gebhart/patrepeval huggingface dataset:
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome (2023)

In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes a DNA lesion in the nucleosome remains enigmatic. In the present study, we inserted an apurinic/apyrimidinic DNA lesion analogue, tetrahydrofuran (THF), in the nucleosomal DNA, where RNAPII stalls at the SHL(-4), SHL(-3.5), and SHL(-3) positions, and determined the structures of these complexes by cryo-electron microscopy. In the RNAPII-nucleosome complex stalled at SHL(-3.5), the nucleosome orientation relative to RNAPII is quite different from those in the SHL(-4) and SHL(-3) complexes, which have nucleosome orientations similar to naturally paused RNAPII-nucleosome complexes. Furthermore, we found that an essential TCR protein, Rad26 (CSB), enhances the RNAPII processivity, and consequently augments the DNA damage recognition efficiency of RNAPII in the nucleosome. The cryo-EM structure of the Rad26-RNAPII-nucleosome complex revealed that Rad26 binds to the stalled RNAPII through a novel interface, which is completely different from those previously reported. These structures may provide important information to understand the mechanism by which RNAPII recognizes the nucleosomal DNA lesion and recruits TCR proteins to the stalled RNAPII on the nucleosome.
What Causes SUDEP (2002)

This article primarily addressed the question of what causes sudden unexpected (or unexplained) death in patients with epilepsy (SUDEP). Researchers
Nonlinear uncertainty analysis in reservoir seismic modeling and inverse problems (2006)

Understanding forward modeling and inverse estimation problems in reservoir seismic analysis can be improved by the consideration of nonlinear uncertainty analysis to quantify the range of expected outcomes (e.g., Tarantola, 1987). In this paper, this requires a quantitative capturing of the a priori uncertainties in the model, parameter and data domains, and physically constrained nonlinear sampling methods (e.g. modified Monte Carlo sampling) to produce large numbers of realizations of each quantity. Application of the forward modeling or inverse estimation operators to the realizations then produces a range of outcomes which can be combined to generate a posteriori uncertainty distributions. A wide variety of statistical measures of uncertainty can then be calculated from the a posteriori distributions to quantify the forward modeling or inverse estimation results.
Mining distance-based outliers from large databases in any metric space (2006)

Let R be a set of objects. An object o ∈ R is an outlier, if there exist less than k objects in R whose distances to o are at most r. The values of k, r, and the distance metric are provided by a user at the run time. The objective is to return all outliers with the smallest I/O cost.This paper considers a generic version of the problem, where no information is available for outlier computation, except for objects' mutual distances. We prove an upper bound for the memory consumption which permits the discovery of all outliers by scanning the dataset 3 times. The upper bound turns out to be extremely low in practice, e.g., less than 1% of R. Since the actual memory capacity of a realistic DBMS is typically larger, we develop a novel algorithm, which integrates our theoretical findings with carefully-designed heuristics that leverage the additional memory to improve I/O efficiency. Our technique reports all outliers by scanning the dataset at most twice (in some cases, even once), and significantly outperforms the existing solutions by a factor up to an order of magnitude.
People and eyes: statistics in ophthalmology. (1998)

In ophthalmic research we have a problem. The collection of data for a project usually involves examining and recording observations on eyes. People generally have two eyes and we often examine both. The problem then comes in the analysis.
Decreasing Incidence of Postcesarean Endometritis With Extended-Spectrum Antibiotic Prophylaxis (2008)

II.
Paradoxical Emboli Secondary to Hepatic Pathology: Common or Coincidental? (2009)

Paradoxical cerebral emboli from cardiac and pulmonary sources are well described in the peer-reviewed literature. We outline a case with a hepatic etiology and describe diagnostic and management options. Though this paper represents the first documentation of such, we believe that transpulmonary shunting with concurrent paradoxical cerebral microemboli is more prevalent than recognized. We introduce this case report to compel practitioners to consider paradoxical emboli in selected cirrhotic patients since it can often be difficult to elicit subtle neurologic changes on clinical examination of patients with end stage liver disease.
Comparison of clinical outcome after cryopreservation of embryos obtained from intracytoplasmic sperm injection and in-vitro fertilization (1998)

The impact of intracytoplasmic sperm injection (ICSI) on cryopreserved zygotes and embryos was evaluated by comparing embryo survival and implantation between embryos derived from ICSI and those derived from standard insemination procedures. The study included patients whose excess zygotes and embryos were cryopreserved between September 1993 and December 1994 and who subsequently underwent a frozen embryo transfer. Embryo survival, clinical pregnancy rates per transfer and pregnancy outcome were compared. Three hundred and thirty eight cryopreservation cycles, during which 1471 embryos were cryopreserved, were included in this study. Of those, 961 were derived from oocytes fertilized by insemination in vitro and 510 were derived from oocytes fertilized by ICSI. A total of 690 of the embryos (451 in the insemination group and 239 in the ICSI group) have since undergone a thaw cycle. The embryo survival rates were similar between the two groups (70.5 and 73.2%, insemination and ICSI respectively) and were not significantly affected by the stage at cryopreservation. There was no significant difference in pregnancy rates per transfer (31.8 and 32.3%), the preclinical pregnancy loss rate (16.7 and 23.8%), or the clinical miscarriage rate (16.7 and 23.8%) between the insemination and the ICSI groups respectively. It is concluded that ICSI does not have an adverse impact on the survival and successful implantation of cryopreserved and thawed embryos.
Heart Rate Variability (2018)

Introduction: Cardiovascular diseases are the highest cause of death in the world. Many of these deaths may be workplace related. Long hours at work seem to be influencing the increased risks of heart diseases. Workplace stress can be defined as the “discrepancies between the physiological demands within a workplace and the inability of employees to either manage or cope with such work demands.” The varied nature and perception of stress are exemplified from literature that shows stress being either a stimulus, or a response, or a stimulus–response combination, also known as a transactional relationship between one or more individuals and the environment, leading to an initiative toward a physiological standpoint. Methods: This research opted for a correlational study which involves 85 full-time employees who were working at least 40 h per week in a large corporation participated in this study. The Personal and Organizational Quality Assessment and Perceived Stress Scale were used to correlate with heart rate variability (HRV). Objectives: The primary objective of this study is to introduce a new quantitative assessment tool emWave Pro Plus (Institute of HeartMath) and compare heart rate variability (HRV) results with the Personal and Organizational Quality Assessment (POQA) and the Perceived Stress Scale (PSS). Results: Astonishing findings emerged. Significant positive correlations were found between emotional stress and HRV and between intention to quit and HRV. In other words, the researcher has to make sense the following surprising findings: (1) The higher the emotional stress an employee faces, the healthier they are. (2) Healthier employees may have higher intentions of quitting their jobs. Conclusion: The surprising results may be attributed to personality, culture, emotional regulation, and age among others.
24 hour plasma Cortisol patterns in growing pigs fed two or three times a day (1988)

Zusammenfassung 24‐Stunden Plasma‐Cortisol‐Profile von zwei‐ und dreimal täglich gefütterten, wachsenden Schweinen An drei weiblichen Schweinen (38–54 kg) wurden die 24‐Stunden Plasmacortisolprofile studiert. Die Tiere erhielten die gleiche tägliche Futtermenge entweder auf zwei (8 und 16 Uhr), oder auf drei Gaben verteilt (8, 16 und 24 Uhr). Beide Behandlungen ergaben minimale Plasmacortisolwerte zwischen 17 und 22 Uhr. Danach erhöhten sich die Plasmacortisolwerte wieder allmählich auf ihre maximalen Werte zwischen 5 und 10 Uhr. Das Anbieten des Futters zum nocturnen Zeitpunkt ergab einen kurzfristig erhöhten Peak im Plasmacortisolgehalt, der sich signifikant von der zweimaligen Fütterung unterschied. Die ernährungsphysiologischen Folgen der Nährstoffresorption einer Nachtfütterung bei gleichzeitig steigendem Plasmacortisolgehalt werden diskutiert.
Early detection of patients at risk of developing diabetic nephropathy. A longitudinal study of urinary albumin excretion (1982)

Abstract. In an attempt to detect patients at high risk of developing diabetic nephropathy, a longitudinal study of urinary albumin excretion rate (radial immunodiffusion) was carried out in 15 female and 8 male long-term insulin-dependent diabetics without proteinuria (negative Albustix test). Five females and 3 males had an elevated urinary albumin excretion at the time of screening, mean 115 ± 26 ( sd ) mg/24 h. Our upper normal range for urinary albumin excretion is ≤ 40 mg/24 h. The 5 patients with the highest albumin excretion subsequently developed persistent albuminuria, 132 → 1007 mg/24 h, P &lt; 0.05, elevated serum creatinine, 83 → 128 μmol/l, P &lt; 0.05, and raised blood pressure, 135/86 → 163/112 mmHg, P &lt; 0.05. One patient developed intermittent albuminuria (positive Albustix test), while the variables in the remaining 2 patients were about the same during the 6 years observation period. Fifteen patients had a normal urinary albumin excretion, mean 17 ± 9 ( sd ) mg/24 h, at the time of the screening. Intermittent and persistent albuminuria developed in 2 patients, while albumin excretion, serum creatinine, and blood pressure were nearly unchanged in the remaining 13 patients after 6 years. Our longitudinal study indicates that early detection of patients at high and low risk of developing persistent proteinuria i.e. diabetic nephropathy, is possible by using a sensitive method for measuring urinary albumin excretion.
Regulation of pulmonary Pseudomonas aeruginosa infection by the transcriptional repressor Gfi1 (2006)

Pulmonary Pseudomonas aeruginosa infections are characterized by the release of proinflammatory mediators, focal induction of apoptosis in respiratory epithelial cells and internalization of the bacteria. Here, we demonstrate that the transcriptional regulator Gfi1 is critically involved in the regulation of proinflammatory cytokine release and the induction of apoptosis in respiratory epithelial cells and macrophages upon P. aeruginosa infection. Gfi1-deficient mice responded to a pulmonary P. aeruginosa infection with uncontrolled pulmonary release of interleukin (IL)-1 and tumour necrosis factor (TNF)-alpha, sepsis and death, which were delayed by injection of IL-1- and TNF-alpha-neutralizing antibodies. The uncontrolled release of cytokines seems to be caused by a failure of Gfi1-deficient respiratory epithelial cells in large to small bronchi and macrophages to respond to P. aeruginosa infection with an induction of apoptosis. Pharmacological inhibition of apoptosis in wild-type mice by intravenous injection of the broad-spectrum caspase inhibitor zVAD-cmk mimicked the phenotype of Gfi1-deficient mice and resulted in a profound sensitization of mice to P. aeruginosa, an increased release of cytokines, sepsis and death of the animals. Thus, Gfi1 controls apoptosis of respiratory epithelial cells and macrophages upon infection with P. aeruginosa. Inhibition of apoptosis by Gfi1 deficiency or caspase blockers sensitizes mice to P. aeruginosa infections, suggesting that apoptosis functions as a novel defence mechanisms in the regulation of the local innate immune response.
Synthesis of Primary Amines from Secondary and Tertiary Amines: Ruthenium‐Catalyzed Amination Using Ammonia (2011)

Splitting of secondary and tertiary amines! The first selective catalytic synthesis of primary amines from secondary and tertiary amines with ammonia is reported. The products are obtained in yields up to 84 %. Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Further Studies of the Mechanism Behind Scopolamine‐induced Reversal of Antistereotypic and Cataleptogenic Effects of Neuroleptics in Rats (1986)

Scopolamine is known to attenuate the amphetamine antagonistic and cataleptogenic effect of selective DA D-2 antagonists. To study further the influence of other receptor systems three approaches were taken: concomitant treatment with receptor blockers (scopolamine, prazosin and ketanserin) and a selective D-2 antagonist YM 09151-2, testing of a neuroleptic droperidol, with mixed D-2, alpha 1 and 5-HT2 antagonistic properties and testing a selective D-1 antagonist SCH 23390. Scopolamine markedly attenuated both effects of YM 09151-2 and droperidol. In contrast neither prazosin nor ketanserin influenced the effects of YM 09151-2. Furthermore, prazosin did not influence the interaction between scopolamine and YM 09151-2 in the tests of stereotypy and catalepsy. Scopolamine did not change the amphetamine antagonistic potency of SCH 23390, but decreased moderately its cataleptogenic potency. It is concluded that 5-HT2 and alpha 1-adrenergic receptor blockade are of minor importance in order to determine the sensitivity of a DA D-2 antagonist to the reversal induced by scopolamine. Thus, our earlier hypothesis, that DA D-1 receptor blockade is the main mechanism stabilizing these neuroleptic effects against scopolamine reversal, are further supported by the present experiments.
Ein fluoriertes Detergens für Membranprotein‐Anwendungen (2015)

Abstract Tenside mit fluorierten Kohlenstoffketten stellen eine vielversprechende milde Alternative zu konventionellen, vollständig hydrierten Detergentien für die Solubilisierung und Handhabung integraler Membranproteine dar. Aufgrund ihrer Inertheit gegenüber Lipidmembranen blieben sie bisher aber von beschränktem Nutzen für solche Anwendungen, in denen eine detergensähnliche Aktivität benötigt wird. Hier zeigen wir, dass Fluorierung an sich Detergensaktivität nicht ausschließt, wie an einem als F 6 OM bezeichneten fluorierten Octylmaltosid‐Derivat veranschaulicht wird. Diese nichtionische Verbindung wechselwirkt mit und solubilisiert Phospholipidvesikel in detergensähnlicher Weise, ohne jedoch die Membranordnung unterhalb der Solubilisierungsgrenze zu beeinträchtigen. Dank dieser sanften und unüblichen Detergensaktivität ist F 6 OM im Gegensatz zu einem lipophoben fluorierten Tensid in der Lage, die funktionelle Rückfaltung eines integralen Membranenzyms durch Förderung der Membraninsertion in Abwesenheit von Mizellen zu unterstützen.
Toxicity profile and early clinical outcome for advanced head and neck cancer patients treated with simultaneous integrated boost and volumetric modulated arc therapy (2015)

RapidArc technology and SIB with 1.65 and 2.12Gy/fraction for 33 fractions showed a good toxicity profile and encouraging trend for OS and DFS for patients with stage III-IV HNC.
Resource-Aware Scheduling of Distributed Ontological Reasoning Tasks in Wireless Sensor Networks (2010)

As the number of wireless sensor network applications continues to grow, the need for specialized task scheduling mechanisms, aware of the sensor devices' capabilities and real-time resource availability, is becoming more and more apparent. In this paper, we therefore propose a generic model for task scheduling in heterogeneous networks, which we subsequently use to schedule distributed reasoning tasks, originating from a real-world WSN monitoring and management application. By means of simulation, we evaluate several developed scheduling heuristics and compare the results to an optimal solution of the same WSN task scheduling problem, obtained using ILP. Experiments show that our heuristics produce acceptable task schedules while maintaining a low resource footprint.
A Prospect for Pyrrolidine Iminosugars as Antidiabetic α-Glucosidase Inhibitors (2012)

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTA Prospect for Pyrrolidine Iminosugars as Antidiabetic α-Glucosidase InhibitorsAna Trapero and Amadeu Llebaria*View Author Information Laboratory of Medicinal Chemistry, Department of Biomedicinal Chemistry, Institut de Química Avançada de Catalunya (IQAC—CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain*Phone: +34-934-006-108. Fax: +34-932045904. E-mail: [email protected]Cite this: J. Med. Chem. 2012, 55, 23, 10345–10346Publication Date (Web):November 28, 2012Publication History Received15 November 2012Published online28 November 2012Published inissue 13 December 2012https://pubs.acs.org/doi/10.1021/jm301682rhttps://doi.org/10.1021/jm301682reditorialACS PublicationsCopyright © 2012 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2960Altmetric-Citations43LEARN 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 PDF (343 KB) Get e-AlertscloseSUBJECTS:Carbohydrates,Inhibition,Inhibitors,Peptides and proteins,Substituents Get e-Alerts
A Rodent Flash FPGA Control System for Closed-loop Optogenetic Stimulation to Suppress Seizures (2018)

in this effort, we report a low power Flash FPGA based control system for benefiting closed-loop neuroscience experiments. A digital implementation of closed-loop proportional-integral-derivative control algorithm has been implemented for offering more flexibility to generate further optogenetic stimulation to stabilize the epileptiform oscillation in epileptiform neuron network. The proposed digital control system receiving recordings from an implantable probe, preformed the closed-loop control algorithm and generating optogenetic stimulation to control epileptic seizures as a closed-loop system. The prototype is capable of satisfying the real time constraints posed by the application when clocked at 20 MHz which costs 4.67 rnA.
Isochronous (CW) Non-Scaling FFAGs: Design and Simulation (2010)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation C. Johnstone, M. Berz, K. Makino, P. Snopok; Isochronous (CW) Non‐Scaling FFAGs: Design and Simulation. AIP Conf. Proc. 4 November 2010; 1299 (1): 682–687. https://doi.org/10.1063/1.3520412 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Target sequence data shed new light on the infrafamilial classification of Araceae (2022)

<strong>PREMISE: </strong>Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered <em>Calla palustris</em>. The main objective of this work was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus <em>Calla</em> in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family. <strong>METHODS: </strong>Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms353 universal probe set. <strong>RESULTS: </strong>The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus <em>Calla</em> is included in subfamily Aroideae which has also been expanded to include Zamioculcadoideae. The new <em>Boycea</em>–<em>Aglaonema </em>Clade is defined. <strong>CONCLUSIONS:</strong> Our results strongly suggest that new research on African genera (<em>Callopsis</em>, <em>Nephthytis </em>and <em>Anubias</em>) and <em>Calla</em> will be important to understand the early evolution of the Aroideae. Also, of particular interest are the phylogenetic positions of the isolated genera <em>Montrichardia</em>, <em>Zantedeschia</em> and <em>Anchomane</em>s, which remain only moderately supported here.
Posterosuperior glenoid internal impingement of the shoulder in the overhead athlete: Pathogenesis, clinical features and MR imaging findings (2015)

Posterosuperior glenoid internal impingement (PGII) is an impingement syndrome of the shoulder that is most commonly seen in the throwing or overhead athlete. The supraspinatus can be normally compressed or impinged between the greater tuberosity and the posterosuperior labrum in the abduction and external rotation position. However, repetitive throwing and biomechanical abnormalities may lead to the intensification of this contact and to the clinical and pathological picture of PGII. The injured athlete usually complains of poor throwing performance and pain located in the posterosuperior aspect of the shoulder. Two main theories regarding the aetiology of PGII have been postulated with differing initial mechanisms. The MRI features of PGII have been described and include supraspinatus and anterior infraspinatus partial undersurface tears, bony changes at the humeral head and labral pathology, including a variation of the type II superior labrum from anterior to posterior lesion. This pictorial essay aims to present cases illustrating the pathophysiology, clinical features and recently described MRI findings, and discuss some of the MR protocol considerations.