gebhart/patrepeval huggingface dataset:
Mammalian Bet3 functions as a cytosolic factor participating in transport from the ER to the Golgi apparatus (2005)

The TRAPP complex identified in yeast regulates vesicular transport in the early secretory pathway. Although some components of the TRAPP complex are structurally conserved in mammalian cells, the function of the mammalian components has not been examined. We describe our biochemical and functional analysis of mammalian Bet3, the most conserved component of the TRAPP complex. Bet3 mRNA is ubiquitously expressed in all tissues. Antibodies raised against recombinant Bet3 specifically recognize a protein of 22 kDa. In contrast to yeast Bet3p, the majority of Bet3 is present in the cytosol. To investigate the possible involvement of Bet3 in transport events in mammalian cells, we utilized a semi-intact cell system that reconstitutes the transport of the envelope glycoprotein of vesicular stomatitis virus (VSV-G) from the ER to the Golgi apparatus. In this system, antibodies against Bet3 inhibit transport in a dose-dependent manner, and cytosol that is immunodepleted of Bet3 is also defective in this transport. This defect can be rescued by supplementing the Bet3-depleted cytosol with recombinant GST-Bet3. We also show that Bet3 acts after COPII but before Rab1, alpha-SNAP and the EGTA-sensitive stage during ER-Golgi transport. Gel filtration analysis demonstrates that Bet3 exists in two distinct pools in the cytosol, the high-molecular-weight pool may represent the TRAPP complex, whereas the other probably represents the monomeric Bet3.
Advances in understanding gonadotrophin-releasing hormone receptor structure and ligand interactions (1997)

Gonadotrophin-releasing hormone (GnRH) is the central regulator of the reproductive system and its analogues are used widely in the treatment of diverse diseases. The GnRH receptor is a member of the large family of G-protein-coupled receptors (GPCRs) which have seven transmembrane domains. Knowledge of these receptors has assisted the development of molecular models of the GnRH receptor that allow prediction of its three-dimensional configuration and the way GnRH binds and activates its receptor. Comparison with other GPCRs led to the discovery that Lys121, in the third transmembrane domain, has a role in agonist binding. The history of GnRH structure-activity studies has allowed the identification of an acidic residue in the third extracellular loop of the receptor that is required for binding of mammalian GnRH, while synthetic GnRH analogues have showed that Asn102, in the second extracellular loop, may interact with the carboxy-terminus of GnRH. These residues can now be incorporated into the receptor models that are being used to design orally active non-peptide GnRH analogues for contraception and treatment of a variety of reproductive disorders.
SpaceWorks’ 2014 Nano/Microsatellite Market Assessment (2014)

Since 2008, SpaceWorks has actively monitored global nano/microsatellite activities, and annually publishes a summary update as a free service to the small satellite development and launch communities. SpaceWorks’ 2014 projection of the 1-50 kg satellite market reflects a significant increase from last year’s projection, with 2-3 times higher quantities of nano/microsatellites needing a launch from 2017 to 2020, driven largely by the advent and continued growth of commercial players.1 This paper presents detailed observations and projections for the nano/microsatellite market based on over 650 satellites with masses between 1 and 50 kilograms in development over the next three years (2014 to 2016). The data source for this assessment is a subset of the SpaceWorks Satellite Launch Demand Database (LDDB), an extensive collection of all known historical missions, announced future satellite projects, and estimated future commercial missions. Analysis of development trends by sector show that the civil sector (including academic) remains strong, and the commercial sector is growing significantly and will likely continue to make large contributions to the global nano/microsatellite market. Analysis of trends by purpose suggests that while Earth observation and remote sensing remain the most widely used applications in the near future, applications for nano/microsatellites are diversifying.
Sclera Recognition - A Survey (2013)

This paper presents a survey on sclera-based biometric recognition. Among the various biometric methods, sclera is one of the novel and promising biometric techniques. The sclera, a white region of connective tissue and blood vessels, surrounds the iris. A survey of the techniques available in the area of sclera biometrics will be of great assistance to researchers, and hence a comprehensive effort is made in this article to discuss the advancements reported in this regard during the past few decades. As a limited number of publications are found in the literature, an attempt is made in this paper to increase awareness of this area so that the topic gains popularity and interest among researchers. In this survey, a brief introduction is given initially about the sclera biometric, which is subsequently followed by background concepts, various pre-processing techniques, feature extraction and finally classification techniques associated with the sclera biometric. Benchmarking databases are very important for any pattern recognition related research, so the databases related with this work is also discussed. Finally, our observations, future scope and existing difficulties, which are unsolved in sclera biometrics, are discussed. We hope that this survey will serve to focus more researcher attention towards the emerging sclera biometric.
Secure verification of location claims (2003)

With the growing prevalence of sensor and wireless networks comes a new demand for location-based access control mechanisms. We introduce the concept of secure location verification, and we show how it can be used for location-based access control. Then, we present the Echo protocol, a simple method for secure location verification. The Echo protocol is extremely lightweight: it does not require time synchronization, cryptography, or very precise clocks. Hence, we believe that it is well suited for use in small, cheap, mobile devices.
Stable Transformation of the Intact Cells of Chlorella Kessleri with High Velocity Microprojectiles (1999)

A transgenic expression system of Chlorella kessleri using the gene for β-glucuronidase (GUS) was developed. Cells of this unicellular green alga were bombarded with the plasmid pBI 121, which bears β-glucuronidase under the control of CaMV 35S promoter and the kanamycin resistant gene. Maximum GUS activity was obtained after 48 h of bombardment using a helium pressure of 900 kPa; GUS activity was then assayed for many generations. The stable transformants were able to grow on kanamycin containing medium after repeated passages between selective and nonselective medium and exhibited GUS activity comparable to that of control cells. Stable transformed cells were confirmed by polymerase chain reaction (PCR) and Southern hybridization of GUS probe with the genomic DNA of C. kessleri.
ChemInform Abstract: Total Synthesis of the Anti Methicillin‐Resistant Staphylococcus aureus Peptide Antibiotics TAN‐1057A—D. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Investigation into the Feasibility of Thioditaloside as a Novel Scaffold for Galectin‐3‐Specific Inhibitors (2013)

Galectin-3 is extensively involved in metabolic and disease processes, such as cancer metastasis, thus giving impetus for the design of specific inhibitors targeting this β-galactose-binding protein. Thiodigalactoside (TDG) presents a scaffold for construction of galectin inhibitors, and its inhibition of galectin-1 has already demonstrated beneficial effects as an adjuvant with vaccine immunotherapy, thereby improving the survival outcome of tumour-challenged mice. A novel approach--replacing galactose with its C2 epimer, talose--offers an alternative framework, as extensions at C2 permit exploitation of a galectin-3-specific binding groove, thereby facilitating the design of selective inhibitors. We report the synthesis of thioditaloside (TDT) and crystal structures of the galectin-3 carbohydrate recognition domain in complexes with TDT and TDG. The different abilities of galactose and talose to anchor to the protein correlate with molecular dynamics studies, likely explaining the relative disaccharide binding affinities. The feasibility of a TDT scaffold to enable access to a particular galectin-3 binding groove and the need for modifications to optimise such a scaffold for use in the design of potent and selective inhibitors are assessed.
High-Throughput Screens for Postgenomics:  Studies of Protein Crystallization Using Microsystems Technology (2002)

This paper describes the fabrication of a micromachined miniaturized array of chambers in a 2-mm-thick single crystal (100) silicon substrate for the combinatorial screening of the conditions required for protein crystallization screening (including both temperature and the concentration of crystallization agent). The device was fabricated using standard photolithography techniques, reactive ion etching (RIE) and anisotropic silicon wet etching to produce an array of 10 x 10 microchambers, with each element having a volume of 5 microL. A custom-built temperature controller was used to drive two peltier elements in order to maintain a temperature gradient (between 12 and 40 degrees C) across the device. The performance of the microsystem was illustrated by studying the crystallization of a model protein, hen egg white lysozyme. The crystals obtained were studied using X-ray diffraction at room temperature and exhibited 1.78 A resolution. The problems of delivering a robust crystallization protocol, including issues of device fabrication, delivery of a reproducible temperature gradient, and overcoming evaporation are described.
Standard reference strains of Escherichia coli from natural populations (1984)

A set of 72 reference strains of Escherichia coli isolated from a variety of hosts and geographical locations has been established for use in studies of variation and genetic structure in natural populations. The strains, which have been characterized by multilocus enzyme electrophoresis, are representative of the range of genotypic variation in the species as a whole.
An Orally Bioavailable Chemical Probe of the Lysine Methyltransferases EZH2 and EZH1 (2013)

EZH2 or EZH1 is the catalytic subunit of the polycomb repressive complex 2 that catalyzes methylation of histone H3 lysine 27 (H3K27). The trimethylation of H3K27 (H3K27me3) is a transcriptionally repressive post-translational modification. Overexpression of EZH2 and hypertrimethylation of H3K27 have been implicated in a number of cancers. Several selective inhibitors of EZH2 have been reported recently. Herein we disclose UNC1999, the first orally bioavailable inhibitor that has high in vitro potency for wild-type and mutant EZH2 as well as EZH1, a closely related H3K27 methyltransferase that shares 96% sequence identity with EZH2 in their respective catalytic domains. UNC1999 was highly selective for EZH2 and EZH1 over a broad range of epigenetic and non-epigenetic targets, competitive with the cofactor SAM and non-competitive with the peptide substrate. This inhibitor potently reduced H3K27me3 levels in cells and selectively killed diffused large B cell lymphoma cell lines harboring the EZH2(Y641N) mutant. Importantly, UNC1999 was orally bioavailable in mice, making this inhibitor a valuable tool for investigating the role of EZH2 and EZH1 in chronic animal studies. We also designed and synthesized UNC2400, a close analogue of UNC1999 with potency >1,000-fold lower than that of UNC1999 as a negative control for cell-based studies. Finally, we created a biotin-tagged UNC1999 (UNC2399), which enriched EZH2 in pull-down studies, and a UNC1999-dye conjugate (UNC2239) for co-localization studies with EZH2 in live cells. Taken together, these compounds represent a set of useful tools for the biomedical community to investigate the role of EZH2 and EZH1 in health and disease.
In Vitro and in Vivo mRNA Delivery Using Lipid-Enveloped pH-Responsive Polymer Nanoparticles (2011)

Biodegradable core--shell structured nanoparticles with a poly(β-amino ester) (PBAE) core enveloped by a phospholipid bilayer shell were developed for in vivo mRNA delivery with a view toward delivery of mRNA-based vaccines. The pH-responsive PBAE component was chosen to promote endosome disruption, while the lipid surface layer was selected to minimize toxicity of the polycation core. Messenger RNA was efficiently adsorbed via electrostatic interactions onto the surface of these net positively charged nanoparticles. In vitro, mRNA-loaded particle uptake by dendritic cells led to mRNA delivery into the cytosol with low cytotoxicity, followed by translation of the encoded protein in these difficult-to-transfect cells at a frequency of ~30%. Particles loaded with mRNA administered intranasally (i.n.) in mice led to the expression of the reporter protein luciferase in vivo as soon as 6 h after administration, a time point when naked mRNA given i.n. showed no expression. At later time points, luciferase expression was detected in naked mRNA-treated mice, but this group showed a wide variation in levels of transfection, compared to particle-treated mice. This system may thus be promising for noninvasive delivery of mRNA-based vaccines.
Peroxisome proliferator‐activated receptor δ controls muscle development and oxydative capability (2003)

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors exerting several functions in development and metabolism. The physiological functions of PPARdelta remain elusive. By using a CRE-Lox recombination approach, we generated an animal model for muscle-specific PPARdelta overexpression to investigate the role of PPARdelta in this tissue. Muscle-specific PPARdelta overexpression results in a profound change in fiber composition due to hyperplasia and/or shift to more oxidative fiber and, as a consequence, leads to the increase of both enzymatic activities and genes implicated in oxidative metabolism. These changes in muscle are accompanied by a reduction of body fat mass, mainly due to a large reduction of adipose cell size. Furthermore, we demonstrate that endurance exercise promotes an accumulation of PPARdelta protein in muscle of wild-type animals. Collectively, these results suggest that PPARdelta plays an important role in muscle development and adaptive response to environmental changes, such as training exercise. They strongly support the idea that activation of PPARdelta could be beneficial in prevention of metabolic disorders, such as obesity or type 2 diabetes.
PTEN, more than the AKT pathway (2007)

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN)/phosphatidylinositol 3-kinase (PI3K)/AKT constitute an important pathway regulating the signaling of multiple biological processes such as apoptosis, metabolism, cell proliferation and cell growth. PTEN is a dual protein/lipid phosphatase and its main substrate phosphatidyl-inositol 3,4,5 triphosphate (PIP3) is the product of PI3K. Increase in PIP3 recruits AKT to the membrane where is activated by other kinases also dependent on PIP3. Many components of this pathway have been described as causal forces in cancer. PTEN activity is lost by mutations, deletions or promoter methylation silencing at high frequency in many primary and metastatic human cancers. Germ line mutations of PTEN are found in several familial cancer predisposition syndromes. Recently, many activating mutations in the PI3KCA gene (coding for the p110alpha catalytic subunit of PI3K) have been described in human tumors. Activation of PI3K and AKT are reported to occur in breast, ovarian, pancreatic, esophageal and other cancers. Genetically modified mice confirm these PTEN activities. Tissue-specific deletions of PTEN usually provoke cancer. Moreover, an absence of PTEN cooperates with an absence of p53 to promote cancer. However, we have observed very different results with the expression of activated versions of AKT in several tissues. Activated AKT transgenic lines do not develop tumors in breast or prostate tissues and do not cooperate with an absence of p53. This data suggest that an AKT-independent mechanism contributes to PTEN tumorigenesis. Crosses with transgenic mice expressing possible PTEN targets indicate that neither cyclin D1 nor p53 are these AKT-independent targets. However, AKT is more than a passive bridge toward PTEN tumorigenesis, since its expression not only allows but also enforces and accelerates the tumorigenic process in combination with other oncogenes.
Anaemia and cigarette smoking (2008)

Cigarette smoking causes numerous diseases that are associated with anaemia but the resulting low haemoglobin levels may be counterbalanced by increased red blood cell production caused by chronic exposure to carbon monoxide from cigarette smoke. Diverse mechanisms are involved in influencing the development or the course of anaemic disease in smokers. This article presents an evaluation of the current literature on the impact of cigarette smoking on various forms of anaemia.
A technique for measuring the surface area of articular cartilage in acetabular fractures (1994)

The aim of this study was to develop a reliable technique for measuring the area of a curved surface from an axial computed tomography (CT) scan and to apply this clinically in the measurement of articular cartilage surface area in acetabular fractures. The method used was a triangulation algorithm. In order to determine the accuracy of the technique, areas of hemispheres of known size were measured to give the percentage error in area measurement. Seven such hemispheres were machined into a Perspex block and their area measured geometrically, and also from CT scans by means of the triangulation algorithm. Scans of 1, 2 and 4 mm slice thickness and separation were used. The error varied with slice thickness and hemisphere diameter. It was shown that the 2 mm slice thickness provides the most accurate area measurement, while 1 mm cuts overestimate and 4 mm cuts underestimate the area. For a hemisphere diameter of 5 cm, which is of similar size to the acetabulum, the error was -11.2% for 4 mm cuts, +4.2% for 2 mm cuts and +5.1% for 1 mm cuts. As expected, area measurement was more accurate for larger hemispheres. This method can be applied clinically to quantify acetabular fractures by measuring the percentage area of intact articular cartilage. In the case of both column fractures, the percentage area of secondary congruence can be determined. This technique of quantifying acetabular fractures has a potential clinical application as a prognostic factor and an indication for surgery in the long term.
Artificial Noses (2011)

The mammalian olfactory system is able to detect many more odorants than the number of receptors it has by utilizing cross-reactive odorant receptors that generate unique response patterns for each odorant. Mimicking the mammalian system, artificial noses combine cross-reactive sensor arrays with pattern recognition algorithms to create robust odor-discrimination systems. The first artificial nose reported in 1982 utilized a tin-oxide sensor array. Since then, however, a wide range of sensor technologies have been developed and commercialized. This review highlights the most commonly employed sensor types in artificial noses: electrical, gravimetric, and optical sensors. The applications of nose systems are also reviewed, covering areas such as food and beverage quality control, chemical warfare agent detection, and medical diagnostics. A brief discussion of future trends for the technology is also provided.
A concise route to (−)-morphine (2001)

A concise enantio- and diastereocontrolled route to (−)-morphine has been developed starting from a bicyclo[3.2.1]octenone chiral building block through an acid-catalyzed tandem retro-aldol-oxonium ion-mediated hydrophenanthrene formation reaction as the key step.
Ultra low noise low cost octave-band hybrid-tuned VCO (2006)

The application where coarse and fine-tuning is prime requirement, phase noise gets drastically degraded in presence of the fine tuning network if incorporated with a coarse tuning network. A VCO with a frequency that is less sensitive to tuning control voltage fluctuations imparts less phase jitter to the system, but suffers from a narrower tuning range, thereby it is limited by tuning band. This paper describes the unique approach of the hybrid tuning capability of the octave-band VCO (1000-2000 MHz/2000-4000 MHz) without sacrificing the phase noise and the tuning range. The design is based on innovative topology, which supports the fast convergence by using coarse-tuning and fine adjustments, by fine-tuning network. The measured phase noise is better than -103 dBc/Hz @ 10 kHz offset for the frequency band 1000-2000 MHz
Fractional adiabatic passage in two-level systems: Mirrors and beam splitters for atomic interferometry (2007)

Atom interferometers require atom mirrors and beam splitters that can maintain high fidelity even when experimental parameters vary from the ideal. We address the use of chirped laser pulses to provide such elements via rapid adiabatic passage, and present a prescription for practical pulses that offer controlled adiabaticity throughout. Full- and half-adiabatic pulses, providing mirrors and beam splitters, respectively, are derived, and the latter examined for robustness and suitability for experimental implementations.
Targeting the HGF/c-MET Pathway in Hepatocellular Carcinoma (2013)

Hepatocellular carcinoma (HCC) is a significant cause of cancer-related morbidity and mortality worldwide. Despite improvements in local therapies, including surgical resection, liver transplantation, and transarterial embolization, the prognosis remains poor for the majority of patients who develop recurrence or present with advanced disease. Systemic therapy with the tyrosine kinase inhibitor sorafenib represents a milestone in advanced HCC but provides a limited survival benefit. Ongoing efforts to study hepatocarcinogenesis have identified an important role for c-MET signaling in the promotion of tumor growth, angiogenesis, and metastasis. In this review, we summarize the preclinical data from human tissue, cell lines, and animal models that implicate c-MET in the pathogenesis of HCC. We also evaluate potential biomarkers that may estimate prognosis or predict response to c-MET inhibitors for more rational clinical trial design. Finally, we discuss the latest clinical trials of c-MET inhibitors in advanced HCC.
Associative and Segregative Phase Separations of Gelatin/κ-Carrageenan Aqueous Mixtures (2006)

The effects of ionic strength, temperature, and pH on the phase separation behavior of type B pigskin gelatin/sodium-type kappa-carrageenan aqueous mixtures were investigated. Depending on the different combinations of temperature and sodium chloride (NaCl) concentration, the mixtures showed compatible, associative, and segregative phase separation behaviors. Additionally, a coexistence of associative and segregative (associative-co-segregative) phase separations was expected at low temperature and low NaCl concentration. These different phase separation events were observed using confocal scanning laser microscopy. Moreover, it was found that the segregative phase separation when alone is induced by the ordering of kappa-carrageenan chains, while that in the coexistence region is induced by the ordering of gelatin chains. pH had a significant effect on the associative phase separation, resulting in morphologies changing from compatible solution to liquid coacervate and further to solid precipitate with decreasing pH. These were attributed to the dramatic changes of the charge density of amphoteric gelatin during the pH decrease.