gebhart/patrepeval huggingface dataset:
Stability engineering of scFvs for the development of bispecific and multivalent antibodies (2010)

Single-chain Fvs (scFvs) are commonly used building blocks for creating engineered diagnostic and therapeutic antibody molecules. Bispecific antibodies (BsAbs) hold particular interest due to their ability to simultaneously bind and engage two distinct targets. We describe a technology for producing stable, scalable IgG-like bispecific and multivalent antibodies based on methods for rapidly engineering thermally stable scFvs. Focused libraries of mutant scFvs were designed using a combination of sequence-based statistical analyses and structure-, and knowledge-based methods. Libraries encoding these designs were expressed in E. coli and culture supernatants-containing soluble scFvs screened in a high-throughput assay incorporating a thermal challenge prior to an antigen-binding assay. Thermally stable scFvs were identified that retain full antigen-binding affinity. Single mutations were found that increased the measured T(m) of either the V(H) or V(L) domain by as much as 14 degrees C relative to the wild-type scFv. Combinations of mutations further increased the T(m) by as much as an additional 12 degrees C. Introduction of a stability-engineered scFv as part of an IgG-like BsAb enabled scalable production and purification of BsAb with favorable biophysical properties.
DNA-Mediated Transfer of an RNA Polymerase II Gene: Reversion of the Temperature-Sensitive Hamster Cell Cycle Mutant TsAF8 by Mammalian DNA (1982)

Treatment of the TsAF8 temperature-sensitive (TS) mutant of Syrian hamster BHK-21 cells, with calcium phosphate precipitates of genomic TS+ DNAs from a variety of mammalian cell lines permitted the selection of TS+ colonies at 40 degrees C. TS+ transformation events were distinguished from spontaneous TS+ reversions in experiments in which alpha-amanitin-sensitive (Amas) TS+ DNA was used to transform an AmaR derivative of TsAF8 cells and AmaR TS+ DNA was used to transform Amas TsAF8 cells. In each case it was possible to demonstrate the unselected acquisition of the appropriate Amas or AmaR phenotype with the selected TS+ allele. Each of these TS+ transformed cell lines when grown at 40 degrees C contained an RNA polymerase II activity with a sensitivity to inhibition by alpha-amanitin characteristic of the particular DNA used to transform the TS cells, whereas at 34 degrees C the same cells contained a mixture of AmaR and Amas polymerase II activities. Together, these data provide convincing evidence that the RNA polymerase II gene determining sensitivity to inhibition by alpha-amanitin can be transferred to TsAF8 cells and that the TS defect in TsAF8 is a polymerase II mutation.
Use of Onium Salt-Based Coupling Reagents in Peptide Synthesis1 (1998)

Peptide coupling methods derived from onium salts based on 1-hydroxybenzotriazole (HOBt) and 1-hydroxy-7-azabenzotriazole (HOAt) are becoming incorporated in synthetic strategies more frequently than the classical carbodiimide methods. We have correlated the reactivity of various onium salts derived from HOXt (X = A, B), with the structure of the reagents in question. Thus, we confirmed that the aza derivatives are more reactive than the parent benzotriazole derivatives in both activation and coupling. In addition, the activation step is determined by the structure of the carbon skeleton. Thus, pyrrolidino derivatives appear to be reagents of choice relative to the piperidino analogues or those derived from trialkylamines. Furthermore although phosphonium salts are slightly less reactive than the corresponding aminium/uronium salts, the former should be used for the activation of hindered species, since the latter may lead to the formation of guanidino derivatives.
Membrane‐Covered Oxygen Sensors: An Exact Treatment of the Switch‐on Transient (1984)

Equations are derived that exactly describe the current‐time behavior of a membrane‐covered oxygen sensor, following the imposition of a polarizing potential to the previously equilibrated cell. The role of the various geometric, transport, and solubility factors is evaluated without any restriction being placed upon the magnitudes of these factors. The equations are analyzed to predict the duration of cottrellian behavior, and the interval before the onset of the steady state, for sensors of practical importance.
Clustering on the Unit Hypersphere using von Mises-Fisher Distributions (2005)

Several large scale data mining applications, such as text categorization and gene expression analysis, involve high-dimensional data that is also inherently directional in nature. Often such data is L2 normalized so that it lies on the surface of a unit hypersphere. Popular models such as (mixtures of) multi-variate Gaussians are inadequate for characterizing such data. This paper proposes a generative mixture-model approach to clustering directional data based on the von Mises-Fisher (vMF) distribution, which arises naturally for data distributed on the unit hypersphere. In particular, we derive and analyze two variants of the Expectation Maximization (EM) framework for estimating the mean and concentration parameters of this mixture. Numerical estimation of the concentration parameters is non-trivial in high dimensions since it involves functional inversion of ratios of Bessel functions. We also formulate two clustering algorithms corresponding to the variants of EM that we derive. Our approach provides a theoretical basis for the use of cosine similarity that has been widely employed by the information retrieval community, and obtains the spherical kmeans algorithm (kmeans with cosine similarity) as a special case of both variants. Empirical results on clustering of high-dimensional text and gene-expression data based on a mixture of vMF distributions show that the ability to estimate the concentration parameter for each vMF component, which is not present in existing approaches, yields superior results, especially for difficult clustering tasks in high-dimensional spaces.
Plaque-independent disruption of neural circuits in Alzheimer’s disease mouse models (1999)

Autosomal dominant forms of familial Alzheimer's disease (FAD) are associated with increased production of the amyloid beta peptide, Abeta42, which is derived from the amyloid protein precursor (APP). In FAD, as well as in sporadic forms of the illness, Abeta peptides accumulate abnormally in the brain in the form of amyloid plaques. Here, we show that overexpression of FAD(717V-->F)-mutant human APP in neurons of transgenic mice decreases the density of presynaptic terminals and neurons well before these mice develop amyloid plaques. Electrophysiological recordings from the hippocampus revealed prominent deficits in synaptic transmission, which also preceded amyloid deposition by several months. Although in young mice, functional and structural neuronal deficits were of similar magnitude, functional deficits became predominant with advancing age. Increased Abeta production in the context of decreased overall APP expression, achieved by addition of the Swedish FAD mutation to the APP transgene in a second line of mice, further increased synaptic transmission deficits in young APP mice without plaques. These results suggest a neurotoxic effect of Abeta that is independent of plaque formation.
Introduction (1988)

Journal Article Introduction Get access G. C. Harcourt G. C. Harcourt *University of Cambridge Search for other works by this author on: Oxford Academic Google Scholar Cambridge Journal of Economics, Volume 12, Issue 1, March 1988, Pages 1–5, https://doi.org/10.1093/oxfordjournals.cje.a035040 Published: 01 March 1988
Load-aware spectrum distribution in Wireless LANs (2008)

Traditionally, the channelization structure in IEEE 802.11-based wireless LANs has been fixed: Each access point (AP) is assigned one channel and all channels are equally wide. In contrast, it has recently been shown that even on commodity hardware, the channel-width can be adapted dynamically purely in software. Leveraging this capability, we study the use of dynamic-width channels, where every AP adaptively adjusts not only its center-frequency, but also its channel-width to match its traffic load. This gives raise to a novel optimization problem that differs from previously studied channel assignment problems. We propose efficient spectrum-distribution algorithms and evaluate their effectiveness through analysis and simulations using real-world traces. Our results indicate that by allocating more spectrum to highly-loaded APs, the overall spectrum-utilization can be substantially improved and the notorious load-balancing problem in WLANs can be solved naturally.
Is Parallel Programming Hard, And, If So, What Can You Do About It? (2011)

php?content_key=184 http://www.rdrop.com/users/ paulmck/RCU/OLSrtRCU.2006.08. 11a.pdf [Viewed January 1, 2007]. [MSS04] Paul E. McKenney, Dipankar Sarma, and Maneesh Soni. Scaling dcache with RCU. Linux Journal, 1(118):38– 46, January 2004. Available: http: //www.linuxjournal.com/node/7124 [Viewed December 26, 2010]. [MT01] Jose F. Martinez and Josep Torrel- las. Speculative locks for concurrent execution of critical sections in shared-memory multiprocessors. In Workshop on Memory Performance Issues, International Symposium on Computer Architecture, Gothen- burg, Sweden, June 2001. Avail- able: http://iacoma.cs.uiuc.edu/ iacoma-papers/wmpi_locks.pdf [Viewed June 23, 2004]. [Mus04] Museum Victoria Australia. CSIRAC: Australia’s first computer. Avail- able: http://museumvictoria.com. au/CSIRAC/ [Viewed: December 7, 2008], 2004. [MW07] Paul E. McKenney and Jonathan Walpole. What is RCU, fundamen- tally? Available: http://lwn.net/ Articles/262464/ [Viewed December 27, 2007], December 2007. [Nes06a] Oleg Nesterov. Re: [patch] cpufreq: mark cpufreq_tsc() as core_initcall_sync. Available: http://lkml.org/lkml/2006/11/19/ 69 [Viewed May 28, 2007], November 2006. [Nes06b] Oleg Nesterov. Re: [rfc, patch 1/2] qrcu: ”quick” srcu implementation. Available: http://lkml.org/lkml/ 2006/11/29/330 [Viewed November 26, 2008], November 2006. [ONH96] Kunle Olukotun, Basem A. Nayfeh, Lance Hammond, Ken Wilson, and Kunyung Chang. The case for a single- chip multiprocessor. In ASPLOS VII, October 1996. [Ope97] Open Group. The single UNIX specification, version 2: Threads. Available: http://www.opengroup. org/onlinepubs/007908799/xsh/ threads.html [Viewed September 19, 2008], 1997. [Pos08] PostgreSQL Global Development Group. PostgreSQL. Available: http://www.postgresql.org/ [Viewed November 26, 2008], November 2008. [PW07] Donald E. Porter and Emmett Witchel. Lessons from large transactional systems. Personal communication i20071214220521.GA5721@olive- green.cs.utexas.edu?, December 2007. [Rei07] James Reinders. Intel Threading Build- ing Blocks. O’Reilly, Sebastopol, CA, USA, 2007. [RG01] Ravi Rajwar and James R. Good- man. Speculative lock elision: Enabling highly concurrent multithreaded execu- tion. In Proceedings of the 34 An- nual ACM/IEEE International Sympo- sium on Microarchitecture, pages 294– 305, Austin, TX, December 2001. The Institute of Electrical and Electronics Engineers, Inc. [RHP07] Chistopher J. Rossbach, Owen S. Hofmann, Donald E. Porter, Hany E. Ramadan, Aditya Bhandari, and Emmett Witchel. TxLinux: Using and managing hardware transactional memory in an operating system. In SOSP’07: Twenty-First ACM Sympo- sium on Operating Systems Principles. ACM SIGOPS, October 2007. Avail- able: http://www.sosp2007.org/ papers/sosp056-rossbach.pdf [Viewed October 21, 2007].
Is Urban Transport Sustainable? (2003)

Once the privilege of the elite, personal mobility is a freedom bestowed by modernity on the general public through technology. The physical negotiation of space by people in pursuit of social values (access to work, friends, child care, education, recreation and supplying the home) is part of urban social life. Road freight vehicles provide a flexibility of supply that keeps profits up and costs down for businesses in the ‘consuming’ city. But the benefits of freedom and flexibility are illusory if the opportunity costs of providing for unending mobility are never considered, distances to be covered increase, travel becomes a compulsory, stressful, dangerous and expensive routine and the costs of mobility are merely shifted from the individual to society and the environment. This book explores how the real benefits of mobility can be protected and the costs properly allocated and contained. The chapters examine the sustainability of the world’s urban transport systems, bringing a variety of perspectives from different nations and from different fields: engineering, sociology, critical geography, environmental economics, eco-politics, urban planning and transport planning.
Breast cancer phenotypes regulated by tissue factor-factor VII pathway: Possible therapeutic targets (2014)

Breast cancer is a leading cause of cancer death in women, worldwide. Fortunately, breast cancer is relatively chemosensitive, with recent advances leading to the development of effective therapeutic strategies, significantly increasing disease cure rate. However, disease recurrence and treatment of cases lacking therapeutic molecular targets, such as epidermal growth factor receptor 2 and hormone receptors, referred to as triple-negative breast cancers, still pose major hurdles in the treatment of breast cancer. Thus, novel therapeutic approaches to treat aggressive breast cancers are essential. Blood coagulation factor VII (fVII) is produced in the liver and secreted into the blood stream. Tissue factor (TF), the cellular receptor for fVII, is an integral membrane protein that plays key roles in the extrinsic coagulation cascade. TF is overexpressed in breast cancer tissues. The TF-fVII complex may be formed in the absence of injury, because fVII potentially exists in the tissue fluid within cancer tissues. The active form of this complex (TF-fVIIa) may stimulate the expression of numerous malignant phenotypes in breast cancer cells. Thus, the TF-fVII pathway is a potentially attractive target for breast cancer treatment. To date, a number of studies investigating the mechanisms by which TF-fVII signaling contributes to breast cancer progression, have been conducted. In this review, we summarize the mechanisms controlling TF and fVII synthesis and regulation in breast cancer cells. Our current understanding of the TF-fVII pathway as a mediator of breast cancer progression will be also described. Finally, we will discuss how this knowledge can be applied to the design of future therapeutic strategies.
Asymmetric synthesis of 5- and 6-membered lactones from cyclic substrates bearing a C2-chiral auxiliary (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric synthesis of 5- and 6-membered lactones from cyclic substrates bearing a C2-chiral auxiliaryYukio Yamamoto, Akio Sakamoto, Takaaki Nishioka, Junichi Oda, and Yoshimasa FukazawaCite this: J. Org. Chem. 1991, 56, 3, 1112–1119Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://doi.org/10.1021/jo00003a038Request reuse permissionsArticle Views1529Altmetric-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 InReddit PDF (1 MB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Tumor-Infiltrating Regulatory Dendritic Cells Inhibit CD8+ T Cell Function via l -Arginine Metabolism (2009)

Dendritic cells (DC) have a critical effect on the outcome of adaptive immune responses against growing tumors. Whereas it is generally assumed that the presence of phenotypically mature DCs should promote protective antitumor immunity, evidence to the contrary does exist. We describe here a novel mechanism by which tumor-infiltrating dendritic cells (TIDC) actively contribute to the suppression of protective CD8(+) T-cell-based antitumor immunity. Using the BALB/NeuT model of spontaneously arising mammary carcinoma, we found that canonical MHC II(+)/CD11b(+)/CD11c(high) TIDCs act as regulatory DCs to suppress CD8(+) T-cell function, resulting in diminished T-cell-based antitumor immunity in vivo. Stimulation of naive T cells with regulatory TIDCs resulted in an altered cell fate program characterized by minimal T-cell expansion, impaired IFNgamma production, and anergy. Suppression by regulatory TIDCs overcame stimulatory signals provided by standard DCs, occurred in the absence of cognate interactions with T cells, and was mediated primarily by arginase metabolism of l-arginine. Immunosuppressive TIDCs were found in every murine tumor type examined and were phenotypically distinct from tumor-infiltrating CD11c(int-low)/CD11b(+)/Gr-1(+) myeloid-derived suppressor cells. Thus, within the tumor microenvironment, MHC II(+) TIDCs can function as potent suppressors of CD8(+) T-cell immunity.
Cloning, Characterization, Controlled Overexpression, and Inactivation of the Major Tributyrin Esterase Gene of Lactococcus lactis (2000)

The gene encoding the major intracellular tributyrin esterase of Lactococcus lactis was cloned using degenerate DNA probes based on 19 known N-terminal amino acid residues of the purified enzyme. The gene, named estA, was sequenced and found to encode a protein of 258 amino acid residues. The transcription start site was mapped 233 nucleotides upstream of the start codon, and a canonical promoter sequence was identified. The deduced amino acid sequence of the estA product contained the typical GXSXG motif found in most lipases and esterases. The protein was overproduced up to 170-fold in L. lactis by use of the nisin-controlled expression system recently developed for lactic acid bacteria. The estA gene was inactivated by chromosomal integration of a temperature-sensitive integration vector. This resulted in the complete loss of esterase activity, which could then be recovered after complementation of the constructed esterase-deficient strain with the wild-type estA gene. This confirms that EstA is the main enzyme responsible for esterase activity in L. lactis. Purified recombinant enzyme showed a preference for short-chain acyl esters, surprisingly also including phospholipids. Medium- and long-acyl-chain lipids were also hydrolyzed, albeit less efficiently. Intermediate characteristics between esterases and lipases make intracellular lactococcal EstA difficult to classify in either of these two groups of esterolytic enzymes. We suggest that, in vivo, EstA could be involved in (phospho)lipid metabolism or cellular detoxification or both, as its sequence showed significant similarity to S-formylglutathione hydrolase (FGH) of Paracoccus denitrificans and human EstD (or FGH), which are part of a universal formaldehyde detoxification pathway.
The involvement of the JAK-STAT signaling pathway in chronic inflammatory skin disease atopic dermatitis (2013)

Atopic dermatitis (AD), a common chronic inflammatory skin disease, is characterized by inflammatory cell skin infiltration. The JAK-STAT pathway has been shown to play an essential role in the dysregulation of immune responses in AD, including the exaggeration of Th2 cell response, the activation of eosinophils, the maturation of B cells, and the suppression of regulatory T cells (Tregs). In addition, the JAK-STAT pathway, activated by IL-4, also plays a critical role in the pathogenesis of AD by upregulating epidermal chemokines, pro-inflammatroy cytokines, and pro-angiogenic factors as well as by downregulating antimicrobial peptides (AMPs) and factors responsible for skin barrier function. In this review, we will highlight the recent advances in our understanding of the JAK-STAT pathway in the pathogenesis of AD.
Extended Activity in Cynomolgus Monkeys of a Granulocyte Colony‐Stimulating Factor Mutein Conjugated With High Molecular Weight Polyethylene Glycol (2000)

The activity of a granulocyte colony-stimulating factor (G-CSF) mutein (nartograstim; [NTG]) conjugated with an average of two polyethylene glycol (PEG) chains per protein molecule was examined in cynomolgus monkeys following a single s.c. injection. Groups of monkeys were given 10 microg/kg, 30 microg/kg, or 100 microg/kg. For comparison, one group of monkeys was given 5 microg/kg of recombinant human G-CSF (rHuG-CSF) daily for six days. In monkeys given 100 microg/kg of PEG-NTG, neutrophil levels reached a peak one day after injection approximately 20-fold higher than baseline levels. Neutrophil numbers in these animals were still significantly elevated six days after injection. In contrast, peak neutrophil levels in monkeys given six injections of rHuG-CSF reached a peak only on day 6 and were approximately the same as that in monkeys given a single dose of PEG-NTG six days before. Pharmacokinetics of PEG-NTG in these monkeys indicated that the area under the plasma concentration time curve (AUC) increased with increasing the dose from 497 ng x h/ml at 10 microg/kg, 6,140 ng x h/ml at 30 microg/kg to 27,900 ng x h/ml at 100 microg/kg. In a separate study, the effects of single doses of 100 microg/kg of PEG-NTG, rHuG-CSF, and unmodified NTG were compared. In this experiment, peak numbers of neutrophils were reached two days after injection in animals receiving PEG-NTG and one day after in animals given unmodified proteins. The pharmacokinetic parameters demonstrated increased exposure for PEG-NTG relative to the unmodified proteins with an AUC0. of 21,012 ng x h/ml compared with 5,492 ng x h/ml for rHuG-CSF and 5,153 ng x h/ml for NTG. These results demonstrate that conjugation of a G-CSF mutein with high molecular weight PEG results in a preparation that can induce prolonged elevation of neutrophils in normal nonhuman primates following a single injection.
Influence of EDTA and Citrate on Physicochemical Properties of Whey Protein-Stabilized Oil-in-Water Emulsions Containing CaCl2 (2002)

The influence of chelating agents (disodium ethylenediaminetetraacetate (EDTA) and sodium citrate) on the physicochemical properties of whey protein isolate (WPI)-stabilized oil-in-water emulsions containing calcium chloride was determined. The calcium-binding characteristics of EDTA and citrate at 30 degrees C were characterized in aqueous solutions (20 mM Tris buffer, pH 7.0) by isothermal titration calorimetry (ITC). EDTA and citrate both bound calcium ions in a 1:1 ratio, but EDTA had a much higher binding constant. Oil-in-water emulsions (pH 7.0) were prepared containing 6.94% (w/v) soybean oil, 0.35% (w/v) WPI, 0.02% (w/v) sodium azide, 20 mM Tris buffer, 10 mM CaCl(2), and 0-40 mM chelating agent. The particle size, apparent viscosity, creaming stability, free calcium concentration, and particle surface potential of the emulsions were measured. The chelating agents reduced or prevented droplet aggregation in the emulsions. When they were present above a certain concentration (>3.5 mM EDTA or >5 mM citrate), droplet aggregation was prevented. The reduction of aggregation was indicated by decreases in particle size, shear-thinning behavior, apparent viscosity, and creaming. Emulsions containing chelating agents had lower free calcium concentrations and more negatively charged droplets, indicating that the chelating agents improved emulsion stability by binding calcium ions. EDTA could be used at lower concentrations than citrate because of its higher calcium ion binding constant.