gebhart/patrepeval huggingface dataset:
Bdp, a new member of a family of DNA-binding proteins, associates with the retinoblastoma gene product. (1999)

We have cloned a gene, BDP, encoding a protein with homology to the retinoblastoma-binding proteins Rbp1 and Rbp2. It also has homology to DNA-binding proteins such as Bright, a B-cell-specific trans-activator, and the Drosophila melanogaster dead ringer gene product. Like MyoD, Bdp binds to the COOH-terminal region of pRb through its conserved region and to hypophosphorylated pRb. It also binds to the MAR of the immunoglobulin heavy-chain locus. Thus Bdp may contribute to the transcriptional regulation of genes involved in differentiation and tissue-specific expression.
Construction of a Meroterpenoid‐Like Compounds Library Based on Diversity‐Enhanced Extracts (2018)

The structural diversity of natural products and their derivatives have long contributed to the development of new drugs. However, the difficulty in obtaining compounds bearing skeletally novel structures has recently led to a decline of pharmaceutical research into natural products. This paper reports the construction of a meroterpenoid-like library containing 25 compounds with diverse molecular scaffolds obtained from diversity-enhanced extracts. This method constitutes an approach for increasing the chemical diversity of natural-product-like compounds by combining natural product chemistry and diversity-oriented synthesis. Extensive pharmacological screening of the library revealed promising compounds for anti-osteoporotic and anti-lymphoma/leukemia drugs. This result indicates that the use of diversity-enhanced extracts is an effective methodology for producing chemical libraries for the purpose of drug discovery.
Enzymatically Synthesized Electronic and Photoactive Materials (2004)

Electronic and photo-active polymers as a class of advanced materials have attracted a lot of interest during last two decades. Typically these materials are synthesized chemically or electrochemically under harsh conditions such as extremely low pH, toxic catalysts and byproducts. New enzymatic approaches have been developed for the synthesis of electro and photo active polymers such as polyanilines, polyazophenols, and polypyrene derivatives. These enzymatically synthesized materials show interesting optical and electronic properties.
Lymphokines and Monokines in Anti-cancer Therapy (1986)

About 10 years ago, it became evident that many types of cancer cells were causally related to irreversible changes in their genetic makeup. Hence, elimination of these malignant cells was the only possible therapy. Except for surgery, classical treatments like irradiation and chemotherapy are fairly unselective and have unpleasant side effects. Can molecular biology provide drugs and treatments that are more selective and effective while being more biocompatible and less toxic?
Phosphine Oxide Monolayers on SiO2 Surfaces (2008)

Getting a grip: H-bond formation is shown to be the main mode of interaction for monolayer formation of phosphine oxides on SiO2 substrates (see images), with covalent reaction involved to a lesser extent. In contrast to the situation with the more widely studied polar phosphonic acids, formation of these monolayers is self-limiting. The results may have important implications for many applications based on phosphine oxide monolayers.
Simplified perturbation-based approach for predicting the tolerance to intra-channel nonlinear effects (2015)

A broadly applicable perturbation-based approach is demonstrated for estimating the impact of intra-channel fiber nonlinearities on system performance. The estimated performance for DP-QPSK, DP-8QAM, and DP-16QAM exhibits good agreement with both simulation and experimental results.
Modular Hybrid Autoregressive Transducer (2022)

Text-only adaptation of a transducer model remains challenging for end-to-end speech recognition since the transducer has no clearly separated acoustic model (AM), language model (LM) or blank model. In this work, we propose a modular hybrid autoregressive transducer (MHAT) that has structurally separated label and blank decoders to predict label and blank distributions, respectively, along with a shared acoustic encoder. The encoder and label decoder outputs are directly projected to AM and internal LM scores and then added to compute label posteriors. We train MHAT with an internal LM loss and a HAT loss to ensure that its internal LM becomes a standalone neural LM that can be effectively adapted to text. Moreover, text adaptation of MHAT fosters a much better LM fusion than internal LM subtraction-based methods. On Google's large-scale production data, a multi-domain MHAT adapted with 100B sentences achieves relative WER reductions of up to 12.4% without LM fusion and 21.5% with LM fusion from 400K-hour trained HAT.
New Synthesis of Piperidine Derivatives via the Chromacyclobutane (1993)

Piperidine derivatives were synthesized from the enynes and Fischer chromium carbene complex via chromacyclobutanes in moderate yields and the reaction course was controlled by the substituents on the double bond of the enynes
The infrastructure for E-business (2003)

Electronic commerce has obtained its means of spreading out to every corner of the world via the Internet. The article gives an overview of the implementation of Internet-based virtual private networks (VPN), the generic deployment framework and main enabling techniques.
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation (2016)

DNA methylation, a major epigenetic mechanism, may regulate coordinated expression of multiple genes at specific time points during alveolar septation in lung development. The objective of this study was to identify genes regulated by methylation during normal septation in mice and during disordered septation in bronchopulmonary dysplasia. In mice, newborn lungs (preseptation) and adult lungs (postseptation) were evaluated by microarray analysis of gene expression and immunoprecipitation of methylated DNA followed by sequencing (MeDIP-Seq). In humans, microarray gene expression data were integrated with genome-wide DNA methylation data from bronchopulmonary dysplasia versus preterm and term lung. Genes with reciprocal changes in expression and methylation, suggesting regulation by DNA methylation, were identified. In mice, 95 genes with inverse correlation between expression and methylation during normal septation were identified. In addition to genes known to be important in lung development (Wnt signaling, Angpt2, Sox9, etc.) and its extracellular matrix (Tnc, Eln, etc.), genes involved with immune and antioxidant defense (Stat4, Sod3, Prdx6, etc.) were also observed. In humans, 23 genes were differentially methylated with reciprocal changes in expression in bronchopulmonary dysplasia compared with preterm or term lung. Genes of interest included those involved with detoxifying enzymes (Gstm3) and transforming growth factor-β signaling (bone morphogenetic protein 7 [Bmp7]). In terms of overlap, 20 genes and three pathways methylated during mouse lung development also demonstrated changes in methylation between preterm and term human lung. Changes in methylation correspond to altered expression of a number of genes associated with lung development, suggesting that DNA methylation of these genes may regulate normal and abnormal alveolar septation.
Sodium transport and phosphorus metabolism in sodium-loaded yeast: simultaneous observation with sodium-23 and phosphorus-31 NMR spectroscopy in vivo (1987)

Simultaneous 23Na and 31P NMR spectra were obtained from a number of yeast suspensions. Prior to NMR spectroscopy, the yeast cells were Na-loaded: this replaced some of the intracellular K+ with Na+. These cells were also somewhat P-deficient in that they had no polyphosphate species visible in the 31P NMR spectrum. In the NMR experiments, the Na-loaded cells were suspended in media which contained inorganic phosphate, very low Na+, and a shift reagent for the Na+ NMR signal. The media differed as to whether dioxygen, glucose, or K+ was present individually or in combinations and as to whether the medium was buffered or not. The NMR spectra revealed that the cells always lost Na+ and gained phosphorus. However, the nature of the Na+ efflux time course and the P metabolism differed depending on the medium. The Na+ efflux usually proceeded linearly until the amount of Na+ extruded roughly equalled the amount of NH4+ and orthophosphate initially present in the medium (external phosphate was added as NH4H2PO4). Thus, we presume this first phase reflects a Na+ for NH4+ exchange. The Na+ efflux then entered a transition phase, either slowing, ceasing, or transiently reversing, before resuming at about the same value as that of the first phase. We presume that this last phase involves the simultaneous extrusion of intracellular anions as reported in the literature. The phosphorus metabolism was much more varied. In the absence of exogenous glucose, the P taken up accumulated first as intracellular inorganic phosphate; otherwise, it accumulated first in the "sugar phosphate" pool. In most cases, at least some of the P left the sugar phosphate pool and entered the polyphosphate reservoir in the vacuole. However, this never happened until the phase probably representing Na+ for NH4+ exchange was completed, and the P in the polyphosphate pool never remained there permanently but always eventually reverted back to the sugar phosphate pool. These changes are interpreted in terms of hierarchical energy demands on the cells under the different conditions. In particular, the energy for the Na+ for NH4+ exchange takes precedence over that required to produce and store polyphosphate. This conclusion is supported by the fact that when the cells are "forced" to exchange K+, as well as NH4+, for Na+ (by the addition of 5 times as much K+ to the NH4+-containing medium), polyphosphates are never significantly formed, and the initial linear Na+ efflux phase persists possibly 6 times as long.(ABSTRACT TRUNCATED AT 400 WORDS)
Rhinocerebral zygomycosis: an unusual dramatic presentation in a paediatric cardiac patient without risk factors (2016)

Mucormycosis is an angioinvasive infection caused by ubiquitous filamentous fungi of the order Mucorales. We describe a case of rhinocerebral mucormycosis presented in a paediatric patient after cardiac surgery correction of a complete atrioventricular canal defect. The rhinocerebral form of mucormycosis in our patient presented as an important epistaxis that needed immediate intubation due to blood inhalation. Furthermore, due to the worsening of pulmonary function, the patient also needed mechanical support with veno-arterial extracorporeal membrane oxygenation. The patient died as a consequence of a disseminated form of fungal infection. We describe our experience of this rare opportunistic infection and we think that early recognition of the disease could help in proper management.
OSPF Extensions to Advertise Seamless Bidirectional Forwarding Detection (S-BFD) Target Discriminators (2016)

This document defines a new OSPF Router Information (RI) TLV that
allows OSPF routers to flood the Seamless Bidirectional Forwarding
Detection (S-BFD) Discriminator values associated with a target
network identifier. This mechanism is applicable to both OSPFv2 and
OSPFv3.
Colloidal Nanocrystals Embedded in Macrocrystals: Methods and Applications (2016)

Colloidal semiconductor nanocrystals have gained substantial interest as spectrally tunable and bright fluorophores for color conversion and enrichment solids. However, they suffer from limitations in processing their solutions as well as efficiency degradation in solid films. As a remedy, embedding them into crystalline host matrixes has stepped forward for superior photostability, thermal stability, and chemical durability while simultaneously sustaining high quantum yields. Here, we review three basic methods for loading the macrocrystals with nanocrystals, namely relatively slow direct embedding, as well as accelerated methods of vacuum-assisted and liquid-liquid diffusion-assisted crystallization. We discuss photophysical properties of the resulting composites and present their application in light-emitting diodes as well as their utilization for plasmonics and excitonics. Finally, we present a future outlook for the science and technology of these materials.
Trial watch (2013)

Oncolytic virotherapy is emerging as a promising approach for the treatment of several neoplasms. The term "oncolytic viruses" is generally employed to indicate naturally occurring or genetically engineered attenuated viral particles that cause the demise of malignant cells while sparing their non-transformed counterparts. From a conceptual standpoint, oncolytic viruses differ from so-called "oncotropic viruses" in that only the former are able to kill cancer cells, even though both display a preferential tropism for malignant tissues. Of note, such a specificity can originate at several different steps of the viral cycle, including the entry of virions (transductional specificity) as well as their intracellular survival and replication (post-transcriptional and transcriptional specificity). During the past two decades, a large array of replication-competent and replication-incompetent oncolytic viruses has been developed and engineered to express gene products that would specifically promote the death of infected (cancer) cells. However, contrarily to long-standing beliefs, the antineoplastic activity of oncolytic viruses is not a mere consequence of the cytopathic effect, i.e., the lethal outcome of an intense, productive viral infection, but rather involves the elicitation of an antitumor immune response. In line with this notion, oncolytic viruses genetically modified to drive the local production of immunostimulatory cytokines exert more robust therapeutic effects than their non-engineered counterparts. Moreover, the efficacy of oncolytic virotherapy is significantly improved by some extent of initial immunosuppression (facilitating viral replication and spread) followed by the administration of immunostimulatory molecules (boosting antitumor immune responses). In this Trial Watch, we will discuss the results of recent clinical trials that have evaluated/are evaluating the safety and antineoplastic potential of oncolytic virotherapy.
Measurements get together (2008)

This article deals with the synchronized measurement technology that has the potential of becoming the backbone for real-time monitoring system. The secure and reliable operation of modern power systems is an increasingly challenging task due to the ever-increasing demand for electricity, the growing number of interconnections, penetration of variable renewable energy sources, and deregulated energy market conditions. Power companies in different parts of the world are therefore feeling the need for a real-time wide area monitoring, protection, and control (WAMPAC) system. Synchronized measurement technology (SMT) has the potential of becoming the backbone of this system. The major advantages of using SMT are that 1) the measurements from widely dispersed locations can be synchronized with respect to a Global Positioning System (GPS) clock, 2) voltage phase angles can be measured directly, which was so far technically infeasible, and 3) the accuracy and speed of energy management system (EMS) applications increases manifold.
Evidence accumulation relates to perceptual consciousness and monitoring (2021)

A fundamental scientific question concerns the neural basis of perceptual consciousness and perceptual monitoring resulting from the processing of sensory events. Although recent studies identified neurons reflecting stimulus visibility, their functional role remains unknown. Here, we show that perceptual consciousness and monitoring involve evidence accumulation. We recorded single-neuron activity in a participant with a microelectrode in the posterior parietal cortex, while they detected vibrotactile stimuli around detection threshold and provided confidence estimates. We find that detected stimuli elicited neuronal responses resembling evidence accumulation during decision-making, irrespective of motor confounds or task demands. We generalize these findings in healthy volunteers using electroencephalography. Behavioral and neural responses are reproduced with a computational model considering a stimulus as detected if accumulated evidence reaches a bound, and confidence as the distance between maximal evidence and that bound. We conclude that gradual changes in neuronal dynamics during evidence accumulation relates to perceptual consciousness and perceptual monitoring in humans.
Analog circuit for sound localization applications (2003)

We describe an analog CMOS circuit that computes the time (phase) delay between two 10 kHz sinusoids. This circuit can be used in sound localization applications. We realize a locking range of 10 - 170 degrees in less than 1 ms that is robust over process variations. Two receivers placed at a distance from one another intercept a sinusoidal waveform emanating from a sound source. The phase difference between the two signals is detected by the circuit, which gives an estimation of the distance of the source from the receivers. This solution is simpler and more elegant than current digital techniques that require specialized DSP hardware to be implemented in real time.
Prescribed intensity patterns from extended sources by means of a wavefront-matching procedure (2018)

One of the most interesting problems in the illumination research community is the design of optics able to generate prescribed intensity patterns with extended input sources. Such optics would be ideally applied to the current generation of extended, high-brightness, high-CRI LEDs used in general illumination, allowing reduced size of luminaires and improved efficiency. But in 3D, for non-symmetric configurations, how to design optics for prescribed intensity using extended sources remains an open question. We present an alternative approach to this problem, for the case of extended Lambertian sources, in which the design strategy is based on the definition of selected “edge wavefronts” of an illumination system. The extended emitter is represented by input wavefronts originating from selected points belonging to its edge; the prescribed intensity pattern, instead, is put in relationship with specific output edge wavefronts. The optic is calculated by requiring that it transforms the input edge wavefronts exactly into the output ones. This wavefront-matching procedure can be achieved, for example, with the Simultaneous Multiple Surfaces method (SMS). We show examples of freeform optics calculated according to the above procedure, which create non-rotationally symmetric irradiance patterns out of extended sources. A fine tuning of the output design wavefronts allows accurate control over the uniformity and extension of the output patterns, as well as on the definition of cut-offs and intensity gradients.
Software Technology for Adaptable Reliable Systems (STARS). Organization Domain Modeling (ODM) Guidebook, Version 1.0. (1995)

Abstract : This guidebook describes the Organization Domain Modeling (ODM) domain engineering method. ODM has been developed by Mark Simos of Organon Motives to systematize key aspects of the domain modeling process and provide an overall framework for a domain engineering life cycle. ODM is intended as a highly tailorable and configurable domain engineering process model, useful for diverse organizations and domains, and amenable to integration with a variety of software engineering processes, methods, and implementation technologies. In addition to focusing on the strictly technical aspects of domain engineering, the method emphasizes the importance of clearly defining the organization context within which each domain engineering effort is conducted. The primary purposes of the guidebook are to: Provide a definitive ODM reference document which promotes public understanding of the method and its applicability through in-depth descriptions of ODM concepts, processes, and workproducts. Provide substantial practical guidance for using the method by describing ODM activities in detail and offering workproduct templates and examples to get practitioners started. Provide general guidance in tailoring the method for application within a particular project or organization.
Metabolic heterogeneity signature of primary treatment-naïve prostate cancer (2017)

To avoid over- or under-treatment of primary prostate tumours, there is a critical need for molecular signatures to discriminate indolent from aggressive, lethal disease. Reprogrammed energy metabolism is an important hallmark of cancer, and abnormal metabolic characteristics of cancers have been implicated as potential diagnostic/prognostic signatures. While genomic and transcriptomic heterogeneity of prostate cancer is well documented and associated with tumour progression, less is known about metabolic heterogeneity of the disease. Using a panel of high fidelity patient-derived xenograft (PDX) models derived from hormone-naïve prostate cancer, we demonstrated heterogeneity of expression of genes involved in cellular energetics and macromolecular biosynthesis. Such heterogeneity was also observed in clinical, treatment-naïve prostate cancers by analyzing the transcriptome sequencing data. Importantly, a metabolic gene signature of increased one-carbon metabolism or decreased proline degradation was identified to be associated with significantly decreased biochemical disease-free patient survival. These results suggest that metabolic heterogeneity of hormone-naïve prostate cancer is of biological and clinical importance and motivate further studies to determine the heterogeneity in metabolic flux in the disease that may lead to identification of new signatures for tumour/patient stratification and the development of new strategies and targets for therapy of prostate cancer.
An integrated process for the production of 2,5-dimethylfuran from fructose (2015)

2,5-Dimethylfuran was produced in 92% yield from fructose in 1-butanol through a combination of dehydration over Amberlyst-15 and hydrogenolysis over Ru–Sn/ZnO.
The importance of being modified: an unrealized code to RNA structure and function (2015)

A, U, C, and G are boring. Truly, four nucleosides sometimes repeated in seemingly endless sequence has a numbing effect even in a computational and structural context. However, there is nothing boring about the chemistries and structures of post-transcriptional modifications of RNA as indicated by the rising interest and rapidly increasing numbers of publications. A plethora of papers demonstrate that modified nucleosides of RNA are functionally indispensable for RNA processing and translation. Over the last 20 years, efficiency, accuracy, enhanced activity and responsiveness are terms that accompany studies of modifications. Modifications are found in all types of RNAs, in every structural motif and in unstructured regions. The large numbers of modifications in tRNAs are quite familiar. The presence, chemistries and RNA sequence locations of modified nucleosides are only now beginning to be appreciated as both temporal—in response to environmental (internal and external) signals—and spatial, in their effect on RNA conformation, dynamics, and functions. Modifications can be recognition determinants for proteins as well as incredible determiners of RNA structure and function. Unfortunately, we tend to neglect the modified nucleosides. Using amplification and transcription in vitro that disregard the native modified nucleosides, we study the interesting low abundance, non-coding RNAs for which one molecule per cell is sometimes enough to affect gene expression. On the other hand, we lack technologies sensitive enough to explore modifications and their functions in these same low abundance RNAs. Our lack of understanding of RNA modification regrettably limits innovation in the use of modified nucleosides for synthetic biology and medicine. However, the past two decades have led to some of the most interesting of findings.