gebhart/patrepeval huggingface dataset:
[Current status of the treatment of HIV infection]. (1999)

The antiretroviral therapeutic strategy changed in 1996, when the prognostic value of the plasma viral load and the CD4 cell counts were confirmed. Two nucleosides, plus a protease inhibitor or a non-nucleoside, are currently the initial preferred options. Viral resistance, and pharmacokinetic problems, however, have limited the efficacy of these schemes. It should be emphasized that continued use of triple drug therapy regimens have been associated with a decrease of morbidity and mortality associated to AIDS. We have analyzed the different drug combinations used in clinical trials and their results, the definition of therapeutic failure, and its consequences to control the treatment. With the currently available regimens, the virus cannot be totally eradicated from the organism and treatment should be continued for life. The combination of drugs in a single tablet, and the decrease in the number of daily intakes can help the patient with adherence, and allow for supervised treatment programs like the ones already applied with success in the treatment of tuberculosis. The use of virus resistance assays and pharmacokinetic assays will help to select the most appropriate treatment in the near future.
Trends in Down's syndrome live births and antenatal diagnoses in England and Wales from 1989 to 2008: analysis of data from the National Down Syndrome Cytogenetic Register (2009)

Since 1989, expansion of and improvements in antenatal screening have offset an increase in Down's syndrome resulting from rising maternal age. The proportion of antenatal diagnoses has increased most strikingly in younger women, whereas that in older women has stayed relatively constant. This trend suggests that, even with future improvements in screening, a large number of births with Down's syndrome are still likely, and that monitoring of the numbers of babies born with Down's syndrome is essential to ensure adequate provision for their needs.
Colonization of peanut roots by biofilm-forming Paenibacillus polymyxa initiates biocontrol against crown rot disease (2007)

The study highlights the importance of efficient rhizosphere colonization and biofilm formation in biocontrol.
Amino acids in the rhizosphere: From plants to microbes (2013)

Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.
A TENTATIVE TYPOLOGY OF AUDIO SOURCE SEPARATION TASKS (2003)

International audience
Specific tetraspanin functions (2001)

Relatively little attention has been given to the large family of abundantly expressed transmembrane proteins known as tetraspanins. Now, the importance of tetraspanins is strongly supported by emerging genetic evidence, coupled with new insights into the biochemistry and functions of tetraspanin protein complexes.
Grapevine stilbene synthase cDNA only slightly differing from chalcone synthase cDNA is expressed in Escherichia coli into a catalytically active enzyme (1990)

Stilbene synthase is responsible for the formation of resveratrol and other stilbenes which function in grapevine as phytoalexins. A full-length stilbene synthase cDNA was prepared from grapevine mRNA and sequenced. The insert in pSV25 coding for a polypeptide with 392 amino acids was inserted into the vectors pKK233-2 and pDS12/RBSII-2, respectively. Expression of the cDNA in Escherichia coli yielded an enzymatically active dimer exhibiting solely stilbene synthase activity. The protein was characterized by enzyme activity and Western blot analysis.
Survey of the prevalence, diagnosis and treatment of dermatological conditions in small animals in general practice (2006)

A survey was made of the prevalence, diagnosis and treatment of dermatological conditions in small animals in general practice in the UK. Out of 3707 small animal consultations in general practice that were observed and recorded, 795 (21.4 per cent) involved animals that had a dermatological problem. In dogs and exotic species, pruritus was the most common presenting sign, accounting for 30 to 40 per cent of the dermatological consultations. In cats, cutaneous swellings were the most common presentation (36 per cent). A diagnosis or recommendation for treatment was made on the basis of the presenting clinical signs and physical examination alone in 576 (72 per cent) of the cases, and various diagnostic tests were performed in the other cases. In dogs, parasitic infestations, bacterial infections and neoplasia accounted for the majority of the diagnoses. In cats, parasites and bacterial infections were the most common. In exotic species, parasites accounted for over 80 per cent of the dermatological diagnoses. In dogs, the most common final diagnoses were otitis, pyoderma, anal sac impaction, flea infestation and atopic dermatitis. In cats, abscesses, flea infestation, and otitis were the most common diagnoses. In exotic species, the most common diagnosis was an unspecified mite infestation. Systemic antibiotics were prescribed in 196 cases (25 per cent), systemic glucocorticoids were prescribed in 162 cases (20 per cent) and treatment with an ectoparasiticide was prescribed in 167 cases (21 per cent).
A portable approach to last resort parsing and interpretation (1993)

This paper describes an approach to robust processing which is domain-independent in its design, yet which can easily take advantage of domain-specific information. Robust processing is well-integrated into standard processing in this approach, requiring essentially only a single new BNF rule in the grammar. We describe the results of implementing this approach in two different domains.
Automation of user-specific ASIC library development (2002)

Discusses a method to develop a user-specific standard cell library using advanced library development tools. The tools described support library engineering, development, quality assurance and productization. The tools can also automatically support multiple vendor ASIC design tools, including VHDL and Verilog, schematic entry tools, simulators, logic synthesizers, datapath compilers, and other compilation tools.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for potent and allele selective suppression of mutant Huntingtin in the CNS (2013)

Autosomal dominant diseases such as Huntington's disease (HD) are caused by a gain of function mutant protein and/or RNA. An ideal treatment for these diseases is to selectively suppress expression of the mutant allele while preserving expression of the wild-type variant. RNase H active antisense oligonucleotides (ASOs) or small interfering RNAs can achieve allele selective suppression of gene expression by targeting single nucleotide polymorphisms (SNPs) associated with the repeat expansion. ASOs have been previously shown to discriminate single nucleotide changes in targeted RNAs with ∼5-fold selectivity. Based on RNase H enzymology, we enhanced single nucleotide discrimination by positional incorporation of chemical modifications within the oligonucleotide to limit RNase H cleavage of the non-targeted transcript. The resulting oligonucleotides demonstrate >100-fold discrimination for a single nucleotide change at an SNP site in the disease causing huntingtin mRNA, in patient cells and in a completely humanized mouse model of HD. The modified ASOs were also well tolerated after injection into the central nervous system of wild-type animals, suggesting that their tolerability profile is suitable for advancement as potential allele-selective HD therapeutics. Our findings lay the foundation for efficient allele-selective downregulation of gene expression using ASOs-an outcome with broad application to HD and other dominant genetic disorders.
Adoptive transfer of effector CD8+ T cells derived from central memory cells establishes persistent T cell memory in primates (2008)

The adoptive transfer of antigen-specific T cells that have been expanded ex vivo is being actively pursued to treat infections and malignancy in humans. The T cell populations that are available for adoptive immunotherapy include both effector memory and central memory cells, and these differ in phenotype, function, and homing. The efficacy of adoptive immunotherapy requires that transferred T cells persist in vivo, but identifying T cells that can reproducibly survive in vivo after they have been numerically expanded by in vitro culture has proven difficult. Here we show that in macaques, antigen-specific CD8(+) T cell clones derived from central memory T cells, but not effector memory T cells, persisted long-term in vivo, reacquired phenotypic and functional properties of memory T cells, and occupied memory T cell niches. These results demonstrate that clonally derived CD8+ T cells isolated from central memory T cells are distinct from those derived from effector memory T cells and retain an intrinsic capacity that enables them to survive after adoptive transfer and revert to the memory cell pool. These results could have significant implications for the selection of T cells to expand or to engineer for adoptive immunotherapy of human infections or malignancy.
Shear stress-induced changes of membrane transporter localization and expression in mouse proximal tubule cells (2010)

Our previous studies of microperfused single proximal tubule showed that flow-dependent Na(+) and HCO(3)(-) reabsorption is due to a modulation of both NHE3 and vacuolar H(+)-ATPase (V-ATPase) activity. An intact actin cytoskeleton was indicated to provide a structural framework for proximal tubule cells to transmit mechanical forces and subsequently modulate cellular functions. In this study, we have used mouse proximal tubule (MPT) cells as a model to study the role of fluid shear stress (FSS) on apical NHE3 and V-ATPase and basolateral Na/K-ATPase trafficking and expression. Our hypothesis is that FSS stimulates both apical and basolateral transporter expression and trafficking, which subsequently mediates salt and volume reabsorption. We exposed MPT cells to 0.2 dynes/cm(2) FSS for 3 h and performed confocal microscopy and Western blot analysis to compare the localization and expression of both apical and basolateral transporters in control cells and cells subjected to FSS. Our findings show that FSS leads to an increment in the amount of protein expression, and a translocation of apical NHE3 and V-ATPase from the intracellular compartment to the apical plasma membrane and Na/K-ATPase to the basolateral membrane. Disrupting actin by cytochalasin D blocks the FSS-induced changes in NHE3 and Na/K-ATPase, but not V-ATPase. In contrast, FSS-induced V-ATPase redistribution and expression are largely inhibited by colchicine, an agent that blocks microtubule polymerization. Our findings suggest that the actin cytoskeleton plays an important role in FSS-induced NHE3 and Na/K-ATPase trafficking, and an intact microtubule network is critical in FSS-induced modulation of V-ATPase in proximal tubule cells.
Molecular Mechanism of Tissue Factor-mediated Acceleration of Factor VIIa Activity (1996)

The mechanism of the acceleration of the catalytic activity of factor VIIa (VIIa) in the presence of tissue factor (TF) was investigated. To explore the VIIa's site(s) that correlates with TF-mediated acceleration, zymogen VII, VIIa, and active site-modified VIIa were prepared, and dissociation constants (Kd) for their bindings to TF or soluble TF in solution were determined. We found that conversion of zymogen VII to VIIa led to an increase in affinity (DeltaDeltaG = 4.3-4.4 kJ/mol) for TFs. Dansyl-Glu-Gly-Arg chloromethyl ketone (DNS-EGRck) treatment of VIIa led to a further increase in the affinity (DeltaDeltaG = 7.3-12 kJ/mol). Neither removal of the Gla domain from VIIa nor truncation of the COOH-terminal membrane and cytoplasmic regions of TF affected the affinity enhanced after DNS-EGRck treatment of VIIa. Treatment of VIIa with (p-amidinophenyl)methanesulfonyl fluoride also enhanced its affinity for soluble TF, whereas treatment with 4-(2-aminoethyl)benzenesulfonyl fluoride, phenylmethylsulfonyl fluoride, or diisopropyl fluorophosphate had a slight effect on the affinity. On the other hand, DNS-EGRck and (p-amidinophenyl)methanesulfonyl fluoride treatments, but not diisopropyl fluorophosphate treatment, of VIIa led to protection of its alpha-amino group of Ile-153 from carbamylation. Protection of the alpha-amino group was consistent with formation of a critical salt bridge between Ile-153 and Asp-343 in the protease domain of VIIa. Therefore, TF may preferentially bind to the active conformational state of VIIa. When one assumes that free VIIa exists in equilibrium between minor active and dominant zymogen-like inactive conformational states, preferential binding of TF to the active state leads to a shift in equilibrium. We speculate that TF traps the active conformational state of VIIa and converts its zymogen-like state into an active state, thereby accelerating the VIIa activity.
Structural basis of second-generation HIV integrase inhibitor action and viral resistance (2020)

Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.
Inter‐echo variance as a weighting factor for multi‐channel combination in multi‐echo acquisition for local frequency shift mapping (2014)

The primary finding of the present study is that accurate LFS maps are achievable if the data from each channel is processed independently prior to combination followed by a weighted combination using IEV as the weighting term. The software is freely available to the scientific community.
KYC Optimization using Blockchain Smart Contract Technology (2020)

In the present scenario, it is vital for any organization, especially the financial organizations, to understand customers and their financial dealings better. KYC is a process to verify identity and related details of corresponding customers. The current KYC mechanism has a severe concern in financial institutions as it requires separate ledger for the separate financial organizations. Every institution has its KYC process, which sometimes may include third-party, which may cause increased maintenance cost, time and redundancy. There is considerable wastage of costs in the form of opportunity cost, maintenance cost, customer verification cost and many more of around $27 million according to an economic survey. The current KYC process is very time-consuming, and it decreases the user experience. We have proposed an enhanced KYC system using blockchain technology to improve the existing KYC system. An inherent feature of the DLT is used to remove the third-party involvement, and smart contracts are used to build our logic in the mobility of the data. Blockchain technology has various types of cryptographic security which provide a safer place to transact over an unsecured channel. Using the facility of DLT, cryptography and consensus mechanism of blockchain, the proposed model of KYC process can optimize storing, updating, sharing of data and accessing operations along with enhanced security, transparency and privacy. It also enhances customer ownership and improves customer experience. It not only reduces the time duration and document update problem but also saves opportunity cost, aggregation, cost, maintenance cost and many more costs, which can affect the performance of any organization.
Signal Transduction Pathways (1995)

Lithium remains the most widely used treatment for bipolar disorder, and this monovalent cation represents one of psychiatry's most important treatments. Despite its demonstrated efficacy in reducing both the frequency and severity of recurrent affective episodes and decades of clinical use, the molecular mechanisms underlying its therapeutic actions have not fully been elucidated. In this report, we review the exciting recent progress in the identification of key components of signal transduction pathways (in particular, guanine nucleotide-binding proteins [G proteins], adenylyl cyclases, and protein kinase C isozymes) as targets for lithium's actions and attempt to integrate these effects with the large body of data emphasizing alterations in various neurotransmitter (particularly monoaminergic) systems. Regulation of signal transduction within critical regions of the brain by lithium affects the function of multiple neurotransmitter systems and may thus explain lithium's efficacy in protecting susceptible individuals from spontaneous, stress-induced, and drug-induced cyclic affective episodes. Recent evidence has also demonstrated significant effects of lithium on the regulation of gene expression in the central nervous system, effects that may play a major role in the long-term stabilization of mood. The identification of these intracellular targets for lithium's actions offers the potential for the development of novel, improved therapeutic agents and, in conjunction with molecular genetic approaches, may facilitate our understanding of the biological factors predisposing individuals to manic-depressive illness.
The ABC transporter AtrB from Aspergillus nidulans mediates resistance to all major classes of fungicides and some natural toxic compounds (2000)

This paper reports the functional characterization of AtrBp, an ABC transporter from Aspergillus nidulans. AtrBp is a multidrug transporter and has affinity to substrates belonging to all major classes of agricultural fungicides and some natural toxic compounds. The substrate profile of AtrBp was determined by assessing the sensitivity of deletion and overexpression mutants of atrB to several toxicants. All mutants showed normal growth as compared to control isolates. DeltaatrB mutants displayed increased sensitivity to anilinopyrimidine, benzimidazole, phenylpyrrole, phenylpyridylamine, strobirulin and some azole fungicides. Increased sensitivity to the natural toxic compounds camptothecin (alkaloid), the phytoalexin resveratrol (stilbene) and the mutagen 4-nitroquinoline oxide was also found. Overexpression mutants were less sensitive to a wide range of chemicals. In addition to the compounds mentioned above, decreased sensitivity to a broader range of azoles, dicarboximides, quintozene, acriflavine and rhodamine 6G was observed. Decreased sensitivity in overexpression mutants negatively correlated with levels of atrB expression. Interestingly, the overexpression mutants displayed increased sensitivity to dithiocarbamate fungicides, chlorothalonil and the iron-activated antibiotic phleomycin. Accumulation of the azole fungicide [(14)C]fenarimol by the overexpression mutants was lower as compared to the parental isolate, demonstrating that AtrBp acts by preventing intracellular accumulation of the toxicant. Various metabolic inhibitors increased accumulation levels of [(14)C]fenarimol in the overexpression mutants to wild-type levels, indicating that reduced accumulation of the fungicide in these mutants is due to increased energy-dependent efflux as a result of higher pump capacity of AtrBp.
Simple approach to highly oriented ZnO nanowire arrays: large-scale growth, photoluminescence and photocatalytic properties (2006)

A simple and low-cost soft route has been developed to the direct large-scale production of highly oriented ZnO nanowire arrays at 60 degrees C. It has been found that the growth of well-aligned ZnO nanowire arrays is dependent on several parameters, such as the reaction time and the concentration of ammonium ions. The environmentally benign ZnO nanowires obtained, with significant photoluminescence property and interesting photocatalytic activity, are single crystals and have a low defect concentration, which could be expected to find promising potential for optoelectronic and environmental application.
Tau Becomes a More Favorable Substrate for GSK-3 When It Is Prephosphorylated by PKA in Rat Brain (2004)

Microtubule-associated protein tau is abnormally hyperphosphorylated in Alzheimer's disease (AD) and other tauopathies and is believed to lead to neurodegeneration in this family of diseases. Here we show that infusion of forskolin, a specific cAMP-dependent protein kinase A (PKA) activator, into the lateral ventricle of brain in adult rats induced activation of PKA by severalfold and concurrently enhanced the phosphorylation of tau at Ser-214, Ser-198, Ser-199, and or Ser-202 (Tau-1 site) and Ser-396 and or Ser-404 (PHF-1 site), which are among the major abnormally hyperphosphorylated sites seen in AD. PKA activation positively correlated to the extent of tau phosphorylation at these sites. Infusion of forskolin together with PKA inhibitor or glycogen synthase kinase-3 (GSK-3) inhibitor revealed that the phosphorylation of tau at Ser-214 was catalyzed by PKA and that the phosphorylation at both the Tau-1 and the PHF-1 sites is induced by basal level of GSK-3, because forskolin activated PKA and not GSK-3 and inhibition of the latter inhibited the phosphorylation at Tau-1 and PHF-1 sites. Inhibition of cdc2, cdk5, or MAPK had no significant effect on the forskolin-induced hyperphosphorylation of tau. Forskolin inhibited spatial memory in a dose-dependent manner in the absence but not in the presence of R(p)-adenosine 3',5'-cyclic monophosphorothioate triethyl ammonium salt, a PKA inhibitor. These results demonstrate for the first time that phosphorylation of tau by PKA primes it for phosphorylation by GSK-3 at the Tau-1 and the PHF-1 sites and that an associated loss in spatial memory is inhibited by inhibition of the hyperphosphorylation of tau. These data provide a novel mechanism of the hyperphosphorylation of tau and identify both PKA and GSK-3 as promising therapeutic targets for AD and other tauopathies.