gebhart/patrepeval huggingface dataset:
Investigations of the Transport Properties of Gold Nanotubule Membranes (2001)

We have developed a new class of synthetic membranes that consist of a porous polymeric support that contains an ensemble of gold nanotubules that span the complete thickness of the support membrane. The support is a commercially available microporous polycarbonate filter with cylindrical nanoscopic pores. The gold nanotubules are prepared via electroless deposition of Au onto the pore walls; i.e., the pores acts as templates for the nanotubules. We have shown that by controlling the Au deposition time, Au nanotubules that have effective inside diameters of molecular dimensions (<1 nm) can be prepared. Hence, these membranes are a new class of molecular sieves. In addition, because these membranes are composed of an electronically conductive material, excess charge can be applied to the tubules by electrochemical charging in an electrolyte solution. We have shown that this allows for control of ion-transport selectivity in these membranes. Finally, because the tubules are composed of gold, well-known Au-thiol chemistry can be used to change the chemical environment within the tubules. Via this route chemical transport selectivity can be introduced into these membranes. This paper reviews progress on size-based, charge-based, and chemical-interaction-based transport selectivity in this new class of membranes.
Shapes of polyhedra and triangulations of the sphere (1998)

The space of shapes of a polyhedron with given total angles less than 2π at each of its n vertices has a Kähler metric, locally isometric to complex hyperbolic space CH n-3 .The metric is not complete: collisions between vertices take place a finite distance from a nonsingular point.The metric completion is a complex hyperbolic cone-manifold.In some interesting special cases, the metric completion is an orbifold.The concrete description of these spaces of shapes gives information about the combinatorial classification of triangulations of the sphere with no more than 6 triangles at a vertex.
Radiosynthesis of N<sup>5</sup>‐[<sup>18</sup>F]fluoroacetylornithine (N<sup>5</sup>‐[<sup>18</sup>F]FAO) for PET imaging of ornithine decarboxylase (ODC) in malignant tumors (2010)

Abstract Polyamines are naturally occurring polycations derived from amino acids via decarboxylation by ornithine decarboxylase (ODC). Ornithine is a substrate for ODC; decarboxylation of ornithine is inhibited by difluoromethylornithine (DFMO) and its derivatives. Polyamine contents are increased in many epithelial cancers, including breast cancer, melanoma, and prostate cancer. In order to image and measure the levels of ODC expression in malignant tumors, we have synthesized a derivative of ornithine, N 5 ‐[ 18 F]fluoroacetylornithine (N 5 ‐[ 18 F]FAO), for use in positron emission tomography. The precursor compound N 2 ‐Boc‐N 5 ‐bromoacetylornithine‐ t ‐butyl ester 2 was synthesized from 5‐amino‐2‐( tert ‐butoxycarbonylamino)pentanoic acid, which was reacted with bromoacetyl chloride followed by esterification with tert ‐butyl‐2,2,2‐trichloroacetamidate. Fluorination of the precursor produced a fluoro‐derivative, which was hydrolyzed in acid to obtain the desired compound, N 5 ‐fluoroacetylornithine. The radiosynthesis of N 5 ‐[ 18 F]FAO was accomplished by radiofluorination of 2 with n ‐Bu 4 N[ 18 F], followed by high‐performance liquid chromatography (HPLC) purification and then by acid hydrolysis. The radiochemical yield was 6–10% (decay corrected) with an average of 8% ( n =10) at the end of synthesis. The radiochemical purity was >99%, and specific activity was >1500 mCi/µmol. The synthesis time was 95–100 min from the end of bombardment. Copyright © 2010 John Wiley & Sons, Ltd.
Evidence for apoptosis signal-regulating kinase 1 in the regenerating palatal epithelium upon acute injury. (1998)

Apoptosis signal-regulating kinase 1 (ASK1), a recently identified mitogen-activated protein (MAP) kinase kinase kinase, is a key element in the mechanism of stress- and cytokine-induced apoptosis. However, pathophysiologic roles of ASK1 in vivo are poorly understood. In the present study, we analyzed the ASK1 expression in injured rat palate using an immunohistochemical approach to investigate the roles of ASK1 during the process of wound healing. In the normal rat palatal epithelium, a weak cytoplasmic staining of ASK1 was observed in keratinocytes of the prickle cell layer. After mucoperiosteal injury of the palate, ASK1 was clearly observed in the suprabasal keratinocytes surrounding the wound. ASK1 expression was most evident at Day 2 after injury in the edge of the migrating epithelium. Thereafter, the intensity of ASK1 staining decreased gradually until the re-epithelialization was completed at Day 10 to 14. A staining with the terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end-labeling method identified a number of apoptotic keratinocytes in the suprabasal layers at the healing edge. Active induction of epithelial apoptosis was readily detectable from Day 5 after injury. In double-staining analysis, the temporal and spatial pattern of ASK1 expression correlated well with the appearance of apoptotic keratinocytes. p38 MAP kinase, a downstream component of ASK1, was found to be activated at the sites of ASK1 expression, suggesting that increased expression of ASK1 leads to activation of downstream MAP kinase signaling pathway in vivo. These results suggest a significant contribution of ASK1 to the epithelial apoptosis in the process of mucoepithelial wound repair.
Modulation of energy deficiency in Huntington's disease via activation of the peroxisome proliferator-activated receptor gamma (2010)

Huntington's disease (HD) is a neurodegenerative disease caused by the expansion of a CAG trinucleotide repeat in exon 1 of the huntingtin (HTT) gene. Here, we report that the transcript of the peroxisome proliferator-activated receptor-γ (PPARγ), a transcription factor that is critical for energy homeostasis, was markedly downregulated in multiple tissues of a mouse model (R6/2) of HD and in lymphocytes of HD patients. Therefore, downregulation of PPARγ seems to be a pathomechanism of HD. Chronic treatment of R6/2 mice with an agonist of PPARγ (thiazolidinedione, TZD) rescued progressive weight loss, motor deterioration, formation of mutant Htt aggregates, jeopardized global ubiquitination profiles, reduced expression of two neuroprotective proteins (brain-derived neurotrophic factor and Bcl-2) and shortened life span exhibited by these mice. By reducing HTT aggregates and, thus, ameliorating the recruitment of PPARγ into HTT aggregates, chronic TZD treatment also elevated the availability of the PPARγ protein and subsequently normalized the expression of two of its downstream genes (the glucose transporter type 4 and PPARγ coactivator-1 alpha genes). The protective effects described above appear to have been exerted, at least partially, via direct activation of PPARγ in the brain, as TZD was detected in the brains of mice treated with TZD and because a PPARγ agonist (rosiglitazone) protected striatal cells from mHTT-evoked energy deficiency and toxicity. We demonstrated that the systematic downregulation of PPARγ seems to play a critical role in the dysregulation of energy homeostasis observed in HD, and that PPARγ is a potential therapeutic target for this disease.
Blockage and directivity in 60 GHz wireless personal area networks: from cross-layer model to multihop MAC design (2009)

We present a cross-layer modeling and design approach for multiGigabit indoor wireless personal area networks (WPANs) utilizing the unlicensed millimeter (mm) wave spectrum in the 60 GHz band. Our approach accounts for the following two characteristics that sharply distinguish mm wave networking from that at lower carrier frequencies. First, mm wave links are inherently directional: directivity is required to overcome the higher path loss at smaller wavelengths, and it is feasible with compact, low-cost circuit board antenna arrays. Second, indoor mm wave links are highly susceptible to blockage because of the limited ability to diffract around obstacles such as the human body and furniture. We develop a diffraction-based model to determine network link connectivity as a function of the locations of stationary and moving obstacles. For a centralized WPAN controlled by an access point, it is shown that multihop communication, with the introduction of a small number of relay nodes, is effective in maintaining network connectivity in scenarios where single-hop communication would suffer unacceptable outages. The proposed multihop MAC protocol accounts for the fact that every link in the WPAN is highly directional, and is shown, using packet level simulations, to maintain high network utilization with low overhead.
Characterization of the Lactococcus lactis Nisin A Operon Genes nisP, Encoding a Subtilisin-Like Serine Protease Involved in Precursor Processing, and nisR, Encoding a Regulatory Protein Involved in Nisin Biosynthesis (1993)

Biosynthesis of the lantibiotic peptide nisin by Lactococcus lactis NIZO R5 relies on the presence of the conjugative transposon Tn5276 in the chromosome. A 12-kb DNA fragment of Tn5276 including the nisA gene and about 10 kb of downstream DNA was cloned in L. lactis, resulting in the production of an extracellular nisin precursor peptide. This peptide reacted with antibodies against either nisin A or the synthetic leader peptide, suggesting that it consisted of a fully modified nisin with the nisin leader sequence still attached to it. This structure was confirmed by N-terminal sequencing and 1H-nuclear magnetic resonance analysis of the purified peptide. Deletion studies showed that the nisR gene is essential for the production of this intermediate. The deduced amino acid sequence of the nisR gene product indicated that the protein belongs to the family of two-component regulators. The deduced amino acid sequence of NisP, the putative product of the gene upstream of nisR, showed an N-terminal signal sequence, a catalytic domain with a high degree of similarity to those of subtilisin-like serine proteases, and a putative C-terminal membrane anchor. Cell extracts of Escherichia coli overexpressing nisP were able to cleave the nisin precursor peptide, producing active, mature nisin. A similar activation was obtained with whole cells but not with membrane-free extracts of L. lactis strains carrying Tn5276 in which the nisA gene had been inactivated. The results indicate that the penultimate step in nisin biosynthesis is secretion of precursor nisin without cleavage of the leader peptide, whereas the last step is the cleavage of the leader peptide sequence from the fully maturated nisin peptide.
Reproduction of Arbitrary Multipath Environments in Laboratory Conditions (2010)

We discuss the synthesis of arbitrary multipath environments in a spherical volume of space (test zone), with a limited number of feed antennas (probes). The probes can be of any type, e.g., simple dipoles. The required number of probes is proportional to the area of the sphere enclosing the test zone. The signal received by a two-port mobile terminal antenna model placed in the test zone is examined through simulations, using measured real-world propagation channel data. We study how the received signal and the channel capacity are affected by truncation errors and a certain noise level in the probe excitations. This kind of synthesis enables the testing of mobile terminals under realistic operating conditions in laboratory environments. The synthesis is not limited to far-field scenarios, but near-field effects can be generated as well.
The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world (2009)

Biotechnology has empirically established that it is easier to construct and evaluate variant genes and proteins than to account for the emergence and function of wild-type macromolecules. Systematizing this constructive approach, synthetic biology now promises to infer and assemble entirely novel genomes, cells and ecosystems. It is argued here that the theoretical and computational tools needed for this endeavor are missing altogether. However, such tools may not be required for diversifying organisms at the basic level of their chemical constitution by adding, substituting or removing elements and molecular components through directed evolution under selection. Most importantly, chemical diversification of life forms could be designed to block metabolic cross-feed and genetic cross-talk between synthetic and wild species and hence protect natural habitats and human health through novel types of containment.
Sarcosine Oxidase Contains a Novel Covalently Bound FMN (1996)

Sarcosine oxidase from Corynebacterium sp. P-1 is a heterotetrameric protein containing three different coenzymes: noncovalent FAD, noncovalent NAD+, and a covalently bound flavin which is released as 8α-(N 3-histidyl)riboflavin upon complete hydrolysis of the protein. The following results show that the covalent flavin is not at the FAD level, as previously proposed, but is rather an 8α-(N 3-histidyl)FMN coenzyme. First, no AMP is released when the protein moiety is treated with phosphodiesterase or subjected to mild acid hydrolysis. The enzyme contains a total of 5 mol of phosphate. Only one phosphate is covalently bound. The other four phosphates are noncovalent and attributed to noncovalently bound FAD and NAD+. The 31P NMR spectrum of native enzyme exhibits resonances due to a single phosphate monoester and two pyrophosphates. Only a resonance due to phosphate monoester is observed after removal of the noncovalent cofactors and proteolytic digestion of the protein moiety. The 8α-(N 3-histidyl)FMN found in corynebacterial sarcosine oxidase represents a novel type of covalent flavin. Studies with sarcosine oxidases from Arthrobacter sp. and Pseudomonas sp. show that these heterotetrameric enzymes also contain covalently bound FMN plus noncovalently bound FAD and NAD+, similar to corynebacterial sarcosine oxidase. In contrast, two monomeric sarcosine oxidases (from Bacillus sp. and an unidentified microorganism) were found to contain only covalently bound FAD.
Reaction pattern of human anti-Mycoplasma pneumoniae antibodies in enzyme-linked immunosorbent assays and immunoblotting (1986)

In serological diagnosis of Mycoplasma pneumoniae disease the frequently used complement fixation test is based on a cross-reacting glycolipid. Recently enzyme-linked immunoassays have been developed to overcome this lack of specificity. To study the involvement of the various proteins and the influence of age on the level of antiprotein antibodies present, we investigated by enzyme-linked immunoassays (immunoglobulin M [IgM] and IgG) and immunoblotting the sera of healthy persons of different age groups as well as sera of patients (including paired sera) with M. pneumoniae infection. In sera of children with nonrespiratory diseases and in healthy blood donors the IgM antibodies rose during the first 2 years of life to a relatively constant background level (optical density at 405 nm of 0.15 to 0.21). In contrast IgG remained low up to the seventh year and then increased to moderate levels (optical density of 0.15). The blotting patterns showed few IgM bands in the age group of 20 to 30 years. IgG blots revealed, up to 7 years, only very few reactions with a 168-kilodalton protein, but in higher age groups a considerable number of reactions with proteins of 193, 168, 84, 69, and 56 kilodaltons were detected. In the sera of patients, positive IgM blots were most numerous in the third week, whereas the number of IgG blots increased up to the fourth and the fifth week. At this time all sera contained antibodies against the 168-kilodalton protein, which is identical with the adhesin of M. pneumoniae. In a patient with acute infection, who had a high preinfection IgG level, no IgM response developed. The data indicate a relatively high background of antibodies against M. pneumoniae proteins in older age groups, suggesting a requirement for paired sera. Furthermore, reinfections of adults may occur without a concomitant IgM response.
The Hydrostatic Gas Journal Bearing With Journal Rotation and Vibration (1964)

This paper analyzes the load-carrying capacity of the externally pressurized gas journal bearing, including the effect of journal rotation and vibration. The analysis assumes small eccentricity ratio and small vibration amplitude such that a first-order perturbation solution is obtained. The gas is fed to the bearing through orifice-restricted feeding holes around the circumference in one or two feeding planes. The number of feeding holes is sufficiently large to permit treating the feeding planes as line sources. Results are given for the load-carrying capacity and the attitude angle.
Molecular identification of an MHC-independent ligand recognized by a human α/β T-cell receptor (2011)

During an analysis of T-cell responses against human renal cell carcinoma (RCC), we identified a CD4(+) T-cell line that showed TCR-mediated recognition and lysis of nearly all RCC lines regardless of MHC type. We have now elucidated the nature of the ligand for this α/β TCR, and it contains no MHC-related moiety and does not involve classic peptide processing. First, matrix metalloproteinase 14 (MMP14) expressed on RCC cells releases membrane-bound TRAIL expressed by the T cell; then, soluble TRAIL binds to its receptor DR4 (TRAIL-R1), which is expressed on tumor cells, and this TRAIL-DR4 complex is recognized by the TCR through a complementarity-determining region 3α (CDR3α)-mediated interaction. Direct and specific antigen-TCR interaction was demonstrated when the immobilized recombinant TRAIL/DR4 complex stimulated the TCR. In addition, amino acid substitutions in the CDR3α of the TCR either obliterated or enhanced target-specific recognition. This description of the molecular nature of a non-MHC target structure recognized by a naturally occurring α/β TCR not only broadens our concept of what the TCR can recognize, but also raises the question of whether such a T cell could be of clinical utility against RCC.
Natural demodulation of two-dimensional fringe patterns I General background of the spiral phase quadrature transform (2001)

It is widely believed, in the areas of optics, image analysis, and visual perception, that the Hilbert transform does not extend naturally and isotropically beyond one dimension. In some areas of image analysis, this belief has restricted the application of the analytic signal concept to multiple dimensions. We show that, contrary to this view, there is a natural, isotropic, and elegant extension. We develop a novel two-dimensional transform in terms of two multiplicative operators: a spiral phase spectral (Fourier) operator and an orientational phase spatial operator. Combining the two operators results in a meaningful two-dimensional quadrature (or Hilbert) transform. The new transform is applied to the problem of closed fringe pattern demodulation in two dimensions, resulting in a direct solution. The new transform has connections with the Riesz transform of classical harmonic analysis. We consider these connections, as well as others such as the propagation of optical phase singularities and the reconstruction of geomagnetic fields.
Expression of Human Glucocerebrosidase in Long-Term Reconstituted Mice Following Retroviral-Mediated Gene Transfer into Hematopoietic Stem Cells (1990)

A retroviral vector (GTN) in which the glucocerebrosidase (GCase) cDNA is driven by the Moloney murine leukemia virus (Mo-MuLV) long terminal repeat (LTR) was tested for transfer efficiency and expression of the GCase gene in long-term reconstituted mice. Eleven W/Wv mice were transplanted with unselected GTN-infected bone marrow cells and 10 of these mice were analyzed 3 months later. Seven of these 10 mice (70%) contained the intact proviral genome in bone marrow, spleen, and thymus. Of these 7,3 mice contained a high-copy number of the provirus in all the hematopoietic tissues tested. The mice contained anywhere from one to four proviral integration sites that were the same in all three tissues, indicating that these mice have been repopulated by one or more transduced multipotential hematopoietic stem cells. Five months after transplantation, bone marrow from the eleventh mouse was transplanted into secondary recipient animals. The secondary recipients contained the intact proviral genome in the bone marrow, spleen, thymus, and macrophages 4 months after the secondary transplantation. This further supports the conclusion that hematopoietic stem cells have indeed been targeted. Human GCase RNA was detected in all 7 mice containing the proviral DNA. These results demonstrate expression of the human GCase gene in the progeny of repopulating hematopoietic stem cells of mice following gene transfer.
Using risk calculation to implement an extended relative pair analysis (1994)

A new nonparametric method of linkage analysis is described based on identity by descent relationships between all pairs of affected relatives within a pedigree. This approach is an extension of ESPA, which only uses information from pairs of affected siblings. The new method, called ERPA, uses the risk calculation facilities of the LINKAGE programs to obtain the necessary information in a fashion which is simple to implement and which automatically generalizes to allow for marker loci which may be multiple, non-codominant and sex-linked. We have investigated the relative performance of ERPA, ESPA and the lod score method on simulated data. ERPA appears to be more sensitive than ESPA for detecting linkage in pedigrees with small sibships, though both nonparametric methods are inferior to the lod score method when the true mode of transmission can be specified.
Antioxidant capacity of different types of tea products (2007)

In the present study, twelve different types of commercial tea samples were assayed to determine their phenolic composition and antioxidant activity. Reverse phase high performance liquid chromatography using a binary gradient system was used for the identification and quantification of individual catechins. Subsequently, total phenolic content was determined spectrophotometrically according to the Folin-ciocalteus method. Total theaflavins and thearubigins were also determined. The radical scavenging behavior of the polyphenols on 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) was also studied spectrophotometrically. The results showed that total polyphenols, total catechins and antioxi-dant activity were significantly (P<0.05) different in the commercial tea samples. Green tea had the highest levels of catechins, total polyphenols and total antioxidant activity. White tea (silvery tip) a rare specialty type of tea was not significantly different from green tea. Statistical analysis showed an essential catechin content influence of the tea extracts on antioxidant activity. Epigallocatechin gallate (EGCG) was the most potent catechin and the most potent in antioxidant activity (r = 0.989***). Epigallo-catechin (EGC) (r = 0.787, P<0.001), epicatechin (EC) + catechin (+C) and epicatechigallate (ECG) also showed significant (P<0.05) antioxidant activity. Black tea contained high levels of theaflavins and thearubigins, which accounted for most of the antioxidant potential in this type of tea product (r = 0.930*** and r = 0.930*** respectively). These results suggest that conversion of catechins during black tea processing did not affect the free-radical potency of black tea. Gallic acid (GA) also showed significant(r = 0.530*) contribution to the antioxidant activity in black tea. Green, black and white tea products processed from Kenyan tea cultivars originally selected for black tea had significantly (P<0.05) higher antioxidant activity than green tea processed from tea cultivars from Japan and China. These results seem to suggest that the cultivar type is critical in determining the antioxidant potency of tea product and that black teas processed from suitable cultivars could be potent in antioxidant activity when compared to green teas.    Key words: Antioxidant capacity, DPPH, catechins, polyphenols, EGCG, theaflavins.