gebhart/patrepeval huggingface dataset:
phylostratr: A framework for phylostratigraphy (2018)

Abstract Motivation The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. Currently, there are no general pipelines for this task. We present an R package, phylostratr , to fill this gap, making high-quality phylostratigraphic analysis accessible to non-specialists. Results Phylostratigraphic analysis entails searching for homologs within increasingly broad clades. The highest clade that contains all homologs of a gene is that gene’s phylostratum. We have created a general R-based framework, phylostratr , for estimating the phylostratum of every gene in a species. The program can fully automate an analysis: select species for a balanced representation of each strata, retrieve the sequences from UniProt, build BLAST databases, run BLAST, infer homologs for each gene against each subject species, determine phylostrata, and return summaries and diagnostics. phylostratr allows extensive customization. A user may: modify the automatically-generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. phylostratr also offers proteome quality assessments, false-positive diagnostics, and checks for missing organelle genomes. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae . Availability phylostratr source code and vignettes are available on GitHub at https://github.com/arendsee/phylostratr Contact evewurtele@gmail.com
Analysis of a UWB Hemispherical Antenna Array in FDTD With a Time Domain Huygens Method (2012)

Electromagnetic modeling is needed in a wide variety of large and complex situations. Existing numerical techniques such as finite difference time domain (FDTD) can, in principle, solve any problem no matter how large or complicated given a sufficiently powerful computer. However, in practice, there remain problems which require more computer power than is available. Recently, the time-domain Huygens (TDH) approach has been shown to be effective for enabling large problems such as propagation on body area networks (BANs) to be modeled in FDTD. In this paper, it is shown that the much larger problem of the conformal antenna array, which is used in the MARIA breast cancer tumor detection system, is also very amenable to this technique with even greater savings in computer resources. Accurate results are obtained using less that a tenth of the resources needed to solve the same problem using existing advanced FDTD tools. The details of how this method is applied, and the choices which need to be made, are discussed.
Abstract 4238: COnsortium for METabolomics Studies (COMETS): leveraging resources to accelerate scientific discovery (2017)

Abstract Metabolomics is a systems approach to the biology of health and disease and an ‘-omics’ discipline that measures small metabolites representing end products of a variety of metabolic and cellular processes as reflected in available biological specimens (e.g. blood, urine, saliva, feces and tissue). As an increasingly more common approach used for epidemiologic and clinical studies, metabolomics has the potential to improve disease risk assessment, screening, diagnosis, prognosis and predictive response to therapy, as well as provide disease mechanistic insight and help to establish criteria for causation. It is timely to establish mechanisms for leveraging existing resources and data for novel biomarker discovery using metabolomics approaches. To this end, the National Institutes of Health COnsortium of METabolomics Studies (COMETS) was established in 2014 (http://epi.grants.cancer.gov/comets/), and currently includes 34 prospective cohorts and 2 consortia from the United States, Europe, Asia and South America. The COMETS mission is to promote collaborations among prospective cohort studies that follow participants for a range of outcomes and perform metabolomic profiling of individuals. COMETS aims to facilitate an open exchange of ideas, knowledge, and results to accelerate a shared goal of identifying metabolomic profiles associated with chronic disease phenotypes (e.g. heart disease, diabetes, cancer). The structure of COMETS includes a steering committee with one representative from each participating cohort/consortium and a number of working groups, including age analysis, data harmonization, statistics, and trainee. In November 2016, COMETS held their inaugural scientific meeting. As a result of this meeting, more working groups are currently being established to support additional interests/projects among the consortium members. Here we further describe the COMETS structure, including preliminary descriptive data, which aims to advance the use and impact of metabolite profiling in population-based research. Citation Format: Rachael Z. Stolzenberg-Solomon, Steven Moore, Crnelia Ulrich, Elizabeth Poole, Marinella Temprosa, Mukesh Verma, Demetrius Albanes, Clara Barrios Barrera, Eric Boerwinkle, Juan P. Casas, Clary Clish, Robert Gerszten, Christian Gieger, Marc Gunter, Sei Harada, Tamara Harris, David Herrington, Ann Hsing, Mattias Johannson, Claudia Langenberg, Jessica Lasky-Su, Loic Le Marchand, Charles Matthews, Cristina Menni, Matej Oresic, Eric Orwoll, Alexandre Pereira, Kathyrn Rexrode, Svati Shah, Xiao-ou Shu, Victoria Stevens, Bing Yu, Hua Zhao, Krista Zanetti. COnsortium for METabolomics Studies (COMETS): leveraging resources to accelerate scientific discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4238. doi:10.1158/1538-7445.AM2017-4238
Polymeric Amphiphile Branching Leads to Rare Nanodisc Shaped Planar Self-Assemblies (2008)

Self-assembly is fundamental to the biological function of cells and the fabrication of nanomaterials. However, the origin of the shape of various self-assemblies, such as the shape of cells, is not altogether clear. Polymeric, oligomeric, or low molecular weight amphiphiles are a rich source of nanomaterials, and controlling their self-assembly is the route to tailored nanosystems with specific functionalities. Here, we provide direct evidence that a particular molecular architecture, polymeric branching, leads to a rare form of self-assembly, the planar nanodisc. Cholesterol containing self-assemblies formed from amphiphilic linear or branched cetyl poly(ethylenimine) (Mn approximately 1000 Da) or amphiphilic cetyl poly(propylenimine) dendrimer derivatives (Mn approximately 2000 Da) show that branching, by reducing the hydrophilic headgroup area, alters the shape of the self-assemblies transforming closed 60 nm spherical bilayer vesicles to rare 50 nm x 10 nm planar bilayer discs. Increasing the hydrophilic headgroup area, by the inclusion of methoxy poly(ethylene glycol) moieties into the amphiphilic headgroup, transforms the planar discs to 100 nm spherical bilayer vesicles. This study provides insight into the key role played by molecular shape on molecular self-organization into rare nanodiscs.
Pumping of 7-Core erbium-doped double-clad fiber amplifier based on higher-order mode coupling (2015)

We investigated the pumping performance of 7-core erbium-doped double-clad fiber amplifier with novel pumping method which we proposed. The pumping method achieves compact assembly of the amplifier based on higher-order mode coupling of pump radiation. BPM calculation shows coupling efficiency of about 95 %.
Improving thermostability and catalytic activity of pyranose 2‐oxidase from <i>Trametes multicolor</i> by rational and semi‐rational design (2008)

The fungal homotetrameric flavoprotein pyranose 2-oxidase (P2Ox; EC 1.1.3.10) catalyses the oxidation of various sugars at position C2, while, concomitantly, electrons are transferred to oxygen as well as to alternative electron acceptors (e.g. oxidized ferrocenes). These properties make P2Ox an interesting enzyme for various biotechnological applications. Random mutagenesis has previously been used to identify variant E542K, which shows increased thermostability. In the present study, we selected position Leu537 for saturation mutagenesis, and identified variants L537G and L537W, which are characterized by a higher stability and improved catalytic properties. We report detailed studies on both thermodynamic and kinetic stability, as well as the kinetic properties of the mutational variants E542K, E542R, L537G and L537W, and the respective double mutants (L537G/E542K, L537G/E542R, L537W/E542K and L537W/E542R). The selected substitutions at positions Leu537 and Glu542 increase the melting temperature by approximately 10 and 14 degrees C, respectively, relative to the wild-type enzyme. Although both wild-type and single mutants showed first-order inactivation kinetics, thermal unfolding and inactivation was more complex for the double mutants, showing two distinct phases, as revealed by microcalorimetry and CD spectroscopy. Structural information on the variants does not provide a definitive answer with respect to the stabilizing effects or the alteration of the unfolding process. Distinct differences, however, are observed for the P2Ox Leu537 variants at the interfaces between the subunits, which results in tighter association.
An Immunohistochemical Study of Gastrointestinal Endocrine Cells in the BALB/c Mouse (2004)

The distributions and frequencies of some endocrine cells in the eight portions of the gastrointestinal tract (GIT) of BALB/c mouse were studied. Endocrine cells were stained using immunohistochemical method with seven types of antisera against bovine chromogranin (BCG), serotonin, gastrin, cholecystokinin (CCK)-8, somatostatin, glucagon and human pancreatic polypeptide (HPP), and the regional distributions and their relative frequencies were observed in the eight portions of the GIT of BALB/c mice. All seven types of immunoreactive (IR) cells were identified. Most of the IR cells in the intestinal portion were generally spherical or spindle in shape (open type cell) while round-shaped cells (closed type cell) were found in the intestinal gland and stomach regions occasionally. Their relative frequencies varied according to each portion of the GIT. BCG-IR cells were observed throughout the whole GIT except for the rectum and they were most predominant in the pylorus. Serotonin-IR cells were detected throughout the whole GIT and they showed the highest frequency in the fundus. Gastrin- and CCK-IR cells were restricted to the pylorus and duodenum with a majority in the pylorus and rare or a few frequencies in the duodenum. Compared with other mammals, somatostatin-IR cells were restricted to the fundus and pylorus with a few frequencies, respectively. In addition, glucagon- and HPP-IR cells were restricted to the fundus and duodenum, respectively, with relative low frequencies. Some species-dependent unique distributions and frequencies of endocrine cells were observed in the GIT of BALB/c mouse compared with other rodents.
A Study on the Mechanical Properties of 3D Printed PLA Specimens According to Infilled Pattern and Printing Direction (2021)

This paper intended to measure the material's rigidity according to the orientation of the PLA specimen produced by the FDM method. To measure the change of strength and stiffness according to the direction of stacking of FDM PLA, the specimen was manufactured and tested not only in the direction of stacking but also infill using line pattern and concentric pattern. The intensity of each direction was 38.11MPa with a 0 degree tensile in the line pattern, 3.45 times higher than 11.9MPa with a 90 degree tensile, and 2.15 times higher shear strength with 28.05MPa and 13.88MPa. In concentric pattern, 0 degree tensile was 50.62MPa, 6.25 times higher than 8.46MPa, and 2.23 times higher in shear strength at 13.52MPa compared to 29.56MPa. The biggest difference in zero-degree concentric pattern tensile was the 37% difference in the 0 degree concentric pattern factor. This shows that the difference in intensity according to direction is more pronounced in concentric patterns than line patterns, and the behavior under load will be similar until the breaking point regardless of the direction.
<i>ETHYLENE RESPONSE FACTOR</i> ( <i>ERF</i> ) genes modulate plant root exudate composition and the attraction of plant parasitic nematodes (2019)

Plant root exudates are compositionally diverse, plastic and adaptive. Ethylene signalling influences the attraction of plant parasitic nematodes (PPNs), presumably through the modulation of root exudate composition. Understanding this pathway could lead to new sources of crop parasite resistance. Here we have used Virus-Induced Gene Silencing (VIGS) to knockdown the expression of two ETHYLENE RESPONSE FACTOR ( ERF ) genes, ERF-E2 and ERF-E3 in tomato. Root exudates are significantly more attractive to the PPNs Meloidogyne incognita , and Globodera pallida following knockdown of ERF-E2 , which has no impact on the attraction of Meloidogyne javanica . Knockdown of ERF-E3 has no impact on the attraction of Meloidogyne or Globodera spp. GC-MS analysis revealed substantial changes in root exudate composition relative to controls. However, these changes do not alter the attraction of rhizosphere microbes Bacillus subtilis or Agrobacterium tumefaciens . This study further supports the potential of engineering plant root exudate for parasite control, through the modulation of plant genes.
It’s Not Just What You Say, But How You Say It: Muiltimodal Sentiment Analysis Via Crowdsourcing (2016)

This paper examines the effect of various modalities of expression on the reliability of crowdsourced sentiment polarity judgments. A novel corpus of YouTube video reviews was created, and sentiment judgments were obtained via Amazon Mechanical Turk. We created a system for isolating text, video, and audio modalities from YouTube videos to ensure that annotators could only see the particular modality or modalities being evaluated. Reliability of judgments was assessed using Fleiss Kappa inter-annotator agreement values. We found that the audio only modality produced the most reliable judgments for video fragments and that across modalities video fragments are less ambiguous than full videos.
Design methodology for multiple domain power distribution systems (2004)

High-speed digital devices require multiple voltage and frequency domains to accommodate the core logic and the input/output (I/O) circuitry for multiple interfaces. In addition, some of these interfaces are programmable to various speeds and signaling modes and they require multiple power supply voltages. These requirements create complex power delivery and signal distribution solutions. This paper proposes a design methodology for fast transient point of load (POL) power distribution architectures for microprocessors and fast switching logic. This paper presents an efficient power distribution system (PDS) design methodology that models the load, its point of load power converter, and the transporting system so that the entire system can be efficiently implemented in circuit simulation as a complete integrated setup for design optimization. Models for the voltage regulator module (VRM) and its transient response and stability, the active load with multiple power supply domains, and the power planes are discussed in detail. System voltage noise margin budgeting is also emphasized.
Enhancing of catalytic properties of vanadia via surface doping with phosphorus using atomic layer deposition (2015)

Atomic layer deposition is mainly used to deposit thin films on flat substrates. Here, the authors deposit a submonolayer of phosphorus on V2O5 in the form of catalyst powder. The goal is to prepare a model catalyst related to the vanadyl pyrophosphate catalyst (VO)2P2O7 industrially used for the oxidation of n-butane to maleic anhydride. The oxidation state of vanadium in vanadyl pyrophosphate is 4+. In literature, it was shown that the surface of vanadyl pyrophosphate contains V5+ and is enriched in phosphorus under reaction conditions. On account of this, V2O5 with the oxidation state of 5+ for vanadium partially covered with phosphorus can be regarded as a suitable model catalyst. The catalytic performance of the model catalyst prepared via atomic layer deposition was measured and compared to the performance of catalysts prepared via incipient wetness impregnation and the original V2O5 substrate. It could be clearly shown that the dedicated deposition of phosphorus by atomic layer deposition enhances the catalytic performance of V2O5 by suppression of total oxidation reactions, thereby increasing the selectivity to maleic anhydride.
Normative rearfoot motion during barefoot and shod walking using biplane fluoroscopy (2014)

II.
Case-control study of debrisoquine 4-hydroxylase, n-acetyltransferase 2, and apolipoprotein e gene polymorphisms in Parkinson's disease (2000)

We investigated the association of Parkinson's disease (PD) with two genes encoding liver-detoxifying enzymes, debrisoquine 4-hydroxylase (CYP2D6) and N-acetyltransferase 2 (NAT2), and with one gene related to Alzheimer's disease, apolipoprotein E (APOE). In a sample of 139 unrelated PD cases and 113 control subjects, the NAT2 M3 allele was associated with PD (odds ratio = 7.9; 95% confidence interval = 1.7-36.3). Case-control analyses for CYP2D6, APOE, and NAT2 M1 or M2 did not show a significant association. However, the age at onset of PD was significantly earlier in cases with the APOE epsilon2/epsilon3 genotype than in cases with the epsilon3/epsilon3 genotype.
Lupus nephritis in juvenile myelomonocytic leukemia. (1999)

A 13-year-old girl developed lupus nephritis and Hashimoto thyroiditis in the chronic phase of juvenile myelomonocytic leukemia (JMML). At age 7 months, she was diagnosed as having JMML based on the hepatosplenomegaly, leukocytosis, thrombocytopenia, increased levels of fetal hemoglobin, and spontaneous in vitro growth of granulocyte-macrophage progenitors. At the onset of JMML, she had hypergammaglobulinemia, antinuclear antibodies, rheumatoid factors and anti-smooth muscle antibody. She had been placed on oral 6-mercaptopurine for about 12 years, with clinical improvement. At age 13 years, she was found to have hematuria and proteinuria. She also developed arthritis and Raynaud's phenomenon as well. She had antinuclear antibodies, rheumatoid factors, LE phenomenon, beta-1C (C3) nephritic factor (C3NeF), antithyroid antibodies, and hypocomplementemia. The renal biopsy specimens revealed a diffuse increase in the mesangial cells and matrix by light microscopy, and intense staining of IgG, Clq and C3 by immunofluorescence microscopy. The hormonal study ultimately showed decreased thyroid functions. So she was diagnosed as lupus nephritis and Hashimoto thyroiditis. The patient is the first example to show close relationship between stem cell abnormalities in JMML and development of overt autoimmune disorders.
Cooperative effects at the interface of nanocrystalline metal–organic frameworks (2016)

Controlling the chemistry at the interface of nanocrystalline solids has been a challenge and an important goal to realize desired properties. Integrating two different types of materials has the potential to yield new functions resulting from cooperative effects between the two constituents. Metal–organic frameworks (MOFs) are unique in that they are constructed by linking inorganic units with organic linkers where the building units can be varied nearly at will. This flexibility has made MOFs ideal materials for the design of functional entities at interfaces and hence allowing control of properties. This review highlights the strategies employed to access synergistic functionality at the interface of nanocrystalline MOFs (nMOFs) and inorganic nanocrystals (NCs).
Diagnostic criteria for hepatocellular carcinoma ⩽3 cm with hepatocyte-specific contrast-enhanced magnetic resonance imaging (2016)

EASL criteria exhibit the best diagnostic performance for HCC ⩽3 cm on hepatocyte-specific contrast-enhanced MRI. A newly identified criterion (arterial-phase hyperintensity and hepatobiliary-phase hypointensity) may increase the diagnostic sensitivity of small (⩽2 cm) HCC.
Potential Involvement of Retroviral Elements in Human Dementias (2007)

Creutzfeldt-Jakob disease (CJD) is a dementia of humans caused by a class of infectious agents with several biological properties similar to those of conventional viruses. The molecular nature of this group of agents is enigmatic, for neither an agent-specific nucleic acid nor a non-host protein has yet been identified. Recent transmissions of familial CJD dementias to rodents suggest that this class of agent can be integrated into the germline. Furthermore, tissue culture studies indicate that CJD causes transformation of cells in a manner reminiscent of slowly oncogenic retroviruses. Currently characterized retroviral-like elements include many forms that do not have 'typical' retroviral ultrastructural morphology; several forms are also known to be resistant to various types of standard physicochemical inactivation. We suggest that CJD agents are either constituted by retroviral-like nucleic acids or interact with endogenous retroviral sequences to elicit a slowly progressive disease of the central nervous system. Several overlapping properties between infectious CJD and 'non-infectious' dementias, such as Alzheimer's disease, implicate potential common pathogenic mechanisms.
A strategy for safe sternal reentry in patients with pseudoaneurysms of the ascending aorta using the PORT-ACCESS EndoCPB system (2009)

Pseudoaneurysms of the ascending aorta developing after previous aortic or aortic valve surgery pose a high risk of exsanguination upon sternal reentry. In the past, femorofemoral bypass and hypothermic circulatory arrest before sternotomy was the preferred approach. Today, however, availability of the PORT-ACCESS EndoCPB system (Edwards Lifesciences, Irvine, CA, USA) allows for endovascular clamping and cardioplegia before sternotomy, avoiding circulatory arrest.
ChemInform Abstract: Catalysis by Electrons and Holes: Formal Potential Scales and Preparative Organic Electrochemistry (2015)

Abstract Review: 145 refs.
Magnetic Seizure Therapy for the Treatment of Depression (2007)

Transcranial magnetic stimulation (TMS) was introduced in the mid 1980s in clinical neurophysiology to study the central motor pathways. Research has been exponentially increased since, and many different methods for brain stimulation have been considered during the last decade. This publication focuses on transcranially applied, non- or low-invasive interventions not requiring an implantable device, i.e. electroconvulsive therapy (ECT), repetitive TMS (rTMS) and transcranial direct current stimulation (tDCS). It provides an excellent overview on this spectrum of fascinating techniques. Many leading experts in this field have contributed to this book. A single chapter summarizes the state of the art in ECT. A series of chapters provides an overview on preclinical research in animals and neuroimaging findings with rTMS and reviews the evidence of efficacy and safety in various psychiatric disorders (affective disorders, schizophrenia and anxiety disorders) also including an article on the application of rTMS in nonpsychiatric diseases, i.e. Parkinson's disease, stroke, pain and tinnitus. Finally, separate reviews discuss very recent innovative approaches in the field of rTMS, i.e. magnetic seizure therapy, theta burst stimulation and deep rTMS.This publication will doubtlessly prove to be essential reading not only to researchers in this field, but also to psychiatrists, neurologists and other clinicians who consider applying these new methods in clinical settings