gebhart/patrepeval huggingface dataset:
The Gene Ontology knowledgebase in 2023 (2023)

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
Filtering slot antenna using coupled line resonator (2014)

This paper presents the design of a novel slot filtering antenna suitable for modern electronic devices integrating various wireless systems that have to coexist. The approach consists in feeding the slot antenna through a filtering microstrip-to-slot-line transition. This transition comprises a coupled line resonator which enables to create two out-of-band transmission zeros and by this way to increase drastically the frequency selectivity of the transition. As proof-of-concept, a slot filtering antenna has been designed for WLAN applications operating in the 2.4GHz band, by using the HFSS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> simulation tool. A prototype has been also fabricated, using a low-cost FR4 substrate, where 2 antennas are printed on a board in order to accommodate the requirements of a 2×2 MIMO system.
The FIGO ovulatory disorders classification system (2022)

Ovulatory disorders are common causes of amenorrhea, abnormal uterine bleeding, and infertility, and are frequent manifestations of polycystic ovary syndrome (PCOS). There are many potential causes and contributors to ovulatory dysfunction that challenge clinicians, trainees, educators, and those who perform basic, translational, clinical, and epidemiological research. Similarly, therapeutic approaches to ovulatory dysfunction potentially involve a spectrum of lifestyle, psychological, medical, and procedural interventions. Collaborative research, effective education, and consistent clinical care remain challenged by the absence of a consensus comprehensive system for classification of these disorders. The existing and complex system, attributed to WHO, was developed more than three decades ago and did not consider more than 30 years of research into these disorders in addition to technical advances in imaging and endocrinology. This manuscript describes the development of a new classification of ovulatory disorders performed under the aegis of the International Federation of Gynecology and Obstetrics (FIGO) and conducted using a rigorously applied Delphi process. The stakeholder organizations and individuals who participated in this process comprised specialty journals, experts at large, national, specialty obstetrical and gynecological societies, and informed lay representatives. After two face-to-face meetings and five Delphi rounds, the result is a three-level multi-tiered system. The system is applied after a preliminary assessment identifies the presence of an ovulatory disorder. The primary level of the system is based on an anatomic model (Hypothalamus, Pituitary, Ovary) that is completed with a separate category for PCOS. This core component of the system is easily remembered using the acronym HyPO-P. Each anatomic category is stratified in the second layer of the system to provide granularity for investigators, clinicians, and trainees using the "GAIN-FIT-PIE" mnemonic (Genetic, Autoimmune, Iatrogenic, Neoplasm; Functional, Infectious and Inflammatory, Trauma and Vascular; Physiological, Idiopathic, Endocrine). The tertiary level allows for specific diagnostic entities. It is anticipated that, if widely adopted, this system will facilitate education, clinical care, and the design and interpretation of research in a fashion that better informs progress in this field. Integral to the deployment of this system is a periodic process of reevaluation and appropriate revision, reflecting an improved understanding of this collection of disorders.
Alcohol-Supported Cu-Mediated 18F-Fluorination of Iodonium Salts under “Minimalist” Conditions (2019)

In the era of personalized precision medicine, positron emission tomography (PET) and related hybrid methods like PET/CT and PET/MRI gain recognition as indispensable tools of clinical diagnostics. A broader implementation of these imaging modalities in clinical routine is closely dependent on the increased availability of established and emerging PET-tracers, which in turn could be accessible by the development of simple, reliable, and efficient radiolabeling procedures. A further requirement is a <i>c</i>GMP production of imaging probes in automated synthesis modules. Herein, a novel protocol for the efficient preparation of <sup>18</sup>F-labeled aromatics via Cu-mediated radiofluorination of (aryl)(mesityl)iodonium salts without the need of evaporation steps is described. Labeled aromatics were prepared in high radiochemical yields simply by heating of iodonium [<sup>18</sup>F]fluorides with the Cu-mediator in methanolic DMF. The iodonium [<sup>18</sup>F]fluorides were prepared by direct elution of <sup>18</sup>F<sup>-</sup> from an anion exchange resin with solutions of the corresponding precursors in MeOH/DMF. The practicality of the novel method was confirmed by the racemization-free production of radiolabeled fluorophenylalanines, including hitherto unknown 3-[<sup>18</sup>F]FPhe, in 22-69% isolated radiochemical yields as well as its direct implementation into a remote-controlled synthesis unit.
Modeling of monolithic RF spiral transmission-line balun (2001)

This paper presents models for monolithic RF spiral transmission-line baluns. The balun consists of a pair of spiral transformers fabricated on high-resistivity silicon. The lumped-element equivalent models are developed. The second-order or higher order models are synthesized from the first-order lumped model. All lumped parameters for the models are extracted from the real physical structures. Simulated behaviors from the second-order models are in good agreement with the measured results within 10% difference.
Activator Protein‐1 Is the Preferred Transcription Factor for Cooperative Interaction with Nuclear Factor‐kB in Respiratory Syncytial Virus‐Induced Interleukin‐8 Gene Expression in Airway Epithelium (1998)

The role of "oxidant-sensitive" transcription factors activator protein (AP)-1, nuclear factor (NF)-kappaB, and NF-IL6 in respiratory syncytial virus (RSV)-induced interleukin (IL)-8 gene expression in A549 epithelial cells was evaluated. RSV infection resulted in increased binding of each of these transcription factors. Transfection of A549 cells with plasmids containing serial truncations of the 5'-flanking region of the IL-8 gene revealed a positive cooperative effect of the binding sites for AP-1 and NF-kappaB. Mutation of either region markedly diminished responsiveness of the promoter to RSV. Mutation of the NF-IL6 site had minimal effect in the presence of intact binding sites for NF-kappaB and AP-1. The antioxidants NAC (N-acetylcysteine), DMSO, and DMPO (5,5-dimethyl-1-pyrroline N-oxide) did not inhibit RSV-induced binding of NF-kappaB; however, binding of AP-1 and NF-IL6 was inhibited. These observations suggest that AP-1 may be the preferred transcription factor (over NF-IL6) for cooperative interaction with NF-kappaB in RSV-induced IL-8 production.
A Learning Approach to Optical Tomography (2015)

We describe a method for imaging 3D objects in a tomographic configuration implemented by training an artificial neural network to reproduce the complex amplitude of the experimentally measured scattered light. The network is designed such that the voxel values of the refractive index of the 3D object are the variables that are adapted during the training process. We demonstrate the method experimentally by forming images of the 3D refractive index distribution of cells.
nec1, a Gene Conferring a Necrogenic Phenotype, Is Conserved in Plant-Pathogenic Streptomyces spp. and Linked to a Transposase Pseudogene (1998)

We are investigating the genetic basis for, and evolution of, plant pathogenicity in Streptomyces spp. The plant-pathogenic species S. scabies, S. acidiscabies, and S. turgidiscabies cause the scab disease of potato and produce the phytotoxins, thaxtomins. Forty-three Streptomyces strains representing the three species were evaluated; all thaxtomin A-producing Streptomyces strains were pathogenic on potato tubers and all but one hybridized to nec1 and ORFtnp, two genes previously cloned from S. scabies ATCC 41973. nec1 confers a pathogenic phenotype on S. lividans TK24, a nonpathogen, and ORFtnp is a transposase pseudogene located 5' to nec1. The eight nonpathogenic strains tested neither produced thaxtomin A nor hybridized to nec1. ORFtnp and nec1 occurred on a single PvuII restriction fragment in all thaxtomin A-producing Streptomyces strains. The nucleotide sequences of the homologs of nec1 and ORFtnp from two pathogenic strains each of S. scabies, S. acidiscabies, and S. turgidiscabies were identical; oligonucleotide primers specific to this gene amplified homologs from all strains that hybridized to nec1. We propose that nec1 and ORFtnp have been horizontally mobilized from S. scabies to S. acidiscabies and S. turgidiscabies, and that nec1 is involved in pathogenicity and physically linked to the thaxtomin A biosynthetic genes.
Dummy design characterization for STI CMP with fixed abrasive (2014)

The Shallow Trench Isolation (STI) Chemical Mechanical Polishing (CMP) process has an essential role in the STI module for the fabrication of the Complementary Metal Oxide Semiconductor (CMOS) transistors. Since the 0.13 μm technology node a direct STI CMP approach is used, where an oxide film is polished to remove the topography after trench fill and to clear the active regions stopping on a silicon nitride layer. One of the approaches for direct STI CMP uses a Fixed Abrasive (FA) web, which provides excellent planarity. Dummy structures are implemented in the device manufacturing layouts in order to overcome the effect of the different patterned densities and feature sizes. The design of the dummy structures plays a critical role for the CMP performance. In this work, a detailed characterization of the impact of the dummy design on the STI CMP performance using FA has been performed. Based on it, CMP optimized dummy designs have been found. The optimum dummy designs are vertical lines with higher patterned density (PD ~> 30 %) and smaller spacing in y (<; 1 μm) as well as segmented squares with bigger size (x = 5 μm, y = 5 μm, s = 1 μm), higher PD (-> 23 %) and smaller width and spacing of the lines.
Oxyhalogenation of Activated Arenes with Nanocrystalline Ceria (2012)

Arenes can be chlorinated, brominated, and iodinated in the presence of CeO2 nanoparticles under aerobic conditions. In a biomimetic approach, active electrophilic halogen species are generated from either organic or inorganic halogen compounds and are trapped by arenes. This C–H transformation can be applied to the synthesis of naturally occurring products.
028 Adherence to the AUA Penile Prosthesis Antibiotic Prophylaxis Guidelines in Diabetic Patients is Associated with Significantly Higher Risks of Device Infection (2020)

The most devastating complication following penile prosthesis (PP) implantation is an infection requiring device explantation. Current AUA guidelines recommend antibiotic prophylaxis before PP implantation with an aminoglycoside and either a 1st/2nd generation cephalosporin or vancomycin. We conducted a multi-institutional study to examine infection rates in diabetic patients undergoing PP implantation with different prophylactic antibiotic regimens, and compared outcomes based on adherence to AUA guidelines. Between April 2003 and August 2018, data was collected from 18 different institutions, and charts of 923 patients with diabetes receiving primary PP implantation were reviewed. Perioperative antibiotic regimen was recorded for each patient and the primary outcome was post-operative infection rates, the secondary outcomes were explantation and revision rates. Patients had a median follow up time of 8 months (range: 0 – 157). Patients were included in the analysis only if they had complete information regarding perioperative antibiotics and outcomes. Univariate comparisons of proportions were completed for rates of infection between different antibiotic regimens. Multivariate analysis controlling for immediate pre-operative blood glucose levels, Hemoglobin A1c, age, diabetes-related complications, and surgical approach was completed for rates of infection, revision, and explantation rates.
Channel and noise compensation for text dependent speaker verification over telephone (2002)

The performance of text dependent, short utterance speaker verification systems degrades significantly with channel and background artifacts. The authors investigate maximum likelihood and adaptive techniques to compensate for a stationary channel and noise. Maximum likelihood channel and noise compensation was introduced by Cox and Bridle (1989), and has been shown to be effective in many other speech applications. For adaptive estimation, a Bussgang like algorithm is developed which is more suitable for real-time implementation. These techniques are evaluated on a speaker verification system that uses the nearest neighbor metric. The results show that for telephone speech with channel differences, channel compensation can provide substantial performance improvement. For un-cooperative speakers, background compensation resulted in a 35% improvement.
Design and Integration Technology for Miniature Medical Microsystems (2008)

The electronic subsystem of wearable and implantable devices is constructed using board-level and package-level integration technology and this limits the achievable miniaturization. We will show that this limitation can be overcome by emerging wafer-level integration methods such as chip-in-wire technology. These technologies can even achieve mechanically bendable and stretchable subsystems.
Protection of optical rings interconnected by an ATM cross-connect (1998)

Wavelength division multiplexing (WDM) technology is investigated as a method to enhance the existing transport network by increasing bit rate transmission. This article focuses on the optical rings network supervision, operation and maintenance. The architecture considered is based on optical rings which are connected by an ATM cross-connect. The proposed operation and maintenance concept deals with the identification of layered network model functions and the maintenance signals required for failure localization.
NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells (2009)

Transformed cells in lymphomas usually maintain the phenotype of the postulated normal lymphocyte from which they arise. By contrast, anaplastic large cell lymphoma (ALCL) is a T-cell lymphoma with aberrant phenotype because of the defective expression of the T-cell receptor and other T-cell-specific molecules for still undetermined mechanisms. The majority of ALCL carries the translocation t(2;5) that encodes for the oncogenic tyrosine kinase NPM-ALK, fundamental for survival, proliferation, and migration of transformed T cells. Here, we show that loss of T-cell-specific molecules in ALCL cases is broader than reported previously and involves most T-cell receptor-related signaling molecules, including CD3epsilon, ZAP70, LAT, and SLP76. We further show that NPM-ALK, but not the kinase-dead NPM-ALK(K210R), downregulated the expression of these molecules by a STAT3-mediated gene transcription regulation and/or epigenetic silencing because this downregulation was reverted by treating ALCL cells with 5-aza-2-deoxycytidine or by knocking down STAT3 through short hairpin RNA. Finally, NPM-ALK increased the methylation of ZAP70 intron 1-exon 2 boundary region, and both NPM-ALK and STAT3 regulated the expression levels of DNA methyltransferase 1 in transformed T cells. Thus, our data reveal that oncogene-deregulated tyrosine kinase activity controls the expression of molecules that determine T-cell identity and signaling.
Aminomethyl substituted thieno[2,3-d]pyrimidines as adenosine A2A receptor antagonists (2011)

A novel series of aminomethyl substituted thieno[2,3-d]pyrimidines have been identified as adenosine A2A receptor antagonists. Analogues show excellent in vitro activities and have excellent activity in vivo in mouse models of Parkinson's disease.
Probing cation intermixing in Li2SnO3 (2016)

A significant amount of intra-layer Li–Sn intermixing was observed. It was shown that the intra-layer Li–Sn was the cause of the suppression of the characteristic high-order super-reflection peaks for the <italic>C</italic>2/<italic>c</italic> structure.
ChemInform Abstract: New Chiral Auxiliaries for Thermal Cycloadditions. (1990)

Abstract A new generation of chiral acrylimide derivatives such as (I) or (V) with improved face‐shielding capabilities providing heretofore unattainable levels of asym.
NGLY1 Deficiency: A Rare Newly Described Condition with a Typical Presentation (2021)

NGLY1 deficiency is the first recognized autosomal recessive disorder of N-linked deglycosylation (NGLY1-CDDG). This severe multisystemic disease is still poorly known and, to date, most cases have been diagnosed through whole exome or genome sequencing. The aim of this study is to provide the clinical, biochemical and molecular description of the first NGLY1-CDDG patient from France along with a literature review. The index case presented with developmental delay, acquired microcephaly, hypotonia, alacrimia, feeding difficulty, and dysmorphic features. Given the complex clinical picture and the multisystemic involvement, a trio-based exome sequencing was conducted and urine oligosaccharides were assessed using mass spectrometry. The exome sequencing revealed a novel variant in the <i>NGLY1</i> gene in a homozygous state. NGLY1 deficiency was confirmed by the identification of the Neu5Ac1Hex1GlcNAc1-Asn oligosaccharide in the urine of the patient. Literature review revealed the association of some key clinical and biological features such as global developmental delay-hypertransaminasemia, movement disorders, feeding difficulties and alacrima/hypolacrima.
LQ-Based Trajectory Tracking of Robotic Manipulators With “Near” Dynamically Feasible Time-Optimal Trajectory (2012)

In this paper we study the trajectory tracking of robotic manipulators using LQ methods. We also present the development of an algorithm that generates “near” dynamically feasible time-optimal trajectories with complete dynamics model, which incorporates both Coulomb and viscous friction. It is shown how to incorporate the viscous-friction term through a convex relaxation of the original non-convex formulation. Viscous friction is traditionally ignored in all existing related formulations due to the intractability in solving the non-convex problem. As a case study, the methodology is applied to a 6-DOF industrial manipulator.
Redox Deposition of Nanoscale MnO2 on Ultraporous Carbon Nanoarchitectures: Correlation of MnO2 Deposition Time and Electrochemical Performance (2007)

The redox reaction of aqueous permanganate with carbon nanofoam substrates at neutral solution pH produces nanoscale MnO2 deposits throughout the nanofoam structure. The MnO2 deposits become thicker with increasing deposition time (5 min to 20 h), with a corresponding enhancement in the electrode capacitance as the deposition progresses. The MnO2 capacitance enhancement is limited at high mass loadings during high rate operation, presumably due to the buildup of thicker MnO2 deposits on and within the carbon nanofoam structure.
Tagging genes with cassette-exchange sites (2005)

In an effort to make transgenesis more flexible and reproducible, we developed a system based on novel 5' and 3' 'gene trap' vectors containing heterospecific Flp recognition target sites and the corresponding 'exchange' vectors allowing the insertion of any DNA sequence of interest into the trapped locus. Flp-recombinase-mediated cassette exchange was demonstrated to be highly efficient in our system, even in the absence of locus-specific selection. The feasibility of constructing a library of ES cell clones using our gene trap vectors was tested and a thousand insertion sites were characterized, following electroporation in ES cells, by RACE-PCR and sequencing. We validated the system in vivo for two trapped loci in transgenic mice and demonstrated that the reporter transgenes inserted into the trapped loci have an expression pattern identical to the endogenous genes. We believe that this system will facilitate in vivo studies of gene function and large-scale generation of mouse models of human diseases, caused by not only loss but also gain of function alleles.
Evolution of human oocyte cryopreservation: slow freezing versus vitrification (2016)

Vitrification has now become the method of choice for oocyte cryopreservation because of better results than slow freezing, but still requires a more standardized utilization. The transfer of fresh or cryopreserved embryo still shows a statistically significant better performance than transfers with embryos obtained with cryopreserved oocytes. Only in a few centers with much experience in cryopreservation are the results between transfers of frozen embryos or embryos obtained from oocyte cryopreservation comparable.
CHOROIDAL NEOVASCULARIZATION IN NORTH CAROLINA MACULAR DYSTROPHY RESPONSIVE TO ANTI–VASCULAR ENDOTHELIAL GROWTH FACTOR THERAPY (2018)

Recognition and treatment of CNV in North Carolina macular dystrophy can result in improved vision. Genetic testing of the PRDM13 gene can confirm a molecular diagnosis for North Carolina macular dystrophy.
Direct Analysis of Daughter Ions (DADI) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.