gebhart/patrepeval huggingface dataset:
<i>De novo</i> design of site-specific protein interactions with learned surface fingerprints (2022)

Abstract Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic, and structural data grows. This knowledge gap has been a major obstacle for the comprehensive understanding of cellular protein-protein interaction (PPI) networks and for the de novo design of protein binders that are crucial for synthetic biology and translational applications. We exploit a geometric deep learning framework operating on protein surfaces that generates fingerprints to describe geometric and chemical features critical to drive PPIs. We hypothesized these fingerprints capture the key aspects of molecular recognition that represent a new paradigm in the computational design of novel protein interactions. As a proof-of-principle, we computationally designed several de novo protein binders to engage four protein targets: SARS-CoV-2 spike, PD-1, PD-L1, and CTLA-4. Several designs were experimentally optimized while others were purely generated in silico , reaching nanomolar affinity with structural and mutational characterization showing highly accurate predictions. Overall, our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling a novel approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
Flower of Adenocaulon bicolor (1915)

The development of the staminate and pistillate flowers is the same up to the development of the ovarian cavity. Both staminate and pistillate flowers have ovarian cavities, but ovules develop only in the pistillate flowers. Stamens are sometimes found in pistillate flowers, but they are always sterile. No gland-hairs are found on staminate flowers. Styles of staminate flowers are cleft. Nothing unusual occurs in the development of the egg, embryo, or pollen grains.
Ethylenediamine. IV.<sup>1</sup> Monoalkyl Derivatives (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEthylenediamine. IV.1 Monoalkyl DerivativesSamuel R. AspinallCite this: J. Am. Chem. Soc. 1941, 63, 3, 852–854Publication Date (Print):March 1, 1941Publication History Published online1 May 2002Published inissue 1 March 1941https://pubs.acs.org/doi/10.1021/ja01848a060https://doi.org/10.1021/ja01848a060research-articleACS PublicationsRequest reuse permissionsArticle Views460Altmetric-Citations31LEARN 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
In vivo expression of mammalian BiP ATPase mutants causes disruption of the endoplasmic reticulum. (1995)

BiP possesses ATP binding/hydrolysis activities that are thought to be essential for its ability to chaperone protein folding and assembly in the endoplasmic reticulum (ER). We have produced a series of point mutations in a hamster BiP clone that inhibit ATPase activity and have generated a species-specific anti-BiP antibody to monitor the effects of mutant hamster BiP expression in COS monkey cells. The enzymatic inactivation of BiP did not interfere with its ability to bind to Ig heavy chains in vivo but did inhibit ATP-mediated release of heavy chains in vitro. Immunofluorescence staining and electron microscopy revealed vesiculation of the ER membranes in COS cells expressing BiP ATPase mutants. ER disruption was not observed when a "44K" fragment of BiP that did not include the protein binding domain was similarly mutated but was observed when the protein binding region of BiP was expressed without an ATP binding domain. This suggests that BiP binding to target proteins as an inactive chaperone is responsible for the ER disruption. This is the first report on the in vivo expression of mammalian BiP mutants and is demonstration that in vitro-identified ATPase mutants behave as dominant negative mutants when expressed in vivo.
The enactive mind, or from actions to cognition: lessons from autism (2003)

Normative-IQ individuals with autism are capable of solving explicit social cognitive problems at a level that is not matched by their ability to meet the demands of everyday social situations. The magnitude of this discrepancy is now being documented through newer techniques such as eye tracking, which allows us to see and measure how individuals with autism search for meaning when presented with naturalistic social scenes. This paper offers an approach to social cognitive development intended to address the above discrepancy, which is considered a key element for any understanding of the pathophysiology of autism. This approach, called the enactive mind (EM), originates from the emerging work on 'embodied cognitive science', a neuroscience framework that views cognition as bodily experiences accrued as a result of an organism's adaptive actions upon salient aspects of the surrounding environment. The EM approach offers a developmental hypothesis of autism in which the process of acquisition of embodied social cognition is derailed early on, as a result of reduced salience of social stimuli and concomitant enactment of socially irrelevant aspects of the environment.
The Preparation and Properties of Some β-Aminopropionic Acid Derivatives (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Preparation and Properties of Some β-Aminopropionic Acid DerivativesJohn A. King and Freeman H. McMillanCite this: J. Am. Chem. Soc. 1946, 68, 8, 1468–1470Publication Date (Print):August 1, 1946Publication History Published online1 May 2002Published inissue 1 August 1946https://pubs.acs.org/doi/10.1021/ja01212a022https://doi.org/10.1021/ja01212a022research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations14LEARN 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
Phenylethylamine and Piperidine Alkaloids in<i>Aloe</i>Species (1992)

Of the approximately 300 species of ALOE (Liliaceae) native to Africa and Arabia, leaf extracts of 224 species have been examined chromatographically for alkaloids using ninhydrin, Dragendorff's reagent, nitroprusside, and iodoplatinate as revealing agents. From these, 48 (21%) species contained compounds giving a strong colorimetric reaction with at least one of these reagents. Tyramine derivatives were identified in 18 species and piperidine derivatives in a further 6 species. The other coloured zones remain unidentified but often appeared to represent common amino acids. Some taxonomic correlations are suggested. The presence of the toxic hemlock alkaloids in aloes readily available for potential medicinal use by local inhabitants sounds a note of caution against the unthinking use of these otherwise useful plants.
BRAZING USING 2.45 GHZ MICROWAVES (2003)

Abstract Not Provided
<i>PANAX NOTOGINSENG </i>SAPONINS ATTENUATE ATHEROSCLEROSIS IN RATS BY REGULATING THE BLOOD LIPID PROFILE AND AN ANTI‐INFLAMMATORY ACTION (2008)

Previous studies have reported on the anti-atherosclerotic effects of Panax notoginseng saponins (PNS). The aim of the present study was to explore the molecular mechanisms responsible for the anti-atherosclerotic effects of PNS and the inflammatory response. Thirty rats were randomly divided into three groups, namely a control group, a group, in which zymosan A was used to induce inflammation (Zym group) and a PNS-treated group. Rats in the three groups were administered liquid paraffin (i.p.), zymosan A (20 mg/kg, i.p., once every 3 days) or zymosan A and PNS (100 mg/kg, i.p., once daily), respectively. All animals were fed a high-fat diet for 9 weeks. At scheduled times, rats were killed, blood was collected and the aorta was removed. Pathological changes in aortas were observed using Sudan IV staining and transmission electron microscopy. Serum lipids were measured enzymatically. Whole-blood viscosity was observed at different shear rates. The expression of cardiovascular disease-specific genes was determined using GEArray (SuperArray, Frederick, MA, USA). Western blotting was used to evaluate the expression levels of nuclear factor (NF)-kappaB/p65 and its inhibitor IkappaBalpha in the aortic wall. In the present study, typical pathological changes associated with atherosclerosis in rats following induction by zymosan A were alleviated by PNS treatment. In the PNS-treated group, there was a marked reduction in total serum cholesterol, triglycerides and blood viscosity. In addition, PNS treatment significantly decreased the gene expression of some inflammatory factors, such as integrins, interleukin (IL)-18, IL-1beta and matrix metalloproteinases 2 and 9. The expression of NF-kappaB/p65 was attenuated, whereas the expression of IkappaBalpha was significantly increased, after treatment with PNS. In conclusion, it appears that PNS exerts its therapeutic effects on atherosclerosis through an anti-inflammatory action and regulation of the blood lipid profile and that an NF-kappaB signalling pathway is involved.
HK cartel leniency powers are unclear (2015)

Counsel in Hong Kong have criticised the lack of clarity on the treatment of subsequent whistleblowers under the city's first leniency policy
[Legal aspects and bed sores]. (2009)

An overall summary of this article was submitted at the VII National Symposium on Bed Sores and Chronic Wounds and at the First Latin American Congress on Ulcers and Wounds. This article consists of an introductory first part followed by a series of numbered questions and answers in which the authors more extensively develop the hottest topics which may affect nurses' daily practice.
Retinal transplantation of photoreceptors results in donor–host cytoplasmic exchange (2016)

Pre-clinical studies provided evidence for successful photoreceptor cell replacement therapy. Migration and integration of donor photoreceptors into the retina has been proposed as the underlying mechanism for restored visual function. Here we reveal that donor photoreceptors do not structurally integrate into the retinal tissue but instead reside between the photoreceptor layer and the retinal pigment epithelium, the so-called sub-retinal space, and exchange intracellular material with host photoreceptors. By combining single-cell analysis, Cre/lox technology and independent labelling of the cytoplasm and nucleus, we reliably track allogeneic transplants demonstrating cellular content transfer between graft and host photoreceptors without nuclear translocation. Our results contradict the common view that transplanted photoreceptors migrate and integrate into the photoreceptor layer of recipients and therefore imply a re-interpretation of previous photoreceptor transplantation studies. Furthermore, the observed interaction of donor with host photoreceptors may represent an unexpected mechanism for the treatment of blinding diseases in future cell therapy approaches.
Clay stabilizers improve EOR injection rates (1984)

In laboratory and field tests, Halliburton Services has used cationic organic polymers to help prevent clay swelling and fines migration. Improved injection rates for waterflooding and enhanced oil recovery (EOR) projects have resulted from clay stabilization by adsorption of polymers onto clay particles. The rate of oil production from EOR and waterflooding projects is related to the rate of aqueous fluid injection. Failure of one or more wells to accept injection at the scheduled rates can reduce the rate of oil production and distort the pattern of fluid movement within the reservoir such that the ultimate oil recovery could also be decreased. Poor injectivity can be due to one or more of the following: Formation damage due to clay swelling and fines migration; Plugging of the face of the formation by solids in drilling, completion, or injection fluids; Scale formation due to incompatibility of formation and injection waters; Casing and tubing corrosion; Bacterial growth; and In situ formation of precipitates caused by an improperly designed acid stimulation. Properly designed remedial well treatment and adequate filtration of injection fluids performed early in the life of the project will help prevent permeability damage due to all of the above causes except claymore » swelling and fines migration.« less
Processing of Rigidized Rei-mullite Insulative Composites (1973)

Systematic development and evaluation of ceramic fiber Mullite are summarized: (1) Major reductions in thermal protection system weight have been achieved by reducing the density and thermal conductivity of the insulation by 20 and 25 percent; (2) already adequate structural margins-of-safety have been greatly enhanced by increasing the tensile strength and strain-to-failure capabilities of the insulation by factors of 3 and 2; (3) cost effectiveness has been increased through the achievement of a high degree of uniformity and reproducibility of properties and through process simplification and binder modifications; and (4) maximization of multimission capability at surface temperatures of 1644 K has been achieved through firing cycle adjustments and the development of a material with high dimensional stability.
Accuracy of the Modified Continuous Glucose Monitoring (CGMS <sup>®</sup> ) Sensor in an Outpatient Setting: Results from a Diabetes Research in Children Network (DirecNet) Study (2005)

These data confirm the improved accuracy previously reported for the modified version of the CGMS sensor.
Altitude-Insensitive Femto Slider Design (2006)

We present an advanced sub-ambient Femto slider that is less sensitive to altitude change. The air bearing design strategy, analysis and optimization are presented. All air bearing simulations were carried out using Data Storage Institute in-house-developed air bearing simulation software.
Regulation of vascular smooth muscle cell proliferation and migration by sphingosine-1-phosphate (2004)

Vascular smooth muscle cells (VSMC) exhibit a range of functional phenotypes important in cardiovascular development and disease. Recently, sphingosine-1-phosphate (S1P), a platelet-derived sphingolipid metabolite, has been demonstrated to regulate VSMC function both in vitro and in vivo . ^ In order to improve our understanding of S1P signaling in VSMC, we determined the expression of S1P receptor isoforms (S1Pn/EDG-n) in two different rat VSMC phenotypes: Pup-intimal VSMC and adult-medial VSMC. ^ Herein, pup-intimal VSMC were found to express higher levels of S1P 1/EDG-1 mRNA than adult-medial VSMC. Exogenous expression of S1P 1/EDG-1 in adult-medial cells enhanced S1P-induced proliferation, concomitant with activation of p70 S6 kinase and increases in cyclin D1. Pertussis toxin impaired S1P-induced p70 S6 kinase activation, cyclin D1 induction and proliferation, suggesting that S1P1/EDG-1-coupling to Gi is critical. Furthermore, blocking p70 S6 kinase phosphorylation with rapamycin reduced cyclin D1 induction and proliferation, suggesting that p70 S6 kinase activation is also critical in S1P1/EDG-1/Gi-mediated proliferation. ^ Recently, sphingosine kinase (SK), the enzyme which synthesizes S1P by phosphorylating sphingosine, has been reported to regulate VSMC function in vitro. In order to elucidate the role of SK in VSMC function in vivo, we attempted to develop transgenic mice expressing a sphingosine kinase/β-galactosidase transgene in arterial VSMC. Transgenic mice were successfully generated and transmitted the transgene to offspring. (Abstract shortened by UMI.) ^
Steering car-like systems with trailers using sinusoids (2003)

Methods for steering car-like robots with trailers are investigated. A connection is demonstrated between Murray and Sastry's (1990, 1991) work of steering with integrally related sinusoids and Sussmann and Liu's (1991) recent work on asymptotic behavior of systems with high-frequency sinusoids as inputs. The merits of coordinate transformations, relative to the convergence properties, are discussed. Simulation results for a car-like robot with two trailers are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An unilateral master-slave hand system with a force-controlled slave hand (2002)

We have developed a new unilateral master-slave hand system. The master system consists of a master arm which has a 3-DOF parallel link mechanism and a 3-DOF wrist mechanism, and a dataglove that is usually used for a virtual reality system. The slave system has a 6-DOF arm and a 16-DOF four-fingered hand. In general, a slave system is controlled by position with reference to a master system position. In this system, when an operator makes the slave system work on a complicated task, he must look at the slave carefully and let his arm and hand manipulate discretely. In the new master-slave system, each finger of the slave hand has a fingertip tactile sensor, and it is controlled by position and force. When an operator has knowledge of a task and handling objects and sets the slave fingertip stiffness, the operation can be performed easily by handling the master arm and hand to a rough position.
Dendritic Cells Induce Autoimmune Diabetes and Maintain Disease via De Novo Formation of Local Lymphoid Tissue (1998)

Activation of autoreactive T cells can lead to autoimmune diseases such as insulin-dependent diabetes mellitus (IDDM). The initiation and maintenance of IDDM by dendritic cells (DC), the most potent professional antigen-presenting cells, were investigated in transgenic mice expressing the lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) under the control of the rat insulin promoter (RIP-GP mice). We show that after adoptive transfer of DC constitutively expressing the immunodominant cytotoxic T lymphocyte (CTL) epitope of the LCMV-GP, RIP-GP mice developed autoimmune diabetes. Kinetic and functional studies of DC-activated CTL revealed that development of IDDM was dependent on dose and timing of antigenic stimulation. Strikingly, repeated CTL activation by DC led to severe destructive mononuclear infiltration of the pancreatic islets but also to de novo formation of islet-associated organized lymphoid structures in the pancreatic parenchyma. In addition, repetitive DC immunization induced IDDM with lymphoid neogenesis also in perforin-deficient RIP-GP mice, illustrating that CD8(+) T cell-dependent inflammatory mechanisms independent of perforin could induce IDDM. Thus, DC presenting self-antigens not only are potent inducers of autoreactive T cells, but also help to maintain a peripheral immune response locally; therefore, the induction of autoimmunity against previously ignored autoantigens represents a potential hazard, particularly in DC-based antitumor therapies.
New interpath interference model for DS-CDMA indoor transmissions with distributed antennas (2002)

In channels where the delay spread is smaller than the chip interval, spread spectrum signals do not give rise to path diversity. In this situation, distributed antennas systems may be used to provide path diversity, significantly improving the system performance. The interference component caused by the same cell-site users, or interpath interference (IPI), is a dominant factor in the performance of these systems. In their analysis it is typically assumed that the probability density function (PDF) of the IPI can be approximated by the Gaussian distribution. This is called the Gaussian approximation (GA). We show that the GA for the IPI does not provide an accurate characterization of the performance of the downlink of DS-CDMA indoor systems with distributed antennas. The bit error rate (BER) at the output of a practical RAKE receiver is computed using an accurate approach for the IPI. We show that when the IPI density is thus modeled, the signal to noise ratio (SNR) at the output of the combiner is well approximated by a random variable with a Weibull distribution. Comparison of the BER obtained by the new approach for the IPI with those obtained by the GA shows that the latter method incurs in considerable error when used to evaluate performance of DS-CDMA indoor systems with distributed antennas.
Ultrathin foils used for low-energy neutral atom imaging of the terrestrial magnetosphere (1993)

Magnetospheric imaging by remote detection of low-energy neutral atoms (LENA5) that are created by charge exchange between magnetospheric plasma ions and neutral geocoronal atoms has been proposed as a method to provide global information of magnetospheric dynamics. For LENA detection, carbon foils can be implemented to (1) ionize the LENAs and electrostatically remove them from the large background of solar UV scattered by the geocorona to which LENA detectors (e.g. , microchannel plates) are sensitive and (2) generate secondary electrons to provide coincidence and/or LENA trajectory information. Quantification of LENA-foil interactions are crucial in defining LENA imager performance. We present equilibrium charge state and angular scatter distributions for 1- to 30-keV atomic hydrogen, helium, and oxygen transiting nominal 0.5 μg cm<sup>2</sup> carbon foils. Results obtained after coating the exit surface of foils with either aluminum or gold suggest that the intended alteration of the exit surface chemistry has no effect on the charge state distributions due to foil contamination from exposure to air. Angular scattering that results from the projectile-foil interaction is quantified and is shown to be independent of the charge state distribution.