gebhart/patrepeval huggingface dataset:
Single-step genomic evaluation of milk production traits in Canadian Alpine and Saanen dairy goats (2022)

Genomic evaluations are routine in most plant and livestock breeding programs but are used infrequently in dairy goat breeding schemes. In this context, the purpose of this study was to investigate the use of the single-step genomic BLUP method for predicting genomic breeding values for milk production traits (milk, protein, and fat yields; protein and fat percentages) in Canadian Alpine and Saanen dairy goats. There were 6,409 and 12,236 Alpine records and 3,434 and 5,008 Saanen records for each trait in first and later lactations, respectively, and a total of 1,707 genotyped animals (833 Alpine and 874 Saanen). Two validation approaches were used, forward validation (i.e., animals born after 2013 with an average estimated breeding value accuracy from the full data set ≥0.50) and forward cross-validation (i.e., subsets of all animals included in the forward validation were used in successive replications). The forward cross-validation approach resulted in similar validation accuracies (0.55 to 0.66 versus 0.54 to 0.61) and biases (-0.01 to -0.07 versus -0.03 to 0.11) to the forward validation when averaged across traits. Additionally, both single and multiple-breed analyses were compared, and similar average accuracies and biases were observed across traits. However, there was a small gain in accuracy from the use of multiple-breed models for the Saanen breed. A small gain in validation accuracy for genomically enhanced estimated breeding values (GEBV) relative to pedigree-based estimated breeding values (EBV) was observed across traits for the Alpine breed, but not for the Saanen breed, possibly due to limitations in the validation design, heritability of the traits evaluated, and size of the training populations. Trait-specific gains in theoretical accuracy of GEBV relative to EBV for the validation animals ranged from 17 to 31% in Alpine and 35 to 55% in Saanen, using the cross-validation approach. The GEBV predicted from the full data set were 12 to 16% more accurate than EBV for genotyped animals, but no gains were observed for nongenotyped animals. The largest gains were found for does without lactation records (35-41%) and bucks without daughter records (46-54%), and consequently, the implementation of genomic selection in the Canadian dairy goat population would be expected to increase selection accuracy for young breeding candidates. Overall, this study represents the first step toward implementation of genomic selection in Canadian dairy goat populations.
Small regulatory RNAs control the multi‐cellular adhesive lifestyle of Escherichia coli (2012)

Small regulatory RNA molecules have recently been recognized as important regulatory elements of developmental processes in both eukaryotes and bacteria. We here describe a striking example in Escherichia coli that can switch between a single-cell motile lifestyle and a multi-cellular, sessile and adhesive state that enables biofilm formation on surfaces. For this, the bacterium needs to reprogramme its gene expression, and in many E. coli and Salmonella strains the lifestyle shift relies on control cascades that inhibit flagellar expression and activate the synthesis of curli, extracellular adhesive fibres important for co-aggregation of cells and adhesion to biotic and abiotic surfaces. By combining bioinformatics, genetic and biochemical analysis we identified three small RNAs that act by an antisense mechanism to downregulate translation of CsgD, the master regulator of curli synthesis. Our demonstration that basal expression of each of the three RNA species is sufficient to downregulate CsgD synthesis and prevent curli formation indicates that all play a prominent role in the curli regulatory network. Our findings provide the first clue as to how the Rcs signalling pathway negatively regulates curli synthesis and increase the number of small regulatory RNAs that act directly on the csgD mRNA to five.
Unusual Electrochemical Response of Oligoalkylthiophene Films: Involvement of Bipolarons (2006)

Cyclic voltammograms of π-conjugated oligoalkylthiophene (13T) films are found to show two oxidation peaks during the 1st potential cycling up to 0.8 V. In the subsequent cycles, however, the 2nd oxidation peak disappears completely and the 1st peak shifts by ca. 0.1 V to the cathodic direction. This finding along with spectroscopic measurements of 13T film before and after electrochemical stimulus suggests first that two different phases to be oxidized at separate potentials coexist in a pristine 13T film and second that one phase can be switched to the other by being oxidized to generate bipolarons.
β-Lactam Drug Allergens: Fine Structural Recognition Patterns of Cephalosporin‐Reactive IgE Antibodies (1996)

Lack of experimental findings on the spectrum of cephalosporin allergenic determinants has hindered diagnosis of adverse reactions to these drugs and retarded understanding of allergenic cross-reactions between cephalosporins and between cephalosporins and penicillins. Subjects allergic to the widely used cephalosporin antibiotic cefaclor have serum immuno globulin (Ig) E antibodies that react with the drug. Quantitative hapten inhibition studies employing sera from subjects allergic to cefaclor revealed fine structual recognition differences between the combining site specificities of cefaclor-reactive IgE antibodies in the sera of different subjects. Unlike penicillins, where discrete side chain or thiazolidine ring determinants alone may be recognized, IgE binding determinants on cefaclor encompassed the entire molecule. Fine structural recognition specificity differences at positions R1 (side-chain) and R2 (substituent attached to dihydrothiazine ring) were detected between IgE antibodies in different sera. Some antibodies showed clear preferential recognition of the aminobenzyl group at position R1 and Cl at R2 while with others, a greater degree of recognition tolerance was seen at R1 where, for example, the aminohydroxybenzyl or aminodihydrobenzyl groups were recognized, and at R2 where a methyl or even an ester group was tolerated. As with the penicillins, cephalosporins as allergens cannot simply be considered as a group of compounds with a common allergenic determinant structure. IgE antibodies that bind to cefaclor show great heterogeneity indicated by clear, fine structural differences in recognition of the R1 and R2 groups on the drug.
Structural Characterization of LRRK2 Inhibitors (2015)

Kinase inhibition is considered to be an important therapeutic target for LRRK2 mediated Parkinson's disease (PD). Many LRRK2 kinase inhibitors have been reported but have yet to be optimized in order to qualify as drug candidates for the treatment of the disease. In order to start a structure-function analysis of such inhibitors, we mutated the active site of Dictyostelium Roco4 kinase to resemble LRRK2. Here, we show saturation transfer difference (STD) NMR and the first cocrystal structures of two potent in vitro inhibitors, LRRK2-IN-1 and compound 19, with mutated Roco4. Our data demonstrate that this system can serve as an excellent tool for the structural characterization and optimization of LRRK2 inhibitors using X-ray crystallography and NMR spectroscopy.
Application of photothermal ionization spectroscopy to the study of epitaxially grown germanium on silicon (1992)

We have applied the technique of photothermal ionization spectroscopy to the study of a 1-μm-thick p-Ge epilayer, grown by molecular beam epitaxy on a n-Si substrate, 500 μm in thickness. The spectra indicate that in the Ge layer there exists a series of charged acceptor defects with an ionization energy continuum starting at 15 meV, an ionization energy somewhat larger than those of the elemental substitutional acceptors. Our results show that photothermal ionization spectroscopy can be applied very advantageously to epitaxial layers of the Si1−xGex alloys that are Ge-like, i.e., for x≥0.85. For these layers, charged impurity centers and defects have their spectral features well separated from those of the Si substrate.
Optimizing geometric multigrid method computation using a DSL approach (2017)

The Geometric Multigrid (GMG) method is widely used in numerical analysis to accelerate the convergence of partial differential equations solvers using a hierarchy of grid discretizations. Multiple grid sizes and recursive expression of multigrid cycles make the task of program optimization tedious. A high-level language that aids domain experts for GMG with effective optimization and parallelization support is thus valuable.
The Rise of American Nationalism (2006)

Nitric oxide (NO) is a short-lived molecule required for many physiological functions, produced from L-arginine by NO synthases (NOS). It is a free radical, producing many reactive intermediates that account for its bioactivity. Sustained induction of the inducible form of NOS (iNOS) in chronic inflammation may be mutagenic, through NO-mediated DNA damage or hindrance to DNA repair, and thus potentially carcinogenic. Expression of iNOS is positively associated with P53 mutation in tumours of the colon, lung, and oropharynx. Progression of a large majority of human and experimental tumours seems to be stimulated by NO resulting from activation of iNOS or constitutive NOS, whereas inhibition is documented in others. This discrepancy is largely explained by differential sensitivity of tumour cells to NO-mediated cytostasis or apoptosis and clonal evolution of NO-resistant and NO-dependent cells. P53 mutation or loss is one of many events linked with NO resistance and dependence. NO can stimulate tumour growth and metastasis by promoting migratory, invasive, and angiogenic abilities of tumour cells, which may also be triggered by activation of cyclo-oxygenase (COX)-2. Thus, selective inhibitors of NOS, COX, or both may have a therapeutic role in certain cancers.
Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system (2022)

<i>Bst</i> DNA polymerase is a DNA polymerase derived from <i>Geobacillus stearothermophilus,</i> has a strand-displacement activity, and is used in loop-mediated isothermal amplification (LAMP) for rapid detection of COVID-19. Despite its potential to be employed in the detection of COVID-19, using commercially available enzymes is not economically feasible. The use of noncommercial enzyme for routine use is desirable. However, research on <i>Bst</i> DNA polymerase is still limited in Indonesia. For those reasons, a preliminary study of scale-up production of recombinant <i>Bst</i> polymerase was conducted. Therefore, the optimization of expression conditions was performed. The optimum conditions for <i>Bst</i> polymerase expression were as follows: 1 mM of IPTG, post-induction incubation time of 6 h, and induction at OD<sub>600</sub> 1.1. Employing optimum conditions could result in 2.8 times increase in protein yield compared to the initial conditions. Subsequently, an operation in 1 L working volume by a lab-scale bioreactor had been performed, followed by purification and dialysis. The optimum result for a 1 L lab-scale bioreactor was achieved by applying 100 rpm and 3 vvm, giving 11.7 mg/L of protein yield. <i>Bst</i> polymerase was successfully purified showing 813.56 U/mg of polymerase activity.
Morphology of n-type macroporous silicon: doping density dependence (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMorphology of n-type macroporous silicon: doping density dependenceE. Galun, C. Reuben, S. Matlis, R. Tenne, and C. Levy-ClementCite this: J. Phys. Chem. 1995, 99, 12, 4132–4140Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/j100012a038https://doi.org/10.1021/j100012a038research-articleACS PublicationsRequest reuse permissionsArticle Views200Altmetric-Citations13LEARN 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 options Get e-Alerts
Microdissection and SAGE as a combined tool to reveal gene expression in ductal carcinoma in situ of the breast (2004)

The interplay between cancer cells and the normal surrounding tissue is believed to influence the biological behavior of the tumor. However, the presence of multiple cell types within the prelevated tumor specimen may attenuate changes that occur specifically in the malignant cells within their microenvironment. To study gene expression of the malignant cells in situ, we used a new microdissection method to separate ductal carcinoma in situ (DCIS) cells from the surrounding stroma, immunological infiltrates, and endothelial cells. We applied an adapted microSAGE protocol, without total mRNA amplification, to study their gene expression profile. Three thousand two hundred one different transcripts were identified in a total of 29 534 observed tags. Of these unique tags, 88.3% matched known GenBank sequences and 11.7% represented unknown transcripts. As compared to a total DCIS SAGE library, microdissection combined with SAGE revealed additional genes expressed only in normal surrounding, probably stromal, cells and not or significantly less in DCIS tumor cells. This study demonstrates that microdissection can be combined with SAGE as a tool to study transcriptomes. This approach provides important new information on differential gene expression both in tumor cells and normal surrounding tissue. Several of the observed differences indeed disappear when the total tumor mass is analyzed.
Multigeneic QTL: the laccase encoded within the soybean Rfs2/rhg1 locus inferred to underlie part of the dual resistance to cyst nematode and sudden death syndrome. (2009)

Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isolated from resistant cultivar 'Forrest' that were different among susceptible cultivars 'Asgrow 3244' and 'Williams 82' at four residues R/H168, I/M271, R/H330, E/K470. Additional differences were found in six of the seven introns and the promoter region. Transcript abundance (TA) among genotypes that varied for resistance to SDS or SCN did not differ significantly. Therefore the protein activity was inferred to underlie resistance. Protein expressed in yeast pYES2/NTB had weak enzyme activity with common substrates but good activity with root phenolics. The Forrest isoform may underlie both QRfs2 and rhg1.
RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma (2015)

The conserved RNA-binding protein Musashi1 (MSI1) has emerged as a key oncogenic factor in numerous solid tumors, including glioblastoma. However, its mechanism of action has not yet been established comprehensively. To identify its target genes comprehensively and determine the main routes by which it influences glioblastoma phenotypes, we conducted individual-nucleotide resolution cross-linking and immunoprecipitation (iCLIP) experiments. We confirmed that MSI1 has a preference for UAG sequences contained in a particular structural context, especially in 3' untranslated regions. Although numerous binding sites were also identified in intronic sequences, our RNA transcriptome sequencing analysis does not favor the idea that MSI1 is a major regulator of splicing in glioblastoma cells. MSI1 target mRNAs encode proteins that function in multiple pathways of cell proliferation and cell adhesion. Since these associations indicate potentially new roles for MSI1, we investigated its impact on glioblastoma cell adhesion, morphology, migration, and invasion. These processes are known to underpin the spread and relapse of glioblastoma, in contrast to other tumors where metastasis is the main driver of recurrence and progression.
Finite-element-based parametric study on welding-induced distortion of TIG-welded stainless steel 304 sheets (2011)

Finite element (FE) simulation of welding processes enables the prediction of component distortions which significantly reduces the need for physical trials. This facilitates reduction in lead time and costs associated with process planning. In this paper, FE modelling of tungsten inert gas welding is performed using SYSWELD for a butt joint between 2 mm thick stainless steel 304 (SS304) sheets. A three-dimensional double ellipsoid (Goldak) heat source is used to model the heat flow during welding. The heat source definition as validated against an experimentally obtained grain structure (macrograph) and thermal history. The isotropic hardening material behaviour model is used in the mechanical analysis and the annealing is considered at 1300 °C. FE-predicted distortion for an unclamped situation is compared with an experimental trial. The FE-predicted fusion zone, thermal histories, and residual distortion are found to be in reasonably good agreement with experimental results. The validated FE methodology is further used to perform a parametric study on the effect of natural and forced cooling, clamp release times, and welding sequence on distortion.
Nearly data-based optimal control for linear discrete model-free systems with delays via reinforcement learning (2014)

In this paper, a nearly data-based optimal control scheme is proposed for linear discrete model-free systems with delays. The nearly optimal control can be obtained using only measured input/output data from systems, by reinforcement learning technology, which combines Q-learning with value iterative algorithm. First, we construct a state estimator by using the measured input/output data. Second, the quadratic functional is used to approximate the value function at each point in the state space, and the data-based control is designed by Q-learning method using the obtained state estimator. Then, the paper states the method, that is, how to solve the optimal inner kernel matrix P‾$\bar{P}$ in the least-square sense, by value iteration algorithm. Finally, the numerical examples are given to illustrate the effectiveness of our approach.
Tipos de interés y déficit presupuestarios futuros esperados en EEUU (1992)

We report the case of a 54 years old male diagnosed as ethmoidal epidermoid carcinoma which, after almost 1 year--asymptomatic period, debuted with facial pain (cluster headache) without another associated clinic. Sino-nasal malignant tumours represent about 5%-6% in all ENT carcinomas and they use to be of later diagnosis, with high probability of local recurrence and invasiveness on structures like orbit and skull base. The main treatment for ethmoidal squamous carcinomas is surgery and depending on staging can require radiotherapy and/or chemotherapy. A bibliographic review is done at this respect.
DO CORTICOSTEROIDS REDUCE THE RISK OF FAT EMBOLISM SYNDROME IN POLY-TRAUMA PATIENTS?: A META-ANALYSIS (2009)

Fat embolism syndrome (FES) is a potentially lethal condition commonly seen in poly-traumatised patients, particularly those with multiple long-bone fractures. Treatment has centered around supportive care and early fracture fixation. Several clinical small trials have suggested corticosteroids benefit patients with FES but its use remains controversial. Our objective was to determine the effect of corticosteroids in preventing FES in patients with multiple long-bone fractures. We conducted a meta-analysis of randomised trials, searching computerised databases for published studies from 1966–2006. Additionally, we performed hand searches of major orthopaedic journals, meeting proceedings, and texts. Our primary outcome was the rate of FES. Secondary outcomes included presence of hypoxia, petechiae, mortality, infection, and delayed union. Of the one hundred and four studies identified, nine were potentially eligible, and only seven met all our eligibility criteria. From our pooled analysis of three hundred and eighty-nine patients, we found that corticosteroids reduced the risk of FES by 78% (95%CI: 43–92%, heterogeneity p-value=0.62, I2=10%) and that only eight patients needed to be treated (NNT=7.5) to prevent one case of FES (95%CI: five to thirteen patients). We did not find any significant differences in the rates of mortality, infection, or delayed union. The current evidence suggests that the use of corticosteroids is beneficial in the prevention of fat embolism syndrome in patients with multiple long-bone fractures. The use of corticosteroids does not appear to significantly increase the risk of complications although a confirmatory large randomised trial is needed.
Signal amplitude conditioned density function for monopulse measurements of fixed-amplitude targets (2002)

Since the measured amplitude of the sum-signal of a monopulse radar is known in the receiver, the probability density function (PDF) for the monopulse measurements can be conditioned on the measured amplitude. The conditional PDF and related statistical properties are developed for the in-phase and quadrature parts of the monopulse measurements of fixed-amplitude targets. Conditions under which the conditional PDF can be approximated as Gaussian are considered. A decoupling of the estimation of the target amplitude and the monopulse processing is proposed for estimating the direction-of-arrival (DOA) for moderate to low SNR targets. Estimators of the variances of the monopulse measurements and the DOA estimate are also given for use in decision and control algorithms such as target tracking with a Kalman filter.
Ubiquitous support of multi path probing: Preventing man in the middle attacks on Internet communication (2014)

Digital certificates issued by certification authorities (CAs) which are part of the Web Public Key Infrastructure (Web PKI) are the indispensable basis for secure communication on the Internet. The certificates are used in TLS to authenticate web servers. However, as past incidents have shown, CA failures and the issuance of malicious certificates threatens the security of communication, as it allows for man in the middle attacks (MitM) and server impersonation. All known mitigations so far are only niche solutions having their own weaknesses and problems which prevented a wide deployment. Thus, additional methods must be natively supported by common web servers to mitigate threats imposed by CA failures. We propose to integrate multi path probing of certificates as a fundamental mechanism into the web infrastructure. This enables the reconfirmation of certificates whenever their authenticity is in doubt. We describe how this can be realized with minor efforts and without infrastructural changes, while the overhead arising from these reconfirmations can be kept at a small rate.