gebhart/patrepeval huggingface dataset:
Thiohydantoins. I. The Preparation of Some 2-Thiohydantoins from Amino Acids and Acylamino Acids (1952)

A reinvestigation of the stepwise degradation of peptides and proteins by the Schlack and Kumpf (1926) procedure, which involves conversion of the terminal carboxyl residue to a 5-substituted-2-thiohydantoin; has been undertaken. The following amino acids or their aoetyl derivatives have been converted by warming with acetic anhydride and ammonium thiocyanate into the corresponding 1-acetyl-2-thio-hydantoins: valine, methionine, isoleucine, α-aminophenylacetic acid, tryptophane, histidine, and tyrosine. These new 1-acetyl-2-thiohydantoins, as well as others, have been deacetylated by an improved procedure. Certain 1-acyl-5-carbethoxy-2-thio- hydantoins on hydrolysis give 2-thiohydantoin only. N-acetylthreonine, acetic anhydride, and ammonium thiocyanate produce 5-ethylidene-2-thiohydantoin, also obtained by the condensation of acetaldehyde with 2-thiohydantoin or its 1-acyl derivatives, or from the interaction of ammonium thiocyanate with 2-phenyl-4-ethylideneoxazol-5-one. This type of rearrangement occurs in other cases.
Automated characterization of bacteria in confocal microscope images (2008)

The problem of bacteria characterization from images acquired in microscopy is considered. The proposed approach consists of four consecutive steps: 1) images enhancement; 2) segmentation based on Watershed algorithm; 3) optimization of the initial segmentation; 4) bacteria quantification using a template matching procedure. Additionally, a modified version of this first approach allows to characterize bacteria colonies. Finally, an analysis of results is performed by comparing the estimated results with respect to results obtained manually by the expert.
Seed Storage Oil Mobilization Is Important But Not Essential for Germination or Seedling Establishment in Arabidopsis (2011)

Triacylglycerol (TAG) is a major storage reserve in many plant seeds. We previously identified a TAG lipase mutant called sugar-dependent1 (sdp1) that is impaired in TAG hydrolysis following Arabidopsis (Arabidopsis thaliana) seed germination (Eastmond, 2006). The aim of this study was to identify additional lipases that account for the residual TAG hydrolysis observed in sdp1. Mutants were isolated in three candidate genes (SDP1-LIKE [SDP1L], ADIPOSE TRIGLYCERIDE LIPASE-LIKE, and COMPARATIVE GENE IDENTIFIER-58-LIKE). Analysis of double, triple, and quadruple mutants showed that SDP1L is responsible for virtually all of the residual TAG hydrolysis present in sdp1 seedlings. Oil body membranes purified from sdp1 sdp1L seedlings were deficient in TAG lipase activity but could still hydrolyze di- and monoacylglycerol. SDP1L is expressed less strongly than SDP1 in seedlings. However, SDP1L could partially rescue TAG breakdown in sdp1 seedlings when expressed under the control of the SDP1 or 35S promoters and in vitro assays showed that both SDP1 and SDP1L can hydrolyze TAG, in preference to diacylglycerol or monoacylglycerol. Seed germination was slowed in sdp1 sdp1L and postgerminative seedling growth was severely retarded. The frequency of seedling establishment was also reduced, but sdp1 sdp1L was not seedling lethal under normal laboratory growth conditions. Our data show that together SDP1 and SDP1L account for at least 95% of the rate of TAG hydrolysis in Arabidopsis seeds, and that this hydrolysis is important but not essential for seed germination or seedling establishment.
Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity. (1991)

We have identified an amino-proximal sequence motif, Phe-Asp-Ile-Glu-Thr, in Saccharomyces cerevisiae DNA polymerase II that is almost identical to a sequence comprising part of the 3'----5' exonuclease active site of Escherichia coli DNA polymerase I. Similar motifs were identified by amino acid sequence alignment in related, aphidicolin-sensitive DNA polymerases possessing 3'----5' proofreading exonuclease activity. Substitution of Ala for the Asp and Glu residues in the motif reduced the exonuclease activity of partially purified DNA polymerase II at least 100-fold while preserving the polymerase activity. Yeast strains expressing the exonuclease-deficient DNA polymerase II had on average about a 22-fold increase in spontaneous mutation rate, consistent with a presumed proofreading role in vivo. In multiple amino acid sequence alignments of this and two other conserved motifs described previously, five residues of the 3'----5' exonuclease active site of E. coli DNA polymerase I appeared to be invariant in aphidicolin-sensitive DNA polymerases known to possess 3'----5' proofreading exonuclease activity. None of these residues, however, appeared to be identifiable in the catalytic subunits of human, yeast, or Drosophila alpha DNA polymerases.
Endonuclease IV (nfo) mutant of Escherichia coli (1986)

A cloned gene, designated nfo, caused overproduction of an EDTA-resistant endonuclease specific for apurinic-apyrimidinic sites in DNA. The sedimentation coefficient of the enzyme was similar to that of endonuclease IV. An insertion mutation was constructed in vitro and transferred from a plasmid to the Escherichia coli chromosome. nfo mutants had an increased sensitivity to the alkylating agents methyl methanesulfonate and mitomycin C and to the oxidants tert-butyl hydroperoxide and bleomycin. The nfo mutation enhanced the killing of xth (exonuclease III) mutants by methyl methanesulfonate, H2O2, tert-butyl hydroperoxide, and gamma rays, and it enhanced their mutability by methyl methanesulfonate. It also increased the temperature sensitivity of an xth dut (dUTPase) mutant that is defective in the repair of uracil-containing DNA. These results are consistent with earlier findings that endonuclease IV and exonuclease III both cleave DNA 5' to an apurinic-apyrimidinic site and that exonuclease III is more active. However, nfo mutants were more sensitive to tert-butyl hydroperoxide and to bleomycin than were xth mutants, suggesting that endonuclease IV might recognize some lesions that exonuclease III does not. The mutants displayed no marked increase in sensitivity to 254-nm UV radiation, and the addition of an nth (endonuclease III) mutation to nfo or nfo xth mutants did not significantly increase their sensitivity to any of the agents tested.
Map building with mobile robots in populated environments (2003)

The problem of generating maps with mobile robots has received considerable attention over the past years. However, most of the approaches assume that the environment is static during the data-acquisition phase. In this paper we consider the problem of creating maps with mobile robots in populated environments. Our approach uses a probabilistic method to track multiple people and to incorporate the results of the tracking technique into the mapping process. The resulting maps are more accurate since corrupted readings are treated accordingly during the matching phase and since the number of spurious objects in the resulting maps is reduced. Our approach has been implemented and tested on real robot systems in indoor and outdoor scenarios. We present several experiments illustrating the capabilities of our approach to generate accurate 2D and 3D maps.
Administration of soluble activin receptor 2B increases bone and muscle mass in a mouse model of osteogenesis imperfecta (2015)

Osteogenesis imperfecta (OI) comprises a group of heritable connective tissue disorders generally defined by recurrent fractures, low bone mass, short stature and skeletal fragility. Beyond the skeletal complications of OI, many patients also report intolerance to physical activity, fatigue and muscle weakness. Indeed, recent studies have demonstrated that skeletal muscle is also negatively affected by OI, both directly and indirectly. Given the well-established interdependence of bone and skeletal muscle in both physiology and pathophysiology and the observations of skeletal muscle pathology in patients with OI, we investigated the therapeutic potential of simultaneous anabolic targeting of both bone and skeletal muscle using a soluble activin receptor 2B (ACVR2B) in a mouse model of type III OI (oim). Treatment of 12-week-old oim mice with ACVR2B for 4 weeks resulted in significant increases in both bone and muscle that were similar to those observed in healthy, wild-type littermates. This proof of concept study provides encouraging evidence for a holistic approach to treating the deleterious consequences of OI in the musculoskeletal system.
Generation of monospecific antibodies based on affinity capture of polyclonal antibodies (2011)

A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.
Seeing the heat – preliminary studies of cryocrystallography using infrared imaging (2002)

As preparation for an extensive study that aims to image the cryocooling process of macromolecular crystals, the ability to thermally image solid objects and liquids at temperatures far below 273 K is demonstrated. In the case of a large lysozyme crystal (1.0 x 0.7 x 0.2 mm), qualitative measurements show the cooling process to take about 0.6 s with the cooling taking place in a wave starting from the face of the crystal nearest to the origin of the cryostream and ending at the point furthest away from the origin. Annealing of this lysozyme crystal, cooled under good cryoprotectant conditions, shows that cold striations form perpendicular to the cooling stream. These striations become more pronounced after successive annealing. Cryocooling of a non-cryoprotected crystal of glucose isomerase displayed an 'S-shaped' cold front wave traveling across the sample. These preliminary results are qualitative but show the power of infrared imaging as a new tool for fundamental and practical cryocrystallography studies.
Surface, corrosion and biocompatibility aspects of Nitinol as an implant material. (2002)

The present review surveys studies on physical-chemical properties and biological response of living tissues to NiTi (Nitinol) carried out recently, aiming at an understanding of the place of this material among the implant alloys in use. Advantages of shape memory and superelasticity are analyzed in respect to functionality of implants in the body. Various approaches to surface treatment, sterilization procedures, and resulting surface conditions are analyzed. A review of corrosion studies conducted both on wrought and as-cast alloys using potentiodynamic and potentiostatic techniques in various corrosive media and in actual body fluids is also given. The parameters of localized and galvanic corrosion are presented. The corrosion behavior is analyzed with respect to alloy composition, phase state, surface treatment, and strain and compared to that of conventional implant alloys. Biocompatibility of porous Nitinol, Ni release and its effect on living cells are analyzed based on understanding of the surface conditions and corrosion behavior. Additionally, the paper offers a brief overview of the comparative toxicity of metals, components of commonly used medical alloys, indicating that the biocompatibility profile of Nitinol is conducive to present in vivo applications.
Modeling and Management of Firewall Policies (2004)

Firewalls are core elements in network security. However, managing firewall rules, especially for enterprise networks, has become complex and error-prone. Firewall filtering rules have to be carefully written and organized in order to correctly implement the security policy. In addition, inserting or modifying a filtering rule requires thorough analysis of the relationship between this rule and other rules in order to determine the proper order of this rule and commit the updates. In this paper we present a set of techniques and algorithms that provide automatic discovery of firewall policy anomalies to reveal rule conflicts and potential problems in legacy firewalls, and anomaly-free policy editing for rule insertion, removal, and modification. This is implemented in a user-friendly tool called "Firewall Policy Advisor." The Firewall Policy Advisor significantly simplifies the management of any generic firewall policy written as filtering rules, while minimizing network vulnerability due to firewall rule misconfiguration.
RNase H cleavage of RNA hybridized to oligonucleotides containing methylphosphonate, phosphorothioate and phosphodiester bonds (1989)

Three types of 14-mer oligonucleotides were hybridized to human beta-globin pre-mRNA and the resultant duplexes were tested for susceptibility to cleavage by RNase H from E. coli or from HeLa cell nuclear extract. The oligonucleotides contained normal deoxynucleotides, phosphorothioate analogs alternating with normal deoxynucleotides, or one to six methylphosphonate deoxynucleosides. Duplexes formed with deoxyoligonucleotides or phosphorothioate analogs were susceptible to cleavage by RNase H from both sources, whereas a duplex formed with an oligonucleotide containing six methylphosphonate deoxynucleosides alternating with normal deoxynucleotides was resistant. Susceptibility to cleavage by RNase H increased parallel to a reduction in the number of methylphosphonate residues in the oligonucleotide. Stability of the oligonucleotides in the nuclear extract from HeLa cells was also tested. Whereas deoxyoligonucleotides were rapidly degraded, oligonucleotides containing alternating methylphosphonate residues remained unchanged after 70 minutes of incubation. Other oligonucleotides exhibited intermediate stability.
A Comprehensive Study of Physical Parameters, Biomechanical Properties, and Statistical Correlations of Iliac Crest Bone Wedges Used in Spinal Fusion Surgery (1994)

The effects of gamma irradiation on mechanical and material properties of iliac crest wedges used in spinal fusion surgery were studied using uniaxial compression testing. The irradiated iliac crest wedges were exposed to 2-2.5 mrad as fresh-frozen and freeze-dried tissues. There were no significant differences in mechanical or material properties of the iliac crest wedges exposed to dosages of 2-2.5 mrad when compared to the nonirradiated wedges. It is suggested that 2-2.5 mrad is an acceptable dose for gamma irradiation sterilization of iliac crest wedges used in spinal fusion surgery and that these tissues may be treated at either the preprocessing or postprocessing stage of wedge production.
LBM–DEM modeling of fluid–solid interaction in porous media (2012)

SUMMARY Three porous media flow problems, in which the fluid mechanical interactions are critical, are studied in a mesoscopic–microscopic coupling system. In this system, fluid flow in the pore space is explicitly modeled at mesoscopic level by the lattice Boltzmann method, the geometrical representation and the mechanical behavior of the solid skeleton are modeled at microscopic level by the particulate distinct element method (DEM), and the interfacial interaction between the fluid and the solids is resolved by an immersed boundary scheme. In the first benchmark problem, the well‐known and frequently utilized Ergun equation is validated in periodic particle and periodic pore models. In the second problem, the upward seepage problem is simulated over three stages: The settlement of the column of sphere under gravity loading is measured to illustrate the accuracy of the DEM scheme; the system is solved to hydrostatic state with pore space filled with fluid, showing that the buoyancy effect is captured correctly in the mesoscopic–microscopic coupling system; then, the flow with constant rate is supplied at the bottom of the column; the swelling of the ground surface and pore pressure development from the numerical simulation are compared with the predictions of the macroscopic consolidation theory. In the third problem, the fluid‐flow‐induced collapse of a sand arch inside a perforation cavity is tested to illustrate a more practical application of the developed system. Through comparing simulation results with analytical solutions, empirical law and physical laboratory observations, it is demonstrated that the developed lattice Boltzmann–distinct element coupling system is a powerful fundamental research tool for investigating hydromechanical physics in porous media flow. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Preshaping photoresist for refractive microlens array fabrication (1993)

Refractive microlenses are fabricated by the P<SUP>2</SUP>ROM (Preshaped Photoresist Refractive Optics by Melting) process. A polar coordinate HeCd laser beam lithography system (laser writer) is used to directly expose a continuous spheroidal profile into photoresist to fabricate 200 micrometers diameter microlenses with speeds between F/1.5 and F/5. Interferometric surface measurements, used to determine optical quality of the preshaped microlenses, indicate reduced spherical aberration in slow lenses fabricated by this method.
Expression of survivin, a novel inhibitor of apoptosis and cell cycle regulatory protein, in pancreatic adenocarcinoma (2002)

Survivin is unique for its expression in human malignancies but not in normal adult cells. It has been implicated in sensitisation to chemotherapy and as a prognostic marker in several common cancers. Immunohistochemistry for Survivin, P53 and BCL-2 expression as well as cell proliferative index (Ki-67) and apoptosis index (TUNEL) was conducted on 52 pancreatic and 12 ampullary adenocarcinomas. Survivin was detected in the cytoplasm of carcinoma cells in 46 (88%) of pancreatic tumours. P53 and BCL-2 were detected in 54% and 12% of pancreatic tumours, respectively. Proliferative index was 26.2+/-10.5% and apoptosis index was 1.38+/-0.69%. Prevalence of Survivin expression was significantly higher in P53-positive than in P53-negative cases (P=0.05) but was not associated with BCL-2 expression. Incrementally higher weighted scores of Survivin expression were associated with increased proliferative index (P=0.001). Furthermore, there was linear correlation between increased proliferative index and higher apoptosis index (P<0.001). Surprisingly, higher scores of Survivin expression were associated with increased apoptosis index (P=0.007). Survival characteristics were not influenced by Survivin, P53 or BCL-2 expression, apoptosis index or proliferative index. Ampullary carcinoma showed Survivin expression in 83% of cases. However, unlike pancreatic carcinoma, there was no correlation between Survivin and P53 expression or proliferative index. In conclusion, Survivin is expressed in the majority of pancreatic adenocarcinomas and correlates with both cellular proliferation and apoptosis. Molecular manipulation of Survivin expression may enhance chemotherapy and radiation therapy for pancreatic cancer.
Apical NA+/H+ exchangers in the mammalian gastrointestinal tract. (2006)

The Slc9a family of nine Na(+)/H(+) exchangers (NHE) plays a critical role in neutral sodium absorption in the mammalian intestine as well as other absorptive and secretory epithelia of digestive organs. These transport proteins mediate the electroneutral exchange of Na(+) and H(+) and are crucial in a variety of physiological processes, including the fine tuning of intracellular pH, cell volume control and systemic electrolyte, acid-base and fluid volume homeostasis. Here, we review the role of the Na(+)/H(+) exchange mechanism as it relates to the physiology of organs and cells involved in nutrient absorption, and we describe physiological and molecular aspects of individual isoforms, including their structure, tissue-, and subcellular distribution, as well as their regulation by physiological stimuli at the transcriptional and post-transcriptional levels. A particular emphasis is placed on Na(+)/H(+) exchanger isoforms expressed on the apical (brush border) membrane of the epithelial cells, and the consequences of gene-targeted mutation of individual isoforms are discussed in the context of the physiology of digestive organs. Where available, we also provide a review of pathophysiological states related to aberrant expression and/or activity of Na(+)/H(+) exchangers within the confines of the digestive system.
Teatro, Mauá, SP. (1991)

Many human tumors of epithelial origin contain cells overexpressing the epidermal growth factor (EGF) receptor, and there is convincing evidence that cancer cell growth is correlated with the loss of the normal regulation of the EGF receptor signal transduction pathway. Some cancers are clearly dependent on activation of the EGF receptor for their proliferation. Recently, a class of compounds, tyrphostins, which inhibit the protein tyrosine kinase activity of the growth factor receptor, have been described. In this report, we have examined the antiproliferative effects of potent new tyrphostins on a well-characterized human squamous cell carcinoma in vitro and in vivo. We found that two of these compounds (RG-13022 and RG-14620) suppressed not only EGF-stimulated cancer cell proliferation in vitro but also tumor growth in nude mice. RG-13022 also increased the life span of these tumor-bearing nude mice. When administered to tumor-bearing nude mice together with monoclonal antibodies to the EGF receptor at a suboptimal dose which had no effect alone, inhibition of tumor growth was markedly enhanced. These data suggest that tyrphostins have potential as anticancer agents.
Networked intelligent robots through the internet: issues and opportunities (2003)

Intelligent robotic systems have been extensively applied in factory automation, space exploration, intelligent buildings, surgery, military service, and also in our daily life. Various remote control methods have been performed for intelligent robotic systems, such as radio, microwave, computer networks, etc. Nowadays, the computer network services have broadly used in our daily life, such as FTP, Telnet, the World Wide Web, e-mail, etc. Consequently, it is very convenient to use the Internet to control intelligent robot, and the users will increase in the future. In the past few years, many researchers have been using the Internet as a command transmission medium which can control the intelligent robot and obtain feedback signals. Although the Internet has many advantages in a variety of fields, using the Internet to control intelligent robots also has some limitations, such as the uncertain time-delay problem, the uncertain data-loss problem, and the data-transmission security problem. In the literature, many experts proposed various methods to solve these problems. This paper will discuss these methods and analyze the effects on the remote control systems caused by these problems. The intelligent robot can simultaneously present low-level navigational capabilities, medium-level self-positioning capabilities, high-level motion-planning capabilities, and the ability to be controlled through the Internet. The issues for controlling intelligent robots through the Internet will be discussed in terms of direct control, behavior programming control, supervisory control, and learning control. Finally, we enumerate some opportunities for the application of network-based intelligent robots, and present some successful examples of networked intelligent robots in our laboratory. Future trends and concluding remarks appear at the end of this paper.