gebhart/patrepeval huggingface dataset:
Identification of Cleavage Sites Leading to the Shed Form of the Anti-Aging Protein Klotho (2014)

Membrane protein shedding is a critical step in many normal and pathological processes. The anti-aging protein klotho (KL), mainly expressed in kidney and brain, is secreted into the serum and CSF, respectively. KL is proteolytically released, or shed, from the cell surface by ADAM10 and ADAM17, which are the α-secretases that also cleave the amyloid precursor protein and other proteins. The transmembrane KL is a coreceptor with the FGF receptor for FGF23, whereas the shed form acts as a circulating hormone. However, the precise cleavage sites in KL are unknown. KL contains two major cleavage sites: one close to the juxtamembrane region and another between the KL1 and KL2 domains. We identified the cleavage site involved in KL release by mutating potential sheddase(s) recognition sequences and examining the production of the KL extracellular fragments in transfected COS-7 cells. Deletion of amino acids T958 and L959 results in a 50-60% reduction in KL shedding, and an additional P954E mutation results in further reduction of KL shedding by 70-80%. Deletion of amino acids 954-962 resulted in a 94% reduction in KL shedding. This mutant also had moderately decreased cell surface expression, yet had overall similar subcellular localization as that of WT KL, as demonstrated by immunofluorescence. Cleavage-resistant mutants could function as a FGFR coreceptor for FGF23, but they lost activity as a soluble form of KL in proliferation and transcriptional reporter assays. Cleavage between the KL1 and KL2 domains is dependent on juxtamembrane cleavage. Our results shed light onto mechanisms underlying KL release from the cell membrane and provide a target for potential pharmacologic interventions aimed at regulating KL secretion.
Datalution: a tool for continuous schema evolution in NoSQL-backed web applications (2016)

When an incremental release of a web application is deployed, the structure of data already persisted in the production database may no longer match what the application code expects. Traditionally, eager schema migration is called for, where all legacy data is migrated in one go. With the growing popularity of schema-flexible NoSQL data stores, lazy forms of data migration have emerged: Legacy entities are migrated on-the-fly, one at-a-time, when they are loaded by the application. In this demo, we present Datalution, a tool demonstrating the merits of lazy data migration. Datalution can apply chains of pending schema changes, due to its Datalog-based internal representation. The Datalution approach thus ensures that schema evolution, as part of continous deployment, is carried out correctly.
Production of recombinant proteins in E. coli by the heat inducible expression system based on the phage lambda pL and/or pR promoters (2010)

The temperature inducible expression system, based on the pL and/or pR phage lambda promoters regulated by the thermolabile cI857 repressor has been widely use to produce recombinant proteins in prokaryotic cells. In this expression system, induction of heterologous protein is achieved by increasing the culture temperature, generally above 37 degrees C. Concomitant to the overexpression of heterologous protein, the increase in temperature also causes a variety of complex stress responses. Many studies have reported the use of such temperature inducible expression system, however only few discuss the simultaneous stress effects caused by recombinant protein production and the up-shift in temperature. Understanding the integral effect of such responses should be useful to develop improved strategies for high yield protein production and recovery. Here, we describe the current status of the heat inducible expression system based on the pL and/or pR lambda phage promoters, focusing on recent developments on expression vehicles, the stress responses at the molecular and physiological level that occur after heat induction, and bioprocessing factors that affect protein overexpression, including culture operation variables and induction strategies.
Flight Control of a Quadrotor Vehicle Subsequent to a Rotor Failure (2014)

In this paper, the problem of designing a control law in case of rotor failure in quadrotor vehicles is addressed. First, a nonlinear mathematical model for a quadrotor vehicle is derived, which includes translational and rotational dynamics. Then a robust feedback linearization controller is developed, which sacrifices the controllability of the yaw state due to rotor failure to linearize the closed-loop system around a working point, where roll and pitch angles are zero and the angular speed around the vertical axis is a nonzero constant. An loop shaping technique is adopted to achieve regulation of these variables around the chosen working point. Finally, an outer loop is proposed for achieving control of the linear displacement under the assumption of small angles approximation for the pitch and roll angles. The proposed control strategy allows the vehicle to use the remaining three functional rotors to enter a constant angular speed around its vertical axis, granting stability and representing an effective way to deal with a rotor failure in quadrotor vehicles.
Achieving overlay budgets for double patterning (2009)

The problem of the alignment tree for double patterning (DP) is presented. When the 2nd DP exposure is aligned to the underlying zero layer, the space CD uniformity is shown to be well outside the budget for the 32 nm HP node. Aligning the 2nd DP layer to the zero layer gives better overlay results, but aligning the 2nd DP pattern to the 1st DP pattern gives results well within the overlay requirements for the 32 nm HP. Aligning the 2nd DP layer to the 1st DP layer is recommended to give the best CD uniformity and overlay results. Experimental results show, qualitatively, the CD uniformity is significantly worse when the 2nd pattern is aligned to the zero layer, but the overlay for both alignment trees could be corrected to roughly the same levels. The raw overlay data shows a significantly different signature for the two alignment trees, possibly caused by alignment mark signal differences between the marks on the zero and 1st layers, or distortion of the zero layer after the first etch. The requirements for a DP exposure tool were reviewed and can be summarized as improved dose control, improved overlay performance, and significantly higher throughput.
Inhibition of serotonin uptake by optical isomers of fluoxetine (1985)

Abstract The optical isomers of fluoxetine, a selective inhibitor of serotonin (5‐hydroxytryptamine, 5HT) uptake, have been compared pharmacologically. As inhibitors of 3 H‐5HT uptake in cortical synaptosomes and of 3 H‐fluoxetine binding in cortical membranes, the (+)‐isomer of fluoxetine was slightly more potent than the (−)‐isomer. The potencies to inhibit 3 H‐5HT uptake ex vivo in synaptosomal preparations of cerebral cortex and brain stem were about the same, except that the (−)‐isomer had a much shorter duration of action than the (+)‐isomer in rats.
Dependence clusters in source code (2009)

A dependence cluster is a set of program statements, all of which are mutually inter-dependent. This article reports a large scale empirical study of dependence clusters in C program source code. The study reveals that large dependence clusters are surprisingly commonplace. Most of the 45 programs studied have clusters of dependence that consume more than 10% of the whole program. Some even have clusters consuming 80% or more. The widespread existence of clusters has implications for source code analyses such as program comprehension, software maintenance, software testing, reverse engineering, reuse, and parallelization.
Large Blue Shift of the Biexciton State in Tellurium Doped CdSe Colloidal Quantum Dots (2008)

The exciton-exciton interaction energy of tellurium doped CdSe colloidal quantum dots is experimentally investigated. The dots exhibit a strong Coulomb repulsion between the two excitons, which results in a huge measured biexciton blue shift of up to 300 meV. Such a strong Coulomb repulsion implies a very narrow hole wave function localized around the defect, which is manifested by a large Stokes shift. Moreover, we show that the biexciton blue shift increases linearly with the Stokes shift. This result is highly relevant for the use of colloidal QDs as optical gain media, where a large biexciton blue shift is required to obtain gain in the single exciton regime.
.pi.-Dicarbollyl derivatives of the transition metals. Metallocene analogs (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.pi.-Dicarbollyl derivatives of the transition metals. Metallocene analogsM. Frederick Hawthorne, Donald Clifford Young, Timothy D. Andrews, David V. Howe, Richard L. Pilling, A. Denise Pitts, Marten Reintjes, Leslie F. Warren Jr., and Patrick A. WegnerCite this: J. Am. Chem. Soc. 1968, 90, 4, 879–896Publication Date (Print):February 14, 1968Publication History Published online1 May 2002Published inissue 14 February 1968https://pubs.acs.org/doi/10.1021/ja01006a008https://doi.org/10.1021/ja01006a008research-articleACS PublicationsRequest reuse permissionsArticle Views1472Altmetric-Citations583LEARN 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
Long-term patency of venous sinus stents for idiopathic intracranial hypertension (2013)

Background Recent reports suggest that placement of a venous sinus stent improves symptoms in selected patients with idiopathic intracranial hypertension (IIH). We report our evaluation of the long-term patency of venous stents placed for IIH. Methods We retrospectively reviewed our clinical database for 30 patients (mean age 33±10 years) with IIH who underwent placement of 36 venous sinus stents between October 2006 and December 2012. Relevant clinical, demographic and radiographic data were extracted after review of these records. All patients underwent retrograde venography to confirm a >50% stenosis and a trans-stenosis pressure gradient. Follow-up catheter angiography was performed beginning 3 months after the procedure. Results Follow-up imaging was available for 23 (77%) of the 30 patients (mean 23 months). For seven patients, angiographic follow-up of >2 years (mean 45 months) was available. All stents remained patent with mild (<25%) in-stent stenosis observed in four patients. In five patients, however, we observed a narrowing of the sinus proximal to the stent. Although no patient underwent repeat stent placement for persistent or recurrent symptoms, cerebrospinal fluid diversion was performed in five cases. Conclusions Venous sinus stent placement has emerged as a promising treatment option for the subgroup of patients with IIH with a pressure gradient across a stenotic venous sinus. We observed long-term patency of all stents placed in this patient population. Further prospective investigation is necessary to improve our understanding of the phenomenon of sinus narrowing upstream of a patent stent and to establish definitively the long-term clinical efficacy of venous sinus stent placement for IIH.
Protective effect of mitochondria-targeted peptide MTP-131 against oxidative stress-induced apoptosis in RGC-5 cells (2017)

The retina of the human eye is extremely vulnerable to oxidative damage. Previous studies have demonstrated that oxidative stress is the predominant mechanism associated with the pathogenesis of age‑related macular degeneration, diabetic retinopathy, glaucoma and retinitis pigmentosa. MTP‑131, a novel mitochondria‑targeted peptide, has been demonstrated to specifically concentrate in the inner mitochondria membrane and to exhibit remarkable antioxidant effects both in vitro and in animal models. In the present study, the protective effect of MTP‑131 was evaluated in response to hydrogen peroxide (H2O2)‑induced oxidative damage in a retinal ganglion cell line, RGC‑5. Cell viability was measured by lactate dehydrogenase (LDH) assay. Changes of mitochondrial membrane potential and generation of intracellular reactive oxygen species (ROS) were measured by flow cytometry and confocal microscopy, respectively. Annexin V‑fluorescein isothiocyanate/propidium iodide staining was used for assessment of apoptosis. Release of cytochrome c was analyzed by confocal microscopy. Pretreatment of cells with MTP‑131 inhibited H2O2‑induced cytotoxicity and reduced LDH release in a dose‑dependent manner, compared with cells treated with H2O2 alone. Mitochondrial depolarization and ROS generation were also prevented by MTP‑131 pretreatment. In addition, MTP‑131 pretreatment inhibited cytochrome c release from mitochondria to cytoplasm, and significantly reduced apoptosis in RGC‑5 cells, compared with cells treated with H2O2 alone. In conclusion, mitochondria‑targeted peptide MTP‑131 exhibited a protective effect against oxidative stress‑induced apoptosis in RGC‑5 cells, which may provide a novel approach for the treatment of age‑associated retinal diseases.
A Survey of Multi-Access Edge Computing in 5G and Beyond: Fundamentals, Technology Integration, and State-of-the-Art (2019)

Driven by the emergence of new compute-intensive applications and the vision of the Internet of Things (IoT), it is foreseen that the emerging 5G network will face an unprecedented increase in traffic volume and computation demands. However, end users mostly have limited storage capacities and finite processing capabilities, thus how to run compute-intensive applications on resource-constrained users has recently become a natural concern. Mobile edge computing (MEC), a key technology in the emerging fifth generation (5G) network, can optimize mobile resources by hosting compute-intensive applications, process large data before sending to the cloud, provide the cloud computing capabilities within the radio access network (RAN) in close proximity to mobile users, and offer context-aware services with the help of RAN information. Therefore, MEC enables a wide variety of applications, where the real-time response is strictly required, e.g., driverless vehicles, augmented reality, robotics, and immerse media. Indeed, the paradigm shift from 4G to 5G could become a reality with the advent of new technological concepts. The successful realization of MEC in the 5G network is still in its infancy and demands for constant efforts from both academic and industry communities. In this survey, we first provide a holistic overview of MEC technology and its potential use cases and applications. Then, we outline up-to-date researches on the integration of MEC with the new technologies that will be deployed in 5G and beyond. We also summarize testbeds and experimental evaluations, and open source activities, for edge computing. We further summarize lessons learned from state-of-the-art research works as well as discuss challenges and potential future directions for MEC research.
The Importance of Free-Hand Sketching in Conceptual Design: Automatic Sketch Input (1993)

Abstract Free-hand drawing (sketching) is important in the conceptual design stage. Current CAD tools are not well suited to sketching. This statement is supported by an examination of free-hand drawing, a brief overview of some commercially available drawing packages and a discussion of other authors’ work in this area. Finally we present objectives for automatic sketch input and their partial realisation in our drawing system called Easel.
Exterminating bugs via collective information recycling (2011)

End-user software is executed billions of times daily, but the corresponding execution details (“by-products”) are discarded. We hypothesize that, if suitably captured and aggregated, these by-products could substantially speed up the process of testing programs and proving them correct. Ironically, both testing and debugging involve simulating real-world conditions and executions, in essence trying to recreate in the lab some of these (previously available, but discarded) execution details. This position paper proposes a way to recoup the execution information that is lost during everyday software use, aggregate it, and automatically turn it into bug fixes and proofs. The goal is to enable software to improve itself by “learning” from past failures and successes, leveraging the information-rich execution by-products that today are being wasted. We view every execution of a program as a test run and aggregate executions across the lifetime of a program into one gigantic test suite - i.e., we remove the distinction between software use and software testing and verification - with the purpose of substantially reducing software bug density.
Global Transcriptional Responses of Fission Yeast to Environmental Stress (2003)

We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression profiles of all known and predicted genes in response to five stress conditions: oxidative stress caused by hydrogen peroxide, heavy metal stress caused by cadmium, heat shock caused by temperature increase to 39 degrees C, osmotic stress caused by sorbitol, and DNA damage caused by the alkylating agent methylmethane sulfonate. We define a core environmental stress response (CESR) common to all, or most, stresses. There was a substantial overlap between CESR genes of fission yeast and the genes of budding yeast that are stereotypically regulated during stress. CESR genes were controlled primarily by the stress-activated mitogen-activated protein kinase Sty1p and the transcription factor Atf1p. S. pombe also activated gene expression programs more specialized for a given stress or a subset of stresses. In general, these "stress-specific" responses were less dependent on the Sty1p mitogen-activated protein kinase pathway and may involve specific regulatory factors. Promoter motifs associated with some of the groups of coregulated genes were identified. We compare and contrast global regulation of stress genes in fission and budding yeasts and discuss evolutionary implications.
Poor Mexican Cinema, So Far From "Cahiers du Cinéma" and So Close to Latino U.S.A.: a Cantankerous Essay (2003)

The title of this essay is inspired by a remark attributed to Porfirio Díaz, dictatorial president of Mexico from 1876 to 1910. The actual quote is ""Poor Mexico, so far from God and so close to the United States"-a reflection on the always problematic relationship between the two neighboring countries. Of course, I am not implying that Cahiers du Cinémaenjoys any kind of divine status. I simply use it as a symbol of serious international cinema, where films are appreciated for their individuality and artistry. The title should also broadcast that this is an opinion piece (well, an unabashed rant, really-especially in the reference notes) against certain broad-based cultural perceptions in the United States and how they may affect the distribution of foreign and domestic movies.
Messages versus messengers in distributed programming (2002)

Messengers are autonomous objects, each capable of navigating through the underlying network and performing various tasks at each node. Messenger applications are written using navigational commands rather than the send/receive primitives of conventional message-passing approaches. In this paper we contrast the two programming styles. The navigational style generally results in a smaller semantic gap between abstract algorithm descriptions and their actual implementations, which makes programs easier to construct, understand, and maintain. Other advantages of the navigational programming style include the ability to compute in unknown or dynamically changing network topologies.
Role of lipopolysaccharide and tumor necrosis factor-alpha in induction of hepatocyte necrosis (1995)

The occurrence of acute hepatic failure during systemic inflammatory response syndrome (SIRS) is related to the extent of hepatocyte (HC) damage and cell death resulting from necrosis or apoptosis. We hypothesized that proinflammatory mediators such as lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-alpha) can, either directly or indirectly through neutrophil (PMN) and Kupffer cell (KC) activation, induce HC damage and cell death, and that the mechanism is cellular necrosis rather than apoptosis. The results in this study demonstrated that LPS and TNF-alpha alone and in combination are directly cytotoxic to cultured rat HC as indicated by the hepatocellular enzyme release and HC necrosis. However, LPS and TNF-alpha, in the presence of sodium arsenite (a heat shock inducer), were unable to induce HC apoptosis. Both KC and PMN activated by either LPS or TNF-alpha induced significant hepatocellular enzyme release and HC necrosis, which was dependent on the ratio of KC and PMN to HC. It is concluded that LPS and TNF-alpha may play a central role in the development of acute hepatic failure after severe trauma and sepsis by directly or indirectly inducing HC necrosis rather than apoptosis.
Anti‐circumsporozoite protein antibodies measure age related exposure to malaria in Kataragama, Sri Lanka (1992)

Antibodies to two peptides DDAAD and (NANP)40 representing the repetitive sequence of circumsporozoite antigens (CS protein) of P. vivax and P. falciparum respectively were measured in a cohort of 149 and 107 individuals respectively at four, 6 monthly blood surveys performed on residents of Kataragama, a P. vivax malaria endemic region in southern Sri Lanka. The prevalence of antibodies to the CS protein of both species was relatively low being less than 20% to either peptide in the population as a whole, this being consistent with the low entomological inoculation rates in the area. A marked age related prevalence pattern was evident, with the prevalence of antibodies increasing with age to reach between 25 to 30% in the 25-50 year age group in both P. vivax and P. falciparum. The population had had a life long exposure to P. vivax malaria but not to P. falciparum, an epidemic of which occurred in this region a few months prior to the beginning of this study. Nevertheless, the age-related prevalence of these antibodies was identical with respect to the two species. This suggests that the age-related prevalence pattern reflected differences in inoculation rates between the age groups due to differences in exposure to inoculation rather than an age acquired response resulting from a cumulative experience over several years. An analysis of antibody prevalence in individuals showed first, that sporozoite inoculations must have been clustered rather than homogeneously distributed in the population and secondly, that sero-conversion did not correlate with malaria infections in these individuals.
Undergraduate organic and polymer lab experiments that exemplify structure determination by NMR (1991)

Where in the curriculum is the best place to teach experimental NMR methods that are so essential to chemists and chemistry? These authors are of the opinion that NMR must be given more than a cursory introduction involving a single experiment, and present a series of experiments.