gebhart/patrepeval huggingface dataset:
Identification of pathogenic variant enriched regions across genes and gene families (2019)

Abstract Missense variant interpretation is challenging. Essential regions for protein function are conserved among gene family members, and genetic variants within these regions are potentially more likely to confer risk to disease. Here, we generated 2,871 gene family protein sequence alignments involving 9,990 genes and performed missense variant burden analyses to identify novel essential protein regions. We mapped 2,219,811 variants from the general population into these alignments and compared their distribution with 65,034 missense variants from patients. With this gene family approach, we identified 398 regions enriched for patient variants spanning 33,887 amino acids in 1,058 genes. As a comparison, testing the same genes individually we identified less patient variant enriched regions involving only 2,167 amino acids and 180 genes. Next, we selected de novo variants from 6,753 patients with neurodevelopmental disorders and 1,911 unaffected siblings, and observed a 5.56-fold enrichment of patient variants in our identified regions (95% C.I. =2.76-Inf, p-value = 6.66×10 −8 ). Using an independent ClinVar variant set, we found missense variants inside the identified regions are 111-fold more likely to be classified as pathogenic in comparison to benign classification (OR = 111.48, 95% C.I = 68.09-195.58, p-value &lt; 2.2e −16 ). All patient variant enriched regions identified (PERs) are available online through a user-friendly platform for interactive data mining, visualization and download at http://per.broadinstitute.org . In summary, our gene family burden analysis approach identified novel patient variant enriched regions in protein sequences. This annotation can empower variant interpretation.
Nearly constant loss effects in borate glasses (2009)

Different nearly constant loss phenomena are investigated in borate glasses with compositions xNa(2)O.(1-x)B(2)O(3), for 0 < or =x< or = 0.3. The ionic conductivities caused by these effects are studied in wide ranges of temperature and frequency, spanning 4.3 K to 573 K and 100 mHz to 1 MHz, respectively. In a first step, we show how to identify the nearly constant loss (NCL) in 0.3Na(2)O.0.7B(2)O(3) glass. In the procedure, the scaling property of the conductivity caused by ordinary hopping is used to remove this component from the total conductivity as measured as a function of temperature at fixed frequency. The resulting NCL component is seen to be proportional to frequency and to display no temperature dependence. In a second step, a broad-band relaxation process is shown to exist in amorphous boron oxide and in sodium borate glasses with x< or = 0.1. It is most probably due to the presence of traces of water, with hydrogen ions behaving as reorienting and interacting local dipoles. In a third step, we propose a simple formal treatment of the NCL phenomenon, tracing it back to a large number of interacting ions, each of them moving locally. The key aspect is a "see-saw-type" time dependence of their individual single-particle double-well potentials, which is due to their Coulomb interactions. The individual ion does, therefore, not require thermal activation and is thus kept in motion even at cryogenic temperatures.
IMPACTO DA CAPTAÇÃO D’ ÁGUA NUM LAGO: O CASO DA LAGOA DO BONFIM, RN - BRASIL (2000)

O presente estudo compreende o desenvolvimento de um modelo computacional de balan&ccedil;o h&iacute;drico para simular o comportamento de um Lago submetido a diferentes vaz&otilde;es de capta&ccedil;&atilde;o d&rsquo;&aacute;gua, possibilitando a avalia&ccedil;&atilde;o dos impactos efetivos associados ao processo de esvaziamento do reservat&oacute;rio. A metodologia desenvolvida foi aplicada &agrave; quest&atilde;o da avalia&ccedil;&atilde;o dos impactos provocados pelo Sistema Adutor Trair&iacute;, na Lagoa do Bonfim, maior reservat&oacute;rio do Estado do Rio Grande do Norte. O modelo computacional foi desenvolvido em duas etapas: 1) determina&ccedil;&atilde;o dos saldos de fluxo, o qual engloba os fluxos subterr&acirc;neos de entrada e sa&iacute;da da lagoa e outros consumos antr&oacute;picos (exceto o bombeamento da adutora) de dif&iacute;cil determina&ccedil;&atilde;o direta, simplificando a abordagem do problema; 2) c&aacute;lculo dos rebaixamento na lagoa associados com um determinado regime de vaz&otilde;es bombeadas. Os resultados mostraram que o volume captado para a Adutora foi respons&aacute;vel por 48% do rebaixamento do n&iacute;vel d&rsquo;&aacute;gua na Lagoa do Bonfim no per&iacute;odo de bombeamento, que foi de 1,17 m. O impacto seria muito maior se a vaz&atilde;o utilizada fosse, neste per&iacute;odo, a prevista para o final do plano, o que implicaria num rebaixamento de 1,913 m, correspondendo a aumento de 71,3% em rela&ccedil;&atilde;o ao rebaixamento observado.
Radio Resource Management in 3G+ Systems (2006)

1Department of Electrical and Computer Engineering, Ryerson University, Toronto, ON, Canada, M5B 2K3 2 Intel Corporation, 2111 NE 25th Avenue, Hillsboro, OR 97229, USA 3Department of Electrical and Computer Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada N2L 3G1 4 INRS-EMT, Universite du Quebec, Place Bonaventure, 800 de la Gauchetiere Ouest, Suite 6900, Montreal, QC, Canada H5A 1K6
Personal monitoring of cutaneous vitamin D3 production through a printable UV molecular dosimeter (2022)

Cutaneous production of vitamin D by exposure of the skin to solar radiation can provide more than 90% of the daily dose needed by the human body, thanks to the range of UV radiation covered by its spectrum and may be the best option to reduce oral supplementation. The process can be monitored by personal UV dosimetry since this is the range of solar radiation related to its production. Aiming to monitor UVB dose looking for correlation with skin production of vitamin D3, a printed strip with the molecular dosimetry device was used to produce a photonic signal as input for calculations in software developed here to run on a smartphone. For this, the molecular dosimeter Eu(btfa)3·bipy was prepared to be printed as a functional ink with a MEMS-based Drop-on-Demand Dimatix DMP2831 Materials Printer to produce the functional paper strips. To use our personal UV molecular dosimeter photonic signal as input data, a correlation curve must be established to convert the UV dose into the amount of vitamin D3 produced. There is a promising solution for personal monitoring of cutaneous vitamin D production by printable UV dosimeter targets, aiming to contribute to a better immune response of individuals. In addition, the creation of a cloud data lake capable of mapping population data on vitamin D deficiency can help define public health policies.
EMM-23: A Stable High-Silica Multidimensional Zeolite with Extra-Large Trilobe-Shaped Channels (2014)

Stable, multidimensional, and extra-large pore zeolites are desirable by industry for catalysis and separation of bulky molecules. Here we report EMM-23, the first stable, three-dimensional extra-large pore aluminosilicate zeolite. The structure of EMM-23 was determined from submicron-sized crystals by combining electron crystallography, solid-state nuclear magnetic resonance (NMR), and powder X-ray diffraction. The framework contains highly unusual trilobe-shaped pores that are bound by 21-24 tetrahedral atoms. These extra-large pores are intersected perpendicularly by a two-dimensional 10-ring channel system. Unlike most ideal zeolite frameworks that have tetrahedral sites with four next-nearest tetrahedral neighbors (Q(4) species), this unusual zeolite possesses a high density of Q(2) and Q(3) silicon species. It is the first zeolite prepared directly with Q(2) species that are intrinsic to the framework. EMM-23 is stable after calcination at 540 °C. The formation of this highly interrupted structure is facilitated by the high density of extra framework positive charge introduced by the dicationic structure directing agent.
Toward a unified design of pattern recognizers (2002)

Finding salient features is one of the most important steps in designing a pattern recognizer. Although this issue has long been studied from the early days of research on pattern recognition, no study has yet provided a well-formalized satisfying solution which is able to be easily used in practical conditions. In this paper, we discuss in detail a new family of discriminative feature design methods, namely, discriminative feature extraction, the minimum error learning subspace method and discriminative metric design. Tracing the development of these methods clarifies a desirable research direction toward a solution to the problem.
Automative surround view aided parking system and surveillance (2013)

Automotive Surround View is a project that add vision system to a car and using it allow to have complete view of the surrounding of the vehicle. The system consist of receiving four video streams from the cameras and then use this data to create a full navigable 3d view of the surrounding of the car, this is helpful for aiding parking and for surveillance purpose. In this thesis is described the entire design of the embedded system, form the mechanical analysis to the computer vision algorithms. In this project are used smart camera module called RVS2.0 made by AST Robotics Group in ST Microelectronics and a platform called Orly to compute data. The result of this project is an embedded system that can assist the driver of the car when the rear view is needed or register the top view to have a complete visual control of the surrounding of the vehicle.
Infrared On-orbit RCC Inspection with the EVA IR Camera: Development of Flight Hardware from a COTS System (2005)

In November 2004, NASA’s Space Shuttle Program approved the development of the Extravehicular (EVA) Infrared (IR) Camera to test the application of infrared thermography to on-orbit reinforced carbon-carbon (RCC) damage detection. A multi-center team composed of members from NASA’s Johnson Space Center (JSC), Langley Research Center (LaRC), and Goddard Space Flight Center (GSFC) was formed to develop the camera system and plan a flight test. The initial development schedule called for the delivery of the system in time to support STS-115 in late 2005. At the request of Shuttle Program managers and the flight crews, the team accelerated its schedule and delivered a certified EVA IR Camera system in time to support STS-114 in July 2005 as a contingency. The development of the camera system, led by LaRC, was based on the Commercial-Off-the-Shelf (COTS) FLIR S65 handheld infrared camera. An assessment of the S65 system in regards to space-flight operation was critical to the project. This paper discusses the space-flight assessment and describes the significant modifications required for EVA use by the astronaut crew. The onorbit inspection technique will be demonstrated during the third EVA of STS-121 in September 2005 by imaging damaged RCC samples mounted in a box in the Shuttle’s cargo bay.
Assay and purification of S-adenosyl-L-methionine:precorrin-2 methyltransferase from Pseudomonas denitrificans (1990)

S-Adenosyl-L-methionine:precorrin-2 methyltransferase (SP2MT), which catalyzes the C-20 methylation of precorrin-2 to precorrin-3, was purified to homogeneity from extracts of a recombinant strain of Pseudomonas denitrificans derived from a cobalamin-overproducing strain. Ammonium sulfate fractionation followed by chromatography on DEAE-Trisacryl, hydroxyapatite, and Mono Q HR purified the enzyme about 110-fold, with a 28% yield. For enzyme purification and characterization, a coupled-enzyme assay was developed which generated in situ the highly oxygen-sensitive substrate, precorrin-2, from delta-aminolevulinic acid. Evidence is given that the chemically reduced form of sirohydrochlorin (dihydrosirohydrochlorin) is methylated at C-20 to precorrin-3 by pure SP2MT. No subsequent SP2MT-dependent methylation reaction of precorrin-3 was detected. The native enzyme has an apparent molecular weight of 53,000, as estimated by gel filtration, and consists of two identical subunits of Mr 26,000, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Stepwise Edman degradation provided the N-terminal sequence of the first 17 amino acids.
Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria (2019)

UDP-3-<i>O</i>-((<i>R</i>)-3-hydroxymyristoyl)-<i>N</i>-glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need created by multidrug resistant Gram-negative bacteria. By using a scaffold hopping approach on a known family of methylsulfone hydroxamate LpxC inhibitors, several hit series eliciting potent antibacterial activities against Enterobacteriaceae and <i>Pseudomonas aeruginosa</i> were identified. Subsequent hit-to-lead optimization, using cocrystal structures of inhibitors bound to <i>Pseudomonas aeruginosa</i> LpxC as guides, resulted in the discovery of multiple chemical series based on (i) isoindolin-1-ones, (ii) 4,5-dihydro-6<i>H</i>-thieno[2,3-<i>c</i>]pyrrol-6-ones, and (iii) 1,2-dihydro-3<i>H</i>-pyrrolo[1,2-<i>c</i>]imidazole-3-ones. Synthetic methods, antibacterial activities and relative binding affinities, as well as physicochemical properties that allowed compound prioritization are presented. Finally, in vivo properties of lead molecules which belong to the most promising pyrrolo-imidazolone series, such as <b>18d</b>, are discussed.
Opposed regulation of type I IFN‐induced STAT3 and ISGF3 transcriptional activities by histone deacetylases (HDACS) 1 and 2 (2011)

The antiviral and antiproliferative responses mediated by type I interferons (IFNs) depend on JAK/STAT signaling and ISGF3 (STAT1:STAT2:IRF9)-dependent transcription. In addition, type I IFNs stimulate STAT3 activation in many cell types, an event generally associated with cell cycle progression, survival, and proliferation. To gather more insight into this functionally contradictive phenomenon, we studied the regulation of STAT3 transcriptional activity upon type I IFN treatment. We show that IFNα2 stimulation strongly induces STAT3 phosphorylation, nuclear translocation, and promoter binding, yet the activation of transcription of a STAT3-dependent reporter and endogenous genes, such as SOCS3 and c-FOS, is impaired. Simultaneous treatment with IFNα2 and trichostatin A, as well as combined HDAC1/HDAC2 silencing, restores STAT3-dependent reporter gene and endogenous gene expression, strongly suggesting that HDAC1 and HDAC2 are directly involved in repressing IFNα2-activated STAT3. Of note, single silencing of only one of the two HDACs does not lead to enhanced STAT3 activity, supporting a functional redundancy between these two enzymes. In sharp contrast, HDAC1 and HDAC2 activities are required for ISGF3-dependent gene expression. We conclude that HDAC1 and HDAC2 differentially modulate STAT activity in response to IFNα2: while they are required for the induction of ISGF3-responsive genes, they impair the transcription of STAT3-dependent genes.
West Germany (RLE: German Politics) (2014)

This book, originally published in 1981,&nbsp;provides the student and general reader alike with a fascinating account of the dynamic re-emergence of Germany after the Second World War as one of the world’s leading and most powerful states. The book gives extensive coverage to all aspects of the former West Germany’s political, social and economic arrangements. As well as dealing with the Basic Law, political parties, Bundestag and government, it also discusses neglected subjects, such as education, the armed forces, welfare services, the role of women, the economy and industrial relations and the mass media.
Confinement of Nucleic Acid Bases and Related Compounds Using Tetra-p-sulfonatocalix[4]arene (2006)

Supramolecular complexes of tetra-p-sulfonatocalix[4]arene and guanine, cytosine, benzimidazole, and 2-hydroxybenzimidazole have been isolated in the solid state, and their structures have been elucidated using single-crystal X-ray diffraction data, as have 2-hydroxybenzimidazole complexes and complexes with large cations tetraphenylphosphonium (Ph4P+) and triethylbenzylammonium (Et3BzN+). These large cations disrupt the usual bilayer arrangement of the sulfonated calixarenes, as can benzimadole itself, and a combination of guanine and cytosine, in the absence of the large cations. Some of the structures show a “molecular capsule” type arrangement with two calixarenes arranged with their cavities directed toward each other, effectively shrouding two nucleic acid bases.
Power supply with extended output voltage intended for the electric welding and cutting (2016)

Electric arc welding and cutting processes require delivery of the electrical power covering the broad range of the output voltage and the output current. Direct approach in the design to cover all required range leads to oversizing of the applied elements of the power conversion. The solution of the coverage the high voltage in the low current range, needed for the welding by means of the electrodes with cellulosic coating and other purposes was proposed, investigated and implemented in the market device.
Nonthyroidal Illness Syndrome: To Treat or Not to Treat? Have We Answered the Question? A Review of Metanalyses (2022)

NTIS is a frequent finding in critical ill patients. Despite several available IRCTs, it is still unclear whether NTIS should be treated or not. New primary endpoints should be identified to adequately validate the efficacy of TH treatment and to obtain a clear answer to the question raised some years ago.
60 GHz Reflection Type Phase Shifter based on liquid crystal (2010)

For the first time, a compact 60 GHz band phase shifter incorporating liquid crystal (LC) is presented. Based on the Reflection Type Phase Shifter (RTPS) structure, it comprises a 3-dB coupler and tunable reflective loads formed on a nematic LC substrate. The LC used to form the substrate is known as E7. Biasing of the LC is achieved using an external electric field, allowing for the control of the reactance of the reflective loads. To facilitate on-wafer measurements and the application of the electric field to the LC, a transition from the microstrip line to the CPW is used. Preliminary measurement results for this RTPS show a differential phase shift of over 130 degrees, a figure of merit of 11.4°/dB and return losses better than -10 dB at 61 GHz.
Replacement of [RuH2(PMe3)4] by [RuH2(PEt3)4] switches reaction products: synthesis of fluoride-bridged diruthenium complexes (2003)

The fluoride-bridged ruthenium dimers [Ru2(μ-F)3(PR3)6][F(HF)n] (R = Et, Pr, Bu; n ≈ 3) were synthesised by the reactions of the cis-[RuH2(PR3)4] complexes with NEt3·3HF in THF; the crystal structure of [Ru2(μ-F)3(PEt3)6]OTf, formed by subsequent reaction with NH4OTf, reveals Ru–F distances in the range 2.132(2)–2.170(2) Å and Ru–F–Ru angles in the range 91.72(7)–93.02(7)°.
The pneumococcal eukaryotic-type serine/threonine protein kinase StkP co-localizes with the cell division apparatus and interacts with FtsZ in vitro (2010)

The importance of serine/threonine phosphorylation in signalling and regulation of gene expression in prokaryotes has been widely recognized. Driven by our interest in StkP (the pneumococcal serine/threonine kinase homologue) for vaccine development, we studied its cellular localization. We found that the C-terminally located PASTA (penicillin-binding protein and serine/threonine kinase associated) domains, but not the N-terminal kinase domain of StkP, were located on the surface of live pneumococcal cells grown in vitro and were also accessible to antibodies during pneumococcal infection in mice and man. Most importantly, we discovered, by immunofluorescence microscopy, that StkP co-localized with the cell division apparatus. StkP and FtsZ, the prokaryotic tubulin homologue, co-localized at mid-cell in most cells. Formation and constriction of the ring-like structure of StkP followed the dynamic changes of FtsZ in dividing cells. This pattern resembles that of the 'late' divisome protein penicillin-binding protein 2X. The lack of StkP in gene deletion mutants did not disturb FtsZ ring formation, further suggesting that StkP joins the divisome after the FtsZ ring is assembled. We also present evidence that StkP binds and phosphorylates recombinant FtsZ in vitro; however, we could not detect changes in the phosphorylation of FtsZ in a stkP deletion strain relative to wild-type cells. Based on its cell-division-dependent localization and interaction with FtsZ, we propose that StkP plays a currently undefined role in cell division of pneumococcus.
Supplemental Figure Legends from Histone Deacetylase HDAC8 Promotes Insulin Resistance and β-Catenin Activation in NAFLD-Associated Hepatocellular Carcinoma (2023)

&lt;p&gt;Legend for Supplemental Figures S1-S8.&lt;/p&gt;
Learning shallow semantic rules for textual entailment (2007)

In this paper we present a novel technique for integrating lexical-semantic knowledge in systems for learning textual entailment recognition rules: the typed anchors. These describe the semantic relations between words across an entailment pair. We integrate our approach in the cross-pair similarity model. Experimental results show that our approach increases performance of cross-pair similarity learning systems. 1
Successful Endoscopic Closure of Pyeloduodenal Fistula Using an Over-the-Scope Clip (2019)

A 62-year-old woman underwent a series of urologic procedures for nephrolithiasis and was diagnosed with a pyeloduodenal fistula (PDF) on computed tomography urography. After the placement of a metallic ureteral stent and nephrostomy tube, an esophagogastroduodenoscopy was performed to evaluate for PDF resolution. Two areas of mucosal defects within the anterior duodenal sweep were closed using the over-the-scope clip system and hemostasis clips. We review the literature and discuss the etiologies, presentation, diagnosis, and treatment of PDF. This is the second documented case of endoscopic PDF closure using the over-the-scope clip system and the third case of endoscopically treated PDF.
Inflow quantification in three‐dimensional cardiovascular MR imaging (2008)

There is significant loss of CNR between blood and myocardium when using larger 3D slabs due to saturation of inflowing spins. The loss of contrast is less pronounced for SSFP than for GRE, though both acquisition techniques suffer.
Isolation and Structural Characterization of New Samarium(III) Bromide–HMPA Complexes (2001)

Abstract The crystal structures of new samarium(III) bromide–HMPA complexes were accurately determined by single crystal X-ray analysis. The Lewis acidity of samarium(III) cation is discussed based on the crystal structures of several samarium(III)–HMPA complexes.