gebhart/patrepeval huggingface dataset:
Trastuzumab-Associated Cardiac Adverse Effects in the Herceptin Adjuvant Trial (2007)

Given the clear benefit in disease-free survival, the low incidence of cardiac adverse events, and the suggestion that cardiac dysfunction might be reversible, adjuvant trastuzumab should be considered for treatment of breast cancer patients who fulfill the HERA trial eligibility criteria.
Prediction model for suitability of resource deployment using complex templates in OpenStack (2017)

Enterprises are moving into cloud, so deployment and configuration of virtual machines and application software are becoming highly complex. The solution to this problem is to automate the deployment and configuration using templates. These templates allow the users to specify the information about resource requirements of an application. In this paper, firstly, we present the methods for development of complex templates that consist of various properties like input parameters and conditional logic, lacking in existing simple templates. OpenStack is the popularly used private Cloud deployment tool and many other similar tools lack in providing the complex templates in their architecture. The complex templates proposed in this paper are generic in nature and designed keeping OpenStack in mind. Using the proposed complex templates, based on user defined input values and conditional logic, various infrastructure stacks can be created in simple templates and can be directly fed into heat engine for deployment. The complex templates can be developed to accept input parameters, including conditional logic or auto scaling constructs. Though the complex template allows us to specify the requirement in an easy way but it is difficult and sometimes inaccurate, to visualize the outcome. Under such circumstances estimating the billing cost of the infrastructure stack is extremely difficult. In order to alleviate this problem, in this paper secondly, we propose a system that can automate the cost estimation of a stack before its creation. In order to assess the cost estimates, we have implemented machine learning using decision trees on the templates data that can produce the output in the form of two classes and give the decision that whether it is good to deploy templates or not. The preliminary assessment is done on the proposed model and results achieved are produced.
Spectral unmixing of multiply stained fluorescence samples T (2010)

The widespread use of fluorescence microscopy along with the vast library of available fluorescent stains and staining\nmethods has been extremely beneficial to researchers in many fields, ranging from material sciences to plant biology. In\nclinical diagnostics, the ability to combine different markers in a given sample allows the simultaneous detection of the\nexpression of several different molecules, which in turn provides a powerful diagnostic tool for pathologists, allowing a\nbetter classification of the sample at hand. The correct detection and separation of multiple stains in a sample is achieved\nnot only by the biochemical and optical properties of the markers, but also by the use of appropriate hardware and software\ntools. In this chapter, we will review and compare these tools along with their advantages and limitations.
2.4 Å Crystal Structure of an Oxaliplatin 1,2-d(GpG) Intrastrand Cross-Link in a DNA Dodecamer Duplex (2001)

(1R,2R-Diaminocyclohexane)oxalatoplatinum(II) (oxaliplatin) is a third-generation platinum anticancer compound that produces the same type of inter- and intrastrand DNA cross-links as cisplatin. In combination with 5-fluorouracil, oxaliplatin has been recently approved in Europe, Asia, and Latin America for the treatment of metastatic colorectal cancer. We present here the crystal structure of an oxaliplatin adduct of a DNA dodecanucleotide duplex having the same sequence as that previously reported for cisplatin (Takahara, P. M.; Rosenzweig, A. C.; Frederick, C. A.; Lippard, S. J. Nature 1995, 377, 649-652). Pt-MAD data were used to solve this first X-ray structure of a platinated DNA duplex derived from an active platinum anticancer drug other than cisplatin. The overall geometry and crystal packing of the complex, refined to 2.4 A resolution, are similar to those of the cisplatin structure, despite the fact that the two molecules crystallize in different space groups. The platinum atom of the [Pt(R,R-DACH)](2+) moiety forms a 1,2-intrastrand cross-link between two adjacent guanosine residues in the sequence 5'-d(CCTCTGGTCTCC), bending the double helix by approximately 30 degrees toward the major groove. Both end-to-end and end-to-groove packing interactions occur in the crystal lattice. The latter is positioned in the minor groove opposite the platinum cross-link. A novel feature of the present structure is the presence of a hydrogen bond between the pseudoequatorial NH hydrogen atom of the (R,R)-DACH ligand and the O6 atom of the 3'-G of the platinated d(GpG) lesion. This finding provides structural evidence for the importance of chirality in mediating the interaction between oxaliplatin and duplex DNA, calibrating previously published models used to explain the reactivity of enantiomerically pure vicinal diamine platinum complexes with DNA in solution. It also provides a new kind of chiral recognition between an enantiomerically pure metal complex and the DNA double helix.
The Viral Mimetic Polyinosinic:Polycytidylic Acid Alters the Growth Characteristics of Small Intestinal and Colonic Crypt Cultures (2020)

Background & AimsThe intestinal epithelium is the first line of defense against enteric pathogens. We investigated the response of small intestinal and colonic crypt cultures to a panel of toll-like receptor ligands to assess the impact of microbial pattern recognition on epithelial growth.MethodsPrimary murine jejunal enteroids and colonoids were cultured with lipopeptide Pam3CSK4, lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (Poly I:C) for 4 to 6 days. Surface area, budding and survival were assessed. Proliferation and numbers of lysozyme positive cells were quantified by flow cytometry. Gene expression was assessed by Nanostring and qRT-PCR.ResultsExposure to Pam3CSK4 and LPS had minimal impact on either enteroids or colonoids. In contrast, Poly I:C increased the surface area of enteroids, while colonoids demonstrated decreased budding. Survival was decreased by Poly I:C in enteroids but not in colonoids. Both enteroids and colonoids exhibited upregulated gene expression of chemokines, but these were increased in magnitude in enteroids. Decreases in gene expression associated with epithelial differentiation and lysozyme positive cells were more apparent in enteroids than in colonoids. Baseline gene expression between enteroids and colonoids differed markedly in levels of stem cell and inflammatory markers. The changes in morphology induced by Poly I:C were mediated by the toll-like receptor adaptor molecule 1 (Ticam1) in enteroids but not in colonoids.ConclusionsPoly I:C alters the molecular program of epithelial cells and shifts from absorption and digestion towards defense and inflammation. Diversity of responses to microbial patterns in enteroids and colonoids may underlie differences in susceptibility to infection along the intestinal tract.
Toughness-Durability of Glass Fiber Reinforced Concrete Systems (1988)

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Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) for Studying Dynamics of Protein Abundance and Posttranslational Modifications (2005)

Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a tag into proteins for relative quantitation by mass spectrometry. SILAC is a simple, yet powerful, method for investigating the dynamics of protein abundance and posttranslational modifications. Here, we provide detailed instructions for using this method to study protein complexes, protein-protein interactions, and the dynamics of protein abundance and posttranslational modifications. We expect that SILAC will become a routine technique because of its applicability to most areas of cell biology. We have also developed a Web site (http://www.silac.org) to provide researchers with updated information about this method and related resources.
Interactions Between Cognitive and Sensorimotor Functions in the Motor Cortex: Evidence from the Preparatory Motor Sets Anticipating a Perturbation (2004)

The many signs of cognitive processes in the activation pattern of the primary motor cortex or in corticospinal (CS) excitability gave rise to the idea that the motor cortex is a crucial node in the processing of cognitive information related to sensorimotor functions. Moreover, it became clear that the preparatory motor sets offer a privileged window to investigate the interaction between cognitive and sensorimotor function in the motor cortex. In the present review, we examine how the study of the preparatory motor sets anticipating a mechanical movement perturbation contributes to enlightening this question. Following the initial observation made by Hammond that some components of the stretch reflex can be modulated by a prior intention either to resist or to relax in response to a subsequent perturbation, first evidence of the phenomenon was obtained in behaving monkeys. Moreover, this study related this peripheral fact to the observed anticipatory activity of motor cortex neurons after a prior instruction telling the animal how to respond to the subsequent perturbation, which triggered the instructed movement. Indeed, this anticipatory activity was found to be different according to the instruction. In the 1980s, this work inspired a lot of studies in human beings that brought support to the idea of a cognitive tuning of the long latency stretch response (LLSR). Specifically, the MI component of the response was shown to be modulated by a prior intent to resist versus to let go when faced with the perturbation. Recently, new approaches have been developed to obtain evidence of a cognitive tuning of CS excitability, thanks to transcranial magnetic stimulation (TMS). TMS has been used both as a reliable tool for quantifying the CS excitability via the motor evoked potentials (MEPs), and to centrally perturb the organization of movement. Such central perturbations offer the unique opportunity to activate the descending motor tracts while shunting, for a short time period, the ascending tracts assisting the movement. Thus, CS excitability was measured before the movement was perturbed. These studies demonstrated the readiness of the CS tract to be involved in anticipatory compensatory responses to central movement perturbations induced by TMS in relation to the subject's cognitive attitudes. The question of the cerebral regions upstream of the motor cortex that could be responsible for this modulation in CS excitability remains largely open.
Marked elevation in plasma osteoprotegerin constitutes an early and consistent feature of cerebral malaria (2016)

Adherence of infected erythrocytes to vascular endothelium causes acute endothelial cell (EC) activation during Plasmodium falciparum infection. Consequently, proteins stored in Weibel-Palade (WP) bodies within EC are secreted into the plasma. Osteoprotegerin (OPG) binds to VWF and consequently is stored within WP bodies. Given the critical role of EC activation in the pathogenesis of severe malaria, we investigated plasma OPG levels in children with P. falciparum malaria. At presentation, plasma OPG levels were significantly elevated in children with cerebral malaria (CM) compared to healthy controls (means 16.0 vs 0.8 ng/ml; p< 0.01). Importantly, OPG levels were also significantly higher in children with CM who had a fatal outcome, compared to children with CM who survived. Finally, in children with CM, plasma OPG levels correlated with other established prognostic indices (including plasma lactate levels and peripheral parasite density). To further investigate the relationship between severe malaria and OPG, we utilised a murine model of experimental CM in which C57BL/6J mice were infected with P. berghei ANKA. Interestingly, plasma OPG levels were increased 4.6 fold within 24 hours following P. berghei inoculation. This early marked elevation in OPG levels was observed before any objective clinical signs were apparent, and preceded the development of peripheral blood parasitaemia. As the mice became increasingly unwell, plasma OPG levels progressively increased. Collectively, these data suggest that OPG constitutes a novel biomarker with prognostic significance in patients with severe malaria. In addition, further studies are required to determine whether OPG plays a role in modulating malaria pathogenesis.
MobiSweep (2016)

In this paper, we explore quick 3D shape composition during early-phase spatial design ideation. Our approach is to re-purpose a smartphone as a hand-held reference plane for creating, modifying, and manipulating 3D sweep surfaces. We implemented MobiSweep, a prototype application to explore a new design space of constrained spatial interactions that combine direct orientation control with indirect position control via well-established multi-touch gestures. MobiSweep leverages kinesthetically aware interactions for the creation of a sweep surface without explicit position tracking. The design concepts generated by users, in conjunction with their feedback, demonstrate the potential of such interactions in enabling spatial ideation.
Delinquency and Abuse Among Juvenile Sexual Offenders (1988)

Background information obtained from 450 male juvenile sexual offenders and their families was examined to explore two important questions: Are juvenile sexual offenders referred for more serious offenses more likely to have a history of aggressiveness or delinquency? Are more serious sexual offenses committed by juveniles who themselves have previously been victims of abuse? The results did not indicate a strong association between the more serious referral sexual offenses and histories of aggressive or property-destructive behavior, but did confirm that the more serious offenses were committed by juveniles who had themselves been abused. Violence and abuse within offenders' families, even though not directly involving the offender himself, were also found to be associated with more serious offenses.
Lysozyme deficiency-an inherited disorder of rabbits. (1974)

A genetic disorder of rabbits consisting of a deficiency of the enzyme lysozyme is characterized. The condition appears to be inherited as an autosomal recessive trait. Most of the tissues of lysozyme-deficient rabbits including bone marrow, liver, lung. spleen and bone had levels of lysozyme which were 1% or less of the levels in the corresponding tissues of normal rabbits when measured with the lysoplate method. Levels of lysozyme in the kidney and serum were 6% of controls, but the thymus of the lysozyme-deficient rabbits had normal levels of the enzyme. All leukocytes of the lysozyme-deficient rabbits were negative for lysozyme when examined by a histobacterial technic. No morphologic lesions could be detected in any of the tissues of the lysozyme-deficient rabbits. Although several species of animals have been reported to be lysozyme deficient, this appears to be the first report of lysozyme deficiency occurring as a mutant condition. It is suggested that these mutant rabbits may be useful as a resource for experiments designed to delineate the biologic role of lysozyme.
Electropolymeric materials incorporating subsite structures related to iron-only hydrogenase: active ester functionalised poly(pyrroles) for covalent binding of {2Fe3S}-carbonyl/cyanide assemblies (2007)

We report the assembly of the first electropolymeric materials incorporating catalytic diiron subsites related to those of the iron-only hydrogenases.
Chloroperoxidase, a Janus Enzyme (2008)

Chloroperoxidase is a versatile fungal heme-thiolate protein that catalyzes a variety of one-electron and two-electron oxidations. We report here that the alkylation of an essential histidine residue showed no effect on the one-electron peroxidations but inhibited two-electron oxidations. The pH profiles of different peroxidative substrates showed optimal activities at varying pH values for the same enzyme. 2-Allylphenol and substituted ortho-phenolics showed efficient peroxidations. Also, substrates excluded from the active site (or with no favorable positioning at the heme center or heme edge) were converted in the peroxidation reaction. While hydrogen peroxide serves as the superior activator in the two-electron oxidations, small alkylhydroperoxides give much better rates for peroxidation reactions. All the above observations indicate that one-electron oxidations are mechanistically quite different from the two-electron oxidations catalyzed by chloroperoxidase. We propose that the peroxidatic substrates interact predominantly outside the heme active site, presumably at the surface of the enzyme.
Extract prepared from the bark of Cinnamomum cassia Blume prevents glutamate-induced neuronal death in cultured cerebellar granule cells (2000)

We studied the protective effect of a water extract from the bark of Cinnamomum cassia Blume on glutamate-induced neuronal death by MTT assay and its action on (45)Ca(2+) influx using cultured rat cerebellar granule cells. In a dose-dependent manner, this extract (10(-5)-10(-4) g/mL) significantly protected against glutamate-induced cell death and also inhibited glutamate-induced (45)Ca(2+) influx. These results suggest that the bark of Cinnamomum cassia has a protective effect on glutamate-induced neuronal death through the inhibition of Ca(2+) influx.
An efficient HARQ retransmission algorithm in OFDMA based wireless networks (2009)

In wireless transmission, hybrid automatic repeat request (HARQ) can improve the throughput performance by using error correction and error detection techniques when the signal quality is poor. In this paper, the effectiveness of HARQ in orthogonal frequency division multiple access (OFDMA) based wireless networks is studied. In OFDMA networks, every channel is split into a set of orthogonal sub-carriers collectively. Every user is assigned a set of sub-carriers for data transmission. When the network is overloaded, some of the packet retransmissions could be delayed. For applications with critical delay and jitter requirement, such as video and VoIP, packets with large delay because of too many retransmission attempts are usually discarded. If those retransmissions are assigned to sub-carriers with better signal quality, the transmission efficiency can be improved. In this paper, we propose an enhanced HARQ algorithm to schedule retransmissions to subcarriers to achieve higher throughput. A timestamp, determined by delay requirements, is attached to the retransmission request. The OFDMA scheduler allocates sub-carriers and time offsets to retransmission packets based on channel properties and the timestamp value. Retransmissions with smaller timestamp value than the estimated propagation time will be aborted. Therefore, the traffic load introduced by unnecessary retransmissions is reduced and the throughput can be improved.
Toughness and Transparency of Poly(vinyl chloride)/Methyl Methacrylate-Butadiene-Styrene Blends with Varied Shell Phase Composition of Core-Shell Theories (2009)

Methyl methacrylate-butadiene-styrene (MBS) were prepared by emulsion polymerization method through grafting of styrene (St) and methyl methacrylate (MMA) with varied ratio on polybutadiene (PB) particles. The effect of St/MMA weight ratio of the shell in MBS on the property of PVC/MBS blends was investigated. It was found that when St/MMA weight ratio was 0/40 and 10/30, brittle-ductile transition occurred firstly for PVC/MBS blends. Transparency of PVC/MBS blends enhanced with the increase of St content in the shell of MBS. TEM results showed that MBS composition in the shell affected disperse morphology of MBS particles in PVC matrix and the deformation behavior of PVC/MBS blends. With the increase of MMA content of the shell in MBS, the deformation mechanism of PVC/MBS blends take place transition from debonding in the interface between MBS particle and PVC matrix to the cavitation of MBS followed by shear deformation of PVC matrix.
Higher order loop corrections for short range magnetoquasistatic position tracking (2011)

Magnetoquasistatic position tracking has been shown to be an excellent technique to measure distances between an emitting and receiving loop for distances up to 50 m along a direction perpendicular to the surface normal of the loops. For short distances from the emitting loop (i.e., less than about ten loop radii) there is an error in the estimated distance. In this paper, we examine the cause of this error and show that a significant portion is due to the simplification of the emitting loop as a simple magnetic dipole. By including a more accurate expression of the source field, errors can be significantly reduced. We show that the first correction term results in a reduction in rms and peak distance estimation error of 12.51 cm (54.44 %) and 11.27 cm (44.72 %), respectively, for distances less than 1.5δ, where δ is the skin depth.
Three dimensional electromechanical model of porcine heart with penetrating wound injury. (2005)

The aim of this study is development a prototype computational model of the pig heart that can be used to predict physiological responses to a penetrating wound injury. The pig has been chosen for this model studies because it shares many anatomical similarities with humans. Three-dimensional cubic Hermite finite element meshes based on detailed measurements of porcine anatomy combined into an integrated anatomic model. The pig ventricular model includes detailed left and right ventricular geometry and myofiber and laminar sheet orientations throughout the mesh. The cardiac mesh was refined and monodomain equations for action potential propagation solved using well-established collocation-Galerkin finite element methods. The membrane kinetic equations for the action potential model was based on detailed cellular models of transmembrane ionic fluxes and intracellular calcium fluxes in canine ventricular myocytes and human atrial myocytes. We modified the anisotropic myocardial conductivity tensor on the endocardial surface of the ventricles by making use of a surface model fitted to measured of Purkinje fiber network anatomy. The mechanical model compute regional three-dimensional stress and strain distributions using anisotropic constitutive laws referred to local material coordinate axes defined by local myofiber and laminar sheet orientations. Passive myocardial mechanics modeled using exponential orthotropic strain energy functions. Active systolic myocardial stresses computed from a multi-scale model that uses crossbridge theory to predict calcium-activated sarcomere length- and velocity-dependent tension filament tension. Since the electrical and mechanical models use a common finite element mesh as the parent parametric framework and both models are solved within our custom finite element package, it is straightforward to couple these models, as we have recently done for a model of coupled ventricular electromechanics. We apply the coupled electromechanical model to predict alterations in regional diastolic and systolic wall mechanics associated with rhythm disturbances and possible arrhythmias with decreased blood volume, tamponade, myocardial injury, and regional ischemia caused by a penetrating wound.