gebhart/patrepeval huggingface dataset:
The Divergent Caenorhabditis elegans β-Catenin Proteins BAR-1, WRM-1 and HMP-2 Make Distinct Protein Interactions but Retain Functional Redundancy in Vivo (2001)

beta-Catenins function both in cell adhesion as part of the cadherin/catenin complex and in Wnt signal transduction as transcription factors. Vertebrates express two related proteins, beta-catenin and plakoglobin, while Drosophila has a single family member, Armadillo. Caenorhabditis elegans expresses three beta-catenin-related proteins, BAR-1, HMP-2, and WRM-1, which are quite diverged in sequence from each other and other beta-catenins. While BAR-1 and WRM-1 are known to act in Wnt-mediated processes, and HMP-2 acts in a complex with cadherin/alpha-catenin homologs, it is unclear whether all three proteins retain the other functions of beta-catenin. Here we show that BAR-1, like vertebrate beta-catenin, has redundant transcription activation domains in its amino- and carboxyl-terminal regions but that HMP-2 and WRM-1 also possess the ability to activate transcription. We show via yeast two-hybrid analysis that these three proteins display distinct patterns of protein interactions. Surprisingly, we find that both WRM-1 and HMP-2 can substitute for BAR-1 in C. elegans when expressed from the bar-1 promoter. Therefore, although their mutant phenotypes and protein interaction patterns strongly suggest that the functions of beta-catenin in other species have been segregated among three diverged proteins in C. elegans, these proteins still retain sufficient similarity to display functional redundancy in vivo.
Acquisition and Transmission of the Agent of Human Granulocytic Ehrlichiosis by Ixodes scapularis Ticks (1998)

The purpose of the present study was to investigate the transmission of a human isolate of the agent of human granulocytic ehrlichiosis (HGE agent) from infected mice to larval ticks and to examine the population kinetics of the HGE agent in different stages of the tick life cycle. The HGE agent was quantitated by competitive PCR with blood from infected mice and with Ixodes scapularis ticks. The median infectious dose for C3H mice was 10(4) to 10(5) organisms when blood from an infected severe combined immunodeficient mouse was used as an inoculum. Uninfected larval ticks began to acquire infection from infected mice within 24 h of attachment, and the number of HGE agent organisms increased in larval ticks during feeding and after detachment of replete ticks. Molted nymphal ticks, infected as larvae, transmitted infection to mice between 40 and 48 h of attachment. Onset of feeding stimulated replication of the HGE agent within nymphal ticks. These studies suggest that replication of the HGE agent during and after feeding in larvae and during feeding in nymphs is a means by which the HGE agent overcomes inefficiencies in acquisition of infection by ticks and in tick-borne transmission to mammalian hosts.
Human Evolution, Life History Theory, and the End of Biological Reproduction (2014)

Throughout primate history there have been three major life history transitions towards increasingly delayed sexual maturation and biological reproduction, as well as towards extended life expectancy. Monkeys reproduce later and live longer than do prosimians, apes reproduce later and live longer than do monkeys, and humans reproduce later and live longer than do apes. These life history transitions are connected to increased encephalization. During the last life history transition from apes to humans, increased encephalization co-evolved with increased dependence on cultural knowledge for energy acquisition. This led to a dramatic pressure for more energy investment in growth over current biological reproduction. Since the industrial revolution socioeconomic development has led to even more energy being devoted to growth over current biological reproduction. I propose that this is the beginning of an ongoing fourth major primate life history transition towards completely delayed biological reproduction and an extension of the evolved human life expectancy. I argue that the only fundamental difference between this primate life history transition and previous life history transitions is that this transition is being driven solely by cultural evolution, which may suggest some deeper evolutionary transition away from biological evolution is already in the process of occurring.
<title>Token-based information security for commercial and federal information networks</title> (1996)

The planning of cryptographic solutions for messaging and electronic commerce applications in the United States during the past few years has been motivated by a high level of interest in the technology on the part of potential users. It has been marked by a high level of controversy over algorithms, patent rights and escrow policy. The diverse needs of the government and commercial sectors have led to mutually exclusive solutions based on different algorithms and policy; this phenomenon is fairly unique to the United States. Because of the strong requirement to preserve the differences that make these solutions unique for the two environments, the near-term evolution of a single standard appears unlikely. Furthermore, the need on the part of some government agencies and some commercial establishments exists to operate in both environments. This paper deals with the technical definition and design approach to a dual-use cryptographic device and the migration paths to the dual-use device from both environments. Such a device is further considered as a component of a secure cryptographic translation facility.
Noncoherent Low-Power Upconversion in Solid Polymer Films (2007)

Noncoherent low-power photon upconversion has been realized in solid thin films composed of an ethyleneoxide/epichlorohydrin copolymer doped with palladium octaethylporphyrin (PdOEP) and 9,10-diphenylanthracene (DPA). Selective excitation of PdOEP at 544 nm generates easily visualized DPA fluorescence in the blue with noncoherent light sources under ambient laboratory conditions. The incident excitation power dependence is quadratic in nature, exemplifying that sequential one-photon absorption by PdOEP leads to the sensitization of two triplet DPA chromophores, which in turn annihilate to produce the upconverted singlet DPA fluorescence. Time-resolved emission experiments confirm that the solid host facilitates these sequential bimolecular reactions leading to delayed DPA fluorescence; however, these processes are notably slower than the analogous photochemistry in fluid solution.
The epigenetic network regulating muscle development and regeneration (2005)

This review focuses on our current knowledge of the epigenetic changes regulating gene expression at the chromatin and DNA level, independently on the primary DNA sequence, to reprogram the nuclei of muscle precursors during developmental myogenesis and muscle regeneration. These epigenetic marks provide the blueprint by which the extra-cellular cues are interpreted at the nuclear level by the transcription machinery to select the repertoire of tissue-specific genes to be expressed. The reversibility of some of these changes necessarily reflects the dynamic nature of skeletal myogenesis, which entails the progression through two antagonistic processes--proliferation and differentiation. Other epigenetic modifications are instead associated to events conventionally considered as irreversible--e.g. maintenance of lineage commitment and terminal differentiation. However, recent results support the possibility that these events can be reversed, at least upon certain experimental conditions, thereby revealing a dynamic nature of many of the epigenetic modifications underlying skeletal myogenesis. The elucidation of the epigenetic network that regulates transcription during developmental myogenesis and muscle regeneration might provide the information instrumental to devise pharmacological interventions toward selective manipulation of gene expression to promote regeneration of skeletal muscles and possibly other tissue.
Nitroxide-Mediated Controlled/Living Free-Radical Surfactant-Free Emulsion Polymerization of Methyl Methacrylate Using a Poly(methacrylic acid)-Based Macroalkoxyamine Initiator (2008)

Water-soluble, SG1 nitroxide-capped poly(methacrylic acid-co-styrene) macroalkoxyamines with ∼10 mol % of styrene subunits were used as initiators in the surfactant-free, ab initio, batch, emulsion homopolymerization of methyl methacrylate and its copolymerization with a low percentage of styrene, in alkaline conditions at temperatures below 90 °C. The polymerizations were well-controlled, with a very high initiating efficiency, due to the high dissociation rate constant of the macroalkoxyamines. It led to the in situ formation of amphiphilic block copolymers that self-assembled into small particles with diameter below 100 nm, according to a polymerization-induced micellization process. The polymerization kinetics, the control over molar mass and molar distribution, and the colloidal characteristics of the so-formed block copolymer micelles were studied in detail. This work represents a breakthrough in controlled/living radical polymerization in aqueous emulsion with the development of new, very efficient macroinitiators used as the sole additive for initiation, stabilization, and chain-growth control. It is also the first development of nitroxide-mediated emulsion polymerization of methyl methacrylate performed at low temperature.
[Preparative separation of the tryptic hydrolysate of a protein by high-pressure liquid chromatography. The primary structure of a monoclonal L-chain of k-type, subgroup I (Bence-Jones Protein Wes) (author's transl)]. (1980)

The tryptic hydrolysate of Bence-Jones protein Wes (Mr = 23000) was separated by high-pressure liquid chromatography in a volatile buffer system on a reversed-phase column. From the resulting 22 peptides 18 yielded integer numbers after amino acid analysis. They could be used directly for a modified Edman degradation. Two peptides were not separated by this procedure, two were missing. Under different conditions these four peptides could also be prepared in pure form. 3 mg was sufficient to elucidate the primary structure of the variable part of this protein completely. The arrangement of the tryptic peptides was deduced by homology to other k=chains. Protein Wes contains 214 residues and belongs to subgroup I of the k-chains. The valine residue in position 191 indicates that it belongs to allotype Inv b+.
The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development (1998)

Fruit morphogenesis is a process unique to flowering plants, and yet little is known about its developmental control. Following fertilization, fruits typically undergo a dramatic enlargement that is accompanied by differentiation of numerous distinct cell types. We have identified a mutation in Arabidopsis called fruitfull (ful-1), which abolishes elongation of the silique after fertilization. The ful-1 mutation is caused by the insertion of a DsE transposable enhancer trap element into the 5' untranslated leader of the AGL8 MADS-box gene. beta-glucuronidase (GUS) reporter gene expression in the enhancer trap line is observed specifically in all cell layers of the valve tissue, but not in the replum, the septum or the seeds, and faithfully mimics RNA in situ hybridization data reported previously. The lack of coordinated growth of the fruit tissues leads to crowded seeds, a failure of dehiscence and, frequently, the premature rupture of the carpel valves. The primary defect of ful-1 fruits is within the valves, whose cells fail to elongate and differentiate. Stomata, which are frequent along the epidermis of wild-type valves, are completely eliminated in the ful mutant valves. In addition to the effect on fruit development, ful cauline leaves are broader than those of wild type and show a reduction in the number of internal cell layers. These data suggest that AGL8/FUL regulates the transcription of genes required for cellular differentiation during fruit and leaf development.
Seed-Mediated Synthesis of Gold Nanorods:  Role of the Size and Nature of the Seed (2004)

We report studies on the synthesis of gold nanorods by a three-step seeding protocol method using a variety of different gold seeds. The synthetic method is adapted from one we published earlier (Jana et al. J. Phys. Chem. B 2001, 105, 4065). The seeds chosen for these studies have average diameters in the range from 4 to 18 nm, with positively charged as well as negatively charged surface groups. In all the cases, along with a large concentration of long rods, a small number of different shapes such as triangles, hexagons, and small rods are observed. The proportion of small rods increases with an increase in the seed size used for nanorod synthesis. For long nanorods synthesized by different seeds a comparison of various parameters such as length, width, and aspect ratio has been made. A dependence of the nanorod aspect ratio on the size of the seed is observed. Increasing the seed size results in lowering of the gold nanorod aspect ratios for a constant concentration of reagents. The charge on the seed also plays a role in determining the nanorod aspect ratio. For positively charged seeds variation in the aspect ratio is not as pronounced as that for negatively charged seeds. The gold nanorods synthesized were characterized by transmission electron microscopy (TEM), UV−vis spectroscopy, and Fourier transform infrared spectroscopy. The role of seed size in the size and shape evolution of the nanocrystal, at different growth stages, has been studied by TEM.
Abstract 4612: JQ1 suppresses tumor growth in tumorgraft models of pancreatic ductal adenocarcinoma (2014)

Abstract Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is one of the most deadly of malignancies. Patients often present late in the course of disease limiting treatment options, with the majority of patients receiving chemotherapy. However, currently available chemotherapy has not impacted overall patient survival, and new therapies are urgently needed. Recently, our lab has documented that tumorgrafts derived specifically from primary PDAC tumors retain characteristics of the tumors of origin. In terms of drug evaluation, tumorgraft models have been shown to be predictive of clinical utility because these models retain tumor heterogeneity, recapitulate tumor architecture, and contain human stroma. To date, most efforts to use tumorgraft models to identify effective agents for the treatment of PDAC have taken an “all comers approach”; but this approach has thus far identified no effective therapies. We proposed that JQ1, a compound that targets the oncogene c-Myc, would be efficacious for the treatment of PDAC, based on molecular characteristics of these tumors. The oncogene c-Myc is amplified or overexpressed in a 30-45% of primary or metastatic PDAC tumors. Also, overexpression of this oncogene is sufficient to induce tumor formation in a genetically engineered mouse model of PDAC, suggesting a critical role in the tumorigenesis of this tumor type. JQ1 is a novel compound in that it is a relatively specific bromodomain inhibitor. Bromodomain containing proteins recognize acetylated lysine residues on histones and direct the assembly of macromolecular molecules to the chromatin for transcription. A specific subfamily of these proteins, known as BETs (bromodomain and extra-terminal), recruit c-Myc to specific sites for transcription. Exposure of PDAC cells to JQ1 decreases the expression and therefore the activity of c-Myc. To test the effectiveness of JQ1 in vivo, we administered 50 mg/kg of JQ1 i.p. once a day for 28 days and monitored tumor growth in a panel of 5 PDAC tumorgraft models. This dose and schedule of JQ1 administration was well tolerated in mice with no significant toxicity. Our data indicate that JQ1 suppressed tumor growth in all 5 models, compared to vehicle control treated mice. The data also showed a modest, JQ1-induced down regulation of c-Myc and NFkB. We conclude that JQ1 and other bromodomain inhibitors warrant further investigation as potentially effective agents for the treatment of PDAC. This work was supported by UAB/UMN SPORE in pancreatic cancer (P50 CA101955). Citation Format: Patrick L. Garcia, Tracy Gamblin, Leona N. Council, John D. Christein, J. Pablo Arnoletti, Martin J. Heslin, Joseph H. Richardson, Jun Qi, Jay E. Bradner, Karina J. Yoon. JQ1 suppresses tumor growth in tumorgraft models of pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4612. doi:10.1158/1538-7445.AM2014-4612
Fast imaging using subencoding data sets from multiple detectors (1993)

A new fast imaging method using a subencoding data acquisition scheme and a multiple coil receiver system is proposed and demonstrated. In this method, a set of aliased images are produced from receiver coils by using the subencoded data without sacrificing the desired resolution, and resolved to an aliasing-free image by using the distance-dependent sensitivity information of each coil. The reduction rate of data acquisition time is proportional to the number of receiver coils. This method can be easily adapted to conventional imaging methods including fast imaging to further reduce the scan time.
An evaluation of methods to study the gut bacterial community composition of freshwater zooplankton (2008)

The occurrence of gut bacteria in freshwater and marine zooplankton has long been recognized, but knowledge about the composition of the gut “microflora” and its permanent presence in different zooplankters is still inadequate. In this study, we tested the suitability of fluorescence in situ hybridization (FISH), catalysed reporter deposition (CARD)-FISH, cultivation and transmission electron microscopy (TEM) on homogenates and whole-specimen sections to assess the presence and identity of gut bacteria in several freshwater copepod and cladoceran species. Unambiguous results about the presence of a permanent gut “microflora” were obtained for freshly caught Daphnia pulex by TEM. CARD-FISH on gut homogenates from Acanthodiaptomus denticornis and D. pulex revealed a very similar bacterial composition to that present in the water column. Major bacterial groups found in cladocerans and copepods were alpha-, beta-, gamma-Proteobacteria and Cytophaga–Flavobacteria. The high contribution of alpha-Proteobacteria in A. denticornis suggested a specific niche for this group, but probably in association with its carapace. FISH on paraffin semithin sections had the potential to provide quantitative and qualitative information about the composition of the gut “microflora”, but loss of bacteria and gut content was significant.
Inhibitory effect of local anaesthetics on reactive oxygen species production by human neutrophils (1997)

In conclusion, in the present in vitro system, only concentrations of lidocaine and mepivacaine 100-fold higher than clinically feasible ones reduced ROS production by human neutrophils. However, the local anaesthetics at clinically relevant blood concentrations had no suppressive effect. Further studies using in vivo systems are required to elucidate the inhibitory effects of local anaesthetics on ROS generation in clinical settings.
Amphipathic DNA polymers exhibit antiviral activity against systemic Murine Cytomegalovirus infection (2009)

These studies indicate that APs exhibit potent, well tolerated antiviral activity against CMV infection in vivo and represent a new class of broad spectrum anti-herpetic agents.
Lisofylline, a Novel Antiinflammatory Compound, Protects Mesangial Cells from Hyperglycemia- and Angiotensin II-Mediated Extracellular Matrix Deposition (2003)

Chronic elevated glucose levels and activation of the renal renin-angiotensin system have been implicated in the pathogenesis of diabetic nephropathy. We tested the ability of lisofylline (LSF), a novel antiinflammatory compound, to prevent extracellular matrix (ECM) accumulation and growth factor production by human mesangial cells (HMCs) cultured in chronic elevated glucose (HG) or angiotensin II (AngII). HMCs were cultured in normal glucose (NG) (5.5 mm) and in HG (25 mm) for 7 d or with 10-7 m AngII for 4 h with or without LSF. Levels of the ECM protein fibronectin and TGF-beta in media were shown to increase in HG compared with NG. LSF decreased HG-induced fibronectin and TGF-beta production to control levels. Increased expression of collagen type IV and laminin was observed in AngII-cultured HMCs. LSF protected HMCs from the AngII induction of these key matrix proteins. cAMP-responsive binding element phosphorylation was significantly higher in both HG and AngII-cultured HMCs. LSF reduced phosphorylation of both cAMP-responsive binding element and p38 MAPK compared with control. These data demonstrate that LSF protects HMCs from HG- and AngII-mediated ECM deposition by the reduction of matrix protein secretion possibly through regulation of TGF-beta production and modulation of the p38 MAPK pathway. These results suggest that LSF may provide therapeutic benefit for prevention or treatment of diabetic nephropathy.
In vitro assessment of 2-fluoro-2-deoxy-D-glucose, L-methionine and thymidine as agents to monitor the early response of a human adenocarcinoma cell line to radiotherapy. (1993)

The tumor cell uptake of three tracers that can be labeled with isotopes suitable for PET imaging--FDG, L-methionine and thymidine--were examined in vitro in a human ovarian carcinoma cell line (HTB77IP3) at varying times following 30 Gy 60Co irradiation and were compared to a nonirradiated control group. FDG, methionine and thymidine uptake per tissue culture well all increased following irradiation when compared to basal values, although to a much lower extent than the increases in uptake seen in a nonirradiated group. This increase in tracer uptake occurred despite a 6.25-fold decline in viable cell numbers. When examined per cell, FDG uptake per cell increased 9.77-fold, methionine 7.82-fold and thymidine 9.48-fold over basal levels from Day 0 to Day 12 following irradiation. Part of these increases may be due to giant cell formation and/or radiation repair processes that require energy, protein and DNA substrates. While the in vitro system differs from in vivo systems due to the absence of a blood supply in vitro, a lack of infiltrating leukocytes and other factors, our data suggest that early assessment of human adenocarcinoma response to radiotherapy by PET with these tracers may be complicated by this normal increase in tracer uptake postirradiation. Clearly, in this human cancer cell line, early radiation-induced cell death is not associated with an early decline in tumor cell uptake of FDG, methionine or thymidine.
Determination of viral proteins present in the human immunodeficiency virus type 1 preintegration complex (1991)

Cytoplasmic extracts prepared from cells infected with metabolically radiolabeled virions of human immunodeficiency virus type 1 contain viral DNA in association with labeled viral proteins. Viral DNA can be purified from these extracts by gel filtration chromatography and sucrose gradient sedimentation as a part of a nucleoprotein complex containing integrase as the only viral protein detectable by immunoprecipitation and gel electrophoretic analysis. The purified complex contains no detectable gag gene products, including p17, p24, p7, or p6, and contains no additional pol gene products, including the p10 protease, p66 and p51 polymerase, or the p15 RNase H. Nearly all of the purified nucleoprotein complexes are capable of integrating into heterologous DNA targets in vitro. These observations demonstrate that integrase is a component of the human immunodeficiency virus type 1 preintegration complex and suggest that integrase may be the only viral protein necessary for the integration of retroviral DNA.
Is Beta Radiation Better than 5 Flurouracil as an Adjunct for Trabeculectomy Surgery When Combined with Cataract Surgery? A Randomised Controlled Trial (2016)

ISRCTN Registry ISRCTN36436933.