gebhart/patrepeval huggingface dataset:
Identification of functionalsine oculismotifs in the autoregulatory element of its own gene, in theeyelessenhancer and in the signalling genehedgehog (2005)

In Drosophila, the sine oculis (so) gene is important for the development of the entire visual system, including Bolwig's organ, compound eyes and ocelli. Together with twin of eyeless, eyeless, eyes absent and dachshund, so belongs to a network of genes that by complex interactions initiate eye development. Although much is known about the genetic interactions of the genes belonging to this retinal determination network, only a few such regulatory interactions have been analysed down to the level of DNA-protein interactions. Previous work in our laboratory identified an eye/ocellus specific enhancer of the sine oculis gene that is directly regulated by eyeless and twin of eyeless. We further characterized this regulatory element and identified a minimal enhancer fragment of so that sets up an autoregulatory feedback loop crucial for proper ocelli development. By systematic analysis of the DNA-binding specificity of so we identified the most important nucleotides for this interaction. Using the emerging consensus sequence for SO-DNA binding we performed a genome-wide search and have thereby been able to identify eyeless as well as the signalling gene hedgehog as putative targets of so. Our results strengthen the general assumption that feedback loops among the genes of the retinal determination network are crucial for proper development of eyes and ocelli.
Spectral narrowing and optical soliton formation in SOI waveguides (2007)

We observe, for the first time to our knowledge, spectral narrowing due to the formation of optical solitons inside a short 5 mm long silicon waveguide with sub-picojoule pulse energies.
Aspects of Heat Transfer during Production of Remelt Ingot Using Chain Casters (2013)

This chapter contains sections titled: Introduction Past Work on Ingot Casting Fundamentals of heat flow Discussion Acknowledgments
Design and Simulation of a Multilayer Chemical Neural Network That Learns via Backpropagation (2023)

The design and implementation of adaptive chemical reaction networks, capable of adjusting their behavior over time in response to experience, is a key goal for the fields of molecular computing and DNA nanotechnology. Mainstream machine learning research offers powerful tools for implementing learning behavior that could one day be realized in a wet chemistry system. Here we develop an abstract chemical reaction network model that implements the backpropagation learning algorithm for a feedforward neural network whose nodes employ the nonlinear "leaky rectified linear unit" transfer function. Our network directly implements the mathematics behind this well-studied learning algorithm, and we demonstrate its capabilities by training the system to learn a linearly inseparable decision surface, specifically, the XOR logic function. We show that this simulation quantitatively follows the definition of the underlying algorithm. To implement this system, we also report ProBioSim, a simulator that enables arbitrary training protocols for simulated chemical reaction networks to be straightforwardly defined using constructs from the host programming language. This work thus provides new insight into the capabilities of learning chemical reaction networks and also develops new computational tools to simulate their behavior, which could be applied in the design and implementations of adaptive artificial life.
A Novel Therapeutic Combination Using PD 0332991 and Bortezomib: Study in the 5T33MM Myeloma Model (2008)

Multiple myeloma (MM) remains incurable partly because no effective cell cycle-based therapy has been available to both control tumor cell proliferation and synergize with cytotoxic killing. PD 0332991 is an orally active small molecule that potently and specifically inhibits Cdk4 and Cdk6. It has been shown to induce rapid G(1) cell cycle arrest in primary human myeloma cells and suppress tumor growth in xenograft models. To improve therapeutic targeting of myeloma progression, we combined tumor suppression by PD 0332991 with cytotoxic killing by bortezomib, a proteasome inhibitor widely used in myeloma treatment, in the immunocompetent 5T33MM myeloma model. We show that 5T33MM tumor cells proliferate aggressively in vivo due to expression of cyclin D2, elevation of Cdk4, and impaired p27(Kip1) expression, despite inhibition of Cdk4/6 by p18(INK4c) and the maintenance of a normal plasma cell transcription program. PD 0332991 potently inhibits Cdk4/6-specific phosphorylation of Rb and cell cycle progression through G(1) in aggressively proliferating primary 5T33MM cells, in vivo and ex vivo. This leads to tumor suppression and a significant improvement in survival. Moreover, induction of G(1) arrest by PD 0332991 sensitizes 5T33MM tumor cells to killing by bortezomib. Inhibition of Cdk4/6 by PD 0332991, therefore, effectively controls myeloma tumor expansion and sensitizes tumor cells to bortezomib killing in the presence of an intact immune system, thereby representing a novel and promising cell cycle-based combination therapy.
[The development of cognitive functions in children with Hurler phenotype mucopolysaccharidosis type I on enzyme replacement therapy with laronidase]. (2010)

1. Among children with MPS type I, there was a measurable decrease in IQ associated with advancing age. 2. In spite of lower IQ, the acquisition of new abilities does occur, but the pace of that development is slower than that expected for the child's age. 3. The study reveals the need for functional diagnosis of development, in order to assess the progress made by the child.
Growth and properties of tungsten-bronze ferroelectric potassium lithium niobate single crystals (2002)

Potassium lithium niobate (KLN) single crystals were grown from a melt with potassium and lithium enriched composition using the rf-heating Czochralski technique. The growth and electric poling conditions were discussed. The transparent crystal was pale-yellow with an absorption edge at 376 nm, and showed a very small optical absorption in the 420-900 nm region. The electrooptic and nonlinear optic coefficients were measured. The deviation of composition in the crystals was investigated by measuring the change of the temperature and phase matching angle of the harmonic generation.
Mucosal Immune Responses Against an Oral Enterotoxigenic Escherichia coli Vaccine Evaluated in Clinical Trials (2021)

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of mortality and morbidity in children in low-income countries. We have tested an oral ETEC vaccine, ETVAX, consisting of inactivated E coli overexpressing the most prevalent colonization factors and a toxoid, LCTBA, administered together with a mucosal adjuvant, double-mutant heat-labile toxin (dmLT), for capacity to induce mucosal immune responses and immunological memory against the primary vaccine antigens, ie, colonization factors, heat-labile toxin B-subunit and O antigen. The studies show that ETVAX could induce strong intestine-derived and/or fecal immune responses in a majority of vaccinated Swedish adults and in different age groups, including infants, in Bangladesh.
Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation (2010)

The infrequently feeding Burmese python (Python molurus) experiences significant and rapid postprandial cardiac hypertrophy followed by regression as digestion is completed. To begin to explore the molecular mechanisms of this response, we have sequenced and assembled the fasted and postfed Burmese python heart transcriptomes with Illumina technology using the chicken (Gallus gallus) genome as a reference. In addition, we have used RNA-seq analysis to identify differences in the expression of biological processes and signaling pathways between fasted, 1 day postfed (DPF), and 3 DPF hearts. Out of a combined transcriptome of ∼2,800 mRNAs, 464 genes were differentially expressed. Genes showing differential expression at 1 DPF compared with fasted were enriched for biological processes involved in metabolism and energetics, while genes showing differential expression at 3 DPF compared with fasted were enriched for processes involved in biogenesis, structural remodeling, and organization. Moreover, we present evidence for the activation of physiological and not pathological signaling pathways in this rapid, novel model of cardiac growth in pythons. Together, our data provide the first comprehensive gene expression profile for a reptile heart.
The applicability of ultra thin silicon films as interlayers for CVD diamond deposition on steels (2003)

In this study, the use of thin Si interlayers (35–150 nm) for promoting diamond deposition onto steel is investigated. The diamond films are deposited by hot filament CVD onto AISI type 316 stainless and high-speed steels. Single stage deposition at substrate temperatures ranging from as low as 475 to 750 °C is found to result only in non-continuous films with low number densities of diamond crystallites. A composite film of diamond and carbides is formed at intermediate temperatures of about 650 °C. It is believed that the formation of iron silicide phases at the exposed steel substrate surfaces leads to diffusion barriers for free iron from the steel matrix, so that graphitic soot formation is significantly avoided.Utilizing a two-stage deposition process, the density and uniformity of the deposited diamond films areincreased and a nearly continuous cauliflower shaped diamond film is obtained. Micro-Raman spectros-copy, scanning electron microscopy and X-ray diffraction techniques are employed to study the phases, morphology, composition, quality and residual stresses of the grown diamond layers.
Analyses of antibody responses to asexual blood stages of Plasmodium falciparum in ethnic tribes living in sympatry (2004)

Analyses of antibody responses to asexual blood stages of Plasmodium falciparum in ethnic tribes living in sympatry
Quantum enhanced metrology in the presence of arbitrary loss (2013)

We introduce the concept of entanglement enhanced interferometry from the viewpoint of the detected photons. The standard quantum limit is achieved when sequentially detected photons are assumed to be in an uncorrelated product state. However when we access the correlations between the detected photons that existed before the interferometer it becomes clear that entanglement enhanced measurement beyond the quantum limit could be achieved independent of loss. We describe possible realisations of this post-measurement entanglement detection using a small array of spin photon entangling gates. We then describe a proof of principle experiment using only linear optics resources.
2D Electrical Imaging of an LNAPL Contamination, Al Amiriyya Fuel Station, Jordan (2004)

The detection of organic contaminants such as light non-aqueous phase liquid (LNAPL) in the subsurface using geophysical methods, particularly electrical resistivity methods has been the subject of considerable interest in recent years. Their detection is based principally upon the electrical properties of the hydrocarbons. During 2002, direct current resistivity data were collected with the Iris Syscal R2 resistivity instrument at the location of Al Amiriyya fuel station site, Jordan. The objective of this study was to evaluate the resolution of resistivity techniques in detecting and locating anomalies of organic contamination. Resistivity measurements were carried out utilizing the Wenner and dipole-dipole array configurations in order to achieve good vertical and lateral resistivity distributions for the investigated site. The interpretations obtained from 2D-modelling of the field data show a highly conductive region in areas with LNAPL contamination. This explanation was supported by the presence of hydrocarbon sheens floated on the surface of water filling the subsidence feature and by excavation works. Correlation between field results obtained shows that the dipole-dipole array is the most reliable since it showed details over the fuel station site that were poorly indicated by the Wenner array.
Audio-tutorial lessons. An alternative to the second course in high school chemistry (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAudio-tutorial lessons. An alternative to the second course in high school chemistryRoger M. Records Cite this: J. Chem. Educ. 1975, 52, 4, 243Publication Date (Print):April 1, 1975Publication History Received3 August 2009Published online1 April 1975Published inissue 1 April 1975https://doi.org/10.1021/ed052p243RIGHTS & PERMISSIONSArticle Views27Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Improving the selectivity of pyrolysis by pyrolytic acid leaching of biomass : the role of AAEMs, anhydrosugar production and process design & evaluation (2016)

The research described in this thesis was conducted in the Sustainable Process Technology (SPT) group at the University of Twente, The Netherlands. The research
In-situ Heat Flux Measurements in Buildings: Applications and Interpretations of Results, Proceedings of a Workshop Held in Hanover, New Hampshire on 22-23 May 1990 (1991)

Abstract : This publication contains papers that were the subjects of presentations at the Workshop on In-Situ Heat Flux Measurements in Buildings, held at the U.S. Army Cold Regions Research and Engineering Laboratory in Hanover, New Hampshire, on May 22-23, 1990. Stephen N. Flanders presided as workshop chairman and is the editor of this publication.
FKS2 and FKS3 Genes of Opportunistic Human Pathogen Candida albicans Influence Echinocandin Susceptibility (2018)

<i>Candida albicans</i>, a prevailing opportunistic fungal pathogen of humans, has a diploid genome containing three homologous <i>FKS</i> genes that are evolutionarily conserved. One of these, the essential gene <i>FKS1</i>, encodes the catalytic subunit of glucan synthase, which is the target of echinocandin drugs and also serves as a site of drug resistance. The other two glucan synthase-encoding genes, <i>FKS2</i> and <i>FKS3</i>, are also expressed, but their roles in resistance are considered unimportant. However, we report here that expression of <i>FKS1</i> is upregulated in strains lacking either <i>FKS2</i> or <i>FKS3</i> Furthermore, in contrast to what is observed in heterozygous <i>FKS1</i> deletion strains, cells lacking <i>FKS2</i> or <i>FKS3</i> contain increased amounts of cell wall glucan, are more resistant to echinocandin drugs, and consistently are tolerant to cell wall-damaging agents. Our data indicate that <i>C. albicans</i><i>FKS2</i> and <i>FKS3</i> can act as negative regulators of <i>FKS1</i>, thereby influencing echinocandin susceptibility.
Topology Perturbation for Detecting Malicious Data Injection (2012)

Bad measurement data exists in power systems for a number of reasons. Malicious data injection attacks, which alter the values of measurements without being detected, are one potential cause of bad data and may have serious consequences. A solution for bad data detection in power systems is proposed in this work, particularly designed to detect malicious data attacks. By applying known perturbations to the system and measuring the changes elsewhere, the approach 'probes' the system for unexpected responses in terms of measurement values. Using a developed 'key space' approach, the perturbation used is rendered unpredictable to the attacker, making it difficult for the attacker to adapt his attacks. Thus, unexpected measurement values after a probe provide an indication of both bad and malicious data. The proposed approach is analyzed for sample systems using MATLAB.
PRADC1: a novel metabolic‐responsive secretory protein that modulates physical activity and adiposity (2019)

Interorgan communication mediated by secreted proteins plays a pivotal role in metabolic homeostasis, yet the function of many circulating secretory proteins remains unknown. Here, we describe the function of protease-associated domain-containing 1 (PRADC1), an enigmatic secretory protein widely expressed in humans and mice. In metabolically active tissues (liver, muscle, fat, heart, and kidney), we showed that <i>Pradc1</i> expression is significantly suppressed by refeeding and reduced in kidney and brown fat in the context of obesity. PRADC1 is dispensable for whole-body metabolism when mice are fed a low-fat diet. However, in obesity induced by high-fat feeding, PRADC1-deficient female mice have reduced weight gain and adiposity despite similar caloric intake. Decreased fat mass is attributed, in part, to increased metabolic rate, physical activity, and energy expenditure in these animals. Reduced adiposity in PRADC1-deficient mice, however, does not improve systemic glucose and lipid metabolism, insulin sensitivity, liver steatosis, or adipose inflammation. Thus, in PRADC1-deficient animals, decreased fat mass and enhanced physical activity are insufficient to confer a healthy metabolic phenotype in the context of an obesogenic diet. Our results shed light on the physiologic function of PRADC1 and the complex regulation of metabolic health.-Rodriguez, S., Stewart, A. N., Lei, X., Cao, X., Little, H. C., Fong, V., Sarver, D. C., Wong, G. W. PRADC1: a novel metabolic-responsive secretory protein that modulates physical activity and adiposity.
The NH4F-induced morphology control of hierarchical CoO@MnO2 core–shell arrays for high performance supercapacitor electrodes (2019)

High-performance hierarchical CoO@MnO<sub>2</sub> core–shell arrays with controllable morphology were fabricated by a facile two-step hydrothermal method.
122-OR: Insulin and C-Peptide in Human Choroid Plexus of Type 1 Diabetes Mellitus (2021)

The choroid plexus (CP) produces cerebrospinal fluid (CSF) and forms a blood-CSF barrier. We already reported that mouse CP epithelial (CPE) cells synthesize and secrete insulin in response to serotonin but not glucose. We now report that insulin expression is present in human postmortem CP samples of humans - nondiabetic, T2DM, and T1DM - by RT-qPCR, in situ hybridization and LC-MS/MS based Selected Reaction Monitoring assay. Human CPE contains all the INS splicing machinery and the major INS splicing variants that are present in islets. Known β-cell specific transcription factors are also expressed in CPE, except for PDX1 and PAX4, which are absent. The SRM assay detected INS A-chain, B-chain, and C-peptide at similar levels in nondiabetic, T2DM, and T1DM islets and CP postmortem samples. Islet amyloid polypeptide (IAPP) expression was not detected in CPE in contrast to human islets where INS and IAPP mRNA, as expected, colocalize in β-cells. Furthermore, INS colocalizes with transthyretin (TTR) mRNA in CPE cells but in islets, TTR is expressed in α-cells and not β-cells. We found less or no expression of T1DM autoantigens in CPE compared to β-cells, with the exception of ICA1 (islet cell autoantigen1), which has similar expression in both tissues. In conclusion, human CPE expresses and synthesizes insulin, it is protected from autoimmune destruction and from IAPP amyloidogenic fibril formation. Disclosure Q. Liu: None. M. Zhu: None. C. Mazucanti: None. S. Marenco: None. J. M. Egan: None. Funding National Institute on Aging
Phenotype of autosomal dominant spastic paraplegia linked to chromosome 2 (1996)

We report the clinical features of 12 families with autosomal dominant spastic paraplegia (ADSP) linked to the SPG4 locus on chromosome 2p, the major locus for this disorder that accounts for approximately 40% of the families. Among 93 gene carriers, 32 (34%) were unaware of symptoms but were clinically affected. Haplotype reconstruction showed that 90% of the asymptomatic gene carriers presented increased reflexes and/or extensor plantar responses independent of age at examination. The mean age at onset was 29 years, ranging from 1 to 63 years. Intra- as well as inter-familial variability of age at onset was important, but did not result from anticipation. Phenotype-genotype correlations and comparison with SPG3 and SPG5 families indicated that despite the variability of age at onset, SPG4 is a single genetic entity but no clinical features distinguish individual SPG4 patients from those with SPG3 or SPG5 mutations.
Light‐Responsive Bilayer Cell Culture Platform for Reversible Cell Guidance (2021)

In vivo, cells are surrounded by a constantly changing microenvironment, which regulates many cell functions such as differentiation, migration, and cell death. Stimuli-responsive biomaterials aim to mimic this interaction between cells and extracellular matrix in vitro. However, reproducing dynamic signaling noninvasively without affecting the cell viability remains a challenge. Herein, a dynamic cell culturing platform consisting of a light-responsive azobenzene molecular glass film and a protective polydimethylsiloxane (PDMS) coating is developed. By tuning the PDMS layer thickness, surface relief gratings (SRGs) can be efficiently photoinscribed on the platform surface. The SRGs can also be erased with light in the presence of PDMS, i.e., the topography can be reversibly photomodulated. The inscribed SRGs can guide epithelial cell orientation along the topography. The erasure parameters are targeted toward cell culturing environment, enabling experiments with live cells. Finally, the photoresponsive platform is patterned with proteins by microcontact printing, allowing its biofunctionalization and the combination of microtopography and protein patterns. This study paves the way for using reconfigurable cell culture platforms for the dynamic control of cell-material interactions. The PDMS coating has potential to protect underneath material, broadening the spectrum of possible materials for dynamic cell culture platforms.
Short paper (2014)

The Android permissions system provides all-or-nothing access to users' photos stored on smartphones, and the permissions which control access to stored photos can be confusing to the average user. Our analysis found that 73% of the top 250 free apps on the Google Play store have permissions that may not reflect their ability to access stored photos. We propose CHIPS, a unique content-based fine-grained run-time access control system for stored photos for Android which requires minimal user assistance, runs entirely locally, and provides low-level enforcement. CHIPS can recognize faces with minimal user training to deny apps access to photos with known faces. CHIPS's privacy identification has low overheads as privacy checks are cached, and is accurate, with false-positive and false-negative rates of less than 8%.