gebhart/patrepeval huggingface dataset:
Characterization of the 3- <i>O</i> -Methylgallate Dioxygenase Gene and Evidence of Multiple 3- <i>O</i> -Methylgallate Catabolic Pathways in <i>Sphingomonas paucimobilis</i> SYK-6 (2004)

Sphingomonas paucimobilis SYK-6 is able to grow on various lignin-derived biaryls as the sole source of carbon and energy. These compounds are degraded to vanillate and syringate by the unique and specific enzymes in this strain. Vanillate and syringate are converted to protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by the tetrahydrofolate-dependent O-demethylases. Previous studies have suggested that these compounds are further degraded via the PCA 4,5-cleavage pathway. However, our subsequent analysis of the ligB insertion mutant, which encodes the beta subunit of PCA 4,5-dioxygenase, suggested that at least one alternative route is involved in 3MGA degradation. In the present study, we isolated the desZ gene, which confers 3MGA degradation activity on Escherichia coli. The deduced amino acid sequence of desZ showed ca. 20 to 43% identity with the type II extradiol dioxygenases. Gas chromatography-mass spectrometry analysis suggested that DesZ catalyzes the 3,4-cleavage of 3MGA. Disruption of both desZ and ligB in SYK-6 resulted in loss of the dioxygen-dependent 3MGA transformation activity, but the resulting mutant retained the ability to grow on syringate. We found that the cell extract of the desZ ligB double mutant was able to convert 3MGA to gallate when tetrahydrofolate was added to the reaction mixture, and the cell extract of this mutant degraded gallate to the same degree as the wild type did. All these results suggest that syringate is degraded through multiple 3MGA degradation pathways in which ligAB, desZ, 3MGA O-demethylase, and gallate dioxygenase are participants.
Manipulating and squeezing the photon local density of states with plasmonic nanoparticle networks (2010)

In this Brief Report, we show that when interconnected networks of gold particles are deposited onto a clean planar surface, they strongly modify the photonic local density of states (LDOS) in the immediate proximity of the self-assembled nanoparticles. They represent unique architectures for the subwavelength patterning of initially flat photonic LDOS. Moreover, we show that their local spectral signatures are well suited for the generation of sites able to enhance molecular fluorescence intensity.
New approaches to prevention and treatment of radial artery graft vasospasm. (1998)

Diltiazem, which is used empirically to prevent RA vasospasm, had little effect on human RA contractions (receptor-independent and receptor-dependent). Organic nitrates inhibited and reversed RA contractions. Adenoviral transfer of NOS suggests that future clinical application of gene therapy may play an important role in prevention of RA vasospasm.
Structure‐Based Repurposing of FDA‐Approved Drugs as TNF‐α Inhibitors (2011)

Old dogs, new tricks! We applied structure-based virtual screening methods to identify small-molecule inhibitors of tumor necrosis factor-α (TNF-α) from a database of 3 000 US Food and Drug Administration (FDA)-approved drugs. Darifenacin (Enablex) and ezetimibe (Zetia) were identified as direct TNF-α inhibition, representing only the fifth and sixth examples of small-molecule TNF-α inhibitors. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Oral History and the Evolution of Thakuri Political Authority in A Subregion of Far Western Nepal (1984)

1974 discussed the evolution of caste organization in Nepal in light of Tucci's investigations of the Ma lia Kingdom of Western Nepal.My dissertation research, of which the following material is a part, was an outgrowth of questions John had raised on this subject.At first glance the material written in 1978 may appear removed f r om the interests of a management development specialist in a contemporary Dallas high technology company.At closer inspection, however, its central themes -the legitimization of hierarchical relationships, the "her o" as an organizational symbol, and th~ impact of local culture on organizational function and design -are issues that are relevant to industrial as well as caste organization.This continuity speaks to the depth of John's insight into the fundamental .nature of the questions involved in the study of hierarchy in Nepal.Under his guidance the topic became for me a continuing framework of analysis involving what John, in The Magars of Banyan Hill, referred to as the interaction between the experience of "sensuous reality" and the abstractions through which we attempt to order it.
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers (2006)

Hy3S is a powerful suite of simulation programs for simulating the stochastic dynamics of networks of biochemical reactions. Its first public version enables computational biologists to more efficiently investigate the dynamics of realistic biological systems.
Anisotropy in the hydrophobic and oleophilic characteristics of patterned surfaces (2017)

A significant difference in the wetting angles of water and oil was observed on patterned substrates, combining interstitial spaces along with hydrophobic solid surfaces, as a function of the orientation. The difference was ascribed to a modification of the liquid–interstice interfacial surface energy due to different degrees of penetration of the liquid. A roughness metric related to the extent to which the liquid infiltrates the interstice normalized by the geometrically determined area is proposed. This study has implications in modulating surface slip behavior and would be of importance in guiding liquid droplets.
Technological Advances in Renal Replacement Therapy (2009)

The worldwide epidemic of chronic kidney disease shows no signs of abating in the near future. Current dialysis forms of renal replacement therapy (RRT), even though successful in sustaining life and improving quality of life somewhat for patients with ESRD, have many limitations that result in still unacceptably high morbidity and mortality. Transplantation is an excellent option but is limited by the scarcity of organs. An ideal form of RRT would mimic the functions of natural kidneys and be transparent to the patient, as well as affordable to society. Recent advances in technology, although generally in early stages of development, might achieve these goals. The application of nanotechnology, microfluidics, bioreactors with kidney cells, and miniaturized sorbent systems to regenerate dialysate makes clinical reality seem closer than ever before. Finally, stem cells hold much promise, both for kidney disease and as a source of tissues and organs. In summary, nephrology is at an exciting crossroad with the application of innovative and novel technologies to RRT that hold considerable promise for the near future.
Direct or indirect skin lipid-ordering effect of pyrrolidone carboxylate sodium after topical treatment with penetration enhancers. (1995)

The structural changes in the lipid of the excised skin of nude mice and the porcine stratum corneum was investigated by in vitro treatment with vitamin C, oleic acid, or DMSO. The CH2 stretching vibrational peaks of lipid near 2920 cm-1 (asymmetric) and 2850 cm-1 (symmetric) shifted to higher wavenumber due to the lipid-disorder after in vitro treatment with above enhancers. The spectral shift of the asymmetric CH2 band was more sensitive than that of the symmetric CH2 band. The higher wavenumber of CH2 stretching bands decreased gradually to the lower region after co-treatment or posttreatment with pyrrolidone carboxylate sodium (PCA Na). Such a decrease was dependent on the PCA Na concentration and the time of treatment. The higher the concentration of PCA Na used, the lower value of the permeability coefficient of vitamin C through the excised skin and the downward spectral shift of asymmetric CH2 band were obtained. When PCA Na coexisted with vitamin C in the cell donor compartment, a competitive effect between PCA Na and vitamin C was found. The oleic acid was supposed to directly insert it into the lipid structure to form a rigid structure, leading to larger spectral shift of both stretching bands but lesser restoring ability after PCA Na treatment. However, DMSO only displaces water from the lipid head groups and protein domain of skin to indirectly loosen the lipid structure, resulting in lesser spectral shift of the CH2 stretching bands to higher region, which was easier and better restoration after PCA Na application. The PCA Na enabled to restore the disordered lipid structure to order state might be attributed to PCA Na previously penetrated into skin and then absorbed water to directly or indirectly rearrange the disordered lipid bilayer structure.
The prevalence of nosocomial infection in intensive care units in Europe. Results of the European Prevalence of Infection in Intensive Care (EPIC) Study. EPIC International Advisory Committee. (1995)

ICU-acquired infection is common and often associated with microbiological isolates of resistant organisms. The potential effects on outcome emphasize the importance of specific measures for infection control in critically ill patients.
An overview of nanolime as a consolidation method for calcareous substrates (2017)

Ca(OH)2 particles with submicrometric dimensions (nanolimes) represent one of the most promising consolidants for the conservation of calcareous substrates. The nanolime treatment is similar to the limewater technique, traditionally used for its durability and high compatibility with the calcareous matrix but requiring a large number of applications and not always yielding a highly effective consolidation. Since 2001, alcohol-based dispersions of Ca(OH)2 nanoparticles have been synthesised to overcome the limitations of the limewater treatment. Nanolimes present the same high compatibility and durability of the traditional technique but superior properties in terms of higher consolidation, penetration and reactivity, and fewer side effects. Since their discovery, nanolimes have been investigated by several research groups with the aim of refining their synthesis process, properties and applications. This paper presents an overview of the most relevant literature about nanolime as a consolidant for calcareous substrates.
Function, occurrence and inhibition of different forms of BAFF (2021)

B cell activating factor (BAFF or BLyS), an important cytokine for B cell survival and humoral immune responses, is targeted in the clinic for the treatment of systemic lupus erythematosus. This review focuses on the structure, function and inhibition profiles of membrane-bound BAFF, soluble BAFF 3-mer and soluble BAFF 60-mer, all of which have distinct properties. BAFF contains a loop region not required for receptor binding but essential for receptor activation via promotion of BAFF-to-BAFF contacts. This loop region additionally allows formation of BAFF 60-mer, in which epitopes of the BAFF inhibitor belimumab are inaccessible. If 60-mer forms in humans, it is predicted to be short-lived and to act locally because adult serum contains a BAFF 60-mer dissociating activity. Cord blood contains elevated levels of BAFF, part of which displays attributes of 60-mer, suggesting a role for this form of BAFF in the development of foetal or neonate B cells.
Epigenetic therapies in acute myeloid leukemia: where to from here? (2019)

A hallmark of acute myeloid leukemia (AML) is epigenetic dysregulation, which is initiated by recurrent translocations and/or mutations in transcription factors and chromatin regulators. This manifests as a block in myeloid differentiation and an increase in malignant self-renewal. These common features of AML have led to widespread optimism that epigenetic therapies would dramatically change the natural history of this disease. Although preclinical studies with these drugs fueled this optimism, results from early clinical trials have offered a more sobering message. Here, we provide an overview of epigenetic therapies that are currently approved by therapeutic regulatory authorities across the world and those undergoing early-phase clinical trials. We also discuss the conceptual and molecular factors that may explain some of the disparity between the bench and bedside, as well as emerging avenues for combining the current generation of epigenetic therapies with other classes of agents and the development of novel epigenetic therapies. With further research and development of this exciting class of drugs, we may finally be able to dramatically improve outcomes for patients afflicted with this aggressive and often incurable malignancy.
Stereospecific 6-alkylation of oestradiol derivatives via Cr(CO)3 complexes (1984)

The increased kinetic acidity of benzylic hydrogen atoms of aromatic steroids temporarily modified by the Cr(CO)3 group provides access to 6-alkylated oestradiol derivatives with controlled stereochemistry; the relative binding affinities of these modified hormones with receptor to the oestradiol respect have been measured.
Tetrameric repeat units associated with virulence factor phase variation in<i>Haemophilus</i>also occur in<i>Netsseria</i>spp. and<i>Moraxella catarrhalis</i> (1996)

The tetrameric repeat units 5'-CAAT-3' and 5'-GCAA-3' are associated with phase variable expression of lipopolysaccharide biosynthetic genes in Haemophilus influenzae. Four other tetrameric repeat units have also been reported from H. influenzae strain Rd, 5'-CAAC-3', 5'-GACA-3', 5'-AGCT-3', and 5'-TTTA-3', which are also associated with putative virulence factors. Using oligonucleotide probes corresponding to five tandem copies of each of these tetramers, we have screened three strains of Neisseria meningitidis and one each of Neisseria gonorrhoeae, Neisseria lactamica, Haemophilus parainfluenzae, Bordetella pertussis, Bordetella parapertussis, Bordetella bronchiceptica and Moraxella catarrhalis for the presence of these motifs. We have demonstrated the presence of multiple copies of the 5'-GCAA-3' motif in all the Neisseria strains tested, and also the repeated motif 5'-CAAC-3' in M. catarrhalis. We have further demonstrated by Southern blot analysis that the 5'-CAAC-3' repeats detected in M. catarrhalis are probably associated with the same genes as in H. influenzae, but that the 5'-GCAA-3' motifs in N. meningitidis are not. The use of characterised tetrameric DNA sequences as hybridisation probes may prove useful in the identification of novel phase variable virulence determinants in organisms other than H. influenzae.
Does ionizing radiation stimulate cancer invasion and metastasis? (2008)

Radiotherapy (RT) is a form of local treatment used mainly for malignant tumors. Such tumors originate from mutated stem cells. During their development they do attract a variety of host cells, coined tumor-associated host cells. Malignant tumors are characterized by uncontrolled growth, invasion and metastasis, the latter being the major cause of death of patients, even when their primary tumor is under control. RT inhibits growth. There are, however, clinical data suggesting that, under some circumstances, it may stimulate metastasis. DNA is a target of ionizing radiation (IR), though not the only one. IR produces cascades of growth factors and chemokines; it activates molecules initiating multiple signaling pathways that modulate several cellular functions. We consider cancer as a network of ecosystems, including at least the founder primary tumor, the site of metastasis and the bone marrow. As these ecosystems are in continuous communication, it is not surprising that RT of the primary tumor influences metastasis. Indeed, experiments with cells in culture and with animal tumors have shown that IR stimulates invasion and metastasis and activates pro-invasive and prometastatic cellular activities through upregulation of key molecules. At certain doses and within certain time frames, IR enhances the activities of the tumor-associated host cells that support invasion and metastasis, namely: endothelial cells building new vessels; leucocytes and macrophages causing inflammation; myofibroblasts initiating desmoplasia; osteoblasts and osteoclasts establishing bone metastasis; nerve cells producing efferent growth- and invasion-promoting molecules. Techniques such as spatially fractioned radiotherapy and hadron therapy may have different effects on metastasis. Taking into consideration the dose- and time-dependency of the IR-induced tumor-associated host cell reactions, these techniques, as well as the conventional ones, should be combined with repetitive biological imaging, reevaluation of planning and eventual replanning during the course of the treatment.
CRC look-up table optimization for single-bit error correction (2007)

Many communication systems use the cyclic redundancy code (CRC) technique for protecting key data fields from transmission errors by enabling both single-bit error correction and multi-bit error detection. The look-up table design is very important for the error-correction implementation. This paper presents a CRC look-up table optimization method for single-bit error correction. The optimization method minimizes the address length of the pre-designed look-up table while satisfying certain restrictions. The circuit implementation is also presented to show the feasibility of the method in the application specific integrated circuit design. An application of the optimization method in the generic framing procedure protocol is implemented using field programmable gate arrays. The result shows that the memory address length has been minimized, while keeping a very simple circuit implementation.
Modulation of the Pharmacokinetic Properties of PNA:  Preparation of Galactosyl, Mannosyl, Fucosyl,<i>N</i>-Acetylgalactosaminyl, and<i>N</i>-Acetylglucosaminyl Derivatives of Aminoethylglycine Peptide Nucleic Acid Monomers and Their Incorporation into PNA Oligomers (2003)

A series of N-(2-aminoethyl)-alpha-amino acid thymine peptide nucleic acid (PNA) monomers bearing glycosylated side chains in the alpha-amino acid position have been synthesized. These include PNA monomers where glycine has been replaced by serine and threonine (O-glycosylated), derivatives of lysine and nor-alanine (C-glycosylated), and amide derivatives of aspartic acid (N-glycosylated). The Boc and Fmoc derivatives of these monomers were used for incorporation in PNA oligomers. Twelve PNA decamers containing the glycosylated units in one, two, or three positions were prepared, and the thermal stability (T(m)) of their complexes with a complementary RNA was determined. Incorporation of the glycosyl monomers reduced the duplex stability by 0-6 degrees C per substitution. A cysteine was attached to the amino terminus of eight of the PNA decamers (Cys-CTCATACTCT-NH(2)) for easy conjugation to a [(18)F]radiolabeled N-(4-fluorobenzyl)-2-bromoacetamide. The in vivo biodistribution of these PNA oligomers was determined in rat 2 h after intravenous administration. Most of the radioactivity was recovered in the kidneys and in the urine. However, N-acetylgalactosamine (and to a lesser extent galactose and mannose)-modified PNAs were effectively targeting the liver (40-fold over unmodified PNA). Thus, the pharmacodistribution in rats of PNA oligomers can be profoundly changed by glycosylation. These results could be of great significance for PNA drug development, as they should allow modulation and fine-tuning of the pharmacokinetic profile of a drug lead.
Multi-stream Network With Temporal Attention For Environmental Sound Classification (2019)

Environmental sound classification systems often do not perform robustly across different sound classification tasks and audio signals of varying temporal structures. We introduce a multi-stream convolutional neural network with temporal attention that addresses these problems. The network relies on three input streams consisting of raw audio and spectral features and utilizes a temporal attention function computed from energy changes over time. Training and classification utilizes decision fusion and data augmentation techniques that incorporate uncertainty. We evaluate this network on three commonly used data sets for environmental sound and audio scene classification and achieve new state-of-the-art performance without any changes in network architecture or front-end preprocessing, thus demonstrating better generalizability.
Rhodium(<scp>iii</scp>)-catalyzed C–H allylation of electron-deficient alkenes with allyl acetates (2014)

Rhodium-catalyzed C-H allylation of acrylamides with allyl acetates is reported. The use of weakly coordinating directing group resulted in high reaction efficiency, broad functionality tolerance and excellent γ-selectivity, which opens a new synthetic pathway for the access of 1,4-diene skeletons.
L-SIGN (CD 209L) is a liver-specific capture receptor for hepatitis C virus (2003)

Hepatitis C virus (HCV) infects nearly 3% of the population of the world and is a major cause of liver disease. However, the mechanism whereby the virus targets the liver for infection remains unknown, because none of the putative cellular receptors for HCV are both expressed specifically in the liver and capable of binding HCV envelope glycoproteins. Liver/lymph node-specific intercellular adhesion molecule-3-grabbing integrin (L-SIGN) is a calcium-dependent lectin expressed on endothelial cells of liver and lymph nodes. Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN), a homologous molecule expressed on dendritic cells, binds HIV and promotes infection. By using a virus-binding assay, we demonstrate that L-SIGN and DC-SIGN specifically bind naturally occurring HCV present in the sera of infected individuals. Further studies demonstrate that binding is mediated by the HCV envelope glycoprotein E2 and is blocked by specific inhibitors, including mannan, calcium chelators, and Abs to the lectin domain of the SIGN molecules. Thus, L-SIGN represents a liver-specific receptor for HCV, and L-SIGN and DC-SIGN may play important roles in HCV infection and immunity.
Pillars article: the dorsoventral regulatory gene cassette spätzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell. 1996. 86: 973-983. (2012)

The cytokine-induced activation cascade of NF-kappaB in mammals and the activation of the morphogen dorsal in Drosophila embryos show striking structural and functional similarities (Toll/IL-1, Cactus/I-kappaB, and dorsal/NF-kappaB). Here we demonstrate that these parallels extend to the immune response of Drosophila. In particular, the intracellular components of the dorsoventral signaling pathway (except for dorsal) and the extracellular Toll ligand, spätzle regulatory gene cassette, control expression of the antifungal peptide gene drosomycin in adults. We also show that mutations in the Toll signaling pathway dramatically reduce survival after fungal infection. Antibacterial genes are induced either by a distinct pathway involving the immune deficiency gene (imd) or by combined activation of both imd and dorsoventral pathways.