gebhart/patrepeval huggingface dataset:
Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations (2010)

Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using α-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 Å resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.
Rate Control for Communication Networks: Shadow Prices, Proportional Fairness and Stability (1998)

F. P. Kelly, A. K. Maulloo, D. K. H. Tan, Rate Control for Communication Networks: Shadow Prices, Proportional Fairness and Stability, The Journal of the Operational Research Society, Vol. 49, No. 3 (Mar., 1998), pp. 237-252
Phase I study of high‐dose thiotepa with busulfan, etoposide, and autologous stem cell support in children with disseminated solid tumors (1999)

Background The aim of this phase I study was to define the maximum tolerated dose (MTD) of thiotepa (TT), administered with busulfan (BU) 480 mg/m2 and etoposide 2,400 mg/m2, followed by autologous bone marrow transplantation (ABMT) or peripheral blood stem cell transplantation (APBSCT) support in children with solid tumors either disseminated at diagnosis or after relapse. Procedure Nineteen patients, between 2 and 16 years of age, received a high-dose chemotherapy regimen including escalating doses of TT starting from 150 mg/m2. Subsequent dose escalation was determined by a modified Fibonacci scheme. Whenever one patient at one dosage level showed a grade III or grade IV reversible toxicity, additional patients were admitted (one by one) up to a maximum number of 6. Upon observing grade III or IV reversible toxicity in two or more systems, in 3 of the 6 patients, no further escalation was performed, and the corresponding dosage was taken as the MTD. WHO criteria were adopted to assess grade of toxicity. Results All patients had hematological recovery; and neutrophils and platelet engraftment were observed after median times of 12 and 29 days from stem cell infusion, respectively. The MTD of TT was determined to be 750 mg/ m2. At this level, 3 of 6 patients experienced grade III mucositis and/or grade III gastrointestinal toxicity. No patient died of treatment-related toxicity. Conclusions A dose of 750 mg/m2 TT is the MTD when it is associated with BU 480 mg/m2 and etoposide 2,400 mg/m2. This ablative regimen represents a feasible and tolerable combination for high-dose chemotherapy followed by hematopoietic stem cell rescue (HSCR). Phase II studies in children with poor-prognosis solid tumors are required to evaluate the effectiveness of this treatment. Med. Pediatr. Oncol. 33:450–454, 1999. © 1999 Wiley-Liss, Inc.
Acid Fracturing: The Effect of Formation Strength on Fracture Conductivity (2009)

Abstract A few studies considered the role of rock strength on fracture conductivity retained at elevated closure strengths. Based on experimental results and field data, many correlations were derived with a consideration of both the surface roughness and rock mechanical properties. These studies found that acid fracture conductivity is sometimes lower with longer acid contact times than with shorter ones. This is apparently the result of the weakening of the rock structure along the face of the fracture with increased acid exposure, such that the conductivity decreases more rapidly with increasing the closure stress. Based on extensive literature survey of three types of carbonate rocks, it was found that chalk has the lowest rock embedment strength and the fractures closed at much lower stresses compared with limestone or dolomite. Dolomite has the highest rock embedment strength and best conductivity results compared with other rocks tested. A sensitivity analysis was performed to determine the effect of rock embedment strength, and dissolved rock equivalent conductivity on the fracture conductivity. The results of this analysis showed that dissolved rock equivalent conductivity determines the maximum conductivity at a closure stress equal to zero, while the value of rock embedment strength determines the decline in conductivity with increasing the closure stress. This analysis shows that the value of dissolved rock embedment conductivity doesn't affect the difference that exists in some of the developed correlations, while the value of rock equivalent strength has a significant impact on this difference. Finally, the rock embedment strength is a key parameter that affects the fracture conductivity. This paper discusses current correlations to predict fracture conductivity, and addresses the influences of several key parameters on the fracture conductivity.
Conformal microstrip antennas and microstrip phased arrays (1974)

A new class of antennas using microstrips to form the feed networks and radiators is presented in this communication. These antennas have four distinct advantages: 1) cost, 2) performance, 3) ease of installation, and 4) the low profile conformal design. The application of these antennas is limited to small bandwidths. Phased arrays using these techniques are also discussed.
Architectural considerations for a new generation of protocols (1990)

The current generation of protocol architectures, such as TCP/IP or the ISO suite, seem successful at meeting the demands of todays networks. However, a number of new requirements have been proposed for the networks of tomorrow, and some innovation in protocol structuring may be necessary. In this paper, we review some key requirements for tomorrow's networks, and propose some architectural principles to structure a new generation of protocols. In particular, this paper identifies two new design principles, Application Level Framing and Integrated Layer Processing. Additionally, it identifies the presentation layer as a key aspect of overall protocol performance.
In vitro study of endogenous CEST agents at 3 T and 7 T (2015)

Chemical exchange saturation transfer (CEST) has been an intensive research area in MRI, providing contrast mechanisms for the amplified detection and monitoring of biomarkers and physiologically active molecules. In biological tissues and organs, many endogenous CEST agents coexist, and their CEST effects may overlap. The interpretation of such overlapped CEST effects can be addressed when the individual CEST effects originating from various metabolites are characterized. In this work, we present the in vitro measurements of the CEST effects from endogenous CEST agents that are commonly found in biological tissues and organs, at the external magnetic fields of 3 T and 7 T and under various pH conditions. Together with the proton NMR spectra measured at 11.7 T, these CEST effects have been evaluated in consideration of the chemical exchange rates, chemical shifts, and acidities of the labile protons. Amine protons of small metabolites might not be visible at 3 T, but some of them can be probed at 7 T, wherein their CEST effects may overlap with those from coexisting amide and hydroxyl protons.
Identifying parental substance use and misuse in clinical practice (2008)

While it is difficult to ascertain how extensive the problem of parental substance misuse is in Australia today, international estimates from the USA indicate that approximately 9% of children live in families with parental alcohol abuse or dependence and substance dependence (Office of Applied Studies, 2003). UK estimates of illicit drug use (excluding alcohol) suggest that 2-3% of children in England, and 4-6% of children in Scotland, have parents with drug problems (Advisory Council on the Misuse of Drugs [ACMD], 2003). It seems likely that at least 10% of Australian children also live in families with parental substance misuse (Dawe et al., 2007). However, parental substance misuse rarely occurs in isolation. Parents are often experiencing a range of other problems that affect children's outcomes, including a range of psychological problems that affect mood. Spousal relationships are often strained and, in many families, accompanied by domestic violence. Children of these relationships develop a range of behavioural problems from early childhood and these, in turn, often result in difficulties in settling into the school system. By middle childhood, if little is done, children may be failing to meet minimum literacy and numeracy standards, and engaging in behaviour and conduct problems that make classroom management difficult (see Dawe et al., 2007, for an extensive review of this literature). Given the elevated risk of poor outcomes for children, it is imperative to develop a range of strategies, both at a policy level and in clinical practice, that will reduce the risk of such outcomes. The issue is a complex one and will require a range of treatment responses offered across health, child protection and drug and alcohol services. This brief article will address the issue of identification of substance misuse. How does a clinician determine if a parent is a problematic substance user within the context of routine clinical practice? For those in drug and alcohol treatment agencies, this is a relatively straightforward matter, as such information is clearly core business. But what of those in agencies who come into contact with multi-problem families but are not directly presented with a substance use issue (e.g., general practice or child health services)? Alternatively, how does a practitioner who learns of parental substance use gauge whether this use may be adversely affecting children?
Lymphocytopenia in a hospital population ‐ what does it signify? (1997)

Lymphocytopenia in hospital patients is most frequently reversible, and due to acute illness, notably sepsis and trauma (including surgery). Malignancy, with or without chemotherapy, and steroid use are also common causes, but HIV infection is a relatively uncommon cause in our hospital.
How to Build an Embodiment Lab: Achieving Body Representation Illusions in Virtual Reality (2014)

Advances in computer graphics algorithms and virtual reality (VR) systems, together with the reduction in cost of associated equipment, have led scientists to consider VR as a useful tool for conducting experimental studies in fields such as neuroscience and experimental psychology. In particular virtual body ownership, where the feeling of ownership over a virtual body is elicited in the participant, has become a useful tool in the study of body representation, in cognitive neuroscience and psychology, concerned with how the brain represents the body. Although VR has been shown to be a useful tool for exploring body ownership illusions, integrating the various technologies necessary for such a system can be daunting. In this paper we discuss the technical infrastructure necessary to achieve virtual embodiment. We describe a basic VR system and how it may be used for this purpose, and then extend this system with the introduction of real-time motion capture, a simple haptics system and the integration of physiological and brain electrical activity recordings.
Sodium Transport: Inhibitory Factor in Sweat of Patients with Cystic Fibrosis (1967)

A factor inhibitory to sodium transport exists in the sweat of patients with cystic fibrosis of the pancreas. When the duct system of the rat parotid was perfused with sweat from patients, marked inhibition of sodium reabsorption was observed. Perfusion with sweat from normal subjects caused no change in sodium reabsorption. The factor thus demonstrated may be responsible for the increased sodium concentrations in the sweat of patients with cystic fibrosis.
Anisotropic critical currents in Ba2YCu3O7 analyzed using an extended Bean model (1989)

We have extended Bean’s critical state model to explicitly include anisotropic critical currents. Measurements at 30 K of the critical currents parallel to the Cu-O planes but with vortex motion either parallel or across twin boundaries show twin boundaries are probably not an important cause of vortex pinning. In the critical state, current flow perpendicular to the Cu-O planes is about 30 times smaller than flow parallel to these planes.
Human implantation : cell biology and immunology (1995)

1. Introduction. 2. Evolution of the maternal-fetal interaction 3. Decidulisation 4. Human trophoblast development 5. Isolation and characterisation of cells from the early pregnant uterus 6. Trophoblast expression of major histocompatibility complex class 1 antigens 7. Uterine mucosal leucocytes 8. Maternal systemic and local immune response to trophoblast 9. Trophoblast interaction with extracellular matrix 10. Cytokines and their receptors in implantation 11. Clinical implications of defective implantation Index.
Re‐imagining motor imagery: Building bridges between cognitive neuroscience and sport psychology (2011)

One of the most remarkable capacities of the mind is its ability to simulate sensations, actions, and other types of experience. A mental simulation process that has attracted recent attention from cognitive neuroscientists and sport psychologists is motor imagery or the mental rehearsal of actions without engaging in the actual physical movements involved. Research on motor imagery is important in psychology because it provides an empirical window on consciousness and movement planning, rectifies a relative neglect of non-visual types of mental imagery, and has practical implications for skill learning and skilled performance in special populations (e.g., athletes, surgeons). Unfortunately, contemporary research on motor imagery is hampered by a variety of semantic, conceptual, and methodological issues that prevent cross-fertilization of ideas between cognitive neuroscience and sport psychology. In this paper, we review these issues, suggest how they can be resolved, and sketch some potentially fruitful new directions for inter-disciplinary research in motor imagery.
Push-pull mode magnetostrictive/piezoelectric laminate composite with an enhanced magnetoelectric voltage coefficient (2005)

A magnetoelectric (ME) laminate composite consisting of a symmetric longitudinally poled piezoelectric Pb(Mg1∕3Nb2∕3)O3–PbTiO3 crystal and two longitudinally magnetized magnetostrictive Tb1−xDyxFe2 layers has been developed that has a notably superior ME voltage coefficient, relative to previous laminate configurations. The symmetric nature of the longitudinally poled piezoelectric layer allows for operation in a push-pull mode that optimizes elastic coupling between layers. Our small laminate has a giant ME voltage coefficient of ∼1.6V∕Oe at low frequencies, a significant enhancement of this coefficient to ∼20V∕Oe under resonance drive, and an exceptional low-level magnetic field sensitivity of ∼10−12T at f=f0.
Regulation of Complement Activity by Vaccinia Virus Complement-Control Protein (1992)

A major protein secreted by vaccinia virus-infected cells has structural similarity to the super-family of complement-control proteins. This vaccinia complement-control protein (VCP) was studied to determine how it regulates complement activation. VCP was bound by C4b and C3b and served as a cofactor with factor I in cleaving these two molecules. VCP inhibited the formation and accelerated the decay of the classical C3 convertase. It also accelerated decay of the alternative pathway convertase, although higher concentrations were apparently needed. In vitro, therefore, VCP interfered with the classical and alternative complement pathways at several steps. In vivo, this interference may increase the virulence of vaccinia virus by enabling it to escape attack by the host's complement system.
Intervention of crescentic glomerulonephritis by antibodies to monocyte chemotactic and activating factor (MCAF/MCP‐1) (1996)

We investigated the pathophysiological role of a potent macrophage (M(phi)) chemotactic cytokine (chemokine), monocyte chemotactic and activating factor/monocyte chemoattractant protein-1 (MCAF/MCP-1), in an animal model of crescentic glomerulonephritis. Administration of a small dose of nephrotoxic sera induced severe proliferative and necrotizing glomerulonephritis, with crescentic formation in the early phase and glomerulosclerosis in the later phase, in Wistar-Kyoto rats. MCAF/MCP-1 protein was detected immunohistochemically in glomeruli, vascular endothelial cells, and tubular epithelial cells in the early phase of injured kidney tissues but not in normal ones. Anti-MCAF/MCP-1 antibodies decreased the number of M(phi) in glomeruli, and prevented crescentic formation and the fusion of epithelial cell foot process in nephritic rats, thereby decreasing the excreted amounts of protein to normal levels on days 3 and 6. Furthermore, anti-MCAF/MCP-1 antibodies remarkably reduced glomerulosclerosis and improved renal dysfunction as well as proteinuria in the later phase (56 days). These results indicate that MCAF/MCP-1 essentially participates in the impairment of renal functions associated with crescentic glomerulonephritis by recruiting and activating M(phi).
Biochip technologies in cancer research (2001)

Development of high-throughput 'biochip' technologies has dramatically enhanced our ability to study biology and explore the molecular basis of disease. Biochips enable massively parallel molecular analyses to be carried out in a miniaturized format with a very high throughput. This review will highlight applications of the various biochip technologies in cancer research, including analysis of 1) disease predisposition by using single-nucleotide polymorphism (SNP) microarrays, 2) global gene expression patterns by cDNA microarrays, 3) concentrations, functional activities or interactions of proteins with proteomic biochips, and 4) cell types or tissues as well as clinical endpoints associated with molecular targets by using tissue microarrays. One can predict that individual cancer risks can, in the future, be estimated accurately by a microarray profile of multiple SNPs in critical genes. Diagnostics of cancer will be facilitated by biochip readout of activity levels of thousands of genes and proteins. Biochip diagnostics coupled with informatics solutions will form the basis of individualized treatment decisions for cancer patients.
Lysosomal degradation of Asn‐linked glycoproteins (1989)

Catabolism of Asn-linked glycoproteins to monosaccharides and amino acids occurs in lysosomes. Break-down must be complete to avoid lysosomal storage diseases that occur when fragments as small as dimers are left undigested. Recent results have clarified several aspects of Asn-linked glycoprotein catabolism in mammals. First, degradation of the oligosaccharide portion is accomplished by exo-glycosidases, which act only from the nonreducing end of chains to release sugar monomers as products. In contrast, proteolysis can proceed from both end and internal points along the polypeptide to eventually yield free amino acids. A second important feature of the glycoprotein disassembly pathway is that the hydrolytic steps can be grouped into two sets of ordered reactions: I) stepwise hydrolysis of the major portion of the oligosaccharide chains by a set of exoglycosidases, and II) ordered disassembly of the protein and the oligosaccharide-to-protein linkage region. Process II can vary at a single reaction step depending on the species in which degradation takes place. Thus, the last step of reaction sequence II can be either: 1) hydrolysis of the actual peptide-to-carbohydrate linkage, or 2) removal of the reducing-end GlcNAc from a previously freed oligosaccharide. The latter cleavage is catalyzed by the lysosomal glycosidase chitobiase. Chitobiase has been found only in humans and rats and not in other mammals (dogs, cats, goats, sheep, cats, or cattle). The hydrolytic mechanism of this enzyme is unique as it appears to be a reducing-end glycosidase and can be viewed as an accessory step in the human and rat digestive pathways. The species that lack this enzyme likely rely on exo-beta-D-glucosaminidase to cleave GlcNAc from both outer chain residues and the chitobiose moiety at the protein-to-carbohydrate linkage.
W011005 Development of an Autonomous UAV Managed by Virtual Reality (2012)

The purpose of this work is to develop an autonomous Unmanned Aerial Vehicle (UAV) as a platform for several types of applications, including inspection, monitoring. The first project presented in this paper concerns an autonomous UAV used in conjunction of Virtual Reality to monitor crop fields to ensure a healthy growing process. We used the AR.Drone, a widely commercialized UAV, initially designed for video gaming and customized it to suit the project's requirements. The resulting prototype is the AGUL, equipped with a GPS and a compass for localization as well as other sensors for real-time monitoring of crops (temperature sensor, humidity sensor, high vision camera). The first tests performed indoor showed promising results regarding the autonomous capability of this drone. The next step will be to perform outdoor tests to assess the robustness of the drone to perturbations like wind or GPS localization errors.
Multimedia Analysis + Visual Analytics = Multimedia Analytics (2010)

To deal with the extent and variety of digital media, researchers are combining multimedia analysis and visual analytics to form the new field of multimedia analytics. This article gives some historical background, discusses surveys of related research, describes initial multimedia analytics research, and reports on benchmark datasets.
Metal-organic frameworks with high capacity and selectivity for harmful gases (2008)

Benchmarks have been established for the performance of six metal-organic frameworks (MOFs) and isoreticular MOFs (IRMOFs, which have the same underlying topology as MOF-5), MOF-5, IRMOF-3, MOF-74, MOF-177, MOF-199, and IRMOF-62, as selective adsorbents for eight harmful gases: sulfur dioxide, ammonia, chlorine, tetrahydrothiophene, benzene, dichloromethane, ethylene oxide, and carbon monoxide. Kinetic breakthrough measurements are used to determine the calculated dynamic adsorption capacity of each "benchmark" MOF for each gas. The capacity of each MOF is compared to that of a sample of Calgon BPL activated carbon. We find that pore functionality plays a dominant role in determining the dynamic adsorption performance of MOFs. MOFs featuring reactive functionality outperform BPL carbon in all but one case and exhibit high dynamic adsorption capacities up to 35% by weight.
Nitrilimine cycloadditions in aqueous media (2000)

Nitrilimine cycloadditions onto a variety of alkenyl dipolarophiles were performed for the first time in aqueous media. The observed cycloaddition outcome was markedly dependent on several factors, including the electronic features and the solubility in water of the dipolarophiles, as well as the presence of a cationic surfactant or an organic cosolvent in the reaction mixture.