gebhart/patrepeval huggingface dataset:
Receptor Targeting for Tumor Localisation and Therapy with Radiopeptides (2000)

Receptor targeting with radiolabeled peptides has become very important in nuclear oncology in the past few years. The most frequently used peptides in the clinic are analogs of somatostatin (SRIF), e.g. OctreoScan, which contain chelators for the radioisotopes 111In, 86Y, 90Y, 67Ga, 68Ga and 64Cu or for 99mTc and 188Re. and were labelled with the halogens 123I and 18F. Radiolabeled analogs of &alpha-melanocyte-stimulating hormone (&alpha-MSH), neurotensin, vasoactive intestinal peptide (VIP), bombesin (BN), substance P (SP) and gastrin/cholecystokinin (CCK) are also being developed, evaluated in vitro and in vivo and tested for clinical application. This review focuses on the expression in tumors and the regulation of receptors for these neuropeptides as well as the development of novel chelator-peptide conjugates suitable for in vivo scintigraphy or internal radiotherapy. The state of the art of radiopeptide pharmaceuticals is illustrated with four SRIF analogs, modified with the macrocyclic chelator 1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetraacetic acid (DOTA): [D-Phe1]-octreotide (DOTAOC), [D-Phe1, Tyr3]-octreotide (DOTATOC), vapreotide (DOTAVAP) and lanreotide (DOTALAN). DOTA is almost a universal chelator capable of strongly encapsulating hard metals such as 111In and 67Ga for Single Photon Emission Tomography (SPET), 68Ga, 86Y and 64Cu for Positron Emission Tomography (PET) as well as 90Y for receptor-mediated radionuclide therapy and radiolanthanides which exhibit different interesting decay schemes. From biodistribution studies in experimental animals and from clinical data it is concluded that DOTATOC is currently the most suitable SRIF radiopeptide with the best potential in the clinic.
Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation (2008)

According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-beta (Abeta) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Abeta assemblies is accompanied by a conformational change toward a high content of beta-structure. Here, we report the solution structure of Abeta(1-40) in complex with the phage-display selected affibody protein Z(Abeta3), a binding protein of nanomolar affinity. Bound Abeta(1-40) features a beta-hairpin comprising residues 17-36, providing the first high-resolution structure of Abeta in beta conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Abeta. Z(Abeta3) stabilizes the beta-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Abeta hairpin within a large hydrophobic tunnel-like cavity. Consequently, Z(Abeta3) acts as a stoichiometric inhibitor of Abeta fibrillation. The selected Abeta conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates.
What happens to Helicobacter pylori after vagotomy and drainage? (1999)

H. pylori is currently identified as the dominant risk factor for chronic duodenal ulcer. The effect of surgery in the form of truncal vagotomy and drainage on the H. pylori status is not well known. Forty three patients with obstructed duodenal ulcer who were positive for H. pylori preoperatively by the urease test on the antral mucosal biopsy specimens were recalled for repeat endoscopy and urease test from the same site at 1 month, 3 months, 6 months and more than 1 year after surgery. The H. pylori positivity declined from 100% preoperatively to 69%, 71%, 73% and 80% at these intervals postoperatively respectively. The fall in H. pylori status after surgery was significant at all intervals. Since surgery for duodenal ulcer in the form of truncal vagotomy and drainage is curative for duodenal ulcer in over 90% of patients whereas H. pylori is suppressed in approximately 20% of patients only, it appears that its effect is independent of H. pylori status. Further studies are required to confirm whether a fall in H. pylori positivity in the antrum is absolute or is due to proximal migration of the organism.
Lipolysis of Triglycerides of Human Milk During Storage at Low Temperatures (1983)

Human milk samples were divided at collection and stored at -70 degrees C or -20 degrees C, or extracted immediately with organic solvent, to compare lipid class composition. Storage at -20 degrees C was not satisfactory for maintaining milk lipid composition, for it resulted in hydrolysis of triglycerides and the appearance of free fatty acids.
Synergistic effect of WRI1 and DGAT1 coexpression on triacylglycerol biosynthesis in plants (2013)

Metabolic engineering approaches to increase plant oil levels can generally be divided into categories which increase fatty acid biosynthesis ('Push'), are involved in TAG assembly ('Pull') or increase TAG storage/decrease breakdown ('Accumulation'). In this study, we describe the surprising synergy when Push (WRI1) and Pull (DGAT1) approaches are combined. Co-expression of these genes in the Nicotiana benthamiana transient leaf expression system resulted in TAG levels exceeding those expected from an additive effect and biochemical tracer studies confirmed increased flux of carbon through fatty acid and TAG synthesis pathways. Leaf fatty acid profile also synergistically shifts from polyunsaturated to monounsaturated fatty acids.
Muscle hypertrophy driven by myostatin blockade does not require stem/precursor-cell activity (2009)

Myostatin, a member of the TGF-beta family, has been identified as a powerful inhibitor of muscle growth. Absence or blockade of myostatin induces massive skeletal muscle hypertrophy that is widely attributed to proliferation of the population of muscle fiber-associated satellite cells that have been identified as the principle source of new muscle tissue during growth and regeneration. Postnatal blockade of myostatin has been proposed as a basis for therapeutic strategies to combat muscle loss in genetic and acquired myopathies. But this approach, according to the accepted mechanism, would raise the threat of premature exhaustion of the pool of satellite cells and eventual failure of muscle regeneration. Here, we show that hypertrophy in the absence of myostatin involves little or no input from satellite cells. Hypertrophic fibers contain no more myonuclei or satellite cells and myostatin had no significant effect on satellite cell proliferation in vitro, while expression of myostatin receptors dropped to the limits of detectability in postnatal satellite cells. Moreover, hypertrophy of dystrophic muscle arising from myostatin blockade was achieved without any apparent enhancement of contribution of myonuclei from satellite cells. These findings contradict the accepted model of myostatin-based control of size of postnatal muscle and reorient fundamental investigations away from the mechanisms that control satellite cell proliferation and toward those that increase myonuclear domain, by modulating synthesis and turnover of structural muscle fiber proteins. It predicts too that any benefits of myostatin blockade in chronic myopathies are unlikely to impose any extra stress on the satellite cells.
Organization of the human protein S genes (1990)

Human genomic clones that span the entire protein S expressed gene (PS alpha) and the 3' two-thirds of the protein S pseudogene (PS beta) have been isolated and characterized. The PS alpha gene is greater than 80 kilobases in length and contains 14 introns and 15 exons, as well as 6 repetitive "Alu" sequences. Exons I and XV contain 112 and 1139 bp 5' and 3' noncoding segments in addition to the amino and carboxyl termini, respectively. Exons I-VIII encode protein segments that are homologous to the vitamin K dependent clotting proteins and are bounded by introns whose position and type are identical with other members of this protein family. Exons IX-XV encode protein segments homologous to sex hormone binding globulin (SHBG) and are bounded by introns of identical type and position as in the SHBG gene. Genomic clones for the PS beta gene cover a distance of greater than 55 kilobases and contain segments corresponding to amino acids 46-635 of the mature protein and the 1.1-kb 3' noncoding region of the cDNA. The presence of multiple base changes in the coding portions of this gene, resulting in termination codons and frame shifts, suggests that it is a pseudogene. Comparison of DNA sequences for the two genes reveals 97% identity for coding and 3' noncoding, and 95.4% for intronic regions, suggesting divergence of the two genes is a relatively recent event.
Genetic and Biochemical Characterization of the UGP1 Gene Encoding the UDP‐Glucose Pyrophosphorylase from Saccharomyces cerevisiae (1995)

We report here that the open reading frame YKL248 , previously identified during the systematic sequencing of yeast chromosome XI [Purnelle B., Skala, J., Van Dijck, L. &amp; Goffeau, A. (1992) Yeast 8 , 977–986] encodes UDP‐glucose pyrophosphorylase (UGPase), the enzyme which catalyses the reversible formation of UDP‐Glc from glucose 1‐phosphate and UTP. Proof for this function come from sequence alignment of the YKL248 product with UGPase of other species, from complementation studies of an Escherichia coli galU mutant deficient in UGPase activity, and from overexpression studies. In particular, the amino acid sequence motifs involved in the binding of glucose 1–phosphate and UDP‐Glc are entirely conserved between the yeast, bovine, human and potato tuber UGPases, and multi‐copy expression of YKL248 resulted in a 40‐fold increase in UGPase activity. This gene was, therefore, renamed UGP1. Gene disruption at the UGP1 locus in a diploid strain, followed by tetrad analysis, showed that UGPase is essential for cell viability. Functional analysis of UGP1 was, therefore, carried out by generating strains in which UGPase could be either overexpressed or depleted. This was done by generating haploid strains carrying either UGP1 on a multicopy vector or the chromosomal deletion of UGP1 , and rescued by a vector bearing the wild‐type gene under the control of the glucose‐repressible galactose‐inducible promoter. The effects of overproducing UGPase on the cell metabolism and morphology were carbon‐source dependent. On glucose medium, the 40–fold increase of UGPase activity was restricted to a twofold increase in the concentration of glycogen and UDP‐Glc, with no significant effect on growth. In contrast, on galactose, the 40–fold increase in UGPase activity was accompanied by several effects, including a threefold reduction of the growth rate, a 3–5–fold increase in the concentrations of UDP‐Glc, UDP‐Gal and galactose 1–phosphate, a higher sensitivity to calcofluor white and an increase in the degree of protein glycosylation. Depletion of UGPase activity was performed by transferring the mutant strains from galactose to glucose medium. Unexpectedly, growth of these mutants on glucose was as efficient as that of the control, although the mutants contained only 5–10% wild‐type UGPase activity, and a growth defect could never been obtained, even after serial transfers of the mutants to a 10% glucose medium. However, the 10–fold reduction of UGPase activity induced a multi‐budding pattern, a higher resistance to zymolyase, a slight increase in the calcofluor sensitivity and a decrease in the cell‐wall β‐glucan content. All these alterations, induced by manipulating the UGP1 gene, are discussed in the context of the strategic position of UDP‐Glc in yeast metabolism.
Glucose Control and Vascular Complications in Veterans with Type 2 Diabetes (2008)

Intensive glucose control in patients with poorly controlled type 2 diabetes had no significant effect on the rates of major cardiovascular events, death, or microvascular complications with the exception of progression of albuminuria (P = 0.01) [added]. (ClinicalTrials.gov number, NCT00032487.)
Recent Advances in Natural Language Generation: A Survey and Classification of the Empirical Literature (2017)

Natural Language Generation (NLG) is defined as the systematic approach for producing human understandable natural language text based on non-textual data or from meaning representations. This is a significant area which empowers human-computer interaction. It has also given rise to a variety of theoretical as well as empirical approaches. This paper intends to provide a detailed overview and a classification of the state-of-the-art approaches in Natural Language Generation. The paper explores NLG architectures and tasks classed under document planning, micro-planning and surface realization modules. Additionally, this paper also identifies the gaps existing in the NLG research which require further work in order to make NLG a widely usable technology.
Macrophage oxidation of L-arginine to nitrite and nitrate: nitric oxide is an intermediate (1988)

Previous studies have shown that murine macrophages immunostimulated with interferon gamma and Escherichia coli lipopolysaccharide synthesize NO2-, NO3-, and citrulline from L-arginine by oxidation of one of the two chemically equivalent guanido nitrogens. The enzymatic activity for this very unusual reaction was found in the 100,000g supernatant isolated from activated RAW 264.7 cells and was totally absent in unstimulated cells. This activity requires NADPH and L-arginine and is enhanced by Mg2+. When the subcellular fraction containing the enzyme activity was incubated with L-arginine, NADPH, and Mg2+, the formation of nitric oxide was observed. Nitric oxide formation was dependent on the presence of L-arginine and NADPH and was inhibited by the NO2-/NO3- synthesis inhibitor NG-monomethyl-L-arginine. Furthermore, when incubated with L-[guanido-15N2]arginine, the nitric oxide was 15N-labeled. The results show that nitric oxide is an intermediate in the L-arginine to NO2-, NO3-, and citrulline pathway. L-Arginine is required for the activation of macrophages to the bactericidal/tumoricidal state and suggests that nitric oxide is serving as an intracellular signal for this activation process in a manner similar to that very recently observed in endothelial cells, where nitric oxide leads to vascular smooth muscle relaxation [Palmer, R. M. J., Ashton, D. S., & Moncada, S. (1988) Nature (London) 333, 664-666].
Evidence for RNA-RNA cross-link formation in Escherichia coli ribosomes (1978)

Evidence is presented in three separate cases for the formation of RNA-RNA cross-links in intact E. coli ribosomes and ribosomal subunits. The first case is a cross-link between the 18S and 13S regions of the 23S RNA, induced by ultraviolet irradiation. The second is a cross-link at the subunit interface, generated by the bifunctional reagent bis-(2-chloroethyl)-amine. The third example is a cross-link between sections O'-D and P-A of the 16S RNA, induced as in the first case by ultraviolet irradiation. The RNA-RNA cross-links can be identified as such, despite the complications introduced by concomitant RNA-protein cross-linking reactions. The experiments represent a first attempt to introduce RNA-RNA cross-linking into studies of the topographical organization of the RNA within the ribosome.
Protein Nanoparticles Engineered to Sense Kinase Activity in MRI (2009)

We introduce a family of protein nanoparticles capable of sensing analytes in conjunction with magnetic resonance imaging (MRI). The new sensors are derived from the iron storage protein ferritin (Ft); they are designed and optimized using facile protein engineering methods, and self-assembled in cells harboring specific combinations of DNA coding sequences. As illustration, we show that suitably constructed Ft-based sensors can report activity of the important neural signaling enzyme protein kinase A (PKA). Phosphorylation of the engineered Ft-based nanoparticles by PKA promotes clustering and changes in T(2)-weighted MRI signal.
Efficient, Verifiable Binary Sandboxing for a CISC Architecture (2005)

Executing untrusted code while preserving security requires enforcement of memory and control-flow safety policies: untrusted code must be prevented from modifying memory or executing code except as explicitly allowed. Software-based fault isolation (SFI) or “sandboxing” enforces those policies by rewriting the untrusted code at the level of individual instructions. However, the original sandboxing technique of Wahbe et al. is applicable only to RISC architectures, and other previous work is either insecure, or has been not described in enough detail to give confidence in its security properties. We present a novel technique that allows sandboxing to be easily applied to a CISC architecture like the IA-32. The technique can be verified to have been applied at load time, so that neither the rewriting tool nor the compiler needs to be trusted. We describe a prototype implementation which provides a robust security guarantee, is scalable to programs of any size, and has low runtime overheads. Further, we give a machine-checked proof that any program approved by the verification algorithm is guaranteed to respect the desired safety property.
Application of hierarchical neural-network-based control to transient stabilization of interconnected power systems (2002)

Flexible AC Transmission Systems (FACTS) research is aimed at increasing transmission capabilities of existing power systems. FACTS devices provide means to dynamically control parameters of the transmission lines. In particular thyristor-controlled series capacitors have been proposed to increase inter-area transient stability margins. Design of a suitable control algorithm for adjusting capacitor compensation level is a challenging task. The power system dynamics, particularly during transients caused by severe faults, are highly nonlinear. A series capacitor affects the system dynamics in nonlinear fashion, further increasing the difficulty of applying traditional linear control. There is also an inherent system uncertainty due to fluctuations of operating conditions and to sudden structural changes caused by faults. A successful controller should be robust with respect to these uncertainties and must accommodate the nonlinear dynamics of the system. The above issues are addressed here using neural-network methodology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Automating Embedded Software Testing on an Emulated Target Board (2007)

An embedded system consists of heterogeneous layers including hardware, HAL (hardware abstraction layer), OS kernel and application layer. Interactions between these layers are the software interfaces to be tested in an embedded system. The identified interfaces are important criterion that selects test cases and monitors the test results in order to detect faults and trace their causes. In this paper, we propose an automated scheme of embedded software interface test based on the emulated target board. The automated scheme enables to identify the location of interface in the source code to be tested, to generate test cases, and to determine 'pass' or fail' on the interface. We implemented the test tool called 'Justitia' based on the proposed scheme. As a case study, we applied the 'Justitia' to mobile embedded software on the S3C2440 microprocessor and Linux kernel v2.4.20.
Use of Conformationally Restricted Benzamidines as Arginine Surrogates in the Design of Platelet GPIIb-IIIa Receptor Antagonists (1997)

The use of 5,6-bicyclic amidines as arginine surrogates in the design of a novel class of potent platelet glycoprotein IIb-IIIa receptor (GPIIb-IIIa) antagonists is described. The additional conformational restriction offered by the bicyclic nucleus results in 20-400-fold increases in potency compared to the freely flexible, acyclic benzamidine counterpart. The design, synthesis, structure-activity relationships (SAR), and in vitro activity of this novel class of GPIIb-IIIa antagonists are presented.
The EXODUS extensible DBMS project: an overview (1989)

This paper presents an overview of EXODUS, an extensible database system project that is addressing data management problems posed by a variety of challenging new applications. The goal of the project is to facilitate the fast development of high-performance, application-specific database systems. EXODUS provides certain kernel facilities, including a versatile storage manager. In addition, it provides an architectural framework for building application-specific database systems; powerful tools to help automate the generation of such systems, including a rule-based query optimizer generator and a persistent programming language; and libraries of generic software components (e.g., access methods) that are likely to be useful for many application domains. We briefly describe each of the components of EXODUS in this paper, and we also describe a next-generation DBMS that we are now building using the EXODUS tools. 1.
Preparation of Mesoscale Hollow Spheres of TiO2 and SnO2 by Templating Against Crystalline Arrays of Polystyrene Beads (2000)

Mesoscale hollow spheres of ceramic materials can be prepared by templating an appropriate sol–gel precursor against a crystalline array of monodisperse polystyrene beads, as demonstrated here. Spheres of well-controlled, uniform size and homogeneous wall thickness result, as can be seen from the Figure, which shows the TEM cross-sectional view of an array of TiO2 hollow spheres.
Structure and Function of HIV-1 Integrase (2004)

HIV-1 integrase is a multidomain enzyme which is required for the integration of viral DNA into the host genome. It is one of three enzymes of HIV, the others being the Reverse Transcriptase and the Protease. It is an attractive target for therapeutic drug design. The enzyme consists of three domains. The N-terminal domain has a His2Cys2 motif which chelates zinc, the core domain has the catalytic DDE motif which is required for its enzymatic activity, and the C-terminal domain has an SH3-like fold which binds DNA nonspecifically. We review the structures of various integrase fragments, the core domain with inhibitors bound, and propose a model for DNA binding.
Visual tracking of an end-effector by adaptive kinematic prediction (1997)

Presents results of a model-based approach to visual tracking and pose estimation for a moving polyhedral tool in position-based visual servoing. This enables the control of a robot in look-and-move mode to achieve six degree of freedom goal configurations. Robust solutions of the correspondence problem-known as "matching" in the static case and "tracking" in the dynamic one-are crucial to the feasibility of such an approach in real-world environments. The object's motion along an arbitrary trajectory in space is tracked using visual pose estimates through consecutive images. Subsequent positions are predicted from robot joint angle measurements. To deal with inaccurate models and to relax calibration requirements, adaptive online calibration of the kinematic chain is proposed. The kinematic predictions enable unambiguous feature matching by a pessimistic algorithm. The performance of the suggested algorithms and the robustness of the proposed system are evaluated on real image sequences of a moving gripper. The results fulfill the requirements of visual servoing, and the computational demands are sufficiently low to allow for real-time implementation.