gebhart/patrepeval huggingface dataset:
Map positions of 47 <i>Arabidopsis</i> sequences with sequence similarity to disease resistance genes (1997)

Map positions have been determined for 42 non-redundant Arabidopsis expressed sequence tags (ESTs) showing similarity to disease resistance genes (R-ESTs), and for three Pto-like sequences that were amplified with degenerate primers. Employing a PCR-based strategy, yeast artificial chromosome (YAC) clones containing the EST sequences were identified. Since many YACs have been mapped, the locations of the R-ESTs could be inferred from the map positions of the YACs. R-EST clones that exhibited ambiguous map positions were mapped as either cleavable amplifiable polymorphic sequence (CAPS) or restriction fragment length polymorphism (RFLP) markers using F8 (Ler x Col-0) recombinant inbred (RI) lines. In all cases but two, the R-ESTs and Pto-like sequences mapped to single, unique locations. One R-EST and one Pto-like sequence each mapped to two locations. Thus, a total of 47 loci were identified in this study. Several R-ESTs occur in clusters suggesting that they may have arisen via gene duplication events. Interestingly, several R-ESTs map to regions containing genetically defined disease resistance genes. Thus, this collection of mapped R-ESTs may expedite the isolation of disease resistance genes. As the cDNA sequencing projects have identified an estimated 63% of Arabidopsis genes, a very large number of R-ESTs (approximately 95), and by inference disease resistance genes of the leucine-rich repeat-class probably occur in the Arabidopsis genome.
P4‐376: Behavioral performance as a predictor of cognitive decline: Detecting the transition from healthy aging to mild cognitive impairment (2012)

It is now recognized that Alzheimer's disease (AD) pathology begins 15–20 years before symptom onset. There remains an urgent need for sensitive cognitive measures for detecting and monitoring subtle changes, especially the changes that occur during the transition from healthy aging to mild cognitive impairment (MCI), a diagnosis that may or may not indicate continued decline to AD. We've used an innovative and sensitive behavioral assay, the Visual Paired Comparison (VPC) task together with eyetracking to address this need. A new picture and a recently presented picture are presented side-by-side, and a subject's spontaneous tendency to look at the pictures is measured. Normal individuals typically look at the new picture about two-thirds of the viewing time. Previous work has shown that MCI subjects spend significantly less time looking at the new pictures than control (CON) subjects. Performance on the VPC task is predictive of worsening cognition regardless of diagnosis at the time of testing, i.e., no matter whether the diagnosis was MCI or CON. Further, scores on the VPC task accurately predicted, up to three years prior to a change in clinical diagnosis, MCI patients who would and would not progress to AD, and CON subjects who would and would not progress to MCI. A Receiver Operating Characteristic (ROC) Curve shows that the task powerfully discriminates between subjects who will worsen and those who will not (AUC = .903, 95% CI, p<.001). Although detecting the transition from MCI to AD is not challenging to the clinician, currently used cognitive measures change little or are too noisy to be very useful for tracking changes from healthy aging to MCI. The present findings show that the VPC task can offer early detection of impending cognitive decline. To our knowledge, this is the first behavioral task that can identify healthy subjects who will soon develop MCI and possibly progress to AD within the next few years. Finally, when combined with biomarker assays, this approach may provide a new way of interrogating the underlying dynamics of AD, as well as other illnesses where impaired cognition is a leading symptom.
Measurements of air pollution emission factors for marine transportation (2012)

Abstract. The chemical composition of the plumes of seagoing ships was investigated during a two weeks long measurement campaign in the port of Rotterdam, Hoek van Holland, The Netherlands, in September 2009. Altogether, 497 ships were monitored and a statistical evaluation of emission factors (g kg−1 fuel) was provided. The concerned main atmospheric components were SO2, NO2, NOx and the aerosol particle number. In addition, the elemental and water-soluble ionic composition of the emitted particulate matter was determined. Emission factors were expressed as a function of ship type, power and crankshaft rotational speed. The average SO2 emission factor was found to be roughly half of what is allowed in sulphur emission control areas (16 vs. 30 g kg−1 fuel), and exceedances of this limit were rarely registered. A significant linear relationship was observed between the SO2 and particle number emission factor. The intercept of the regression line, 0.5 × 1016 (kg fuel)−1, gives the average number of particles formed during the burning of 1 kg zero sulphur content fuel, while the slope, 2 × 1018, provides the average number of particles formed with 1 kg sulphur burnt with the fuel. Water-soluble ionic composition analysis of the aerosol samples from the plumes showed that ~144 g of particulate sulphate was emitted from 1 kg sulphur burnt with the fuel. The mass median diameter of sulphate particles estimated from the measurements was ~42 nm.
Functionalized macrocarbocyclic rings. I. Two fourteen-membered dimethyl macrocycles with trans, cis diene and cis dienophile (1989)

Etude de la structure de deux isomeres de formule brute C 24 H 34 O 8 : 1) cristallise dans P2 1 /c avec affinement jusqu'a 0,049; 2) cristallise dans P1 avec affinement jusqu'a 0,051. Pour les deux composes, les doubles liaisons sont respectivement trans, cis et cis
Further results on DCT-based linear phase paraunitary filter banks (2003)

A DCT-based simplified general structure for a linear phase paraunitary filter bank (LPPUFB) was developed by the pre- and post-processing of the DCT in the time domain. The new structure can be viewed as the dual of the generalized LOT (GenLOT). We generalize the result to odd-channel LPPUFB and LPPUFB with pair-wise mirror image property. Design examples and their application in image compression are presented.
Synchronization of multiple A/D converters based on spectral stretch (2018)

We present a newmethod for synchronization of multiple independent A/D converters for microphone array processing. Since the spectrum obtained in each channel becomes a stretched version of the source spectrum, we construct a probabilistic generative model of spectrum stretch. Synchronization is realized by solving the inverse problem of the probabilistic generative model.
Siah1 Interacts with the Scaffold Protein POSH to Promote JNK Activation and Apoptosis (2005)

Siah proteins are ubiquitin-protein isopeptide ligases (E3) that have been implicated in a variety of cellular actions, including promotion of apoptotic death. Here, we show that Siah1 is a binding partner for POSH (plenty of SH3s), a scaffold component of the apoptotic JNK pathway, and that Siah contributes to death of neurons and other cell types by activating the JNK pathway. Such proapoptotic activity requires the E3 ligase activity of Siah1. Moreover, apoptotic stimuli markedly elevate cellular Siah1 levels by a mechanism reliant on Siah1 protein stabilization. This stabilization requires JNK pathway activation and interaction with POSH and is enhanced by phosphorylation of SIAH1 at tyrosines 100 and 126. Depletion of intracellular Siah proteins via small interference RNA partially protects cells from death evoked by apoptotic stimuli such as trophic factor deprivation and DNA damage. These findings thus reveal a "loop" mechanism in which the JNK pathway promotes SIAH1 stabilization and in which SIAH1 in turn activates the JNK pathway and, ultimately, contributes to cell death.
PCA Based Stress Monitoring of Cylindrical Specimens Using PZTs and Guided Waves (2017)

Since mechanical stress in structures affects issues such as strength, expected operational life and dimensional stability, a continuous stress monitoring scheme is necessary for a complete integrity assessment. Consequently, this paper proposes a stress monitoring scheme for cylindrical specimens, which are widely used in structures such as pipelines, wind turbines or bridges. The approach consists of tracking guided wave variations due to load changes, by comparing wave statistical patterns via Principal Component Analysis (PCA). Each load scenario is projected to the PCA space by means of a baseline model and represented using the <i>Q</i>-statistical indices. Experimental validation of the proposed methodology is conducted on two specimens: (i) a 12.7 mm ( 1 / 2 " ) diameter, 0.4 m length, AISI 1020 steel rod, and (ii) a 25.4 mm ( 1 " ) diameter, 6m length, schedule 40, A-106, hollow cylinder. Specimen 1 was subjected to axial loads, meanwhile specimen 2 to flexion. In both cases, simultaneous longitudinal and flexural guided waves were generated via piezoelectric devices (PZTs) in a pitch-catch configuration. Experimental results show the feasibility of the approach and its potential use as in-situ continuous stress monitoring application.
COVID-19 Serology at Population Scale: SARS-CoV-2-Specific Antibody Responses in Saliva (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of an ongoing pandemic that has infected over 36 million and killed over 1 million people. Informed implementation of government public health policies depends on accurate data on SARS-CoV-2 immunity at a population scale. We hypothesized that detection of SARS-CoV-2 salivary antibodies could serve as a noninvasive alternative to serological testing for monitoring of SARS-CoV-2 infection and seropositivity at a population scale. We developed a multiplex SARS-CoV-2 antibody immunoassay based on Luminex technology that comprised 12 CoV antigens, mostly derived from SARS-CoV-2 nucleocapsid (N) and spike (S). Saliva and sera collected from confirmed coronavirus disease 2019 (COVID-19) cases and from the pre-COVID-19 era were tested for IgG, IgA, and IgM to the antigen panel. Matched saliva and serum IgG responses (<i>n</i> = 28) were significantly correlated. The salivary anti-N IgG response resulted in the highest sensitivity (100%), exhibiting a positive response in 24/24 reverse transcription-PCR (RT-PCR)-confirmed COVID-19 cases sampled at >14 days post-symptom onset (DPSO), whereas the salivary anti-receptor binding domain (RBD) IgG response yielded 100% specificity. Temporal kinetics of IgG in saliva were consistent with those observed in blood and indicated that most individuals seroconvert at around 10 DPSO. Algorithms employing a combination of the IgG responses to N and S antigens result in high diagnostic accuracy (100%) by as early as 10 DPSO. These results support the use of saliva-based antibody testing as a noninvasive and scalable alternative to blood-based antibody testing.
برنامج تدریبی موجه فی ضوء بعض المحددات الکینماتیکیة وتأثیره علی المستوی الرقمی لمتسابقی 400 متر عدو (2020)

برنامج تدريبي موجه في ضوء بعض المحددات الکينماتيکية وتأثيره علي المستوي الرقمي لمتسابقي 400 متر عدوإسم الباحث : أحمد عبد المرضي عبد العزيزهدف البحث تصميم برنامج تدريبي فى ضوء تحليل مقاطع سباق 400 متر عدو ومعرفة تأثيره على الصفات البدنية لمتسابقي 400 متر عدو و بعض المتغيرات الکينماتيکية والمستوى الرقمي لمتسابقي 400 متر عدواستخدم الباحث المنهج التجريبي باستخدام التصميم التجريبي لمجموعة واحدة والذى يعتمد على القياس (القبلي– البعدي ) وذلک لمناسبته وطبيعة البحث. يتکون مجتمع البحث من لاعبي المشروع القومي للموهبة والبطل الأوليمبي ولاعبي نادي بنها من اللاعبين الممارسين لسباق 400 متر عدو والبالغ عددهم 8 لاعبينولجمع البيانات قام الباحث باستخدام جهاز smart speed وعدد 1 کاميرا فيديو للتصوير , برنامج tracker للتحليل وساعاتيين بولر وقد أشارت النتائج توجد فروق دالة احصائياً بين القياس القبلي والقياس البعدي في الصفات البدنية لمتسابقي 400م عدو ولصالح القياس البعدي، ووجود فروق دالة احصائياً بين القياس القبلي والقياس البعدي في بعض المتغيرات الکينماتيکية والمستوى الرقمي لمتسابقي 400 متر عدو ولصالح القياس البعدي.وجاءت أهم التوصيات فى الاهتمام بالتصوير والتحليل للوقوف علي الأمور الدقيقة التي يکون لها أثر في تطوير المستوي الرقمي ، ويجب الاهتمام بتدريب الصفات البدنية الخاصة في المراحل السنية المختلفة وإدراجها ضمن برامج الإعداد للناشئين.
Preference-Based Instrumental Variable Methods for the Estimation of Treatment Effects: Assessing Validity and Interpreting Results (2007)

Observational studies of drugs and medical procedures based on administrative data are increasingly used to inform regulatory and clinical decisions. However, the validity of such studies is often questioned because available data may not contain measurements of many important prognostic variables that guide treatment decisions. Recently, approaches to this problem have been proposed that use instrumental variables (IV) defined at the level of an individual health care provider or aggregation of providers. Implicitly, these approaches attempt to estimate causal effects by using differences in medical practice patterns as a quasi-experiment. Although preference-based IV methods may usefully complement standard statistical approaches, they make assumptions that are unfamiliar to most biomedical researchers and therefore the validity of such analyses can be hard to evaluate. Here, we propose a simple framework based on a single unobserved dichotomous variable that can be used to explore how violations of IV assumptions and treatment effect heterogeneity may bias the standard IV estimator with respect to the average treatment effect in the population. This framework suggests various ways to anticipate the likely direction of bias using both empirical data and commonly available subject matter knowledge, such as whether medications or medical procedures tend to be overused, underused, or often misused. This approach is described in the context of a study comparing the gastrointestinal bleeding risk attributable to different non-steroidal anti-inflammatory drugs.
Measuring Aging and Identifying Aging Phenotypes in Cancer Survivors (2019)

Observational data have shown that some cancer survivors develop chronic conditions like frailty, sarcopenia, cardiac dysfunction, and mild cognitive impairment earlier and/or at a greater burden than similarly aged individuals never diagnosed with cancer or exposed to systemic or targeted cancer therapies. In aggregate, cancer- and treatment-related physical, cognitive, and psychosocial late- and long-term morbidities experienced by cancer survivors are hypothesized to represent accelerated or accentuated aging trajectories. However, conceptual, measurement, and methodological challenges have constrained efforts to identify, predict, and mitigate aging-related consequences of cancer and cancer treatment. In July 2018, the National Cancer Institute convened basic, clinical, and translational science experts for a think tank titled "Measuring Aging and Identifying Aging Phenotypes in Cancer Survivors." Through the resulting deliberations, several research and resource needs were identified, including longitudinal studies to examine aging trajectories that include detailed data from before, during, and after cancer treatment; mechanistic studies to elucidate the pathways that lead to the emergence of aging phenotypes in cancer survivors; long-term clinical surveillance to monitor survivors for late-emerging effects; and tools to integrate multiple data sources to inform understanding of how cancer and its therapies contribute to the aging process. Addressing these needs will help expand the evidence base and inform strategies to optimize healthy aging of cancer survivors.
The Histone Deacetylase Inhibitor Valproic Acid Lessens NK Cell Action against Oncolytic Virus-Infected Glioblastoma Cells by Inhibition of STAT5/T-BET Signaling and Generation of Gamma Interferon (2012)

Tumor virotherapy has been and continues to be used in clinical trials. One barrier to effective viral oncolysis, consisting of the interferon (IFN) response induced by viral infection, is inhibited by valproic acid (VPA) and other histone deacetylase inhibitors (HDACi). Innate immune cell recruitment and activation have been shown to be deleterious to the efficacy of oncolytic herpes simplex virus (oHSV) infection, and in this report we demonstrate that VPA limits this deleterious response. VPA, administered prior to oHSV inoculation in an orthotopic glioblastoma mouse model, resulted in a decline in NK and macrophage recruitment into tumor-bearing brains at 6 and 24 h post-oHSV infection. Interestingly, there was a robust rebound of recruitment of these cells at 72 h post-oHSV infection. The observed initial decline in immune cell recruitment was accompanied by a reduction in their activation status. VPA was also found to have a profound immunosuppressive effect on human NK cells in vitro. NK cytotoxicity was abrogated following exposure to VPA, consistent with downmodulation of cytotoxic gene expression of granzyme B and perforin at the mRNA and protein levels. In addition, suppression of gamma IFN (IFN-γ) production by VPA was associated with decreased STAT5 phosphorylation and dampened T-BET expression. Despite VPA-mediated immune suppression, mice were not at significantly increased risk for HSV encephalitis. These findings indicate that one of the avenues by which VPA enhances oHSV efficacy is through initial suppression of immune cell recruitment and inhibition of inflammatory cell pathways within NK cells.
Thermal Management Integrated With Flat Heat Pipes for In-Slot Stator Windings of Electric Motors (2022)

Increasing electromagnetic loads can improve the torque density and power density of electric motors; however, these enhancements are limited by the resultant thermal problems. This article proposes a cooling concept, where flat heat pipes (FHPs) are inserted into the center of the stator slots to directly remove copper loss without consuming power. Detailed thermal models of the FHPs and an electric motor are established using a lumped-parameter thermal network. The thickness of the vapor chamber is found to be the most critical parameter that simultaneously affects the thermal and electromagnetic performance. A case study is carried out on an existing 6-kW drive motor for a ducted fan, and the simulation results are validated through motorette experiments. Research results have shown that a 70 °C hot-spot temperature reduction can be achieved, and more than 80% of the copper loss can be removed by the FHPs. Moreover, the shaft power that the thermally modified motor can provide is expected to be 2.4 times that of the reference motor, and a continuous power density of 4.8 kW/kg can be achieved using air as a cooling agent.
10,11-Methylenedioxycamptothecin, a Topoisomerase I Inhibitor of Increased Potency: DNA Damage and Correlation to Cytotoxicity in Human Colon Carcinoma (HT-29) Cells (1990)

We had previously shown that 10,11-methylenedioxy-20-(RS)-camptothecin (MDO-CPT) is a more potent inhibitor of purified DNA topoisomerase I than 20-(S)-camptothecin (CPT). The current studies compared the cytotoxicity and DNA damage induced by MDO-CPT and CPT in the human colon carcinoma cell line, HT-29. MDO-CPT was 7- to 10-fold more potent than CPT both for cytotoxicity (ID50 = 25 vs. 180 nM) and production of DNA single-strand breaks (SSB). Kinetics of SSB formation and reversal were similar for MDO-CPT and CPT. DNA-protein crosslinks (DPC) were also produced by both drugs with a SSB/DPC ratio of 1/1. Moreover, no SSB were detected under non-deproteinizing conditions, indicating that both CPT and MDO-CPT produced protein-linked DNA single-strand breaks. A good correlation between cytotoxic potency and protein-linked DNA single-strand break production was observed for CPT and MDO-CPT, implying a causal relationship between drug-induced cytotoxicity and topoisomerase I inhibition. The sensitivity of human colon HT-29 cancer cells to camptothecins may be a selective phenomenon since these cells normally express natural resistance to current chemotherapeutic drugs, including topoisomerase II inhibitors.
Milankovitch orbital forcing control on shallow-water carbonate cyclicity and early dolomitization: insights from the lower Cretaceous Cupido platform, NE Mexico (2007)

Jerry Lucia for great discussion on dolomitization processes, Robert Folk for critical reviews or portions of this manuscript and discussions regarding dolomite characteristics and dolomitization processes, Larry Mack for his assistance and insights in data preparation, collection and interpretation during laboratory analyses, Kitty Milliken for expertise in carbonate petrology, the use of Scanning Electron Microscope and Cathodoluminescence, and great discussion on dolomitization models, Urshela Hammers for critical reviews of manuscripts and lengthy discussion on sequence stratigraphic concepts, Linda Hinnov for interactive tutorials and discussions on spectral analysis techniques and interpretation, Wan Yang for ideas into statistical analysis vi of high-frequency cycles, James Lee Wilson for ideas and critical questioning of Cupido platform sequence stratigraphic framework and evolution, Tina Foster for sharing ideas about facies, depositional model and stratigraphic correlation across the Cupido platform.
Multiple Adducts of C<sub>60</sub> by Tether‐Directed Remote Functionalization and synthesis of soluble derivatives of new carbon allotropes C<sub><i>n</i>(60+5)</sub> (1997)

Abstract A comprehensive series of multiple adducts of C 60 was prepared by tether‐directed remote functionalization. When the tether‐reactive‐group conjugates 2 and 10 were attached to methano[60]fullerenecarboxylic acid ( = cyclopropafullerene‐C 60 ‐ I h ‐carboxylic acid) and C 60 , respectively, the e ‐bis‐adducts 4 and 9 ( Schemes 1 and 2 ) were obtained with complete regioselectivity as predicted by semi‐empirical PM3 calculations ( Fig. 2 ). Attachment of the anchor‐tether‐reactive‐group conjugate 13 to C 60 by Bingel reaction, followed by double intramolecular Diels‐Alder cycloaddition afforded the tris‐adduct 12 ( Scheme 3 ). Starting from 12 , a series of selective e ‐additions led to the tetrakis‐adducts 16 and 19 ( Scheme 4 ), pentakis‐adducts 20 – 23 ( Scheme 5 ), and, ultimately, to hexakis‐adducts 24 and 25 ( Scheme 6 ), and 29 and 30 ( Scheme 7 ) with a pseudo‐octahedral addition pattern on the fullerene core. Oxidative cyclization of diethynylmethanofullerene 30 under Eglinton‐Glaser conditions afforded the trimeric and tetrameric acetylenic macrocycles 26 , with three, and 27 , with four appended C 60 moieties, respectively ( Scheme 8 ). These multinanometer‐sized compounds are the first soluble derivatives of C 195 and C 260 , two members of a new class of fullerene‐acetylene hybrid C‐allotropes with the general formula C n (60 + 5) . The matrix‐assisted laser‐desorption time‐of‐flight mass spectra of 26 and 27 showed a remarkable fragmentation; the sequential loss of fullerene spheres led to the formation of ions corresponding to mono‐fullerene adducts of the cyclocarbons cyclo ‐C 15 and cyclo ‐C 20 ( Fig. 4 ). Large solvent effects were observed in the Bingel addition of 2‐bromomalonates to higher adducts of C 60 , with the use of polar solvents enhancing the reaction rate without loss of regioselectivity. Experimental evidence for the enhanced reactivity of e face over e edge bonds was obtained, which had previously been predicted in computational studies. The correlated series of mono‐ to hexakis‐adducts of C 60 allowed identification of the changes in reactivity and physical properties that occur, when the conjugated π‐electron chromophore of the fullerene is reduced as a result of increasing functionalization; this analysis is the subject of the directly following paper.