gebhart/patrepeval huggingface dataset:
Water adsorption in MOFs: fundamentals and applications (2014)

This review article presents the fundamental and practical aspects of water adsorption in Metal-Organic Frameworks (MOFs). The state of the art of MOF stability in water, a crucial issue to many applications in which MOFs are promising candidates, is discussed here. Stability in both gaseous (such as humid gases) and aqueous media is considered. By considering a non-exhaustive yet representative set of MOFs, the different mechanisms of water adsorption in this class of materials are presented: reversible and continuous pore filling, irreversible and discontinuous pore filling through capillary condensation, and irreversibility arising from the flexibility and possible structural modifications of the host material. Water adsorption properties of more than 60 MOF samples are reported. The applications of MOFs as materials for heat-pumps and adsorbent-based chillers and proton conductors are also reviewed. Some directions for future work are suggested as concluding remarks.
Achromatic quarter-wave plates using the dispersion of form birefringence (1997)

We propose achromatic quarter-wave plates of a subwavelength grating structure. When the period of the grating structure is smaller than the wavelengths of the incident light, the structure is considered to be an optically anisotropic medium. The effective refractive indices strongly depend on the wavelengths, especially when the period is close to the wavelength. Using this feature, we can design a grating quarter-wave plate whose phase retardation is maintained at pi/2 for a wide wavelength range. A design method using the effective medium theory is described, and the wave plates designed were evaluated by numerical calculation with a rigorous electromagnetic grating theory. The calculation results led to the possibility of an achromatic quarter-wave plate whose retardation errors are smaller than 3 degrees for a +/-10% change in wavelength.
Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cells. (1990)

To avoid the mutagenic effect of spontaneous hydrolytic deamination of 5-methylcytosine, G.T mispairs, arising in DNA as a result of this process, should always be corrected to G.C pairs. We describe here the identification of a DNA glycosylase activity present in nuclear extracts from HeLa cells, which removes the mispaired thymine to generate an apyrimidinic (AP) site opposite the guanine. We further show, using a specific antibody and inhibitors, that the single nucleotide gap, created upon processing of the AP site, is filled in by DNA polymerase beta. This finding substantiates the proposed role of this enzyme in short-patch DNA repair.
Transformation in vitro of a nontumorigenic rat urothelial cell line by hydrogen peroxide. (1996)

Chronic infection/inflammation of the urinary tract is a significant risk factor for the development of bladder cancer. The present study examined the hypothesis that hydrogen peroxide (H202) and cytokines released during inflammation are involved in the enhancement of bladder carcinogenesis. Using growth in soft agar and tumorigenicity in athymic nude mice as indices of transformation, we examined the effect of H202 and cytokines on the enhancement of N-methyl-N-nitrosourea (MNU)-initiated transformation of MYP3 cells, an anchorage-dependent nontumorigenic rat bladder epithelial cell line. MYP3 cells pretreated with or without MNU were exposed to H202 (0.001 to 0.1 mM) daily for 1 week in monolayer culture and were then tested for growth in soft agar. A marked increase in colony numbers was observed in the cells that were MNU-initiated and exposed to H202 (P < 0.01). Furthermore, H202 exposure alone at 0.01 mM or 0.1 mM caused colony formation in soft agar. The transformants induced by MNU plus H202 or H202 alone formed high-grade transitional cell carcinomas when injected into nude mice. The growth of these transformants was stimulated by several cytokines (interleukin 1alpha, interleukin 6, and tumor necrosis factor-alpha) better than the parental cells both on a plastic surface and in soft agar. Our results indicate that H202 causes genetic change(s) to induce tumorigenic conversion in urothelial cells and that the transformants are stimulated to grow because of their selective response to several cytokines. We suggest that these mechanisms may be involved in the in vivo carcinogenesis associated with chronic urinary tract infection.
Specific inhibition of c- myc protein biosynthesis using an antisense synthetic deoxy-oligonucleotide in human T lymphocytes. (1988)

C-myc protein expression in human T cells was specifically inhibited by a 15-mer deoxy-oligonucleotide complementary to the 5' end of the human c-myc gene second exon. The oligonucleotide penetrates the cells without any treatment, with a plateau of cell association reached in 2 h. The oligonucleotide specifically blocked the de novo synthesis of c-myc protein, induced by PHA in human resting peripheral T cells, without impairing the overall synthesis of other proteins, as shown by two-dimensional analysis of [35S]methionine pulse-labeled proteins. The specific inhibition of c-myc protein synthesis prevented the entry into S phase of resting T cells, induced to proliferate by PHA, or IL-2-dependent T cells induced by IL-2, as shown by [3H]thymidine incorporation. The inhibition of proliferation was specific since it was not observed with the corresponding sense-oligonucleotide and was reversed by preincubation of the cells with an excess of sense oligonucleotide. These results clearly support a role for c-myc protein in the proliferation process and show that inducible protein expression can be blocked by means of synthetic oligonucleotides complementary to a coding exon.
Shading-based dynamic shape refinement from multi-view video under general illumination (2011)

We present an approach to add true fine-scale spatio-temporal shape detail to dynamic scene geometry captured from multi-view video footage. Our approach exploits shading information to recover the millimeter-scale surface structure, but in contrast to related approaches succeeds under general unconstrained lighting conditions. Our method starts off from a set of multi-view video frames and an initial series of reconstructed coarse 3D meshes that lack any surface detail. In a spatio-temporal maximum a posteriori probability (MAP) inference framework, our approach first estimates the incident illumination and the spatially-varying albedo map on the mesh surface for every time instant. Thereafter, albedo and illumination are used to estimate the true geometric detail visible in the images and add it to the coarse reconstructions. The MAP framework uses weak temporal priors on lighting, albedo and geometry which improve reconstruction quality yet allow for temporal variations in the data.
Characteristics of multiwalled carbon nanotube nanobridges fabricated by poly(methylmethacrylate) suspended dispersion (2002)

We report on the transport characteristics of individual multiwalled carbon nanotube/nanofibers (MWCNTs) grown by plasma-enhanced chemical vapor deposition (PECVD). The measurements were performed on individual MWCNT nanobridges suspended by sputtered Nb contacts. Temperature dependent measurements of conductance revealed that the conductance is dominated by a contribution from thermally activated carriers. High-field measurements show that the PECVD grown MWCNTs are able to carry high current densities (∼108 A/cm2) and after reaching a critical limit, break down in segments of nanotube shells while still being electrically stable. The high-density current transport and reliability make PECVD grown MWCNTs good candidates for applications as field emission cathodes and nanoelectronic interconnects.
Mapping the Prion Protein Using Recombinant Antibodies (1998)

The fundamental event in prion disease is thought to be the posttranslational conversion of the cellular prion protein (PrPC) into a pathogenic isoform (PrPSc). The occurrence of PrPC on the cell surface and PrPSc in amyloid plaques in situ or in aggregates following purification complicates the study of the molecular events that underlie the disease process. Monoclonal antibodies are highly sensitive probes of protein conformation which can be used under these conditions. Here, we report the rescue of a diverse panel of 19 PrP-specific recombinant monoclonal antibodies from phage display libraries prepared from PrP deficient (Prnp0/0) mice immunized with infectious prions either in the form of rods or PrP 27-30 dispersed into liposomes. The antibodies recognize a number of distinct linear and discontinuous epitopes that are presented to a varying degree on different PrP preparations. The epitope reactivity of the recombinant PrP(90-231) molecule was almost indistinguishable from that of PrPC on the cell surface, validating the importance of detailed structural studies on the recombinant molecule. Only one epitope region at the C terminus of PrP was well presented on both PrPC and PrPSc, while epitopes associated with most of the antibodies in the panel were present on PrPC but absent from PrPSc.
Studies on transfer ribonucleic acids and related compounds. XLI. Synthesis of tRNA fragments containing modified nucleosides. (1983)

tRNA fragments containing modified nucleosides have been synthesized either by condensation of nucleotides containing a modified base or by modification of oligonucleotides. Ribothymidine 3'-phosphate was prepared by condensation of the silylated base with protected D-ribose followed by phosphorylation. Ribothymidine-containing trimer, T-Ψ-C, was synthesized by the phosphodiester method. A ribothymidine-containing hexamer T-U-C-A-A-A and a 2'-O-methylcytidine containing hexamer C-G-G-G-Cm-Up were synthesized by the phosphotriester method. A dihydrouridine-containing trimer D-A-G and a 7-methylguanosine-containing trimer m7G-U-C were obtained by modification of the trimers by reduction and methylation, respectively.
Conformational Memories and the Endocannabinoid Binding Site at the Cannabinoid CB1 Receptor (2002)

Endocannabinoid stucture-activity relationships (SAR) indicate that the CB1 receptor recognizes ethanolamides whose fatty acid acyl chains have 20 or 22 carbons, with at least three homoallylic double bonds and saturation in at least the last five carbons of the acyl chain. To probe the molecular basis for these acyl chain requirements, the method of conformational memories (CM) was used to study the conformations available to an n-6 series of ethanolamide fatty acid acyl chain congeners: 22:4, n-6 (K(i) = 34.4 +/- 3.2 nM); 20:4, n-6 (K(i) = 39.2 +/- 5.7 nM); 20:3, n-6 (K(i) = 53.4 +/- 5.5 nM); and 20:2, n-6 (K(i) > 1500 nM). CM studies indicated that each analogue could form both extended and U/J-shaped families of conformers. However, for the low affinity 20:2, n-6 ethanolamide, the higher populated family was the extended conformer family, while for the other analogues in the series, the U/J-shaped family had the higher population. In addition, the 20:2, n-6 ethanolamide U-shaped family was not as tightly curved as were those of the other analogues studied. To quantitate this variation in curvature, the radius of curvature (in the C-3 to C-17 region) of each member of each U/J-shaped family was measured. The average radii of curvature (with their 95% confidence intervals) were found to be 5.8 A (5.3-6.2) for 20:2, n-6; 4.4 A (4.1-4.7) for 20:3, n-6; 4.0 A (3.7-4.2) for 20:4, n-6; and 4.0 A (3.6-4.5) for 22:4, n-6. These results suggest that higher CB1 affinity is associated with endocannabinoids that can form tightly curved structures. Endocannabinoid SAR also indicate that the CB1 receptor does not tolerate large endocannabinoid headgroups; however, it does recognize both polar and nonpolar moieties in the headgroup region. To identify a headgroup orientation that results in high CB1 affinity, a series of dimethyl anandamide analogues (R)-N-(1-methyl-2-hydroxyethyl)-2-(R)-methyl-arachidonamide (K(i) = 7.42 +/- 0.86 nM), (R)-N-(1-methyl-2-hydroxyethyl)-2-(S)-methyl-arachidonamide (K(i) = 185 +/- 12 nM), (S)-N-(1-methyl-2-hydroxyethyl)-2-(S)-methyl-arachidonamide (K(i) = 389 +/- 72 nM), and (S)-N-(1-methyl-2-hydroxyethyl)-2-(R)-methyl-arachidonamide (K(i) = 233 +/- 69 nM) were then studied using CM and computer receptor docking studies in an active state (R) model of CB1. These studies suggested that the high CB1 affinity of the R,R stereoisomer is due to the ability of the headgroup to form an intramolecular hydrogen bond between the carboxamide oxygen and the headgroup hydroxyl that orients the C2 and C1' methyl groups to have hydrophobic interactions with valine 3.32(196), while the carboxamide oxygen forms a hydrogen bond with lysine 3.28(192) at CB1. In this position in the CB1 binding pocket, the acyl chain has hydrophobic and C-H.pi interactions with residues in the transmembrane helix (TMH) 2-3-7 region. Taken together, the studies reported here suggest that anandamide and its congeners adopt tightly curved U/J-shaped conformations at CB1 and suggest that the TMH 2-3-7 region is the endocannabinoid binding region at CB1.
VEGF165b, an Inhibitory Vascular Endothelial Growth Factor Splice Variant (2004)

Growth of new blood vessels (angiogenesis), required for all tumor growth, is stimulated by the expression of vascular endothelial growth factor (VEGF). VEGF is up-regulated in all known solid tumors but also in atherosclerosis, diabetic retinopathy, arthritis, and many other conditions. Conventional VEGF isoforms have been universally described as proangiogenic cytokines. Here, we show that an endogenous splice variant, VEGF(165)b, is expressed as protein in normal cells and tissues and is circulating in human plasma. We also present evidence for a sister family of presumably inhibitory splice variants. Moreover, these isoforms are down-regulated in prostate cancer. We also show that VEGF(165)b binds VEGF receptor 2 with the same affinity as VEGF(165) but does not activate it or stimulate downstream signaling pathways. Moreover, it prevents VEGF(165)-mediated VEGF receptor 2 phosphorylation and signaling in cultured cells. Furthermore, we show, with two different in vivo angiogenesis models, that VEGF(165)b is not angiogenic and that it inhibits VEGF(165)-mediated angiogenesis in rabbit cornea and rat mesentery. Finally, we show that VEGF(165)b expressing tumors grow significantly more slowly than VEGF(165)-expressing tumors, indicating that a switch in splicing from VEGF(165) to VEGF(165)b can inhibit tumor growth. These results suggest that regulation of VEGF splicing may be a critical switch from an antiangiogenic to a proangiogenic phenotype.
n -3 Polyunsaturated fatty acids modulate carcinogen-directed non-coding microRNA signatures in rat colon (2009)

We have hypothesized that dietary modulation of intestinal non-coding RNA [microRNA (miRNA)] expression may contribute to the chemoprotective effects of nutritional bioactives (fish oil and pectin). To fully understand the effects of these agents on the expression of miRNAs, Sprague-Dawley rats were fed diets containing corn oil or fish oil with pectin or cellulose and injected with azoxymethane (AOM, a colon-specific carcinogen) or saline (control). Real-time polymerase chain reaction using miRNA-specific primers and Taq Man probes was carried out to quantify effects on miRNA expression in colonic mucosa. From 368 mature miRNAs assayed, at an early stage of cancer progression (10 week post AOM injection), let-7d, miR-15b, miR-107, miR-191 and miR-324-5p were significantly (P < 0.05) affected by diet x carcinogen interactions. Overall, fish oil fed animals exhibited the smallest number of differentially expressed miRNAs (AOM versus saline treatment). With respect to the tumor stage (34 week post AOM injection), 46 miRNAs were dysregulated in adenocarcinomas compared with normal mucosa from saline-injected animals. Of the 27 miRNAs expressed at higher (P < 0.05) levels in tumors, miR-34a, 132, 223 and 224 were overexpressed at >10-fold. In contrast, the expression levels of miR-192, 194, 215 and 375 were dramatically reduced (< or = 0.32-fold) in adenocarcinomas. These results demonstrate for the first time the utility of the rat AOM model and the novel role of fish oil in protecting the colon from carcinogen-induced miRNA dysregulation.
Inhibition of angiogenesis by tissue inhibitor of metalloproteinase (1994)

Matrix proteases play a critical role in cell invasion and migration, including the process of angiogenesis. The ability of specific factors to induce angiogenic responses correlates with their stimulation of matrix protease synthesis and release. Using an in vivo angiogenesis assay, the endothelial cell response to known angiogenic factors, basic fibroblast growth factor (bFGF) and adipocyte conditioned medium, was blocked by an inhibitor of matrix metalloproteinase activity, TIMP-1. The TIMP effect was mediated, at least in part, through the inhibition of endothelial cell migration, as determined by the ability of TIMP to block chemotaxis in a Boyden chamber assay. These results indicate that the inhibition of migration is a direct effect on the endothelial cells and does not require accessory cells. An additional observation was that the RNA levels for TIMP were significantly reduced in differentiated adipocytes, compared to undifferentiated F442A controls. Therefore, the acquisition of an angiogenic phenotype may involve not only the induction of positive factors, but also the suppression of angiogenesis inhibitors.
The symptom of pain with pressure ulcers: a review of the literature. (2008)

Although wound pain often is described as an important clinical factor by both patients and providers, pain associated with pressure ulcers is poorly understood. To assess the state of knowledge of pain with pressure ulcers, a systematic, integrative review of the literature was conducted to determine: 1) how pain is measured, 2) pain prevalence/incidence, and 3) factors associated with pressure ulcer pain. Bibliographic databases including MEDLINE (1966-2005), HealthSTAR (1975-2005), CINAHL (1982-2005), and seven others were searched using the terms decubitus ulcers, pressure ulcer, pressure sore, bed sore, and pain and then culled to English-language, clinical publications. Of the 417 articles recovered, 26 met the study inclusion criteria, six specifically identified pain prevalence (ranging from 37% and 100%), and none documented the incidence of pain in patients with pressure ulcers. Measurement tools used to assess pain included the Visual Analogue Scale, the Verbal Rating Scale, the Wong-Baker Facial Recognition Scale, the McGill Pain Questionnaire-Short Form, the Numerical Rating Scale, and the Present Pain Intensity scale. Pressure ulcer pain was described as a burning sensation and reported as both constant and transient. Contrary to often-held clinical opinion, the studies reviewed suggest that pain increases with pressure ulcer stage. Although a number of intrinsic and extrinsic factors were studied (eg, age, ulcer stage, and bed surfaces), no conclusions could be drawn from the available research. Because pain is an issue for individuals with pressure ulcers and may present a different profile than other sources of pain, pain assessment should become an integral part of pressure ulcer care and documented to guide pressure ulcer management.
Homing endonucleases from mobile group I introns: discovery to genome engineering (2014)

Homing endonucleases are highly specific DNA cleaving enzymes that are encoded within genomes of all forms of microbial life including phage and eukaryotic organelles. These proteins drive the mobility and persistence of their own reading frames. The genes that encode homing endonucleases are often embedded within self-splicing elements such as group I introns, group II introns and inteins. This combination of molecular functions is mutually advantageous: the endonuclease activity allows surrounding introns and inteins to act as invasive DNA elements, while the splicing activity allows the endonuclease gene to invade a coding sequence without disrupting its product. Crystallographic analyses of representatives from all known homing endonuclease families have illustrated both their mechanisms of action and their evolutionary relationships to a wide range of host proteins. Several homing endonucleases have been completely redesigned and used for a variety of genome engineering applications. Recent efforts to augment homing endonucleases with auxiliary DNA recognition elements and/or nucleic acid processing factors has further accelerated their use for applications that demand exceptionally high specificity and activity.
Sizing it up: Cellular MRI using micron‐sized iron oxide particles (2005)

There is rapidly increasing interest in the use of MRI to track cell migration in intact animals. Currently, cell labeling is usually accomplished by endocytosis of nanometer-sized, dextran-coated iron oxide particles. The limitations of using nanometer-sized particles, however, are that millions of particles are required to achieve sufficient contrast, the label can be diluted beyond observability by cell division, and the label is biodegradable. These problems make it difficult to label cells other than macrophages in vivo, and to conduct long-term engraftment studies. It was recently demonstrated that micron-sized iron oxide particles (MPIOs) can be taken up by a number of cell types. In this study we examined the MRI properties of single MPIOs with sizes of 0.96, 1.63, 2.79, 4.50, and 5.80 microm. Furthermore, the capacity of cells to endocytose these MPIOs was investigated, and the MRI properties of the labeled cells at 7.0 and 11.7 Tesla were measured as a function of image resolution and echo time (TE). Cells labeled with MPIOs generally contained iron levels of approximately 100 pg, which is approximately threefold higher than those obtained with the best strategies to label cells using nanometer-sized particles. On occasion, some cells had levels as high as approximately 400 pg. We demonstrate that these large particles and the cells labeled with them can be detected by spin echo (SE)-based imaging methods. These measurements indicate that MPIOs should be useful for improving cell tracking by MRI.
Applications of Sulfoxides to Asymmetric Synthesis of Biologically Active Compounds (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplications of Sulfoxides to Asymmetric Synthesis of Biologically Active CompoundsM. Carmen CarrenoCite this: Chem. Rev. 1995, 95, 6, 1717–1760Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/cr00038a002https://doi.org/10.1021/cr00038a002research-articleACS PublicationsRequest reuse permissionsArticle Views3759Altmetric-Citations955LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts