gebhart/patrepeval huggingface dataset:
A Real Knot in Protein (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Real Knot in Protein and Shigehiro KamitoriView Author Information Department of Biochemistry University of Kansas Lawrence, Kansas 66045 Cite this: J. Am. Chem. Soc. 1996, 118, 37, 8945–8946Publication Date (Web):September 18, 1996Publication History Received8 April 1996Published online18 September 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja961147mhttps://doi.org/10.1021/ja961147mrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views477Altmetric-Citations69LEARN 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 SUBJECTS:Disulfides,Noncovalent interactions,Peptides and proteins,Protein folding,Protein structure Get e-Alerts
Myasthenic Immunoglobulin Accelerates Acetylcholine Receptor Degradation (1977)

Degradation of acetylcholine receptors by cultured rat skeletal muscle cells was determined from the release of 125I from bound 125I-labeled alpha-bungarotoxin. Addition of immunoglobulin from patients with myasthenia gravis to the culture medium accelerated the degradation rate to a mean of 8.51 +/- 0.44 percent per hour, compared with the mean control rate of 3.97 +/- 0.14 percent per hour (P less than .001). A similar mechanism may possibly be involved in the autoimmune pathogenesis of myasthenia gravis in man.
FLT3-ITD up-regulates MCL-1 to promote survival of stem cells in acute myeloid leukemia via FLT3-ITD–specific STAT5 activation (2009)

Myeloid cell leukemia-1 (MCL-1) is an essential survival factor for hematopoiesis. In humans, hematopoietic stem cells (HSCs) express MCL-1 at the highest level in response to FMS-like tyrosine kinase-3 (FLT3) signaling. We here show that this FLT3-dependent stem cell maintenance system also plays a critical role in survival of leukemic stem cells (LSCs) in acute myeloid leukemia (AML). The CD34(+)CD38(-) LSC fraction expresses high levels of FLT3 as well as MCL-1, even compared with normal HSCs. Treatment with FLT3 ligand induced further MCL-1 up-regulation in LSCs in all AML cases tested. Interestingly, the group of samples expressing the highest levels of MCL-1 constituted AML with FLT3-internal tandem duplications (ITD). In FLT3-ITD AML cell lines, cells expressed a high level of MCL-1, and an inhibition of MCL-1 induced their apoptotic cell death. A tyrosine kinase inhibitor suppressed MCL-1 expression, and induced apoptosis that was reversed by the enforced MCL-1 expression. Finally, transduction of FLT3-ITD into HSCs strongly activated MCL-1 expression through its signal transducer and activator of transcription 5 (STAT5)-docking domains. This effect was completely abrogated when STAT5 activation was blocked. Thus, the acquisition of FLT3-ITD ensures LSC survival by up-regulating MCL-1 via constitutive STAT5 activation that is independent of wild-type FLT3 signaling.
Verapamil and adriamycin in the treatment of drug-resistant ovarian cancer patients. (1987)

Eight patients with refractory ovarian cancer were treated on a pilot protocol of verapamil plus Adriamycin (Adria Laboratories, Columbus, OH). This trial was based on our previous laboratory studies which demonstrated that Adriamycin resistance in human ovarian cancer cell lines could be partially reversed by exposure of the cells to high concentrations of verapamil (3,000 ng/mL). Patients were treated in an intensive care unit with continuous cardiovascular monitoring. The dose of verapamil was escalated in each patient until hypotension or heart block developed, and this dose was maintained for 72 hours. Adriamycin (50 mg/m2) was infused over 24 hours during the second day of the verapamil infusion and verapamil alone was administered on the third day in an effort to block efflux from drug-resistant cells. This intensive approach led to a median plasma verapamil level of 1,273 ng/mL (range, 720 to 2,767). However, the high infusion rates of verapamil (9 micrograms/kg/min) required to achieve these plasma levels produced an unacceptable degree of cardiac toxicity. Two patients developed transient atropine-responsive complete heart block and four patients developed transient congestive heart failure with increases in pulmonary capillary wedge pressure. There was no evidence that the noncardiac toxicities of Adriamycin were enhanced by verapamil. There were no objective responses to therapy. Future studies should use less cardiotoxic calcium channel blockers that can be safely administered to produce the plasma levels required for in vitro sensitization of drug resistant cells.
Robust TCP stream reassembly in the presence of adversaries (2005)

There is a growing interest in designing high-speed network devices to perform packet processing at semantic levels above the network layer. Some examples are layer-7 switches, content inspection and transformation systems, and network intrusion detection/prevention systems. Such systems must maintain perflow state in order to correctly perform their higher-level processing. A basic operation inherent to per-flow state management for a transport protocol such as TCP is the task of reassembling any out-of-sequence packets delivered by an underlying unreliable network protocol such as IP. This seemingly prosaic task of reassembling the byte stream becomes an order of magnitude more difficultto soundly execute when conducted in the presence of an adversary whose goal is to either subvert the higher-level analysis or impede the operation of legitimate traffic sharing the same network path. We present a design of a hardware-based high-speed TCP reassembly mechanism that is robust against attacks. It is intended to serve as a module used to construct a variety of network analysis systems, especially intrusion prevention systems. Using trace-driven analysis of out-of-sequence packets, we first characterize the dynamics of benign TCP trafficand show how we can leverage the results to design a reassembly mechanism that is efficientwhen dealing with non-attack traffic. We then refine the mechanism to keep the system effective in the presence of adversaries. We show that although the damage caused by an adversary cannot be completely eliminated, it is possible to mitigate the damage to a great extent by careful design and resource allocation. Finally, we quantify the trade-off between resource availability and damage from an adversary in terms of Zombie equations that specify, for a given configuration of our system, the number of compromised machines an attacker must have under their control in order to exceed a specified notion of “acceptablecollateral damage.” 1
Spermine Protects Mice Against Lethal Sepsis Partly by Attenuating Surrogate Inflammatory Markers (2009)

The pathogenesis of sepsis is partly attributable to dysregulated inflammatory response mediated by pathogen-associated molecular patterns (PAMPs) (for example, endotoxin) and damage-associated molecular patterns (DAMPs) (for example, high-mobility group box 1 [HMGB1]). An endogenous ubiquitous polyamine, spermine, inhibits endotoxin-induced cytokine release in vitro, but its capacities to attenuate sepsis- and HMGB1-induced inflammatory responses was previously unknown. We thus tested the hypothesis that spermine protects mice against lethal sepsis by attenuating sepsis-induced local and systemic inflammatory responses. Intraperitoneal (i.p.) administration of spermine (10 mg/kg, twice daily, for 3 d) conferred a significant protection against lethal sepsis. The protective effects were associated with a significant reduction in peritoneal and serum levels of several surrogate markers of sepsis (for example, Interleukin-6 [IL-6], keratinocyte-derived chemokine [KC], monocytes chemoattractant protein-1 [MCP-1], macrophage inflammatory protein-2 [MIP-2], tissue inhibitor of metalloproteinase-1 [TIMP-1], soluble tumor necrosis factor-alpha receptor I [sTNFRI], and soluble tumor necrosis factor-alpha receptor II [sTNFRII]) during a late stage of sepsis. In vitro, spermine effectively inhibited HMGB1-induced release of the above surrogate markers in peritoneal macrophages. Thus, spermine confers protection against lethal sepsis partly by attenuating sepsis- and HMGB1-induced inflammatory responses.
Pea proteins: A review of chemistry, technology of production, and utilization (1991)

Abstract Dry peas are an important protein source for people and for animals. This paper reviews various aspects of the protein in dry peas, including variations in protein content, biochemical characteristics of the major protein components, and amino acid composition. The existing technology for the production of concentrated sources of pea protein (i.e., concentrates and isolates) is described. Finally the utilization of dry peas, pea flours, pea protein concentrates, and pea protein isolates is discussed. That discussion includes studies of the nutritonal value of peas and of the functional properties of dry pea ingredients in model systems and in food products. Topics for future research to enhance utilization of dry peas form the conclusion of this paper.
Heat capacity cryostat and novel methods of analysis for small specimens in the 1.5–10 K range (1980)

We describe a method for measuring heat capacity of small specimens in the 1.5–10 K range by means of thermal relaxation over that range. Our methods of calibration and analysis make use of the simple properties of the thermal link between specimen and its surroundings, and offer several advantages. The cryostat has been used in magnetic fields of up to 4.5 T, and simple relationships for the magnetoresistance of heat links and thermometer have been determined. Measurement of the heat capacity of a 90 mg copper sample shows that the method is accurate to 1%.
Global Phenotypic Analysis and Transcriptional Profiling Defines the Weak Acid Stress Response Regulon inSaccharomyces cerevisiae (2003)

Weak organic acids such as sorbate are potent fungistatic agents used in food preservation, but their intracellular targets are poorly understood. We thus searched for potential target genes and signaling components in the yeast genome using contemporary genome-wide functional assays as well as DNA microarray profiling. Phenotypic screening of the EUROSCARF collection revealed the existence of numerous sorbate-sensitive strains. Sorbate hypersensitivity was detected in mutants of the shikimate biosynthesis pathway, strains lacking the PDR12 efflux pump or WAR1, a transcription factor mediating stress induction of PDR12. Using DNA microarrays, we also analyzed the genome-wide response to acute sorbate stress, allowing for the identification of more than 100 genes rapidly induced by weak acid stress. Moreover, a novel War1p- and Msn2p/4p-independent regulon that includes HSP30 was identified. Although induction of the majority of sorbate-induced genes required Msn2p/4p, weak acid tolerance was unaffected by a lack of Msn2p/4p. Ectopic expression of PDR12 from the GAL1-10 promoter fully restored sorbate resistance in a strain lacking War1p, demonstrating that PDR12 is the major target of War1p under sorbic acid stress. Interestingly, comparison of microarray data with results from the phenotypic screening revealed that PDR12 remained as the only gene, which is both stress inducible and required for weak acid resistance. Our results suggest that combining functional assays with transcriptome profiling allows for the identification of key components in large datasets such as those generated by global microarray analysis.
Expression of the CD85j (leukocyte Ig‐like receptor 1, Ig‐like transcript 2) receptor for class I major histocompatibility complex molecules in idiopathic inflammatory myopathies (2008)

CD85j is expressed in PM and sporadic IBM at the sites of partial invasion and in DM in perivascular inflammation, paving the way for dissecting the role of CD85j in the pathogenesis of inflammatory myopathies.
Versatile and scalable parallel histogram construction (2014)

Histograms are used in various fields to quickly profile the distribution of a large amount of data. However, it is challenging to efficiently utilize abundant parallel resources in modern processors for histogram construction. To make matters worse, the most efficient implementation varies depending on input parameters (e.g., input distribution, number of bins, and data type) or architecture parameters (e.g., cache capacity and SIMD width).
Flexible and stretchable electronics (2013)

Conventionally electronics circuits are produced by assembly of packaged components on flat, rigid printed circuit boards. However there is a growing demand for 2.5 dimensional (2.5D free form surfaces) or even full 3D electronics. Applications for such circuits are found in a vast range of fields: such circuits are desirable for comfort and ergonomic reasons (e.g. in wearable or implantable circuits), to respond to design and aesthetics considerations (e.g. 2.5D or 3D light sources), for ecological reasons (more efficient materials usage, less CO2 emissions in automotive applications) etc. In this contribution we will present two technologies, under development at our laboratory, which open the way to industrial production of randomly deformable circuits. These technologies are :\n•\tThe ultra-thin chip package (UTCP) technology, by which bare Si (or other anorganic semiconductor based) chips are thinned down to a thickness of 20-30µm, embedded in a stack of spin-on polyimide layers, and provided with a fan-out metallization, resulting in an extremely miniaturized, lightweight and flexible chip package with a total thickness below 100µm\n•\tA number of technologies for dynamically stretchable (i.e. elastic) circuits, which are based on the interconnection of individual components or component islands with meander shaped thin-film or Printed Circuit Board (PCB) based metal wirings and embedding in elastic polymers like PDMS (silicone rubbers) or PU (polyurethanes). Process flow details, reliability data and applications for these technologies will be presented.
Delayed application of direct current electric fields in experimental spinal cord injuries (1993)

The cutaneus trunci muscle (CTM) reflex of guinea pigs depends on an ascending afferent pathway within the ventrolateral funiculus of the thoracic spinal cord. The expression of this reflex is a phasic contraction of back skin in response to tactile stimulation, which is permanently eliminated by transection of the ventrolateral funiculus. It was shown previously that when a polarized (rostrally negative), weak (300-400 μV/mm) DC electric field is placed across a lateral hemisection of the spinal cord in adult guinea pigs at the time of injury, approximately 13% recover the reflex, while sham-treated animals remain unchanged. In this study, a similar approach was used, except that three months were allowed to pass between the time of hemisection and experimental treatment. No recovery of the CTM reflex was observed in 13 animals with rostrally negative fields, 8 of which were followed for at least 9 months, 5 for 3 months; or in 11 animals with caudally negative applied fields, 8 of which were followed for 9 months and 3 for 3 months.
The preparation and properties of the catalytic subunit of bovine enterokinase. (1984)

A limited reduction of the disulfide bonds of bovine enterokinase (enteropeptidase, EC 3.4.21.9) was accomplished with 50 mM dithioerythritol, at pH 9.0, and at 4 degrees C. The conditions separated the heavy and light subunits quantitatively with improved reliability when compared to the conditions used previously (Savithri, H. S., and Light, A. (1980) Biochim. Biophys. Res. Commun, 94, 360-365). Pancreatic trypsin inhibitor was added to the reaction to ensure that the yield of the heavy subunit was equal to that of the catalytic subunit (light subunit). Otherwise the heavy subunit was subject to extensive degradation. The subunits were alkylated with iodoacetate and then resolved on Sephadex G-150. Amino acid analyses and the incorporation of [14C]carboxymethyl groups showed that 3.1 carboxymethylcysteine residues were in the catalytic subunit and 8.9 in the heavy subunit. The catalytic subunit had normal catalytic activity toward N-benzoyl-L-arginine ethyl ester, enhanced activity toward N-tosyl-L-arginine methyl ester and N-tosyl-L-lysine methyl ester, and lower activity toward N-benzoyl-DL-arginine p-nitroanilide. The catalytic subunit retained the restricted specificity of intact enterokinase, but the rate of activation of trypsinogen was much slower. It is likely that the limited reduction of the disulfide bonds of the catalytic subunit altered the interaction of protein substrates with the specificity site.
Dimensionality reduction by random mapping: fast similarity computation for clustering (2002)

When the data vectors are high-dimensional it is computationally infeasible to use data analysis or pattern recognition algorithms which repeatedly compute similarities or distances in the original data space. It is therefore necessary to reduce the dimensionality before, for example, clustering the data. If the dimensionality is very high, like in the WEBSOM method which organizes textual document collections on a self-organizing map, then even the commonly used dimensionality reduction methods like the principal component analysis may be too costly. It is demonstrated that the document classification accuracy obtained after the dimensionality has been reduced using a random mapping method will be almost as good as the original accuracy if the final dimensionality is sufficiently large (about 100 out of 6000). In fact, it can be shown that the inner product (similarity) between the mapped vectors follows closely the inner product of the original vectors.
That Which Does Not Stabilize, Will Only Make Us Stronger (2007)

Many places in the world are too rugged or enclosed for vehicles to access. Even today, material transport to such areas is limited to manual labor and beasts of burden. Modern advancements in wearable robotics may make those methods obsolete. Lower extremity exoskeletons seek to supplement the intelligence and sensory systems of a human with the significant strength and endurance of a pair of wearable robotic legs that support a payload. This article first outlines the use of Clinical Gait Analysis data as the framework for the design of such a system at UC Berkeley. This data is used to design the exoskeleton degrees of freedom and size its actuators. It will then give an overview of one of the control schemes implemented on the BLEEX. The control algorithm described here increases the system closed loop sensitivity to its wearer’s forces and torques without any measurement from the wearer (such as force, position, or electromyogram signal). The control algorithm uses the inverse dynamics of the exoskeleton, scaled by a number smaller than unity, as a positive feedback controller. This controller almost destabilizes the system since it leads to an overall loop gain slightly smaller than unity and results in a large sensitivity to all wearer’s forces and torques thereby allowing the exoskeleton to shadow its wearer.
Requirement for a beta 2-microglobulin-associated Fc receptor for acquisition of maternal IgG by fetal and neonatal mice. (1995)

There is considerable evidence to suggest that an FcR similar in structure to class I MHC Ags, neonatal Fc receptor (FcRn), transports IgG across the intestinal epithelium of suckling mice. However, this has not previously been shown definitively, nor has it been shown whether FcRn is the only, or even the major, IgG transporter in the neonatal mouse gut. We report here that neonatal mice homozygous for a targeted disruption of the beta 2microglobulin (beta 2m) gene, which encodes one subunit of FcRn, had reduced FcRn alpha-chain at the lumenal plasma membrane of intestinal cells. These mice had strikingly lower serum IgG levels during the first month after birth than littermates that possessed functional FcRn. Furthermore, we found by fostering mice on mothers with a different IgG allotype that all of the IgG in sera of beta 2m-/- mice was endogenous, and that none was obtained from milk. We conclude that FcRn is the only transporter of IgG from mother to young in the mouse. The onset of IgG synthesis in mice that received no milk IgG lagged behind that in siblings with normal IgG transport, suggesting that maternal IgG stimulates Ab production in the neonate. We noted no difference between the IgG concentrations in the milk of beta 2m-/- and beta 2m+/- mice, indicating that FcRn is not involved in the secretion of IgG into milk.
Oxidized Phospholipids, Lp(a) Lipoprotein, and Coronary Artery Disease (2005)

Circulating levels of oxidized LDL are strongly associated with angiographically documented coronary artery disease, particularly in patients 60 years of age or younger. These data suggest that the atherogenicity of Lp(a) lipoprotein may be mediated in part by associated proinflammatory oxidized phospholipids.
A modular system for tracking players in sports games (2009)

Detection, recognition and tracking of the players in sports games which is based on image processing and computer vision is the topic of interest of various research groups. Different approaches regarding choice and placement of the acquisition hardware exist. Regardless of whether a custom set of static cameras is used or the images are acquired from directed TV coverage, player detection and tracking is a complex process. Robustness of such a system is the main goal of its designers. In this paper, a modular system for tracking indoor and outdoor team games using computer vision is proposed and described. Proposed approach is flexible and expandable so it can be said that overall system framework provides robustness of detection, recognition and tracking.
Versatile derivatisation of solid support media for covalent bonding on DNA-microchips (1999)

A chemistry was developed that permits on DNA-arrays both the covalent immobilisation of pre-fabricated nucleic acids-such as oligonucleotides, PCR-products or peptide nucleic acid oligomers-and the in situ synthesis of such compounds on either glass or polypropylene surfaces. Bonding was found to be stable even after some 30 cycles of stripping. Due to a dendrimeric structure of the linker molecule, the loading can be modified in a controlled manner and increased beyond the capacity of glass without negative effects on hybridisation efficiency. Also, the chemistry warrants the modulation of other surface properties such as charge or hydrophobicity. Preferentially, attachment of nucleic acids takes place only via the terminal amino-group of amino-modified oligonucleotides or the terminal hydroxyl-group of unmodified molecules so that the entire molecule is accessible to probe hybridisation. This derivatisation represents a support chemistry versatile enough to serve nearly all current forms of DNA-arrays or microchips.