gebhart/patrepeval huggingface dataset:
Exposure to lead induces hypoxia—like responses in bullfrog larvae <i>(Rana catesbeiana)</i> (1999)

Amphibians collected around mining sites, areas with extensive automobile traffic, and shooting ranges have been documented to contain high levels of lead. Lead-exposed amphibians might respond as if in hypoxic conditions because exposure is known to decrease hemoglobin levels, damage erythrocytes, and alter respiratory surfaces. Therefore, we exposed bullfrog larvae to either 0 or 780 μg/L Pb and either 3.50 or 7.85 mg/L oxygen for 7 d and monitored activity, trips to the surface, and buccal ventilation rates. Activity was significantly decreased in larvae exposed to low oxygen, Pb, or both compared to activity of larvae in high oxygen with no Pb. Larvae exposed to both Pb and low oxygen displayed higher buccal ventilation rates than larvae exposed to either treatment separately. Lead-exposed larvae surfaced significantly more often than unexposed larvae even under high-oxygen conditions. Lead-exposed larvae decreased in mass during the exposure period, whereas unexposed larvae increased in mass. Lead exposure could decrease survival of larvae in the field not only because of physiological problems due to decreased oxygen uptake but also because of greater predation pressure due to increased presence at the surface and reduced growth rates.
Two Approaches for Efficient Synthesis of (‐)‐Colletol. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Identify Optical Proximity Correction (OPC) issue in 0.13 μm technology development (2004)

In this paper, we explained a failure analysis methodology to identify optical proximity correction issues in 0.13 /spl mu/m technology development. Here we used, the continue-on-failure wafer sort technology for yield analysis.
The natural history of calcium urolithiasis (1977)

The course of untreated calcium renal stones, derived from the retrospective study of 300 patients with defined metabolic disorders and from the analysis of two prospective, published studies, is complex and heterogeneous. Generally, stones provoke considerable morbidity; hyperuricosuria is associated with an unusually severe stone disease. Stone recurrence rates usually remain stable, or rise with successive stones; in a minority of patients, the reverse is true. A single stone is likely to be followed by a recurrence. The mean time to recurrence averages 6.78 years, with peaks at 1.56 and eight years. Because the disease is likely to be morbid and chronic and does not wane with age, diagnostic evaluation and treatment should be strongly considered for any patient with recurrent stones, and for those in whom recurrence is likely to pose more than the usual risk. (<i>JAMA</i>238:1519-1523, 1977)
Structure of the <i>Mycobacterium tuberculosis</i> OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall (2010)

The pore-forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline-rich hinge region. As expected, the high-resolution structure of the C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria. The N-terminal domain of OmpATb (73-204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb(73-204) is highly water soluble, current-voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb(73-204) suggest that OmpATb(73-204) can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane-associated rings at the basal body of the secretion machinery.
Computational Prediction of Blood-Brain Barrier Permeability Using Decision Tree Induction (2012)

Predicting blood-brain barrier (BBB) permeability is essential to drug development, as a molecule cannot exhibit pharmacological activity within the brain parenchyma without first transiting this barrier. Understanding the process of permeation, however, is complicated by a combination of both limited passive diffusion and active transport. Our aim here was to establish predictive models for BBB drug permeation that include both active and passive transport. A database of 153 compounds was compiled using in vivo surface permeability product (logPS) values in rats as a quantitative parameter for BBB permeability. The open source Chemical Development Kit (CDK) was used to calculate physico-chemical properties and descriptors. Predictive computational models were implemented by machine learning paradigms (decision tree induction) on both descriptor sets. Models with a corrected classification rate (CCR) of 90% were established. Mechanistic insight into BBB transport was provided by an Ant Colony Optimization (ACO)-based binary classifier analysis to identify the most predictive chemical substructures. Decision trees revealed descriptors of lipophilicity (aLogP) and charge (polar surface area), which were also previously described in models of passive diffusion. However, measures of molecular geometry and connectivity were found to be related to an active drug transport component.
Cell-based Probabilistic Roadmaps (CPRM) for Efficient Path Planning in Large Environments (2007)

Abstract — This paper presents a novel sampling-based path planning method called Cell-based Probabilistic Roadmaps (CPRM). The algorithm has both anytime and replanning characteristics and is superior to classical approaches in that it incrementally builds and reuses the roadmap. Because it maintains a graph structure that is tailored to the queries, CPRM is very fast in answering repeated queries, e.g. in replanning scenarios. Different design parameters allow to control and fine-tune the behavior of the algorithm. I.
Myocardial infarction: diagnosis and vital status prediction using neural networks (2002)

Neural networks (NNs) have been found useful in many biomedical applications. The authors' purpose is to apply NNs to two specific problems in cardiology, namely, diagnosis of echocardiograms for myocardial infarction and prediction of vital status of patients that suffered such. The authors used NNs to discriminate between normal and infarcted myocardium, by looking at intensity changes. The intensities of selected regions are used for training and testing. In predicting the vital status of patients that have suffered acute myocardial infarction, the authors used a large database (MIDAS) with follow-ups. The NN in this case has two hidden layers with 18 patient variables from the MIDAS dataset as inputs. The NN was again trained with the feedback algorithm ALOPEX and tested with unknown data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fertilization and early embryology: Controlled comparison of Earle's balanced salt solution with Ménézo B2 medium for human in-vitro fertilization performance (1994)

In order to optimize the in-vitro fertilization (IVF) procedure and to avoid the batch-to-batch fluctuations of in-house culture medium, we investigated the use of a commercially available medium. In our human IVF programme, a controlled comparison was performed from July 1991 to February 1992 between in-house Earle's medium and commercially available Ménézo B2 medium. The major difference between the two tested media is the additional presence of amino acids and water-soluble vitamins in Ménézo B2 and the different origins of the proteins source, i.e. bovine serum albumin (BSA) in Ménézo B2 and human serum albumin (HSA) in Earle's medium. In the first, auto-controlled study, sibling oocytes cultured in Ménézo B2 showed a significantly higher fertilization rate than those cultured in Earle's medium: 58.1 +/- 37.2% and 52.1 +/- 36.9% respectively. After further culture of the fertilized oocytes, there was no difference in the morphological characteristics of the embryos cultured in the different media, although the rate of development was different. In Ménézo B2 medium, a higher proportion of the embryos had reached at least the 4-cell stage at transfer. In the second, randomized study, effects on the pregnancy and implantation rates of both media were analysed. In the group of oocytes cultured in B2, more excellent or good-quality embryos were available for transfer at a more advanced stage of development. No significant difference in pregnancy rate was observed: 39.1% per transfer in Earle's medium versus 40.5% per transfer in Ménézo B2.(ABSTRACT TRUNCATED AT 250 WORDS)
FeedMAP: Improving Safety and Comfort for In-Vehicle Applications by Map Deviation Detection and Online Map Updating (2008)

Up-to-date map data is a must for current and future navigation and Advanced Driver Assistance System (ADAS) applications. Today, digital maps are normally stored on DVDs or hard disks, with periodic updates only available on replacement disks. However, new mechanisms for updating maps have been investigated and some of them already reached the market. As the real world is changing every day, detecting changes to the road network quickly and at a low cost is a challenge. Although mapmakers continuously survey the European road network for changes, map information is not always up-to-date or accurate.
Intraoperative Use of an External Fixator Distraction Device for Corrective Distal Radius Osteotomy (1999)

Department of Orthopaedics and Rehabilitation, University of Miami School of Medicine, Miami, Florida, U.S.A. Address correspondence and reprint requests to Dr. Richard A. Rogachefsky, 1948 Union Boulevard, Bayshore, NY 11706, USA. No benefits in any form have been received or will be received from a commercial party related directly or indirectly to the subject of this article.
Abstract 4923: Expression of class III beta-tubulin (TUBB3) in 3580 colorectal cancers (CRCs) and correlation with clinico-pathological and molecular features (2016)

Abstract Class III beta-tubulin plays a crucial role in intracellular transport, meiosis and mitosis. High expression of TUBB3 has been shown to associate with poor prognosis and taxane resistance in various cancer types. CRC is known to be generally resistant to taxane therapy. We investigated expression of TUBB3 in 3580 CRCs and made correlations with clinicopathological and molecular parameters. 3580 CRC samples were evaluated by tumor profiling (Caris Life Sciences, Phoenix, AZ). Tests included Sanger or next generation sequencing (NGS), protein expression by immunohistochemistry (IHC) and gene amplification by in situ hybridization (ISH). TUBB3 expression was evaluated by immunohistochemistry (Ab: POLY, Covance) and expression higher than 2+, 30% was scored as positive. TUBB3 positive expression was observed in 37% (1320/3580) of the complete CRC cohort, specifically 27% in mucinous histology (164/617) and 17% in signet ring histology (29/171). While the expression was not associated with average patient age (59 years old) or gender (53% vs. 50% male), TUBB3 was more frequently expressed in tumors that originated from the left colon (370/1016 or 36%) than from the right colon (235/790 or 30%, p = 0.003). In the 1847 tumors taken from metastatic sites, 40% (746) overexpressed TUBB3 while in 1629 CRCs taken from primary tumors, only 34% (547) overexpressed TUBB3 (p&lt;0.0001). Interestingly, in tumors that overexpressed TUBB3, 65% also overexpressed cMET (828/1275) and 33% also overexpressed TLE3 (431/1299). This compares to 50% cMET expression (1096/2207, p&lt;0.0001) and 23% TLE3 expression (517/2225, p&lt;0.0001) in tumors that were negative for TUBB3. Microsatellite instability detected by fragment analysis was more prevalent in the TUBB3-negative cohort than the TUBB3-positive cohort (7.4% or 77/1046 vs. 2.9% or 16/558, p = 0.0002). Mutations in APC (62% vs. 56%, p = 0.0003) and KRAS (55% vs. 46%, p&lt;0.0001) were more frequent in TUBB3-positive tumors, while GNAS (2% vs. 5%, p&lt;0.0001) and SMAD4 (10.1% vs. 14.6%, p = 0.0005) mutations were significantly more frequent in tumors that were negative for TUBB3 expression. Thus, high expression of TUBB3 was found in 37% of CRCs, and was significantly associated with tumors that originated from the left colon and with tumors taken from metastatic sites. Distinct biomarker features detected by IHC and sequencing suggest that TUBB3 expression may carry theranostic importance which warrants further investigation in clinical trials. Citation Format: Joanne Xiu, Sandeep Reddy, Wafik S. El-Deiry. Expression of class III beta-tubulin (TUBB3) in 3580 colorectal cancers (CRCs) and correlation with clinico-pathological and molecular features. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4923.
Canonical models in mathematical neuroscience (1998)

Our approach to mathematical neuroscience is not to consider a single model but to consider a large family of neural models. We study the family by converting every member to a simpler model, which is referred to as being canonical. There are many examples of canonical models. Most of them are derived for families of neural systems near thresholds; that is, near transitions between the rest state and the state of repetitive spiking. The canonical model approach enables us to study frequency and timing aspects of networks of neurons using frequency domain methods. We use canonical (phase) models to demonstrate our theory of frequency modulated (FM) interactions in the brain: Populations of cortical oscillators self-organize by frequencies; same-frequency sub-populations of oscillators can interact in the sense that a change in phase deviation in one will be felt by the others in the sub-population; and oscillators operating at different frequencies do not interact in this way. In our theory, sub-networks are identified by the firing frequency of their constituents. Network elements can change their sub-population membership by changing their frequency, much like tuning to a new station of an FM radio. Also discussed here are mechanisms for changing frequencies obtained in our recent work using similar models to study spatial patterns of theta and gamma rhythm phase locking in the hippocampus.
Emergency Endovascular Repair for a Ruptured Abdominal Aortic Aneurysm Patient (2005)

症例は71歳の男性。意識消失にて近医脳神経外科に緊急入院した。脳梗塞の既往歴,心房細動を伴っていたことから脳梗塞の再発を疑われ抗凝固療法が施行された。翌日になり腹部膨満が出現,腹部CTにて破裂性腹部大動脈瘤(rAAA)と診断された。抗凝固療法による凝固時間の延長,血液型がAB型であり十分な輸血の確保が難しいことから,開腹人工血管置換術は困難と判断された。Stent-graft (SG)内挿術を目的として当科に紹介され救急車にて搬送された。来院時収縮期血圧60mmHgとショック状態であり,直ちに手術室に移動し全身麻酔で手術を開始した。2チームに分かれ,1チームが大腿動脈を露出する間に他の術者がSGを自作した。術中血管造影から破裂はFitzgerald 4型と判明した。aorto-rt. uniiliac SG+交叉バイパス手術を行い,左総腸骨動脈をコイル塞栓した。手術時間2時間1分,出血量60mlにて手術終了。4POD抜管,6POD経口摂取再開,12POD退院となった。SG内挿術は動脈瘤の腎動脈分枝部からの距離や腸骨動脈の性状などの制約を受けること,またエンドリークなどの合併症や,長期のデータがないことなど,人工血管置換術に比し欠点も多い。しかし,症例によっては本症例のようにSGでなければ救命できないものもあり,今後rAAA治療の選択肢の一つとして考慮すべき術式と考えられた。
Differential lectin recognition of glycoproteins in choanomastigote-shaped trypanosomatids: taxonomic implications (2003)

The glycoprotein profiles of seven choanomastigote-shaped trypanosomatids (six Crithidia spp. and one Herpetomonas sp.), which have been suggested to form three distinct taxonomic groups (Crithidia, Angomonas and Strigomonas), were analyzed by Western blotting using the lectins Limax flavus (LFA), Sambucus nigra (SNA) and Maackia amurensis (MAA), which specifically recognize sialic acid residues, and concanavalin A (Con A) that recognizes mannose-like residues in glycoconjugates. All lectins showed a sugar-inhibited recognition with the parasite extracts, with the exception of LFA, which did not show any reactivity with the studied species. The SNA agglutinin presented a characteristic and specific pattern for each taxonomic group. The MAA lectin showed an identical profile for all species analyzed, while Con A grouped the choanomastigote-shaped species in two different patterns, one specific for the Angomonas group, and the other comprehending both Strigomonas and Crithidia groups. These results illustrate the heterogeneity of the genus Crithidia. The possible taxonomic redistribution of the choanomastigote-shaped trypanosomatids is also discussed.
Hélicase RecQ, syndrome de Werner, et réparation de l’ADN par recombinaison homologue (2002)

Le syndrome de Werner est une maladie auto-somique récessive rare qui se traduit par un vieillissement prématuré associé à une instabilité génétique provoquant un risque élevé de cancers. Le gène responsable du syndrome code pour une protéine, WRN, qui comprend deux domaines fonctionnels impliqués dans le métabolisme de l’ADN : un domaine hélicase de type RecQ et un domaine exonucléase. Le rôle de cette protéine dans la réparation de l’ADN par recombinaison homologue a été montré récemment. Nous avons aussi montré que les porteurs sains, hétérozygotes pour le gène <i>WRN<i/>, ont une instabilité génétique augmentée, ce qui pourrait avoir des conséquences importantes dans la sensibilité individuelle aux maladies liées à l’âge ainsi qu’aux traitements anti-tumoraux.
Periodic Formation of FeSi Bands in Diffusion Couples Fe(15 wt.% Si) - Zn (1982)

During the reaction in Fe(15 wt.% Si)-Zn diffusion couples at temperatures between 623 and 723 K thin regularly spaced parallel bands containing very small FeSi precipitates are observed throughout the 6 and ~ reaction layers. The periodic nature of this effect is strongly reminiscent of the well-known Liesegang phenomenon. A detailed analysis of our results with respect to the principles underlying the Liesegang mechanism, however, shows that such a mechanism cannot explain the observed phenomenon in our case. A more probable explanation is found in the action of shear and tenSile stresses in the diffusion couple which lead to a periodic release ofthe continuously formed FeSi precipitates from the Fe(15 wt.% Si) substrate. Preliminary results obtained with substrates of varying thicknesses are strongly in favour of the latter explanation.
Weaving quantum optical frequency combs into hypercubic cluster states (2014)

We present a simple, scalable, top-down method for entangling the quantum optical frequency comb into hypercubic-lattice continuous-variable cluster states up to a maximum size of about 104 modes using existing technology.
Social determinants of adult mortality from non-communicable diseases in northern Ethiopia, 2009-2015: Evidence from health and demographic surveillance site (2017)

In summary, the study indicates that double mortality burden from both NCDs and communicable diseases was evident in northern rural Ethiopia. Public health intervention measures that prioritise disadvantaged NCD patients such as those who are unable to read and write, the elders, the extended family and non-family household co-residents could significantly reduce NCD mortality among the adult population.
Role of WNK1/OSR1 in maintaining endothelial tight junction integrity (2020)

Deletion of the WNK1 (with no lysine kinase‐1) gene in mice causes embryonic lethality due to failed vascular development. This phenotype can be rescued by endothelial‐specific expression of WNK1 or a constitutively active form of its substrate OSR1 (Oxidative Stress Responsive‐1). Additionally, depletion of WNK1/OSR1 decreased in vitro angiogenesis and cell migration in endothelial cells. This indicates an essential function of WNK1/OSR1 in angiogenesis. However, the underlying mechanism by which WNK1/OSR1 mediates this process is unclear. WNK1 is known to regulate TGF‐β/Smad signaling which induces epithelial‐mesenchymal transition (EMT), a process utilized in cell migration and angiogenic sprouting during physiological and pathophysiological vascular remodeling. OSR1 is reported to form a complex with the TGF‐βII receptor at tight junctions which mediates dissolution of tight junction upon activation by TGF‐β. Therefore, we hypothesize that WNK1/OSR1 axis is necessary for TGF‐β/Smad‐induced disruption of cell‐cell adhesion, thereby promoting cell migration and angiogenesis. We found that WNK1 pharmacological inhibition decreased the expression of TGF‐β‐induced EMT mediators such as the receptor tyrosine kinase Axl which is known to be important for maintaining tight junction integrity in HDMECs (Human Dermal Microvascular Endothelial Cells) (Normalized densitometry values; WNKi‐ Axl: 0.2 ± 0.05 vs. siControl: 1, n=3) and in primary HUVECs (Human Umbilical Vein Endothelial Cells) (normalized densitometry values; WNK1i: 0.4 ± 0.1 vs. DMSO: 1, n=3, *p<0.05). We also determined that OSR1 and Occludin, a tight junction protein are co‐localized and that inhibition of WNK1 using a small molecule WNK1 inhibitor, decreased their co‐localization and tight junction breakdown during TGF‐β signaling in primary HUVECs (Pearson’s coefficient; Control; 0.08 ± 0.2 vs. TGF‐β: 0.61 ± 0.15 vs. TGF‐β+WNK1i: 0.12 ± 0.25, n=2, 2 replicates per experiment). Finally, we observed that bands corresponding to phosphorylated form of Occludin on a Western blot were enhanced in WNK inhibited samples compared to control (normalized densitometry values; TGF‐β+WNKi: 1 vs. TGF‐β: 0.21 ± 0.07, n=2). Since Occludin is known to be dephosphorylated during tight junction breakdown, the presence of the phosphorylated form of Occludin with WNK inhibition may indicate the disruption of cellular processes leading to TGF‐β‐dependent tight junction breakdown. These data suggest WNK1‐dependent function of OSR1 in cell migration and angiogenesis through regulating tight junction integrity. Combined, these data indicate the importance of WNK1 function in endothelial cell migration and angiogenesis. Understanding how WNK1 regulates angiogenesis and cell migration is immediately relevant during development, fibrosis as well as cancer. Support or Funding Information American Heart Association postdoctoral fellowship to Ankita Jaykumar and NIH funding R01 HL147661 to Melanie H. Cobb
ChemInform Abstract: LIGAND WRAPPING AROUND CHROMIUM‐ REACTIONS OF DIPHENYLMETHANE, 1,4‐DIPHENYLBUTANE, BENZYL ETHER, AND BENZYL SULFIDE WITH CHROMIUM ATOMS (1978)

Abstract Bei der Überführung in Chromkomplexe erhält man aus den Diarylverbindungen (I) lediglich die Bis‐Verbindungen (II).