gebhart/patrepeval huggingface dataset:
Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-.ANG. resolution [Erratum to document cited in CA113(11):93943z] (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleStructural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-.ANG. resolution [Erratum to document cited in CA113(11):93943z]Raymond C. Stevens, J. Eric Gouaux, and William N. LipscombCite this: Biochemistry 1990, 29, 50, 11146Publication Date (Print):December 18, 1990Publication History Published online1 May 2002Published inissue 18 December 1990https://pubs.acs.org/doi/10.1021/bi00502a021https://doi.org/10.1021/bi00502a021research-articleACS PublicationsRequest reuse permissionsArticle Views24Altmetric-Citations-LEARN 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 optionsGet e-Alertsclose Get e-Alerts
A Widely Tunable Narrow Linewidth RF Source Integrated in a Heterogeneous Photonic Module (2014)

Generating radio-frequency signals over the entire spectrum, from 1 to 100 GHz, typically requires the use of multiple oscillators designed only for specific narrow bands of operation within that spectrum. An optoelectronic system based on modulation side-band-injection-locked lasers is capable of generating RF frequencies tunable over a span of more than seven octaves with low phase noise . We present the results of our efforts to develop a heterogeneously integrated version of this system based on a silicon-photonic integrated circuit coupled to III-V semiconductor gain chips. Towards that end, we have successfully demonstrated an integrated laser module and achieved tunable RF generation with a ~ 1 Hz linewidth.
Toxaphene Residue Composition as an Indicator of Degradation Pathways (1997)

Toxaphene, a mixture of chlorinated bornanes and camphenes with a high proportion of enantiomers, can be used as an indicator for the investigation of environmental conditions which lead to the compositional pattern of toxaphene in environmental samples. Due to its persistence and long range transport, toxaphene is distributed throughout the world. The changes in composition after biotic or abiotic transformation are visible in the gas chromatograms of different environmental samples. These are important clues to translocation and degradation pathways. The results of enantioselective residue analysis and of degradation experiments with single toxaphene components suggest the dominance of photolysis over other abiotic or biotic processes in air, water, and fish.
A Semiconducting Organic Radical Cationic Host–Guest Complex (2012)

The self-assembly and solid-state semiconducting properties of single crystals of a trisradical tricationic complex composed of the diradical dicationic cyclobis(paraquat-p-phenylene) (CBPQT(2(•+))) ring and methyl viologen radical cation (MV(•+)) are reported. An organic field effect transistor incorporating single crystals of the CBPQT(2(•+))⊂MV(•+) complex was constructed using lithographic techniques on a silicon substrate and shown to exhibit p-type semiconductivity with a mobility of 0.05 cm(2) V(-1) s(-1). The morphology of the crystals on the silicon substrate was characterized using scanning electron microscopy which revealed that the complexes self-assemble into "molecular wires" observable by the naked-eye as millimeter long crystalline needles. The nature of the recognition processes driving this self-assembly, radical-radical interactions between bipyridinium radical cations (BIPY(•+)), was further investigated by resonance Raman spectroscopy in conjunction with theoretical investigations of the vibrational modes, and was supported by X-ray structural analyses of the complex and its free components in both their radical cationic and dicationic redox states. These spectroscopic investigations demonstrate that the bond order of the BIPY(•+) radical cationic units of host and guest components is not changed upon complexation, an observation which relates to its conductivity in the solid-state. We envision the modularity inherent in this kind of host-guest complexation could be harnessed to construct a library of custom-made electronic organic materials tailored to fit the specific needs of a given electronic application.
Molecular characterization of a 12q22‐q24 deletion associated with congenital deafness: Confirmation and refinement of the DFNA25 locus (2002)

The DFNA25 locus for autosomal dominant nonsyndromic hereditary hearing loss has been mapped to 12q21-q24 by linkage analysis. A de novo deletion in a six-year-old boy with congenital hearing loss as well as mental and motor retardation now provides independent confirmation of this genetic localization and narrows the critical interval to 13 cM in the 12q22-q24.1 region. Mapping of the deletion was performed using fluorescence in situ hybridization (FISH) analysis with region-specific yeast artificial chromosome (YAC) clones. Ten YACs 929_e_4, 959_c_3, 746_h_7, 817_h_10, 886_a_6, 916_h_9, 969_c_12, 747_e_2, 812_h_12, and 959_f_8 were absent from one chromosome 12 from the patient. Molecular analyses of eight polymorphic markers helped to narrow down the breakpoints and demonstrated that the derivative chromosome 12 is of paternal origin. Several known genes including ATP2A2, UBE3B, and VR-OAC that map in the 12q22-q24.1 region are included in the deletion. These results provide evidence that haploinsufficiency for a gene or genes in 12q22-q24.1 is associated with autosomal dominant deafness.
Approaches to compact quantum cascade laser modules with integrated coolers (2005)

A compact quantum cascade laser module is presented. That is based on conductive as well as convective cooling for efficient heat dissipation. Quantum cascade lasers with selectively doped active regions achieve better thermal behavior.
Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles (2014)

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.
Improved-dynamic-range single-mode OTDR at 1.3 μm (1984)

A high-performance single-mode optical time-domain reflector (OTDR) incorporating a new low-noise receiver design utilising a PIN diode detector and a transimpedance amplifier is described. With a 1.3 μm laser diode source a dynamic range of 30 dB one way is achieved, and using an Nd: YAG laser source the dynamic range is 41 dB one way.
3,3’-Diindolylmethane and its derivatives: nature-inspired strategies tackling drug resistant tumors by regulation of signal transduction, transcription factors and microRNAs (2020)

Indoles of cruciferous vegetables are promising anti-tumor agents. Studies with indole-3-carbinol and its dimeric product, 3,3'-diindolylmethane (DIM), suggest that these compounds have the ability to deregulate multiple cellular signaling pathways that are essential for tumor growth and spread. These natural compounds are also effective modulators of transcription factors and non-coding RNAs. These effects explain their ability to inhibit tumor spread and to overcome drug resistance. In this work, pertinent literature on the effects of DIM and its synthetic derivatives on resistant tumors and resistance mechanisms in tumors is highlighted.
Accurate whole-night sleep monitoring with dry-contact ear-EEG (2019)

Sleep is a key phenomenon to both understanding, diagnosing and treatment of many illnesses, as well as for studying health and well being in general. Today, the only widely accepted method for clinically monitoring sleep is the polysomnography (PSG), which is, however, both expensive to perform and influences the sleep. This has led to investigations into light weight electroencephalography (EEG) alternatives. However, there has been a substantial performance gap between proposed alternatives and PSG. Here we show results from an extensive study of 80 full night recordings of healthy participants wearing both PSG equipment and ear-EEG. We obtain automatic sleep scoring with an accuracy close to that achieved by manual scoring of scalp EEG (the current gold standard), using only ear-EEG as input, attaining an average Cohen's kappa of 0.73. In addition, this high performance is present for all 20 subjects. Finally, 19/20 subjects found that the ear-EEG had little to no negative effect on their sleep, and subjects were generally able to apply the equipment without supervision. This finding marks a turning point on the road to clinical long term sleep monitoring: the question should no longer be whether ear-EEG could ever be used for clinical home sleep monitoring, but rather when it will be.
Flexible Bragg reflectors for the terahertz regime composed of polymeric compounds (2007)

Terahertz technology holds a huge potential for a variety of applications in science and the industry, but still suffers from the lack of widely available system components. Not only active but also passive components like reflectors and filters are needed to advance the maturity of terahertz technology in general. Here, we present high quality, flexible, low-cost terahertz Bragg reflectors and filters based on polymeric compounds. The compounding technology allows to custom tailor dielectric properties as desired for the mirror design, namely a high index of refraction and low absorption at the center frequency of the reflector or filter. Two different base materials are evaluated: poly(propylene) (PP) and poly(vinylidene fluoride co- hexafluoropropylene) (PVDF). In both cases, rutile titania (TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) serves as high refractive index additive. The frequency dependent reflection coefficient of a nine layer PVDF and a five layer PP- based mirror are measured for a set of angles, both in s- and p-polarization, using a fiber coupled terahertz time domain spectrometer. Transfer matrix simulations are in good agreement with the experimental data.
A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative (2023)

Healthcare datasets obtained from Electronic Health Records have proven to be extremely useful for assessing associations between patients' predictors and outcomes of interest. However, these datasets often suffer from missing values in a high proportion of cases, whose removal may introduce severe bias. Several multiple imputation algorithms have been proposed to attempt to recover the missing information under an assumed missingness mechanism. Each algorithm presents strengths and weaknesses, and there is currently no consensus on which multiple imputation algorithm works best in a given scenario. Furthermore, the selection of each algorithm's parameters and data-related modeling choices are also both crucial and challenging. In this paper we propose a novel framework to numerically evaluate strategies for handling missing data in the context of statistical analysis, with a particular focus on multiple imputation techniques. We demonstrate the feasibility of our approach on a large cohort of type-2 diabetes patients provided by the National COVID Cohort Collaborative (N3C) Enclave, where we explored the influence of various patient characteristics on outcomes related to COVID-19. Our analysis included classic multiple imputation techniques as well as simple complete-case Inverse Probability Weighted models. Extensive experiments show that our approach can effectively highlight the most promising and performant missing-data handling strategy for our case study. Moreover, our methodology allowed a better understanding of the behavior of the different models and of how it changed as we modified their parameters. Our method is general and can be applied to different research fields and on datasets containing heterogeneous types.
On the Throughput of Ad Hoc Networks using Connectivity Graphs (2004)

In this paper we propose a set of necessary and sufficient conditions under which the throughput in an ad-hoc network can remain constant as the number of nodes n increases. Throughput refers to the minimum achievable rate between a source-destination pair for a given routing mechanism and physical model, when the network is shared by \\Theta(n) randomly chosen source-destination pairs. The main idea is to use a connectivity graph, that does not represent the actual physical network, but rather the available communication resources.
LINK Experience: Downtown Circulator Design, Implementation, and Evaluation (2006)

This paper describes how the Ann Arbor Transportation Authority (AATA) operated an experimental downtown circulator bus route in Ann Arbor, MI, for 20 months. During this period, the AATA studied and improved the route in order to determine if Ann Arbor could support such a service. City officials, business owners, and residents were all attracted to the many perceived benefits a downtown circulator bus offers. Despite growing interest in downtown circulators from communities across the country, little research or public documentation of these routes currently exists. This paper details the AATA’s efforts in planning and operating the route, from an inclusive planning process, to an innovative marketing campaign, to the survey research used to bring service better in line with riders’ transportation needs. In August 2003, the AATA introduced the 3.2-mile (5.2-kilometer) LINK route, which connected downtown districts and the University of Michigan campus. For the first year of operation ridership remained low, peaking at 282 riders per weekday and 9 passengers per service hour. During this time the AATA conducted two onboard rider surveys to determine if the route met riders’ needs. The results of these surveys inspired several service changes introduced in June and August 2004, which lead to a near doubling in ridership. By March 2005, ridership had hit 821 average weekday riders and 23 passengers per service hour. The success of the service will enable the LINK to continue a modified route with funding shared between the AATA, the University of Michigan, and the Ann Arbor Downtown Development Authority.
SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry (2006)

Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3' terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.
Overview for the First Shared Task on Language Identification in Code-Switched Data (2014)

Thamar Solorio, Elizabeth Blair, Suraj Maharjan, Steven Bethard, Mona Diab, Mahmoud Ghoneim, Abdelati Hawwari, Fahad AlGhamdi, Julia Hirschberg, Alison Chang, Pascale Fung. Proceedings of the First Workshop on Computational Approaches to Code Switching. 2014.
Design of electron guns and focusing structures for THz linear beam tubes (2008)

Results are reported for numerical modeling of concepts for non-circular beam formation for near-THz frequency TWT’s. Several methods for beam compression were examined, and one method appears promising for producing a 12 kV, 8 mA beam with a cross section 70 x 160 microns, while keeping the cathode loading to about 59 A/cm2. This would be suitable for a 650 GHz TWT. The beam loading is significantly lower than in similar frequency backward wave oscillators (BWO) and should result in much longer cathode lifetimes.
Kaplan-Meier analysis of circuit survival for continuous veno-venous hemofiltration (CVVH) and continuous veno-venous dialysis (CVVHD) (2011)

<b>Copyright information:</b>Taken from "Solute removal during continuous renal replacement therapy in critically ill patients: convection versus diffusion"Critical Care 2006;10(2):R67-R67.Published online 28 Apr 2006PMCID:PMC1550874.
Military applications of micro- and nanofibers (2014)

Chemical warfare differs from conventional warfare, such as explosives, in the sense that the toxicity of the chemicals used is very dangerous to the combatants in the battlefield, or to the civil population being affected during a war or as a result of a terrorist attack. The threat is amplified by concealment and low cost and relatively easy production of these agents, which renders them weapons of mass destruction. It becomes essential in such a situation that soldiers wear protective clothing, respirators, face masks, gloves, etc. Initially German troops unleashed chemical warfare agents, such as mustard agent, HD, during World War I in 1915, and this resulted in much more concern during World War II. Thus research on decontamination of chemical and biological warfare agents (CWAs) has been the subject of serious interest in many research laboratories since World War II. Mustard gas or bis(2-chloroethyl) sulfide is one of the highly cytotoxic, readily methylating CWAs that are regulated under the 1993 Chemical Weapons Convention (CWC). It covalently binds to DNA bases or forms disulfide bonds with the thiol groups. This readily leads to programmed cell death or the mutated DNA leads to cancer. The simultaneous danger associated with this toxic agent is its high skin penetration owing to its high lipophilicity, which results in immediate blister formation and huge uptake through skin within a short duration of exposure (Ivarsson et al. 1992).
Hospitalization for pneumonia among individuals with and without HIV infection, 1995-2007: a Danish population-based, nationwide cohort study (2009)

Background Human immunodeficiency virus (HIV)-infected individuals with high CD4(+) cell counts may have increased susceptibility to other infections. We compared incidence rates of pneumonia among individuals with and without HIV infection and explored risk factors for pneumonia in the HIV-infected population. Methods This was an observational cohort study conducted during 1995-2007. Each member of a Danish population-based nationwide cohort of HIV-infected individuals was matched with up to 99 control individuals from the general population. Data on age, mortality, emigration, and hospital discharge diagnoses from 1977 onward were obtained from nationwide administrative databases. Individuals without previous hospitalization for pneumonia were observed from the date of HIV diagnosis until the first hospitalization to treat pneumonia (excluding pneumonia attributable to Pneumocystis jiroveci). Risk factors were assessed by Poisson regression. Results The study included 3516 persons with HIV infection and 328,738 persons without HIV infection, which provided 23,677 person-years and 2,944,760 person-years of observation, respectively. Incidence rates of pneumonia in HIV-infected individuals decreased from 50.6 hospitalizations per 1000 person-years (95% confidence interval [CI], 42.9-59.7 hospitalizations per 1000 person-years) during 1995-1996 to 19.7 hospitalizations per 1000 person-years (95% CI, 16.2-23.8 hospitalizations per 1000 person-years) during 2005-2007. Compared with control individuals, incidence rate ratios were 34.6 (95% CI, 28.4-41.8) during 1995-1996; 6.3 (95% CI, 5.1-7.7) during 2005-2007; and 5.9 (95% CI, 4.2-7.6) during 2005-2007 for the subgroup with a CD4(+) cell count >500 cells/microL. Injection drug use, low current CD4(+) cell count, nadir CD4(+) cell count, increasing age, and no current receipt of highly active antiretroviral therapy increased the risk of pneumonia. Conclusions The risk of pneumonia in persons with HIV infection has decreased substantially since the introduction of highly active antiretroviral therapy, but HIV infection remains a strong risk factor for the need for hospitalization to treat pneumonia, even in persons with high CD4(+) cell counts.
A cost‐effective 60hz FHD LCD using 800Mbps AiPi technology (2009)

Abstract AiPi technology incorporates an embedded clock and control scheme with a point‐to‐point bus topology, thereby having the smallest possible number of interface lines between a timing controller and column drivers. A point‐to‐point architecture boosts the data rate and reduces the number of interface lines, because impedance matching can be easily achieved. An embedded clock and control scheme is implemented by means of multi‐level signalling, which results in a simple clock/data recovery circuitry. A 46” AiPi‐based 10‐bit FHD prototype requires only 20 interface lines, compared to 38 lines for mini‐LVDS. The measured maximum data rate per data pair is more than 800 Mbps.