gebhart/patrepeval huggingface dataset:
Functional Properties and Genomics of Glucose Transporters (2007)

Glucose is the major energy source for mammalian cells as well as an important substrate for protein and lipid synthesis. Mammalian cells take up glucose from extracellular fluid into the cell through two families of structurallyrelated glucose transporters. The facilitative glucose transporter family (solute carriers SLC2A, protein symbol GLUT) mediates a bidirectional and energy-independent process of glucose transport in most tissues and cells, while the NaM(+)/glucose cotransporter family (solute carriers SLC5A, protein symbol SGLT) mediates an active, Na(+)-linked transport process against an electrochemical gradient. The GLUT family consists of thirteen members (GLUT1-12 and HMIT). Phylogenetically, the members of the GLUT family are split into three classes based on protein similarities. Up to now, at least six members of the SGLT family have been cloned (SGLT1-6). In this review, we report both the genomic structure and function of each transporter as well as intra-species comparative genomic analysis of some of these transporters. The affinity for glucose and transport kinetics of each transporter differs and ranges from 0.2 to 17mM. The ability of each protein to transport alternative substrates also differs and includes substrates such as fructose and galactose. In addition, the tissue distribution pattern varies between species. There are different regulation mechanisms of these transporters. Characterization of transcriptional control of some of the gene promoters has been investigated and alternative promoter usage to generate different protein isoforms has been demonstrated. We also introduce some pathophysiological roles of these transporters in human.
A fast local descriptor for dense matching (2008)

We introduce a novel local image descriptor designed for dense wide-baseline matching purposes. We feed our descriptors to a graph-cuts based dense depth map estimation algorithm and this yields better wide-baseline performance than the commonly used correlation windows for which the size is hard to tune. As a result, unlike competing techniques that require many high-resolution images to produce good reconstructions, our descriptor can compute them from pairs of low-quality images such as the ones captured by video streams. Our descriptor is inspired from earlier ones such as SIFT and GLOH but can be computed much faster for our purposes. Unlike SURF which can also be computed efficiently at every pixel, it does not introduce artifacts that degrade the matching performance. Our approach was tested with ground truth laser scanned depth maps as well as on a wide variety of image pairs of different resolutions and we show that good reconstructions are achieved even with only two low quality images.
High Oleic Acid Mutant in Soybean Induced by X-Ray Irradiation (1994)

Dry seeds of soybean [Glycine max (L.) Merr. var. Bay] were irradiated by X-rays (21.4 kR) and the M2 generations were examined for the oleic acid content in their oil. The genetic variability of oleic acid content in the oil of the Bay variety was significantly increased by the X-ray treatment when compared with the Bay control. A mutant, designated as M23, was selected from 2747 M2 plants, having an oleic acid content of 46.1%, twice as much as that in the normal Bay variety. A distinct inverse relationship was observed between the oleic and linoleic acid contents in M23. Mutant M23 isolated from the M2 generations was confirmed to be always associated with a high oleic acid content under different environmental conditions in the M3 generations.
A transformation system for the yeast Candida utilis: use of a modified endogenous ribosomal protein gene as a drug-resistant marker and ribosomal DNA as an integration target for vector DNA (1995)

We have developed a transformation system for the yeast Candida utilis. A novel strategy was applied to construct the transformation system, since auxotrophic mutants which could be used as hosts for transformation are not available. A gene encoding the ribosomal protein L41 was cloned from C. utilis, which is sensitive to cycloheximide, and used as a marker gene conferring cycloheximide resistance after modification of its amino acid sequence. The marker gene was constructed by substitution of the proline codon at position 56 with the glutamine codon by in vitro mutagenesis, as it had been reported previously that the 56th amino acid residue of L41 is responsible for the cycloheximide sensitivity of various organisms (S. Kawai, S. Murao, M. Mochizuki, I. Shibuya, K. Yano, and M. Takagi, J. Bacteriol. 174:254-262 1992). The ribosomal DNA (i.e., DNA coding for rRNA) of C. utilis was also cloned and used as a multiple-copy target for the integration of vector DNA into the genome, which resulted in a high transformation efficiency. Transformants were obtained by electroporation with a maximum efficiency of approximately 1,400 transformants per 1 microgram of linearized DNA carrying the gene for cycloheximide resistance and part of the ribosomal DNA. No transformants were obtained with intact plasmids. Multiple copies of the linearized plasmid were integrated into the host chromosome by homologous recombination. Southern analysis of the transformants in which vector DNA was integrated at the L41 gene locus indicated that there are two copies of gene for the L41 protein per cell, suggesting that C. utilis is diploid. Transformants were obtained from a variety of C. utilis strains, indicating that this method is applicable to the transformation of other C. utilis strains, even though there is significant heterogeneity in chromosomal karyotypes among these strains.
Selective Synthesis of Methylnaphthalenes in HSAPO-34 Cages and Their Function as Reaction Centers in Methanol-to-Olefin Catalysis (2001)

Several recent papers have demonstrated that the conversion of methanol to olefins on the silico-aluminophosphate solid acid catalyst HSAPO-34 usually requires methylbenzenes that function as scaffolds (reaction centers) for carbon−carbon bond making and breaking steps. These benzene rings form in the ca. 1 nm cages through ship-in-a-bottle routes from olefins, and they cannot exit the ca. 0.38 nm windows connecting cages. Here, we report a procedure for the selective (80%) synthesis of naphthalene in the cages of HSAPO-34 based on methanol conversion at 600 °C. These naphthalene molecules are accessible to methanol and react at 400 °C to form methylnaphthalenes in the cages with up to four methyl groups. We find that HSAPO-34 catalysts with methylnaphthalenes as the primary entrained hydrocarbon species eliminate ethylene and propene, much like methylbenzenes. A careful comparison of catalysts prepared with either methylnaphthalenes or methylbenzenes showed the former to be ca. one-third as active as the latter (for comparable numbers of reaction centers), but the methylnaphthalene-based catalysts yielded higher ethylene selectivity (at comparable conversions) than the methylbenzene-based catalysts.
Two-Photon Three-Dimensional Optical Storage Memory (1994)

We present a means for constructing three-dimensional optical memory devices that operate by two-photon interaction. Photochromic molecules and semiconductors have been studied as materials for writing and reading information within the volume of a solid matrix. The mechanism for writing and reading the information, bit density, cycle times, and stability of the materials under various experimental conditions are the topics addressed.
Structure−Activity Relationships of the Didemnins (1996)

Bioactivities of 42 didemnin congeners, either isolated from the marine tunicates Trididemnun solidum and Aplidium albicans or prepared synthetically and semisynthetically, have been compared. The growth inhibition of various murine and human tumor cells and plaque reduction of HSV-1 and VSV grown on cultured mammalian cells were used to assess cytotoxicity and antiviral activity. Biochemical assays for macromolecular synthesis (protein, DNA, and RNA) and enzyme inhibition (dihydrofolate reductase, thymidylate synthase, DNA polymerase, RNA polymerase, and topoisomerases I and II) were also performed to specify the mechanisms of action of each analogue. Immunosuppressive activity of the didemnins was determined using a mixed lymphocyte reaction (MLR) assay. These assays revealed that the native cyclic depsipeptide core is an essential structural requirement for most of the bioactivites of the didemnins, especially for cytotoxicities and antiviral activities. The linear side-chain portion of the peptide can be altered with a gain, in some cases, of bioactivities. In particular, dehydrodidemnin B, tested against several types of tumor cells and in in vivo studies in mice, as well as didemnin M, tested for the mixed lymphocyte reaction and graft vs host reaction in murine systems, showed remarkable gains in their in vitro and in vivo activities compared to didemnin B.
Compression of binary sources with side information at the decoder using LDPC codes (2002)

We show how low-density parity-check (LDPC) codes can be used to compress close to the Slepian-Wolf limit for correlated binary sources. Focusing on the asymmetric case of compression of an equiprobable memoryless binary source with side information at the decoder, the approach is based on viewing the correlation as a channel and applying the syndrome concept. The encoding and decoding procedures are explained in detail. The performance achieved is seen to be better than recently published results using turbo codes and very close to the Slepian-Wolf limit.
PI3K signalling in inflammation (2014)

PI3Ks regulate several key events in the inflammatory response to damage and infection. There are four Class I PI3K isoforms (PI3Kα,β,γ,δ), three Class II PI3K isoforms (PI3KC2α, C2β, C2γ) and a single Class III PI3K. The four Class I isoforms synthesise the phospholipid 'PIP3'. PIP3 is a 'second messenger' used by many different cell surface receptors to control cell movement, growth, survival and differentiation. These four isoforms have overlapping functions but each is adapted to receive efficient stimulation by particular receptor sub-types. PI3Kγ is highly expressed in leukocytes and plays a particularly important role in chemokine-mediated recruitment and activation of innate immune cells at sites of inflammation. PI3Kδ is also highly expressed in leukocytes and plays a key role in antigen receptor and cytokine-mediated B and T cell development, differentiation and function. Class III PI3K synthesises the phospholipid PI3P, which regulates endosome-lysosome trafficking and the induction of autophagy, pathways involved in pathogen killing, antigen processing and immune cell survival. Much less is known about the function of Class II PI3Ks, but emerging evidence indicates they can synthesise PI3P and PI34P2 and are involved in the regulation of endocytosis. The creation of genetically-modified mice with altered PI3K signalling, together with the development of isoform-selective, small-molecule PI3K inhibitors, has allowed the evaluation of the individual roles of Class I PI3K isoforms in several mouse models of chronic inflammation. Selective inhibition of PI3Kδ, γ or β has each been shown to reduce the severity of inflammation in one or more models of autoimmune disease, respiratory disease or allergic inflammation, with dual γ/δ or β/δ inhibition generally proving more effective. The inhibition of Class I PI3Ks may therefore offer a therapeutic opportunity to treat non-resolving inflammatory pathologies in humans. This article is part of a Special Issue entitled Phosphoinositides.
The Society for Immunotherapy of Cancer perspective on regulation of interleukin-6 signaling in COVID-19-related systemic inflammatory response (2020)

The pandemic caused by the novel coronavirus SARS-CoV-2 has placed an unprecedented burden on healthcare systems around the world. In patients who experience severe disease, acute respiratory distress is often accompanied by a pathological immune reaction, sometimes referred to as 'cytokine storm'. One hallmark feature of the profound inflammatory state seen in patients with COVID-19 who succumb to pneumonia and hypoxia is marked elevation of serum cytokines, especially interferon gamma, tumor necrosis factor alpha, interleukin 17 (IL-17), interleukin 8 (IL-8) and interleukin 6 (IL-6). Initial experience from the outbreaks in Italy, China and the USA has anecdotally demonstrated improved outcomes for critically ill patients with COVID-19 with the administration of cytokine-modulatory therapies, especially anti-IL-6 agents. Although ongoing trials are investigating anti-IL-6 therapies, access to these therapies is a concern, especially as the numbers of cases worldwide continue to climb. An immunology-informed approach may help identify alternative agents to modulate the pathological inflammation seen in patients with COVID-19. Drawing on extensive experience administering these and other immune-modulating therapies, the Society for Immunotherapy of Cancer offers this perspective on potential alternatives to anti-IL-6 that may also warrant consideration for management of the systemic inflammatory response and pulmonary compromise that can be seen in patients with severe COVID-19.
Characterization of Ha-Ras, N-Ras, Ki-Ras4A, and Ki-Ras4B as in Vitro Substrates for Farnesyl Protein Transferase and Geranylgeranyl Protein Transferase Type I (1997)

Ras proteins are small GTP-binding proteins which are critical for cell signaling and proliferation. Four Ras isoforms exist: Ha-Ras, N-Ras, Ki-Ras4A, and Ki-Ras4B. The carboxyl termini of all four isoforms are post-translationally modified by farnesyl protein transferase (FPT). Prenylation is required for oncogenic Ras to transform cells. Recently, it was reported that Ki-Ras4B is also an in vitro substrate for the related enzyme geranylgeranyl protein transferase-1 (GGPT-1) (James, G. L., Goldstein, J. L., and Brown, M. S. (1995) J. Biol. Chem. 270, 6221-6226). In the current studies, we compared the four isoforms of Ras as substrates for FPT and GGPT-1. The affinity of FPT for Ki-Ras4B (Km = 30 nM) is 10-20-fold higher than that for the other Ras isoforms. Consistent with this, when the different Ras isoforms are tested at equimolar concentrations, it requires 10-20-fold higher levels of CAAX-competitive compounds to inhibit Ki-Ras4B farnesylation. Additionally, we found that, as reported for Ki-Ras4B, N-Ras and Ki-Ras4A are also in vitro substrates for GGPT-1. Of the Ras isoforms, N-Ras is the highest affinity substrate for GGPT-1 and is similar in affinity to a standard GGPT-1 substrate terminating in leucine. However, the catalytic efficiencies of these geranylgeranylation reactions are between 15- and 140-fold lower than the corresponding farnesylation reactions, largely reflecting differences in affinity. Carboxyl-terminal peptides account for many of the properties of the Ras proteins. One interesting exception is that, unlike the full-length N-Ras protein, a carboxyl-terminal N-Ras peptide is not a GGPT-1 substrate, raising the possibility that upstream sequences in this protein may play a role in its recognition by GGPT-1. Studies with various carboxyl-terminal peptides from Ki-Ras4B suggest that both the carboxyl-terminal methionine and the upstream polylysine region are important determinants for geranylgeranylation. Furthermore, it was found that full-length Ki-Ras4B, but not other Ras isoforms, can be geranylgeranylated in vitro by FPT. These findings suggest that the different distribution of Ras isoforms and the ability of cells to alternatively process these proteins may explain in part the resistance of some cell lines to FPT inhibitors.
Role of the pH on Hyaluronan Behavior in Aqueous Solution (2004)

In this paper, we have examined the behavior of hyaluronan solutions at different pH values. A slight degradation is observed in acidic conditions (pH = 1.6) and basic medium (pH = 12.6) from molecular weight distribution analysis, but the rheological behavior is relatively not influenced much by the pH at the exclusion of two domains: around pH = 2.5, a gel-like behavior is shown and is attributed to cooperative interchain interactions due to the reduction of the polymer net charge and may be the protonation of the acetamido groups; for pH > 12, the decrease of viscosity is mainly attributed to a reduction of the stiffness of the polymeric backbone in alkaline conditions due to the partial breakage of the H-bond network.
SURVEY AND SUMMARY: From DNA biosensors to gene chips (2000)

Wide-scale DNA testing requires the development of small, fast and easy-to-use devices. This article describes the preparation, operation and applications of biosensors and gene chips, which provide fast, sensitive and selective detection of DNA hybridization. Various new strategies for DNA biosensors and gene chips are examined, along with recent trends and future directions. The integration of hybridization detection schemes with the sample preparation process in a 'Lab-on-a-Chip' format is also covered. While the use of DNA biosensors and gene chips is at an early stage, such devices are expected to have an enormous effect on future DNA diagnostics.
An Artificially Intelligent Technique to Generate Synthetic Geomechanical Well Logs for the Bakken Formation (2018)

Artificially intelligent and predictive modelling of geomechanical properties is performed by creating supervised machine learning data models utilizing artificial neural networks (ANN) and will predict geomechanical properties from basic and commonly used conventional well logs such as gamma ray, and bulk density. The predictive models were created by following the approach on a large volume of data acquired from 112 wells containing the Bakken Formation in North Dakota. The studied wells cover a large surface area of the formation containing the five main producing counties in North Dakota: Burke, Mountrail, McKenzie, Dunn, and Williams. Thus, with a large surface area being analyzed in this research, there is confidence with a high degree of certainty that an extensive representation of the Bakken Formation is modelled, by training neural networks to work on varying properties from the different counties containing the Bakken Formation in North Dakota. Shear wave velocity of 112 wells is also analyzed by regression methods and neural networks, and a new correlation is proposed for the Bakken Formation. The final goal of the research is to achieve supervised artificial neural network models that predict geomechanical properties of future wells with an accuracy of at least 90% for the Upper and Middle Bakken Formation. Thus, obtaining these logs by generating it from statistical and artificially intelligent methods shows a potential for significant improvements in performance, efficiency, and profitability for oil and gas operators.
Fast Model Predictive Control Using Online Optimization (2009)

A widely recognized shortcoming of model predictive control (MPC) is that it can usually only be used in applications with slow dynamics, where the sample time is measured in seconds or minutes. A well-known technique for implementing fast MPC is to compute the entire control law offline, in which case the online controller can be implemented as a lookup table. This method works well for systems with small state and input dimensions (say, no more than five), few constraints, and short time horizons. In this paper, we describe a collection of methods for improving the speed of MPC, using online optimization. These custom methods, which exploit the particular structure of the MPC problem, can compute the control action on the order of 100 times faster than a method that uses a generic optimizer. As an example, our method computes the control actions for a problem with 12 states, 3 controls, and horizon of 30 time steps (which entails solving a quadratic program with 450 variables and 1284 constraints) in around 5 ms, allowing MPC to be carried out at 200 Hz.
Topic identification in natural language dialogues using neural networks (2002)

In human-computer interaction systems using natural language, the recognition of the topic from user's utterances is an important task. We examine two different perspectives to the problem of topic analysis needed for carrying out a successful dialogue. First, we apply self-organized document maps for modeling the broader subject of discourse based on the occurrence of content words in the dialogue context. On a Finnish corpus of 57 dialogues the method is shown to work well for recognizing subjects of longer dialogue segments, whereas for individual utterances the subject recognition history should perhaps be taken into account. Second, we attempt to identify topically relevant words in the utterances and thus locate the old information ('topic words') and new information ('focus words'). For this we define a probabilistic model and compare different methods for model parameter estimation on a corpus of 189 dialogues. Moreover, the utilization of information regarding the position of the word in the utterance is found to improve the results.
Candidate vaccines protect macaques against primate immunodeficiency viruses. (1998)

The preclinical evaluation of the efficacy of potential vaccines against AIDS requires challenge models. The experimental infection of macaques with simian immunodeficiency virus, human immunodeficiency virus type 2 (HIV-2) or chimeric viruses have proven to be most valuable. The progress made using simian models to assess the efficacy and identify the correlates or mechanism of protection by whole inactivated virus, live attenuated virus or recombinant sub-unit vaccines is reviewed. It is possible to conclude from these studies that an effective AIDS vaccine is feasible. Furthermore, it is likely that these different vaccine approaches protect through distinct mechanisms. These results provide a scientific basis for the development and selection of suitable candidate human AIDS vaccines for testing in humans.
Multilocular fat cells in WAT of CL-316243-treated rats derive directly from white adipocytes (2000)

Multilocular, mitochondria-rich adipocytes appear in white adipose tissue (WAT) of rats treated with the beta3-adrenoceptor agonist, CL-316243 (CL). Objectives were to determine whether these multilocular adipocytes derived from cells that already existed in the WAT or from proliferation of precursor cells and whether new mitochondria contained in them were typical brown adipocyte mitochondria. Use of 5-bromodeoxyuridine to identify cells that had undergone mitosis during the CL treatment showed that most multilocular cells derived from cells already present in the WAT. Morphological techniques showed that at least a subpopulation of unilocular adipocytes underwent conversion to multilocular mitochondria-rich adipocytes. A small proportion of multilocular adipocytes ( approximately 8%) was positive for UCP1 by immunohistochemistry. Biochemical techniques showed that mitochondrial protein recovered from WAT increased 10-fold and protein isolated from brown adipose tissue (BAT) doubled in CL-treated rats. Stained gels showed a different protein composition of new mitochondria isolated from WAT from that of mitochondria isolated from BAT. Western blotting showed new mitochondria in WAT to contain both UCP1, but at a much lower concentration than in BAT mitochondria, and UCP3, at a higher concentration than that in BAT mitochondria. We hypothesize that multilocular adipocytes present at 7 days of CL treatment have two origins. First, most come from convertible unilocular adipocytes that become multilocular and make many mitochondria that contain UCP3. Second, some come from a cell that gives rise to more typical brown adipocytes that express UCP1.