free filter, where the information state vector and information matrix are propagated rather than the state vector and error covariance matrix. Furthermore, the CH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> IF is extended for multi-sensor state estimation. The efficacy of the CH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> IF is demonstrated by a simulation example of a permanent magnet synchronous motor in the presence of Gaussian and non-Gaussian noises.
Analytically predicted estimates for vitamin D, vitamin A and chromium content in adult multivitamin/mineral products (MVMs) for the Dietary Supplement Ingredient Database (DSID) (2017)

Adult MVMs are the most commonly reported dietary supplements in the US, with ~30% reporting their use. The analytically determined content of these products is ingredient specific, with some ingredients close to labeled levels and others significantly higher. The DSID ( http://dsid.usda.nih.gov ) reports analytically derived national estimates for ingredient content in DS, including adult MVMs. Predicted estimates are based on regression analysis of representative products purchased in 2006–07 (adult MVM‐1). These predictions are linked to NHANES 2003–2008 and can be used instead of labeled levels for more precise nutrient intake assessment in surveys. A second adult MVM study (adult MVM‐2) was initiated to investigate how label information, sales, and quality change over time. Representative products were purchased in 2011, and sent for analysis to qualified laboratories. Final lab results were statistically evaluated. For the 18 ingredients analyzed in both adult MVM studies, overages in mean ingredient content were found for all vitamins (with thiamin a consistent exception) and all minerals, with some ingredients more variable than others. Improvements in analytical methodology for vitamin D, vitamin A (beta‐carotene and retinol), and chromium provide reliable data for these ingredients in adult MVMs for the first time. For vitamin D products labeled from 15 to 2,000 IU per serving, a linear regression model predicts mean analytical content ranging from 45 to 20% above label, with a 40.5% overage at the most common labeled level of 400 IU. For vitamin A products labeled from 1,000 to 20,000 IU per serving, a quadratic regression model predicts mean analytical content ranging from 49% above to 8.5% below label, with a 25.6% estimated overage at the most common labeled level (3,500 IU). For adult MVMs containing chromium, a linear regression model predicts mean overages of 29 to 10% across a 10–250 μg per serving label range, with a 20.4% overage at the most common labeled level (120 μg/serving). For these ingredients, the regression model was significantly better than the label claim at predicting actual product content. For many vitamins and minerals in MVMs, labeled levels are at or above the Recommended Dietary Allowance (RDA). Taking into account ingredient overages, the number of products in the adult MVM‐2 study at or above the RDA increased from 42% to 63% for vitamin A, and 47% to 62% for vitamin D. Most of the labeled and analytical results for chromium were well above the adequate intake (AI) level of 35 μg/day. Since consumers take MVMs over a number of years, and some combine MVM intake with high dose single vitamin or mineral DSs and highly fortified foods, the risk of excessive intakes should be investigated. Support or Funding Information ARS/USDA &amp; ODS/NIH Y1CN501006
Tunable Graphene dc Superconducting Quantum Interference Device (2008)

Graphene exhibits unique electrical properties on account of its reduced dimensionality and "relativistic" band structure. When contacted with two superconducting electrodes, graphene can support Cooper pair transport, resulting in the well-known Josephson effect. We report here the fabrication and operation of a two junction dc superconducting quantum interference device (SQUID) formed by a single graphene sheet contacted with aluminum/palladium electrodes in the geometry of a loop. The supercurrent in this device can be modulated not only via an electrostatic gate but also by an applied magnetic fielda potentially powerful probe of electronic transport in graphene and an ultrasensitive platform for nanomagnetometry.
Trisomy rescue mechanism: the case of concomitant mosaic trisomy 14 and maternal uniparental disomy 14 in a 15‐year‐old girl (2016)

Maternal uniparental disomy of chromosome 14 (upd(14)mat) is responsible for a Prader-Willi-like syndrome with precocious puberty. Although upd(14) is often hypothesized to result from trisomy rescue mechanism, T14 cell lines are usually not found with postnatal cytogenetic investigations. We report the coexistence of both chromosomal abnormalities in a 15-year-old girl.
Therapeutic potential of oxytocin receptor signaling in vascular dementia (2020)

Abstract Background We recently demonstrated a de novo upregulation of the oxytocin receptor (OXTR) in astrocytes located in the peri‐infarct regions of subjects who died with vascular dementia (multi‐infarct subtype). OXTR activation has been linked to antioxidant, anti‐inflammatory, and angiogenic signaling, suggesting that OXTR upregulation is a novel protective target for vascular dementia, mixed dementias, and perhaps even cerebrovascular accidents. To test this hypothesis, we modeled OXTR upregulation in a novel rat model of vascular dementia. Method Four month‐old spontaneously hypertensive, stroke prone rats are being randomized to receive cortical injections of adeno‐associated virus (AAV, serotype 6) bearing either OXTR or green fluorescent protein (GFP) cDNA under control of the astroglial‐specific GFAP promoter, followed by randomization to receive cortical injections of the vasoconstrictor endothelin‐1 (ET‐1) or saline vehicle (n = 16/group, balanced for sex). Following behavioral testing, rats are being analyzed postmortem for infarction lesion size, cerebrovascular pathology, and several mechanistic indices including markers for cell death, inflammation, and oxidative stress. Result Preliminary results ( n = 6‐8/group) showed that rats receiving AAV‐OXTR and ET‐1 displayed a nonsignificant 40% reduction in mean latency time to target on the Barnes maze compared to rats receiving AAV‐GFP and ET‐1 ( p = 0.7). Similarly, OXTR/ET‐1‐treated rats showed a 110% increase in the mean ratio of time spent exploring novel vs. familiar objects on the Novel Object Task compared to GFP/ET‐1‐treated rats ( p = 0.08). Postmortem histological analysis revealed a nonsignificant 60% reduction in infarct size in OXTR/ET‐1 compared to GFP/ET‐1 rats ( p = 0.08). Conclusion Preliminary data are trending to support the concept that astrocytic OXTR signaling may have a therapeutic benefit for dementia resulting from cerebrovascular accidents.