gebhart/patrepeval huggingface dataset:
PrpE, a PPP protein phosphatase from Bacillus subtilis with unusual substrate specificity (2002)

Bacillus subtilis is a Gram-positive bacterium with a relatively large number of protein phosphatases. Previous studies have shown that some Ser/Thr phosphatases play an important role in the life cycle of this bacterium [Losick and Stragier (1992) Nature (London) 355, 601-604; Yang, Kang, Brody and Price (1996) Genes Dev. 10, 2265-2275]. In this paper, we report the biochemical properties of a putative, previously uncharacterized phosphatase, PrpE, belonging to the PPP family. This enzyme shares homology with other PPP phosphatases as well as with symmetrical diadenosine tetraphosphatases related to ApaH (symmetrical Ap(4)A hydrolase) from Escherichia coli. A His-tagged recombinant PrpE was purified from E. coli and shown to have Ni(2+)-dependent and okadaic acid-resistant phosphatase activity against a synthetic phosphorylated peptide and hydrolase activity against diadenosine 5',5"'-tetraphosphate. Unexpectedly, PrpE was able to remove phosphate from phosphotyrosine, but not from phosphothreonine or phosphoserine.
Controllable plasma membrane poration by pulsing tandem microbubble. (2010)

Understanding the dynamic interaction of cavitation bubbles with biological tissue is central to the effective and safe application of therapeutic ultrasound in clinical medicine. Coupled oscillation of two laser generated microbubbles (maximum radius = 28 μm) in constrained media and associated shear stresses are investigated experimentally. Bubble-bubble interaction in a microchannel of 25-μm height is observed using high-speed video cameras and μPIV technique. Two liquid micro-jets moving in opposite directions can be generated when the second bubble is produced at the maximum size of the first one. The interaction of these tandem microbubbles with single cell leads to controllable poration of adjacent cell membrane and dye uptake. Micro-PIV data are compared with cell viability at various bubble-cell distances and azimuthal orientations. This method provides a new approach for highly selective cell treatment in situ applicable to targeted microinjection of macromolecules and gene vectors in microfluidics devices. [This work was supported in part by NIH.]
Interleukin 1 induces endothelial cell synthesis of plasminogen activator inhibitor. (1986)

Human endothelial cells activated with IL-1 express a surface membrane-oriented procoagulant generating system characterized by increased tissue factor synthesis and decreased thrombomodulin activity. We now report that IL-1 also stimulates endothelial cell synthesis of plasminogen activator inhibitor. This array of IL-1-induced activities shifts the balance at the endothelial cell surface to a prothrombotic influence and may reflect an early response of the blood vessel wall to injury.
Supplementary Figure 3 from Tumor-Promoting Desmoplasia Is Disrupted by Depleting FAP-Expressing Stromal Cells (2023)

&lt;p&gt;FAP-CAR T cells restrict AE17.OVA tumor growth through reduced proliferation, increased apoptosis and altered tumor stroma.&lt;/p&gt;
Rapid access to rare natural pyranosides using 1,2-diacetal protected intermediates (1997)

The synthesis of six rare methylpyranosides from common manno- and galacto-pyranoside starting materials has been achieved by the expedient use of 1,2-diacetal protecting group methodology highlighting its compatibility with a number of other common synthetic procedures.
Identification of the Cystic Fibrosis Gene (1990)

ROMMENS, JOHANNA M.; IANNUZZI, MICHAEL C.; KEREM, BAT-SHEVA; DRUMM, MITCHELL L.; MELMER, GEORG; DEAN, MICHAEL; ROXMAHEL, RICHARD; COLE, JEFFERY L.; KENNEDY, DARA; HIDAKA, NORIKO; ZSIGA, MARTHA; BUCHWALD, MANUEL; RIORDAN, JOHN R.; TSUI, LAP-CHEE; COLLINS, FRANCIS S.Author Information
Wafer-fused 1550-nm band VCSELs with fundamental mode output exceeding 6 mW (2008)

We report on 1550-nm fused VCSELs with 6.8 mW SM power at 0degC and 2.6-mW at 80degC. These devices can be tuned with current by 15 nm.
Preparation, characterization, and intramolecular electron transfer in pentaammineruthenium histidine-26 cytochrome b5 derivatives: role of the intervening medium in long-range donor-acceptor electronic coupling (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation, characterization, and intramolecular electron transfer in pentaammineruthenium histidine-26 cytochrome b5 derivatives: role of the intervening medium in long-range donor-acceptor electronic couplingBradley A. Jacobs, Marcia R. Mauk, Walter D. Funk, Ross T. A. MacGillivray, A. Grant Mauk, and Harry B. GrayCite this: J. Am. Chem. Soc. 1991, 113, 12, 4390–4394Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/ja00012a003https://doi.org/10.1021/ja00012a003research-articleACS PublicationsRequest reuse permissionsArticle Views104Altmetric-Citations24LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
JAVACAM: trimming Java down to size (1998)

JavaCam is an embedded sensor device that connects to the Internet and operates with as little as 1.5 Mbytes of total system memory. To determine how small a Java system we could build that would still support a Java Virtual Machine, we wrote the Java Nanokernel, a very thin operating system. We then ported Sun's Java Development Kit 1.0.1 to JN. This port included the complete Java language and all of the core Java packages except java.awt. In this article, we begin by describing JN and the port of JDK 1.0.1 to it. We then describe our first significant application, JavaCam, a camera that is remotely programmable in Java and Internet accessible.
Survival of African Swine Fever Virus in Excretions from Pigs Experimentally Infected with the Georgia 2007/1 Isolate (2015)

African swine fever virus (ASFV) causes a lethal haemorrhagic disease of swine which can be transmitted through direct contact with infected animals and their excretions or indirect contact with contaminated fomites. The shedding of ASFV by infected pigs and the stability of ASFV in the environment will determine the extent of environmental contamination. The recent outbreaks of ASF in Europe make it essential to develop disease transmission models in order to design effective control strategies to prevent further spread of ASF. In this study, we assessed the shedding and stability of ASFV in faeces, urine and oral fluid from pigs infected with the Georgia 2007/1 ASFV isolate. The half-life of infectious ASFV in faeces was found to range from 0.65 days when stored at 4°C to 0.29 days when stored at 37°C, while in urine it was found to range from 2.19 days (4°C) to 0.41 days (37°C). Based on these half-lives and the estimated dose required for infection, faeces and urine would be estimated to remain infectious for 8.48 and 15.33 days at 4°C and 3.71 and 2.88 days at 37°C, respectively. The half-life of ASFV DNA was 8 to 9 days in faeces and 2 to 3 days in oral fluid at all temperatures. In urine, the half-life of ASFV DNA was found to be 32.54 days at 4°C decreasing to 19.48 days at 37°C. These results indicate that ASFV in excretions may be an important route of ASFV transmission.
Properties of a “Split-and-Stuttering” Module of an Assembly Line Polyketide Synthase (2021)

Notwithstanding the "one-module-one-elongation-cycle" paradigm of assembly line polyketide synthases (PKSs), some PKSs harbor modules that iteratively elongate their substrates through a defined number of cycles. While some insights into module iteration, also referred to as "stuttering", have been derived through <i>in vivo</i> and <i>in vitro</i> analysis of a few PKS modules, a general understanding of the mechanistic principles underlying module iteration remains elusive. This report serves as the first interrogation of a stuttering module from a <i>trans</i>-AT subfamily PKS that is also naturally split across two polypeptides. Previous work has shown that Module 5 of the NOCAP (<u><b>noc</b></u>ardiosis <u><b>a</b></u>ssociated <u><b>p</b></u>olyketide) synthase iterates precisely three times in the biosynthesis of its polyketide product, resulting in an all-<i>trans</i>-configured triene moiety in the polyketide product. Here, we describe the intrinsic catalytic properties of this NOCAP synthase module. Through complementary experiments <i>in vitro</i> and in <i>E. coli</i>, the "split-and-stuttering" module was shown to catalyze up to five elongation cycles, although its dehydratase domain ceased to function after three cycles. Unexpectedly, the central olefinic group of this truncated product had a <i>cis</i> configuration. Our findings set the stage for further in-depth analysis of a structurally and functionally unusual PKS module with contextual biosynthetic plasticity.
The structure of the external rectus eye muscles of the carpet shark Cephaloscyllium isabella. (1984)

The external rectus muscles of the carpet shark Cephaloscyllium isabella contain two types of muscle fibre. A core of large white fibres which have regular myofibrils with extensive sarcoplasmic reticulum, triads located at the Z disc and a pronounced H band and M line. Mitochondria are frequent but tend to be smaller and less abundant than mitochondria of the smaller red fibre type. The red fibres which surround the central region are rich in mitochondria, have little sarcoplasmic reticulum and triads which are infrequent and dispersed. Sarcomere banding of red fibres is characterised by a faint H band and M line while the Z disc is thick in comparison with that found on the white muscle fibre sarcomere.
SINGLE CHIP INTEGRATED VIRAL RNA EXTRACTION AND RT-PCR FOR INFECTIOUS DISEASE IDENTIFICATION FROM BLOOD SAMPLE (2010)

This paper presents an integrated lab-on-a-chip (LOC) microdevice that includes viral ribonucleic acid (RNA) extraction from blood samples and RNA amplification through a one-step reverse transcription-polymerase chain reaction (RT-PCR) method for application on point-of-care (POC) infectious disease diagnostics.
The Role of Somatic Hypermutation in the Generation of Antibody Diversity (1989)

The immune system is capable of establishing an enormous repertoire of antibodies before its first contact with antigen. Most antibodies that express germ-line sequences are of relatively low affinity. Once antigen enters the system, it stimulates a somatic mutational mechanism that generates antibodies of higher affinity and selects for the expression of those antibodies to produce a more effective immune response. The details of the mechanism and regulation of somatic hypermutation remain to be elucidated.
Bar coding a must for patient safety (2002)

Journal Article Bar coding a must for patient safety Get access Dennis A. Tribble, Pharm.D. Dennis A. Tribble, Pharm.D. Chief Technology Officer ForHealth Technologies, Inc. 840 Research Parkway, Suite 430 Oklahoma City, OK 73104 Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 59, Issue 7, 1 April 2002, Page 667, https://doi.org/10.1093/ajhp/59.7.667 Published: 01 April 2002
The Efficacy, Longevity, and Safety of Combined Radiofrequency Treatment and Hyaluronic Acid Filler for Skin Rejuvenation (2014)

A new device incorporating RF treatment before HA filler injection may represent a biocompatible and long-lasting advance in skin rejuvenation.
Switched-Current Circuit Design Techniques (1993)

This chapter builds on earlier chapters (Chapters 3 and 4) which described architectures and non-idealities of basic switched-current circuits. In Chapter 3, basic cells were developed (delay, integrator and differentiator modules) and their algorithmic behaviour was described in terms of finite difference equations. In Chapter 4, the effects on circuit performance of imperfections in the MOS transistors used to build the circuits were analysed. In this chapter, circuit techniques are described which enhance performance in terms of precision, dynamic range and linearity.
Hierarchical Wavelet Representations of Ship Radar Returns (1993)

In this paper we investigate the problem of efficient representations of large databases of pulsed radar returns in order to economize memory requirements and minimize search time. We use synthetic radar returns from ships as the experimental data. We motivate wavelet multiresolution representations of such returns. We develop a novel algorithm for hierarchically organizing the database, which utilizes a multiresolution wavelet representation working in synergy with a Tree Structured Vector Quantizer (TSVQ), utilized in its clustering mode. The tree structure is induced by the multiresolution decomposition of the pulses. The TSVQ design algorithm is of the "greedy" type. We show by experimental results that the combined algorithm results in data search times that are logarithmic in the number of terminal tree nodes, with negligible performance degradation (as measured by distortion-entropy curves) from the full search vector quantization. Furthermore we show that the combined algorithm provides an efficient indexing scheme (with respect to variations in aspect, elevation and pulsewidth) for radar data which is equivalent to a multiresolution aspect graph or a reduced target model. Promising experimental results are reported using high quality synthetic data.
An Accountability Interface for the Internet (2007)

The Internet provides no information on the fate of transmitted packets, and end systems cannot determine who is responsible for dropping or delaying their traffic. As a result, they cannot verify that their ISPs are honoring their service level agreements, nor can they react to adverse network conditions appropriately. While current probing tools provide some assistance in this regard, they only give feedback on probes, not actual traffic. Moreover, service providers could, at any time, render their network opaque to such tools. We propose an explicit accountability interface, through which ISPs can pro-actively supply feedback to traffic sources on loss and delay, at administrative-domain granularity. Notably, our interface is resistant to ISP lies and can be implemented with a modest NetFlow modification. On our Click-based prototype, playback of real traces from a Tier-1 ISP reveals less than 2% bandwidth overhead. Finally, our proposal benefits not only end systems, but also ISPs, who can now control the amount and quality of information revealed about their internals.
Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon (2011)

Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical ~20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluorescent protein (GFP) stop codon, GFP expression was similarly reduced. Rap1p mediated this down-regulation, as shown by mutagenesis and chromatin immunoprecipitation. A regular threefold drop is observed in different contexts, suggesting utility for synthetic circuits. A large reduction of RNAP II occupancy on the CO-Ty1 construct was observed 3' to the identified Rap1p site and a novel 3' truncated RNA species was observed. We propose a novel mechanism of transcriptional regulation by Rap1p whereby it serves as a transcriptional roadblock when bound to transcription unit sequences.
Plasma gun injection in the Proto-Cleo stellarator (1981)

Gun injection of plasma parallel to the magnetic field in the Proto-Cleo stellarator results in particle confinement times of 3.5 – 4 ms while injection of plasma perpendicular to the magnetic field results in confinement times of 1.5 – 2 ms. Calculations of confinement times based on convective-cell theory that includes shear show good agreement with experimentally measured values.
Error Bounds for Online Predictions of Linear-Chain Conditional Random Fields: Application to Activity Recognition for Users of Rolling Walkers (2011)

Linear-Chain Conditional Random Fields (L-CRFs) are a versatile class of models for the distribution of a sequence of hidden states ("labels") conditional on a sequence of observable variables. In general, the exact conditional marginal distributions of the labels can be computed only after the complete sequence of observations has been obtained, which forbids the prediction of labels in an online fashion. This paper considers approximations of the marginal distributions which only take into account past observations and a small number of observations in the future. Based on these approximations, labels can be predicted close to real-time. We establish rigorous bounds for the marginal distributions which can be used to assess the approximation error at runtime. We apply the results to an L-CRF which recognizes the activity of rolling walker users from a stream of sensor data. It turns out that if we allow for a prediction delay of half of a second, the online predictions achieve almost the same accuracy as the offline predictions based on the complete observation sequences.
Computational and experimental evidence to the permeability of withanolides across the normal cell membrane (2019)

Abstract Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in the clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs - withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that withaferin-A, but not withanone, could proficiently transverse through the model membrane. The free energy profiles obtained were in accordance with the physico-chemical properties of the investigated drug molecules. It was observed that the polar head group of the bilayer exhibits high resistance for the passage of withanone as compared to withaferin-A, while the interior of the membrane behaves similarly for both withanolides. The solvation analysis revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force. The impact of the favorable interaction of terminal oxygen (O5) of withaferin-A with the phosphate of the membrane led to its smooth passage across the bilayer. The computational predictions were validated by raising and recruiting unique antibodies that react to withaferin-A and withanone. Further, the time-lapsed analyses of control and treated human normal and cancer cells, demonstrated proficient permeation of withaferin-A, but not withanone, through normal cells. These data strongly validated our computational method for predicting permeability and hence bioavailability of candidate compounds in the drug development process. Statement of significance What determines the bioavailability of a drug? Does the ability to cross cell membrane determine this? A combined simulation/experimental study of the permeability of two natural drugs - withanolides (Wi-A and Wi-N) across the cell membrane was conducted. In the computational portion of the study, steered MD simulations were performed to investigate the propensity of the two molecules to permeate across the cell. It is found that Wi-A proceeds relatively simply across the cell compared to Wi-N. This trend was found to be consistent with experiment. This work is an important step towards understanding the molecular basis of permeability of natural drug molecules.
A/C1166 Gene Polymorphism of the Angiotensin II Type 1 Receptor (AT1) and Ambulatory Blood Pressure: The Ohasama Study. (2003)

We previously investigated the relation between hypertension and each of three major genetic polymorphisms in the renin-angiotensin (AGT)-aldosterone system (R-A-A), AGT M235T, angiotensin convert enzyme (ACE) I/D, and CYP11B2 -344C/T, by means of ambulatory blood pressure (ABP) monitoring in a general Japanese population (the Ohasama Study). A/C1166 gene polymorphism in the 3' untranslated region of the angiotensin II type 1 receptor (AT1) gene is the final remaining major target in R-A-A to be examined in the Ohasama Study population. In the present study, the AT1 A/C1166 polymorphism was genotyped by the TaqMan polymerase chain reaction (PCR) method or restriction fragment length polymorphism (RFLP) in 802 Japanese subjects aged 40 and over, who were previously genotyped for the AGT M235T, ACE D/I, CYP11B2 -344C/T polymorphisms. The AA genotype, AC genotype, and CC genotype were present in 678 (84.5%), 121 (15.1%), and 3 (0.4%) of subjects, respectively. Since the frequency of the C allele was quite low (0.079), the genotypes were classified according to the presence or absence of the C allele. Although daytime blood pressure (BP) was higher in subjects with the C allele, the difference was not statistically significant after adjusting for age, gender, body mass index, and smoking status. No significant difference was noted in the prevalence of cardiovascular diseases or nocturnal BP decline between the two groups. These results indicated that AT1 A/C1166 polymorphism was not associated with any clinical parameters associated with hypertension or atherosclerosis in the Japanese population.
Exploiting syntactic structure for language modeling (1998)

The paper presents a language model that develops syntactic structure and uses it to extract meaningful information from the word history, thus enabling the use of long distance dependencies. The model assigns probability to every joint sequence of words-binary-parse-structure with headword annotation and operates in a left-to-right manner -therefore usable for automatic speech recognition. The model, its probabilistic parameterization, and a set of experiments meant to evaluate its predictive power are presented; an improvement over standard trigram modeling is achieved.
A Framework for Exploring Categorical Data (2009)

In this paper, we present a framework for categorical data analysis which allows such data sets to be explored using a rich set of techniques that are only applicable to continuous data sets. We introduce the concept of separability statistics in the context of exploratory categorical data analysis. We show how these statistics can be used as a way to map categorical data to continuous space given a labeled reference data set. This mapping enables visualization of categorical data using techniques that are applicable to continuous data. We show that in the transformed continuous space, the performance of the standard k-nn based outlier detection technique is comparable to the performance of the k-nn based outlier detection technique using the best of the similarity measures designed for categorical data. The proposed framework can also be used to devise similarity measures best suited for a particular type of data set.