gebhart/patrepeval huggingface dataset:
Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon (2018)

Background: Profiling microbiome on low biomass samples is challenging for metagenomics since these samples are prone to present DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA gene - ITS - 23S rRNA gene; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS) and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION (Oxford Nanopore Technologies) using 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using WIMP workflow on EPI2ME (ONT) or Minimap2 software with rrn database. Results: Full-length 16S rRNA and the rrn operon retrieved the microbiota composition from the bacterial isolate, the mock communities and the complex skin samples, even at the genus and species level. For Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with rrn operon as the marker, and ~68% of the cases with 16S rRNA gene respectively. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in the dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, rrn operon would be the best choice.
Predictive ability of host genetics and rumen microbiome for subclinical ketosis (2020)

Subclinical metabolic disorders such as ketosis cause substantial economic losses for dairy farmers in addition to the serious welfare issues they pose for dairy cows. Major hurdles in genetic improvement against metabolic disorders such as ketosis include difficulties in large-scale phenotype recording and low heritability of traits. Milk concentrations of ketone bodies, such as acetone and β-hydroxybutyric acid (BHB), might be useful indicators to select cows for low susceptibility to ketosis. However, heritability estimates reported for milk BHB and acetone in several dairy cattle breeds were low. The rumen microbial community has been reported to play a significant role in host energy homeostasis and metabolic and physiologic adaptations. The current study aims at investigating the effects of cows' genome and rumen microbial composition on concentrations of acetone and BHB in milk, and identifying specific rumen microbial taxa associated with variation in milk acetone and BHB concentrations. We determined the concentrations of acetone and BHB in milk using nuclear magnetic resonance spectroscopy on morning milk samples collected from 277 Danish Holstein cows. Imputed high-density genotype data were available for these cows. Using genomic and microbial prediction models with a 10-fold resampling strategy, we found that rumen microbial composition explains a larger proportion of the variation in milk concentrations of acetone and BHB than do host genetics. Moreover, we identified associations between milk acetone and BHB with some specific bacterial and archaeal operational taxonomic units previously reported to have low to moderate heritability, presenting an opportunity for genetic improvement. However, higher covariation between specific microbial taxa and milk acetone and BHB concentrations might not necessarily indicate a causal relationship; therefore further validation is needed before considering implementation in selection programs.
Crystal Preparation of Ni-Mn-Ga Alloys. (1999)

Partial evaluation of the liquidus diagram of Ni-Mn-Ga by thermal analysis and microstructural evaluation has determined that the primary solidification surface for the Heusler alloy phase exists over a wide range of compositions. The primary solidification surface falls modestly in temperature with either increasing Mn or Ga concentrations. The composition, Ni50Mn25Ga25, melts incongruently over a temperature range of approximately 18 deg C. The small temperature range of solidification allows for the conditions suitable for crystal growth to be easily established and maintained throughout the crystal growth process for a wide variety of compositions. In general, the Mn composition increases as the solid grows with an associated decrease in Ni composition. Analysis of the composition profiles indicated that the compositional changes, and hence, the solidification process, is dominated by convective mixing in the liquid during growth and evaporative losses of Mn. Finally, preliminary experiments were conducted that demonstrated the feasibility of using the Czochralski technique for the preparation of Ni-Mn-Ga alloys. Additional process optimization is required to gain confidence in applying the Czochralski method to the routine preparation of Ni50Mn25Ga25 and its alloys.
RNA splicing analysis contributes to reclassifying variants of uncertain significance and improves the diagnosis of monogenic disorders (2022)

RNA splicing analysis is an important method to assess the impact of sequence variants on splicing in clinical practice and can contribute to the reclassification of a significant proportion of VUSs. RNA splicing analysis should be considered for genetic disease diagnostics.
Vaccination accelerates hepatic erythroblastosis induced by blood-stage malaria (2020)

Abstract Background: Vaccination induces survival of otherwise lethal blood-stage infections of the experimental malaria Plasmodium chabaudi. Blood-stage malaria induces extramedullary erythropoiesis in the liver. This study investigates how vaccination affects the course of malaria-induced expression of erythrocytic genes in the liver. Methods: Female Balb/c mice were vaccinated at week 3 and week 1 before challenging with 106 P. chabaudi-parasitized erythrocytes. The non-infectious vaccine consisted of erythrocyte ghosts isolated from P. chabaudi-infected erythrocytes. Gene expression microarrays and quantitative real-time PCR were used to compare mRNA expression of different erythrocytic genes in the liver of vaccination-protected and non-protected mice during infections on days 0, 1, 4, 8, and 11 p.i. Results: Global transcriptomics analyses reveal vaccination-induced modifications of malaria-induced increases in hepatic gene expression on days 4 and 11 p.i. On these days, vaccination also alters hepatic expression of the erythropoiesis-involved genes Ermap, Kel, Rhd, Rhag, Slc4a1, Gypa, Add2, Ank1, Epb4.1, Epb4.2, Epb4.9, Spta1, Sptb, Tmod1, Ahsp, Acyp1, Gata1, Gfi1b, Tal1, Klf1, Epor, and Cldn13. In vaccination-protected mice, expression of these genes, except Epb4.1, is significantly higher on day 4 p.i. than in un-protected non-vaccinated mice, reaches maximal expression at peak parasitaemia on day 8 p.i., and is slowed down or even decreased towards the end of crisis phase on day 11 p.i.. After day 1 p.i., Epor expression takes about the same course as that of the other erythroid genes. Hepatic expression of Epo, however, is delayed in both vaccinated and non-vaccinated mice for the first 4 days p.i. and is maximal at significantly higher levels in vaccinated mice on day 8 p.i., before declining towards the end of crisis phase on day 11 p.i. Conclusion: The present data indicate that vaccination accelerates malaria-induced erythroblastosis in the liver for 1-2 days. This may contribute to earlier replenishment of peripheral red blood cells by liver-derived reticulocytes, which may favour final survival of otherwise lethal blood-stage malaria, since reticulocytes are not preferred as host cells by P. chabaudi.
The use of crowdfunding and its impact on entrepreneurship in the city of Ambato - Ecuador (2021)

Crowdfunding and its impact on entrepreneurship in the city of Ambato are studied, according to several authors the variables are associated quite well when undertaking an idea and seeking financing. Within this process, the advantages and disadvantages of using crowdfunding are highlighted, as well as the process to undertake and finance projects. The results express that there is still the wrong thinking that financing is a limitation to undertake and they do not look for options in the market that can satisfy their needs. The results to entrepreneurs show that there is ignorance about crowdfunding but there is a real interest in learning about the subject and using it; also that the first financing option is banking. Finally, through the chi square the hypothesis is verified, accepting that crowdfunding does impact the enterprises of the city of Ambato. Keywords: Crowdfunding, Entrepreneurship, Investments, Financing, Economic performance. References [1]R. Abdurrahman, M. Erna amd M. Anang, «Digital Marketing and SMEs: A Systematic Mapping Study,» Library Philosophy and Practice (e-journal), 2 Agosto 2021. [2]Ley Orgániza de Emprendimiento e Innovación, 2020. [3]Crowdfunding ORG, «Crowdfunding una nueva forma de recaudar dinero para los proyectos,» 2020. [4]M. García and J. Saiz, «Concepto de emprendimiento, teorías y nuevos enfoques. Crowdfunding y nuevas formas de financiamiento,» Handbook of Science and Technology, 2017. [5]P. Moina, L. Morales and A. Córdoba, «El crowdfunding un nuevo mecanismo de impulsar la economía en el Ecuador,» Revista de Ciencias de la Administración y Economía, 2020. [6]A. Briones, «Concepto de Crowdfunding,» IEPS, p. 22, 2019. [7]E. Flores, «Diseño de un Centro para Emprendedores en una Escuela Profesional de Ingeniería aplicando el Modelo Lean Canvas,» Perú, http://dx.doi.org/10.4067/S0718-50062019000600151, 2019. [8]A. Kritiko, «Emprendedores y su impacto en el empleo y el crecimiento económico,» DIW Berlin, University of Potsdam, and IZA, Germany, 2019. [9]J. Gallestegui, «Franquicias regionales,» Emprender Revista, México, 2006. [10]E. Tenori, «Jóvenes emprendedores,» IEPS, p. 14, 2017. [11]A. Marin, «Procesos de analisis de emprendimientos y negocios,» USFQ, pp. 35-63, 2017. [12]D. Ricardo, «Emprender en la nueva era,» Emprendedores LATAM, 2017. [13]T. Trang, «Emprendimiento, autoempleo y creación de empleo en Vietnam,» Agricultural Economics and Management-Master's Programme, 2019. [14]A. Villamar, G. Zambrano and A. Regalado, «Medios digitales en el posicionamiento de marca,» Espíritu Emprendedor TES, p. 1, 2019. [15]L. Jiménez and S. Acosta, «El crowdfunding como alternativa para el emprendedor del siglo XXI,» 2019.
Implementation of one-dimensional domain wall dynamics simulator (2017)

We implemented a one-dimensional domain wall (DW) dynamics simulator based on the well-developed collective coordinate approach to demonstrate DW motion under a given magnetic field and/or current flow. The simulator adopted all known influences, including three-dimensional external magnetic fields, spin transfer torque with non-adiabatic contribution, spin Hall effect, Rashba effect, and Dzyaloshinskii-Moriya interaction. The simulator can calculate the position, velocity, internal magnetization angle, and tilting angle of the domain wall to the current direction or wire axis under given simulation conditions and material parameters. It will not only provide physical insights of domain wall dynamics to experimentalists, but also can be used to more easily simulate various physical circumstances before running time-consuming micromagnetic simulations or real experiments.
Immune Response to Coccidioidomycosis and the Development of a Vaccine (2017)

Coccidioidomycosis is a fungal infection caused by <i>Coccidioides posadasii</i> and <i>Coccidioides immitis</i>. It is estimated that 150,000 new infections occur in the United States each year. The incidence of this infection continues to rise in endemic regions. There is an urgent need for the development of better therapeutic drugs and a vaccine against coccidioidomycosis. This review discusses the features of host innate and adaptive immune responses to <i>Coccidioides</i> infection. The focus is on the recent advances in the immune response and host-pathogen interactions, including the recognition of spherules by the host and defining the signal pathways that guide the development of the adaptive T-cell response to <i>Coccidioides</i> infection. Also discussed is an update on progress in developing a vaccine against these fungal pathogens.
P129 Fungal contamination of valved holding chambers (VHCS): potential to prevent, and effect on drug delivery (2016)

<h3>Introduction and objectives</h3> Able Spacerâ−2 VHC (AS2) is one of many accessory devices available to improve pressurised metered dose inhaler (pMDI) drug delivery, but uniquely includes a ∼ 1wt% body polymer silver ion additive ( ∼ 1%Ag+) to combat microbial growth and reduce static. Drug-specific bacterial growth on VHC polymers<sup>1</sup> and the bacterial growth-reducing effects of the Ag+ polymer are known.<sup>2</sup> The fungal pathogen <i>Aspergillus fumigatus</i> causes serious pulmonary disease. We assessed the effect of 4%Ag+ on fungal activity and, subsequently, drug delivery characteristics. <h3>Methods</h3> Determination of fungal sporicidal activity was via modified ISO22196:2011 using flat body polymer discs (n = 3) of AS2 ∼ 1% Ag+ and AS2 4%Ag+, and sterile Control (same polymer minus Ag+, n = 6). 100mL <i>A. fumigatus</i> (5.0 x 10<sup>5</sup> spores/mL distilled water) was pipetted onto disc surfaces. Samples were incubated for 24 h at 35°C/ ≥ 95% relative humidity, with silver ions neutralised thereafter. Colony forming units (CFU) were enumerated by spiral dilution and converted to CFU/cm<sup>2</sup>. Aerosol performance of salbutamol (as salbutamol sulphate) pMDI (Ventolinâ Evohaler, GSK) through AS2 VHC ( ∼ 1% Ag+ as standard) and a newly-developed AS2 4% Ag+ VHC was assessed through a Next Generation Impactor (NGI) at 30 L/min. pMDIs and NGI were operated, and drug determinations made, using standard procedures. <h3>Results</h3> 24 h geometric mean Log<sub>10</sub><i>A. fumigatus</i> CFU/cm<sup>2</sup> were 4.2 × 10<sup>3</sup> (Control), 2.8 × 10<sup>3</sup> ( ∼ 1% Ag+), and 4.5 × 10<sup>2</sup> (4% Ag+), representing Log<sub>10</sub> and% reductions from Control of 0.2 (34%) and 1.0 (89%) for ∼1% Ag+ and 4% Ag+. Key salbutamol aerosol performance data were emitted dose (mg) 95.9 ± 11.0 and 94.9 ± 9.1; fine particle fraction (% &lt; 5.0 mm) 54.0 ± 4.3 and 53.6 ± 1.9; and fine particle dose (mg &lt; 5.0 mm) 52.0 ± 8.7 and 50.7 ± 3.8 for AS2 ∼ 1% Ag+ and AS2 4% Ag+ respectively. NGI recovery (Figure 1) profiles were very similar, including the VHC component: 38.9 ± 4.2 (AS2 ∼ 1% Ag+) and 40.2 ± 5.3 (AS2 4% Ag+). <h3>Conclusions</h3> Use of 4%Ag+ additive did not affect salbutamol aerosol performance and showed greater effect on <i>A. fumigatus</i> spored activity <i>in vitro</i>. VHC fungal <i>Candida</i> spp. and nebuliser <i>Aspergillus</i> spp. have been identified. The moist, anti-static setting of the Chamber may support and, of more concern, promote aerosolisation into the lungs of fungal material. Further research and understanding are necessary. <h3>Reference</h3> Sanders. <i>PCRM</i> 2016;<b>26</b>(16022):16. Sanders MJ, <i>et al</i>. P87 Klebsiella Pneumoniae Survival On Plastic Valved Holding Chamber Bodies. <i>Thorax</i> 2014;<b>69</b>(Suppl 2):A114.
Micelle‐bound conformation of a hairpin‐forming peptide: Combined NMR and molecular dynamics study (2002)

A peptide fragment from a protein hairpin turn region was modified by addition of isoleucine residues to both ends to enhance binding to lipid micelles; the resulting peptide (I(1)-I(2)-C(3)-N(4)-N(5)-P(6)-H(7)-I(8)-I(9)) contains the core sequence I-C-N-N-P-H from an antibody-binding region of hemagglutinin A. Nuclear magnetic resonance (NMR) diffusion measurements indicated partial binding (43-65%) of the peptide to micelles of n-octylglucoside and significantly stronger binding (85%) to dodecylphosphocholine (DPC) micelles. Simulated annealing and conformational analysis using nuclear Overhauser enhancement restraints revealed a type I or III hairpin turn between residues N(5) and I(8) of the DPC-bound peptide. Amide exchange experiments support the possibility that a hydrogen bond forms between N(5) and I(8), stabilizing the turn. In contrast, no discernable structure was observed for the peptide in aqueous solution by either NMR or circular dichroism. Molecular dynamics simulations of DPC micelles and peptide-micelle complexes suggested that the peptide lies flat on the micelle surface and showed rapid rearrangement of the lipids to accommodate the bound peptide. According to a search performed using the basic local alignment search tool (BLAST), the sequences N-P-H-I and N-P-H-V are present as hairpin turns in eight of the nine proteins whose crystal structures were available. The addition of isoleucine residues and the use of lipid micelles to stabilize hairpin conformations equivalent to those found in proteins generates new possibilities for reproducing biologically important hairpin turns from short, linear peptides.
Improved quantification of CSF bilirubin in the presence of hemoglobin using least squares curve-fitting (2011)

Subarachnoid hemorrhage (SAH) is a dangerous neurological event with a very short time window for early diagnosis. Clinical diagnoses performed in a lab seek to quantify bilirubin in cerebrospinal fluid (CSF) as a biomarker for SAHs; however laboratory assays suffer from lengthy protocols, interference from hemoglobin, and the availability of expertise. Substantial improvements in the determination of bilirubin concentration in the presence of hemoglobin in CSF are demonstrated in this work. Concentration estimates within 15% for bilirubin in the range of 0.2 to 1.6 mg /dl were determined for CSF samples containing fresh hemoglobin concentrations ranging from 0.05 to 0.25 g/dl. To demonstrate extensibility of the system with respect to more complete mock SAH samples, sample sets with one additional species of both hemoglobin and bilirubin, methemoglobin and alpha-bilirubin, respectively, were tested and yielded results within 25% of actual values, as measured by standard chemical assays of preparations prior to mixing.
Tecendo Redes pela Igualdade: Meninas Adolescentes de Comunidades de Baixa-renda Debatendo Sobre as Relações de Gênero e a Violência Contra as Mulheres. Doi: 10.5212/Rlagg.v.2.i2.002014 (2011)

A construção do conhecimento nos permite (des) aprender e (re) significar valores, ideais e práticas de vida, especialmente quando é feita a partir do encontro e diálogo entre academia e comunidade. A igualdade de oportunidades entre homens e mulheres também parece possível quando tem nos fundamentados nessa premissa. Este artigo visa, portanto, refletir sobre os discursos construídos por meninas adolescentes, moradoras de duas comunidades de baixa-renda de Recife, com respeito ao tema de gênero e violência contra as mulheres.
IBAKE: Identity-Based Authenticated Key Exchange (2012)

Cryptographic protocols based on public key methods are based on
certificates and large scale public key infrastructure (PKI) to
support certificate management. The emerging field of Identity Based
Encryption protocols allows to simplify the infrastructure
requirements via a Key Generation Function (KGF) while providing the
same flexibility. However one significant limitation of Identity Based
Encryption methods is that the KGF can end up being a de-facto key
escrow server with undesirable consequences. Another observed
deficiency is a lack of mutual authentication of communicating
parties. Here, Identity Based Authenticated Key Exchange (IBAKE)
Protocol is specified which does not suffer from the key escrow
problem and in addition provides mutual authentication and a perfect
forward and backwards secrecy.
Pathogenesis of oedema in chronic severe anaemia: studies of body water and sodium, renal function, haemodynamic variables, and plasma hormones. (1993)

In patients with oedema caused by chronic severe anaemia there is retention of salt and water, reduction of renal blood flow and glomerular filtration rate, and neurohormonal activation similar to that seen in patients with oedema caused by myocardial disease. However, unlike patients with myocardial disease, patients with anaemia have a high cardiac output and a low systemic vascular resistance and blood pressure. It is suggested that the low concentration of haemoglobin in patients with anaemia causes a reduced inhibition of basal endothelium-derived relaxing factor activity and leads to generalised vasodilatation. The consequent low blood pressure may be the stimulus for neurohormonal activation and salt and water retention.
Experimental study of substrate roughness and surfactant effects on the Landau-Levich law (2005)

In this work we present an experimental study of deviations from the classical Landau-Levich law in the problem of dip coating. Among the examined causes leading to deviations are the nature of the liquid-gas and liquid-solid interfaces. The thickness of the coating film created by withdrawal of a plate from a bath was measured gravimetrically over a wide range of capillary numbers for both smooth and well-characterized rough substrates, and for clean and surfactant interface cases. In view of the dependence of the lifetime of a film on the type of liquid and substrate, and liquid-gas and liquid-solid interfaces, we characterized the range of measurability of the film thickness in the parameter space defined by the withdrawal capillary number, the surfactant concentration, and substrate roughness size. We then study experimentally the effect of a film thickening due to the presence of surfactants. Our recent theory based on a purely hydrodynamic role of the surface active substance suggests that there is a sorption-controlled coating regime in which Marangoni effects should lead to film thinning. However, our experiments conducted in this regime demonstrate film thickening, calling into question the conventional wisdom, which is that Marangoni stresses (as accounted by the conventional interfacial boundary conditions) lead to film thickening. Next we examine the effect of well-characterized substrate roughness on the coated film thickness, which also reveals its influence on wetting-related processes and an effective boundary condition at the wall. In particular, it is found that roughness results in a significant thickening of the film relative to that on a smooth substrate and a different power of capillary number than the classical Landau-Levich law.
Comparison of six in‐house tests for the rapid diagnosis of feline immunodeficiency and feline leukaemia virus infections (2001)

Six rapid tests for the diagnosis of feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) infections which have recently been introduced in Europe for use in small animal practice were compared. Eight hundred serum samples were tested and those reacting FIV-positive in at least one of the tests were confirmed by Western blot, and those reacting FeLV-positive were confirmed by virus isolation. The specificity and sensitivity of each test and the quality of the results produced were compared.