gebhart/patrepeval huggingface dataset:
[Cloning and expression of a osmoregulatory gene pro B from halotolerant Bacillus subtilis]. (2002)

A 1.3 kb fragment is cloned from halotolerated Bacillus subtilis 93151 with PCR amplification method, and its positively-directionally inserted fragment can complemented with proB-E. coli by function test. Halotolerated ability of E. coli DH5 alpha having this recombination plasmid rises from 2% to 4% in minimal medium. The nucleotide sequence of this fragment is obtained by primer walking method. Nucleotide sequence of this fragment 167-1269 bp translates a protein which has 370 amino acid by sequence analysis through DNAsis program. There are non-typical-10 sequences, typical-35 sequences and a Ribosome binding site of this fragment in its upstream sequence, and there is flanking sequence, which has best efficiency of beginning translating. Homologues comparision, of nucleotide and amino acid sequences of this fragment and those of gene in gene bank shows that homogenous of Nucleotide sequences and amino acid sequences of this fragement and Bacillus subtilis 168 are respectively 81%, 90%, which prove that this gene is certainly a pro B gene. This protein translated by this fragment has several absoluter conservative domain which have been correlating closely with forming active center of enzyme and tri-dimension structure of active center, compared amino acid sequences of this fragment and pro B genes of thirty kinds of different microorganism.
Molecular Approaches to the Photocatalytic Reduction of Carbon Dioxide for Solar Fuels (2009)

The scientific community now agrees that the rise in atmospheric CO(2), the most abundant green house gas, comes from anthropogenic sources such as the burning of fossil fuels. This atmospheric rise in CO(2) results in global climate change. Therefore methods for photochemically transforming CO(2) into a source of fuel could offer an attractive way to decrease atmospheric concentrations. One way to accomplish this conversion is through the light-driven reduction of carbon dioxide to methane (CH(4(g))) or methanol (CH(3)OH((l))) with electrons and protons derived from water. Existing infrastructure already supports the delivery of natural gas and liquid fuels, which makes these possible CO(2) reduction products particularly appealing. This Account focuses on molecular approaches to photochemical CO(2) reduction in homogeneous solution. The reduction of CO(2) by one electron to form CO(2)(*-) is highly unfavorable, having a formal reduction potential of -2.14 V vs SCE. Rapid reduction requires an overpotential of up to 0.6 V, due at least in part to the kinetic restrictions imposed by the structural difference between linear CO(2) and bent CO(2)(*-). An alternative and more favorable pathway is to reduce CO(2) though proton-assisted multiple-electron transfer. The development of catalysts, redox mediators, or both that efficiently drive these reactions remains an important and active area of research. We divide these reactions into two class types. In Type I photocatalysis, a molecular light absorber and a transition metal catalyst work in concert. We also consider a special case of Type 1 photocatalysis, where a saturated hydrocarbon links the catalyst and the light absorber in a supramolecular compound. In Type II photocatalysis, the light absorber and the catalyst are the same molecule. In these reactions, transition-metal coordination compounds often serve as catalysts because they can absorb a significant portion of the solar spectrum and can promote activation of small molecules. This Account discusses four classes of transition-metal catalysts: (A) metal tetraaza-macrocyclic compounds; (B) supramolecular complexes; (C) metalloporphyrins and related metallomacrocycles; (D) Re(CO)(3)(bpy)X-based compounds where bpy = 2,2'-bipyridine. Carbon monoxide and formate are the primary CO(2) reduction products, and we also propose bicarbonate/carbonate production. For comprehensiveness, we briefly discuss hydrogen formation, a common side reaction that occurs concurrently with CO(2) reduction, though the details of that process are beyond the scope of this Account. It is our hope that drawing attention both to current mechanistic hypotheses and to the areas that are poorly understood will stimulate research that could one day provide an efficient solution to this global problem.
Specificity of Tissue Transglutaminase Explains Cereal Toxicity in Celiac Disease (2002)

Celiac disease is caused by a selective lack of T cell tolerance for gluten. It is known that the enzyme tissue transglutaminase (tTG) is involved in the generation of T cell stimulatory gluten peptides through deamidation of glutamine, the most abundant amino acid in gluten. Only particular glutamine residues, however, are modified by tTG. Here we provide evidence that the spacing between glutamine and proline, the second most abundant amino acid in gluten, plays an essential role in the specificity of deamidation. On the basis of this, algorithms were designed and used to successfully predict novel T cell stimulatory peptides in gluten. Strikingly, these algorithms identified many similar peptides in the gluten-like hordeins from barley and secalins from rye but not in the avenins from oats. The avenins contain significantly lower percentages of proline residues, which offers a likely explanation for the lack of toxicity of oats. Thus, the unique amino acid composition of gluten and related proteins in barley and rye favors the generation of toxic T cell stimulatory gluten peptides by tTG. This provides a rationale for the observation that celiac disease patients are intolerant to these cereal proteins but not to other common food proteins.
COLD-PCR–Enhanced High-Resolution Melting Enables Rapid and Selective Identification of Low-Level Unknown Mutations (2009)

COLD-PCR/HRM improves the mutation-scanning capabilities of HRM and combines high selectivity, convenience, and low cost with the ability to sequence unknown low-level mutations in clinical samples.
Multiple displacement amplification for complex mixtures of DNA fragments (2008)

We believe that this method allows for generation of abundant amounts of good quality genetic material from a complex mixture of short DNA fragments, which can be further used in high throughput genetic analysis.
Object removal by exemplar-based inpainting (2003)

A new algorithm is proposed for removing large objects from digital images. The challenge is to fill in the hole that is left behind in a visually plausible way. In the past, this problem has been addressed by two classes of algorithms: (i) "texture synthesis" algorithms for generating large image regions from sample textures, and (ii) "inpainting" techniques for filling in small image gaps. The former work well for "textures" - repeating two dimensional patterns with some stochasticity; the latter focus on linear "structures" which can be thought of as one dimensional patterns, such as lines and object contours. This paper presents a novel and efficient algorithm that combines the advantages of these two approaches. We first note that exemplar-based texture synthesis contains the essential process required to replicate both texture and structure; the success of structure propagation, however, is highly dependent on the order in which the filling proceeds. We propose a best-first algorithm in which the confidence in the synthesized pixel values is propagated in a manner similar to the propagation of information in inpainting. The actual color values are computed using exemplar-based synthesis. Computational efficiency is achieved by a block-based sampling process. A number of examples on real and synthetic images demonstrate the effectiveness of our algorithm in removing large occluding objects as well as thin scratches. Robustness with respect to the shape of the manually selected target region is also demonstrated. Our results compare favorably to those obtained by existing techniques.
Text Classification using String Kernels (2000)

1 Introduction Standard learning systems (like neural networks or decision trees) operate on input data after they have been transformed into feature vectors x1;:::; x ` 2 X from an n dimensional space. There are cases, however, where the input data can not be readily described by explicit feature vectors: for example biosequences, images, graphs and text documents. For such datasets, the construction of a feature extraction module can be as complex and expensive as solving the entire problem. An effective alternative to explicit feature extraction is provided by kernel methods. Kernel-based learning methods use an implicit mapping of the input data into a high dimensional feature space defined by a kernel function, i.e. a function returning the inner product between the images of two data points in the feature space. The learning then takes place in the feature space, provided the learning algorithm can be entirely rewritten so that the data points only appear inside dot products with other data points.
Analysis of Ehrlichial p28 Gene Expression in a Murine Model of Persistent Infection (2005)

Historically, ehrlichioses were tick-borne diseases of veterinary medical importance and are now important emerging infectious diseases in humans. p28s are encoded by multigene families with ORFs tandemly arranged with intergenic spaces of variable lengths. We reported initial sequencing of the Ehrlichia muris p28 locus. A model of persistent infection was described and provided tools for study of persistent ehrlichial infection. We completed the sequence of the E. muris p28 locus and examined mRNA expression.
Isoprenoid Biosynthesis through the Methylerythritol Phosphate Pathway: The (E)-4-Hydroxy-3-methylbut-2-enyl Diphosphate Synthase (GcpE) is a [4Fe–4S] Protein (2002)

One of the last bottlenecks in the elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis has been solved. A [4Fe–4S] cluster is the prosthetic group of the GcpE protein from E. coli. This enzyme is involved in the conversion of 1 into 2, through two successive one-electron transfers.
Cuidado y curación tradicional de los animales de trabajo en la primera obra de veterinaria mexicana (1575-1579) (2008)

El libro Albeitería, escrito por el mexicano Juan Suárez de Peralta en tre 1575 y 1579, es el primero en Ciencias Veterinarias escrito en América, aunque debido a su rareza ha sido prácticamente desaprovechado por los estudiosos del cuidado animal. El ser originario de la Nueva España le proporcionó al autor, según él mismo declara, la oportunidad de acceder a las fórmulas médicas a base de plantas, tanto exóticas como nativas, conforme a la medicina indígena; aprovechar al máximo el sa ber español y árabe de un "gran albéitar gitano", en el uso de plantas y emplastos, así como el "medir el pulso" y el "curar por la orina" como parte del procedimiento de atención medica al ganado equino, además de múltiples procedimientos de medicina veterinaria tradicional hispanoárabe. En dicho texto están las bases de los cuidados utilizados por los campesinos mexicanos en la atención y curación de sus animales de trabajo, ya que éstas son herederas directas de las prácticas curativas llegadas de la península Ibérica. La identificación de los cuidados y remedios tradicionales, así como también de la farmacopea utilizada por Suárez de Peralta en los animales de trabajo es el objetivo del presente escrito.
Living histamine-containing cells from the bronchial lumens of humans. Description and comparison of histamine content with cells of rhesus monkeys. (1977)

A B
Targeting tumor angiogenesis: comparison of peptide and polymer-peptide conjugates. (2005)

Specific molecular targeting of the alpha(v)beta(3) integrin and nonspecific vascular permeability are both significant in the relative tumor localization of polymeric conjugates of RGD4C. Extravascular leak in nonspecific organs appears to be a major factor in reducing the T/B for the peptide molecules.
Evidence That Aspartic Acid 301 Is a Critical Substrate-Contact Residue in the Active Site of Cytochrome P450 2D6 (1995)

Model building studies have intimated a role for aspartic acid 301 in the substrate binding of cytochrome P450 2D6 (CYP2D6). We have tested this hypothesis by generating a range of CYP2D6 mutants substituting a variety of amino acids at this site. The mutant proteins, which included substitution with a negatively charged glutamic acid residue or neutral asparagine, alanine, or glycine residues, were expressed in Saccharomyces cerevisiae. In addition, a mutant where aspartic acid 301 was deleted was also tested. All the mutants expressed approximately equivalent amounts of recombinant apoprotein and, apart from the alanine 301 and the aspartic acid 301 deletion mutants, gave carbon monoxide difference spectra of similar magnitude to the wild type. In the cases of the alanine and deletion mutants, the amount of holoprotein was significantly reduced or absent relative to the amount of apoprotein, indicating restricted heme incorporation. The glutamic acid mutant was shown to have similar catalytic properties to the wild type enzyme toward the substrates debrisoquine and metoprolol; however, some differences in regioselectivity and ligand binding were observed. The mutants containing neutral amino acids at position 301 exhibited marked reductions in catalytic activity. At low substrate concentrations little, if any, activity toward debrisoquine and metoprolol was measured. However, at a higher substrate concentration (2 mM) some activity was observed (about 10-20% of wild type levels). Consistent with the above findings, the debrisoquine-induced spin changes in the mutant proteins were markedly reduced. These data collectively demonstrate that aspartic acid 301 plays an important role in determining the substrate specificity and activity of CYP2D6 and provide experimental evidence supporting the role of this amino acid in forming an electrostatic interaction between the basic nitrogen atom in CYP2D6 substrates and the carboxylate group of aspartic acid 301.
Conditionally Replicative Adenovirus for Prostate Cancer Therapy (2001)

Abstract : Quantitative tumor transduction represents a major limitation to the achievement of meaningful clinical results in cancer gene therapy protocols. Approaches directed towards the goal of enhancing or amplifying the effects of a genetic transduction event may further enhance the potential efficacy of cancer gene therapy strategies. One way to achieve this amplification effect would be via replication of the delivered viral vector. In this approach, a conditionally replicative competent virus would be utilized to selectively replicate within the transduced tumor cells and not in normal tissues. Adenoviral vectors possess the unique attribute with respect to the in vivo gene delivery recommending their employment as conditionally replicative vectors. It is our hypothesis that a conditionally adenovirus that would replicate selectively and specifically into tumor cells could be developed and utilized as an experimental tumor therapy modality for prostate cancer. In these initial studies, we have shown that improving the infectivity of adenoviral vectors dramatically augments the oncolytic potency of CRAD agents. The establishment of this key principal now feasibilize our original goal to improve the replicative specificity of the CRADs for carcinoma of the prostate.
Specificity of protein kinase inhibitor peptides and induction of long-term potentiation. (1994)

Previous studies have used synthetic peptide analogs, corresponding to sequences within the pseudosubstrate domain of protein kinase C (PKC) or the autoregulatory domain of Ca2+/calmodulin-dependent protein kinase II (CaMKII), in attempts to define the contribution of each of these protein kinases to induction of long-term potentiation (LTP). However, the specificity of these inhibitor peptides is not absolute. Using intracellular delivery to rat CA1 hippocampal neurons, we have determined the relative potency of two protein kinase inhibitor peptides, PKC-(19-36) and [Ala286]CaMKII-(281-302), as inhibitors of the induction of LTP. Both peptides blocked the induction of LTP; however, PKC-(19-36) was 30-fold more potent than [Ala286]CaMKII-(281-302). The relative specificity of PKC-(19-36), [Ala286]CaMKII-(281-302), and several other CaMKII peptide analogs for protein kinase inhibition in vitro was also determined. A comparison of the potencies of PKC-(19-36) and [Ala286]CaMKII-(281-302) in the physiological assay with their Ki values for protein kinase inhibition in vitro indicates that the blockade of induction of LTP observed for each peptide is attributable to inhibition of PKC.
Phosphinimide complexes with pendant hemilabile donors: synthesis, structure and ethylene polymerization activity (2009)

The phosphines tBu(2)P(CH(2))(3)ECH(2)Ph (E = O (1), S (2)) converted to the corresponding phosphinimines (Me(3)SiN)PtBu(2)(CH(2))(3)ECH(2)Ph, E = O (3), S (4)) which were used to prepared the titanium complexes Cp'TiCl(2)NPtBu(2)(CH(2))(3)ECH(2)Ph, (E = O, Cp' = Cp (5), Cp* (6); E = S, Cp' = Cp (7), Cp* (8)). These species were subsequently methylated to the corresponding dimethyl-derivatives (9)-(12). Activation of (9)-(12) with both B(C(6)F(5))(3) and [Ph(3)C][B(C(6)F(5))(4)] was studied. For example, the [CpTiMe(NPtBu(2)(CH(2))(3)OCH(2)Ph)][MeB(C(6)F(5))(3)] (13) reacted with THF to give [CpTiMe(THF)(NPtBu(2)(CH(2))(3)OCH(2)Ph)][MeB(C(6)F(5))(3)] (14). Similar reactions gave the stable ion pairs [Cp'TiMe(NPtBu(2)(CH(2))(3)XCH(2)Ph)][MeB(C(6)F(5))(3)] (X = O, Cp' = Cp*, (15); X = S Cp' = Cp, (16), Cp*(17)) and [Cp'TiMe(NPtBu(2)(CH(2))(3)XCH(2)Ph)][B(C(6)F(5))(4)] (X = O, Cp' = Cp, (18); Cp*(19); X = S, Cp' = Cp, (20), Cp* (21)). The dihalide complexes (5)-(8), activated with MAO, proved to be ethylene polymerization catalysts of moderate activities. The dialkyl titanium complexes (9)-(12) activated with B(C(6)F(5))(3) or [Ph(3)C][B(C(6)F(5))(4)], gave catalysts that exhibited substantially higher activity and high molecular weight polyethylene. Polymerization at 60 degrees C rather than 30 degrees C significantly increased activity as well. The impact of the hemilabile donor with respect to catalyst activity is discussed. Crystallographic studies of (5) and (6) are reported.
Recent Segmental Duplications in the Human Genome (2002)

Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.
Cutaneous melanoma and intervention strategies to reduce tumor-related mortality: what we know, what we don't know, and what we think we know that isn't so (2006)

The care of patients who have cutaneous melanoma (CM) has undergone a dramatic change during the past five decades. In an increasing majority of cases, CM is being discovered in a premetastatic phase of tumor progression. Most patients are being treated in the ambulatory setting with a minimum of inconvenience and economic cost, and modest re-excision margins have largely replaced the mutilating surgical exonerations that were once standard only four decades ago. Histopathologic assessment of the primary tumor is the most widely used staging procedure to determine who is most likely to develop metastatic disease. For patients who develop distant metastases, there is no therapy currently available, based on large-scale randomized trials, that will prolong patient survival. Therefore, establishing an early diagnosis in a premetastatic phase of tumor development must be the overriding goal of any intervention strategy that seeks to reduce CM-related mortality. Unfortunately, as a result of public messages that emphasize the role of ultraviolet radiation (UVR) exposure in tumor development, most general physicians and lay people believe that most if not all cases of CM are the direct result of UVR exposure. In fact, we do not know the case fraction of CM directly attributable to UVR, and the unintended consequences of current messages directly linking UVR exposure and CM development may be thwarting the primary intervention goal of reducing tumor-related mortality. More likely to have an immediate positive impact on CM-related mortality are public messages that encourage skin awareness and self-examination by patients, total skin screening examinations by physicians during routine care, and periodic lifetime surveillance of patients determined to have a high CM risk based on identifiable historic and phenotypic traits.
Systematic design of unitary space-time constellations (2000)

We propose a systematic method for creating constellations of unitary space-time signals for multiple-antenna communication links. Unitary space-time signals, which are orthonormal in time across the antennas, have been shown to be well-tailored to a Rayleigh fading channel where neither the transmitter nor the receiver knows the fading coefficients. The signals can achieve low probability of error by exploiting multiple-antenna diversity. Because the fading coefficients are not known, the criterion for creating and evaluating the constellation is nonstandard and differs markedly from the familiar maximum-Euclidean-distance norm. Our construction begins with the first signal in the constellation-an oblong complex-valued matrix whose columns are orthonormal-and systematically produces the remaining signals by successively rotating this signal in a high-dimensional complex space. This construction easily produces large constellations of high-dimensional signals. We demonstrate its efficacy through examples involving one, two, and three transmitter antennas.
Using polymer blends to fine-tune binder performance (1996)

The glass transition temperature (T{sub g}) of polymeric binders strongly affects ease of forming and mechanical properties of green ceramic parts. The T{sub g} of commercially available binders spans a wide range of temperatures, but the ideal T{sub g} for an application may not be readily available. In this study we demonstrate how blending of polymers with different T{sub g}s can be used to fine tune binder performance in dry pressing and tape casting.