gebhart/patrepeval huggingface dataset:
Electrochemical Generation of Reactive Species and their Application as Chemotherapeutics (2012)

A major limitation in developing a successful cancer treatment is the need for a distinction between normal and cancerous tissue. For solid tumors, this distinction can be made on a spatial basis, and successful treatments have been developed accordingly; however, many of these treatments cause pathologies in healthy tissue, much to the detriment of patient health. To address this issue for solid tumours, a conceptual approach would be to administer the chemotherapeutic drug locally, such that the intra-tumour concentration was high, while the systemic exposure to the drug remained low, thus, minimizing side effects. The present research focuses on providing proof-of-concept for the electrochemical generation of a toxicant from a prodrug, and subsequent use to elicit cytotoxicity in cancer cells, in attempts to electrochemically mimic monooxygenase-catalyzed bioactivation. Electro-oxidation of acetaminophen and cyclophosphamide substrates at graphite and Ti/RuO2 anodes was successful in generating their respective toxicants; however, the graphite anode was superior with respect to current efficiency and toxicant yield. Electrolyses conducted in batch and flow reactors produced effluents which reduced EMT-6 cell viability to the IC99 level. This thesis provides proof-of-concept for electrochemical prodrug activation as a viable area for further cancer research.
Supplementary Materials from Ischemia-Induced K-<i>ras</i> Mutations in Human Colorectal Cancer Cells: Role of Microenvironmental Regulation of MSH2 Expression (2023)

&lt;p&gt;Data on K-ras mutation at codon 12 &amp; 61&lt;/p&gt;
Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane (2001)

Vectorial proton translocation through membranes is a fundamental energy conversion process in biological cells. Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven, voltage-sensitive proton pump in the purple membrane (PM) of Halobacterium salinarum and achieves its biological function by cycling through a reaction sequence that includes ultrafast (∼500 fs) events, intermediate (μs) as well as slow (∼10 ms) steps. bR is of utmost simplicity in comparison with other proton translocating bioenergetic proteins and, therefore, constitutes an ideal model for the study of this process. The PM involves a highly structured supramolecular organization and is fundamental for the in vivo functioning of bR. Over the last 10 years, crystal structures of bR have become available at increasing resolution. The most recent structures resolve many of the lipids of the PM and provide atomic level detail of bR at below 2 Å resolution. Fundamental for an understanding of the function of bR is internal water that participates in proton pumping. Several water molecules have been resolved now crystallographically in two channels, on the extracellular and on the intracellular side of bR. We show that free energy perturbation theory can place water molecules in bR, with results that compare well with the observed water molecules, and we apply the method to predict water movement during bR's photocycle. A preliminary simulation illustrates that water molecules may indeed be displaced during the photocycle, after retinal undergoes an all-trans → 13-cis isomerization, and that this displacement may constitute a mechanism for proton pumping. A key advance reported in this feature article is the integration of the available bR structures into a model for the entire PM. This hexagonally periodic, lamellar model has been hydrated and refined through a constant pressure molecular dynamics simulation. The resulting structure connects extracellular bulk water with water molecules and key side groups in the interior of bR, permitting a seamless overall description of the proton path in the PM, from intracellular to extracellular space. For the first time, a complex cellular reaction can be accounted for in full atomic detail in its complete native environment.
Primary central nervous system lymphoma in a child with acute B‐cell lymphoblastic leukaemia: consecutive Epstein‐Barr virus‐related malignancies (1998)

Primary central nervous system lymphoma (PCNSL), observed among immunocompromised AIDS patients, has not been reported during chemotherapy for acute lymphoblastic leukaemia (ALL). We report a case of PCNSL occurring in a child receiving intensive multiagent chemotherapy for B-cell ALL. In situ hybridization studies demonstrated Epstein-Barr virus genome in both tumours, suggesting a possible link between the two diseases. The clinical response of the PCNSL to conservative therapy highlights the importance of accurately diagnosing such EBV-related disorders, especially in patients where immune compromise can be reversed.
Gaussian-state entanglement in a quantum beat laser (2011)

Recently quantum beat lasers have been considered as a source of entangled radiation [S. Qamar, F. Ghafoor, M. Hillery, and M. S. Zubairy, Phys. Rev. A 77, 062308 (2008)]. We investigate and quantify the entanglement of this system when the initial cavity modes are prepared in a Gaussian two-mode state, one being a nonclassical state and the other a thermal state. It is investigated how the output entanglement varies with the nonclassicality of the input Gaussian state, thermal noise, and the strength of the driving field.
Interactive feature selection for efficient customer recognition in contact centers: Dealing with common names (2018)

We propose an interactive decision-making framework to assist a Customer Service Representative (CSR) in the efficient and effective recognition of customer records in a database with many ambiguous entries. Our proposed framework consists of three integrated modules. The first module focuses on the detection and resolution of duplicate records to improve effectiveness and efficiency in customer recognition. The second module determines the level of ambiguity in recognizing an individual customer when there are multiple records with the same name. The third module recommends the series of feature-related questions that the CSR should ask the customer to enable rapid recognition, based on that level of ambiguity. In the first module, the F-Swoosh approach for duplicate detection is used, and in the second module a dynamic programming-based technique is used to determine the level of ambiguity within the customer database for a given name. In the third module, Levenshtein edit distance is used for feature selection in combination with weights based on the Inverse Document Frequency (IDF) of terms. The algorithm that requires the minimum number of questions to be put to the customer to achieve recognition is the algorithm that is chosen. We evaluate the proposed framework on a synthetic dataset and demonstrate how it assists the CSR to rapidly recognize the correct customer.
Effects of Intramuscular Alfaxalone/Acepromazine on Echocardiographic, Biochemical, and Blood Gas Measurements in Healthy Cats (2019)

The effects of intramuscular injection of alfaxalone ([ALF] 5 mg/kg), acepromazine ([ACE] 0.05 mg/kg), and an ALF-ACE combination ([AA] 0.025 mg/kg ACE followed by 2.5 mg/kg ALF) on the sedation, echocardiographic, biochemical, and blood gas indexes and recovery were evaluated in seven cats. No sedation was obtained with ACE, and sedation scores were higher with ALF than with AA treatment. Compared with baseline, an increase in heart rate occurred after ACE, and all treatments caused a decrease in systemic arterial pressure. Decreased left ventricular internal dimension in diastole, end-diastolic volume of the left ventricle, stroke volume, and left atrial dimension were identified after AA. There were minimal changes in echocardiographic variables after ALF. Biochemical and blood gas analysis showed no significant changes after all treatments. Although the difference in quality of recovery between the AA and ALF treatment groups was insignificant, all cats treated with AA or ALF showed ataxia. The AA combination did not change the recovery score, and tremor and twitching were identified more frequently with AA than ALF. ALF had no significant effects on echocardiographic, biochemical, or blood gas variables. ALF could be considered a useful sedative option for diagnostic procedures and echocardiography in cats.
Role of ectonucleotide pyrophosphatase/phosphodiesterase 2 in the midline axis formation of zebrafish (2016)

Lysophosphatidic acid (LPA) is a unique bioactive lysophospholipid that induces pleiotropic effects in various cell types and organisms by acting on its specific receptors. LPA is mainly synthetised extracellularly by the ectonucleotide pyrophosphatase/phosphodiesterase 2/autotaxin (enpp2). Altered LPA signalling is associated with embryonic abnormalities, suggesting critical roles for LPA during development. However, the role of LPA signalling during early embryogenesis is not well established. We demonstrate that enpp2/LPA signalling in the early zebrafish embryo results in altered axis and midline formation, defects in left right (L-R) patterning, ciliogenesis of the Kupffer's vesicle (KV), through the modulation of cell migration during gastrulation in a lpar<sub>1-3</sub> Rho/ROCK-dependant manner. Overall, this study demonstrates an essential role of enpp2/LPA signalling during early embryogenesis.
CoExp: A Web Tool for the Exploitation of Co-expression Networks (2021)

Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCNA) amongst one of the most widely used R packages. While managing a few network models can be done manually, it is often more advantageous to study a wider set of models derived from multiple independently generated transcriptomic data sets (e.g., multiple networks built from many transcriptomic sources). However, there is no software tool available that allows this to be easily achieved. Furthermore, the visual nature of co-expression networks in combination with the coding skills required to explore networks, makes the construction of a web-based platform for their management highly desirable. Here, we present the CoExp Web application, a user-friendly online tool that allows the exploitation of the full collection of 109 co-expression networks provided by the CoExpNets suite of R packages. We describe the usage of CoExp, including its contents and the functionality available through the family of CoExpNets packages. All the tools presented, including the web front- and back-ends are available for the research community so any research group can build its own suite of networks and make them accessible through their own CoExp Web application. Therefore, this paper is of interest to both researchers wishing to annotate their genes of interest across different brain network models and specialists interested in the creation of GCNs looking for a tool to appropriately manage, use, publish, and share their networks in a consistent and productive manner.
Temperature and Diapause Development in the Egg of Diabrotica barberi (Coleoptera: Chrysomelidae) (1994)

Three independent studies were conducted on the effects of constant temperatures (0, 3, 6, 9, 12, 15, 18, and 25°C) with numerous exposure times (15 to 240 d) on diapausing embryos of the northern corn rootworm, Diabrotica barberi Smith and Lawrence. All three studies had similar results. The temperahlres 15 and 18°C appeared to enhance diapause development and subsequent diapause termination when compared with the lower temperatures (O–3°C). However, the temperature range 9–12°C was optimum for minimum mortality and maximum hatch at nearly all exposure times used. At this range and in particular 9°C, hatch was as high as 60% after 180 d exposure. Exposures of 15 and 30 d produced minimal hatch, <20%, at any temperature. Days to hatch tended to decrease as temperature increased but varied with experiment. Hatching time also decreased as exposure increased for all temperatures. Eggs exposed only to the developmental optima of 25°C had <20% hatch in all studies, and ≥50% of the eggs were still in the diapause state at the conclusion of the studies. We concluded that most D. barberi embryos require low temperature to terminate diapause and complete embryogenesis. These studies support the hypothesis that D. barberi has a propensity to be continuously variable in diapause length. Also, variable diapause length has allowed this species to adapt to natural and artificial perturbations, in particular, crop rotation.
Underwater superoleophobic porous membrane based on hierarchical TiO2 nanotubes: multifunctional integration of oil–water separation, flow-through photocatalysis and self-cleaning (2014)

Superhydrophilic and underwater superoleophobic membranes based on hierarchical TiO<sub>2</sub> nanotubes integrated the functions of oil–water separation, flow-through photocatalysis and self-cleaning.
Recursive tilings and space-filling curves with little fragmentation (2011)

This paper defines the Arrwwid number of a recursive tiling (or space-filling curve) as the smallest number a such that any ball Q can be covered by a tiles (or curve fragments) with total volume O(volume(Q)). Recursive tilings and space-filling curves with low Arrwwid numbers can be applied to optimize disk, memory or server access patterns when processing sets of points inRd. This paper presents recursive tilings and space-filling curves with optimal Arrwwid numbers. For d ≥ 3, we see that regular cube tilings and space-filling curves cannot have optimal Arrwwid number, and we see how to construct alternatives with better Arrwwid numbers.
Imperfect Segmentation Labels: How Much Do They Matter? (2018)

Labeled datasets for semantic segmentation are imperfect, especially in medical imaging where borders are often subtle or ill-defined. Little work has been done to analyze the effect that label errors have on the performance of segmentation methodologies. Here we present a large-scale study of model performance in the presence of varying types and degrees of error in training data. We trained U-Net, SegNet, and FCN32 several times for liver segmentation with 10 different modes of ground-truth perturbation. Our results show that for each architecture, performance steadily declines with boundary-localized errors, however, U-Net was significantly more robust to jagged boundary errors than the other architectures. We also found that each architecture was very robust to non-boundary-localized errors, suggesting that boundary-localized errors are fundamentally different and more challenging problem than random label errors in a classification setting.
Fully-tunable, Purcell-enhanced On-chip Quantum Emitters (2015)

We report the all-electrical control over cavity-emitter systems, consisting in Stark-tunable quantum dots embedded in mechanically reconfigurable photonic crystal membranes. Purcell-effect from a single dot is demonstrated at distinct wavelengths.
Frequency quorum rendezvous for fast and resilient key establishment under jamming attack (2010)

This paper proposes a novel Frequency Quorum Rendezvous (FQR) scheme for fast and resilient pre-key establishment in anti-jamming spread spectrum techniques. While nodes hop over own frequencies during the key establishment phase, using a quorum system improves their rendezvous probability and reduces time latency.
Tissue Distribution of Hesperetin in Rats after a Dietary Intake (2011)

Hesperetin, the aglycone of hesperidin present in citrus fruits, possesses various biological activities. We assessed the tissue distribution of hesperetin in rats fed with a 0.2% hesperetin diet for 4 weeks. Its highest concentration was found in the liver, and the second highest was in the aorta. The aorta is assumed to be one of the main target tissues of hesperetin for exerting its functions.
Abstract 417: Urine as an alternative to blood for germline genomics and cancer genetics (2019)

Abstract Currently, blood is the body fluid of choice to provide comprehensive germline genomics via Peripheral Blood Mononuclear Cells (PBMC) and cancer genetics via the detection of circulating tumor DNA (ctDNA, liquid biopsy) for precision medicine. In this study, we examined if urine can be an alternative to blood for comprehensive germline genomics and for liquid biopsy. We have previously shown that human urine contains DNA derived both from sloughed-off cell debris of the urinary tract (greater than 1 KB/High Molecular weight or HMW) and trans-renal DNA from the circulation (less than 1 KB/Low molecular weight or LMW). We performed whole genome sequencing (WGS) to compare the quality and comprehensiveness of the genomic data between 3 sets of matched PBMC and HMW urine DNA. There was no statistically significant difference between the NGS data obtained from PBMC and urine DNA upon comparing the number of reads, average coverage, percent aligned reads, percent reads passing Phred score Q30 (p value less than 0.05, paired t-test) and coverage of human genome. Next, we compared the detectability of ctDNA in the matching LMW urine and plasma DNA obtained from 44 HCC patients by employing a panel of HCC biomarkers including genetic mutations at TP53 codon 249 [G:C to T:A transversion (TP53 249T)], CTNNB1 exon 3 regions 32-37 (CTNNB1 32-37), and hTERT promoter region position 124 (hTERT 124) and aberrant methylation of RASSF1A (mRASSF1A) promoter. In this study, a systematic analysis of this HCC biomarker panel demonstrated that urine can complement blood for liver cancer screening. A combination of the plasma and urine biomarkers with serum AFP the current most widely used biomarker for HCC can provide higher sensitivity (up to 30% more) for liver cancer detection. In order to characterize and determine if LMW urine DNA is derived from plasma DNA, we performed WGS to compare the size profiles and coverage of these two sources of cell-free DNA in 3 sets of matching HCC urine and plasma samples. Overall shorter read lengths were obtained from urine DNA as compared to the corresponding plasma DNA. A series of peaks occurring at 10 bp periodicity was displayed in both sources of cell-free DNA Further analysis regarding the genome coverage, overlapping fraction and variant detection is ongoing. In conclusion, our data suggests that (i) HMW urine DNA can replace PBMC DNA for providing comprehensive genomic sequencing data and (ii) urine can complement blood for liver cancer liquid biopsy, precision medicine, and potential applications to other cancers. Citation Format: Surbhi Jain, Tai-Jung Lee, Adam Zhang, Jonathan Cheng, Jamin D. Steffen, Chi-Tan Hu, James P. Hamilton, Harry Luu, Hie-Won Hann, Fwu-Shan Shieh, Selena Y. Lin, Wei Song, Ying-Hsiu Su. Urine as an alternative to blood for germline genomics and cancer genetics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 417.
ChemInform Abstract: SYNTHESIS OF FUSED PYRROLINES BY THE INTRAMOLECULAR CYCLOADDITION OF AZIDES. APPLICATION TO THE PYRROLIZIDINE ALKALOIDS (1985)

Abstract Aus dem Aldehyd (I) wird" über (II) und (IIIa)‐(IIIc) das Azid (IV) hergestellt.
Which Domicile? - a Crucial Question for APTs (1995)

Journal Article Which Domicile? – a Crucial Question for APTs Get access Charles A Cain, M.A., A.C.I.B. Charles A Cain, M.A., A.C.I.B. Skye Fiduciary Services Limited Executive OfficeSkye Suite, Mollfort House, 2 Water Street, Ramsey, Isle of Man, IM8 2HP Telephone No: +44 (0)1624 816117 Facsimile No: +44 (0) 1624 816645 Search for other works by this author on: Oxford Academic Google Scholar Trusts & Trustees, Volume 1, Issue 10, October 1995, Pages 6–9, https://doi.org/10.1093/tandt/1.10.6 Published: 01 October 1995
Hypoxia and β-hydroxybutyrate acutely reduce glucose extraction by the brain in anesthetized dogs (1993)

Induced ketosis may acutely prolong hypoxic tolerance by altering glucose and (or) beta-hydroxybutyrate extraction by the brain. Anesthetized dogs were ventilated and instrumental for arterial and cerebral venous blood sampling, taken during baseline, infusion, test, and recovery periods. Each dog received one of four different beta-hydroxybutyrate doses and 25 min of either a normoxic or hypoxic (8% oxygen) test period. Arterial glucose and beta-hydroxybutyrate were stable in the saline and 3 mg.kg-1 x min-1 beta-hydroxybutyrate infusion groups, but glucose declined and beta-hydroxybutyrate increased in the 10 and 20 mg.kg-1 x min-1 beta-hydroxybutyrate infusion groups. During normoxia glucose arteriovenous differences across the brain decreased significantly only in the 20 mg.kg-1 x min-1 beta-hydroxybutyrate infusion groups, and during hypoxia the differences decreased for all groups. beta-Hydroxybutyrate arteriovenous differences tended to increase with a 100-fold increase in beta-hydroxybutyrate concentrations, but the trend was not statistically significant. Hypoxia further decreased glucose extraction, but did not change beta-hydroxybutyrate extraction. We conclude that beta-hydroxybutyrate may protect during hypoxia by depressing glucose uptake and consumption rather than by acting as an alternative cerebral energy substrate.
Effect of Upper Abdominal Surgery and Cirrhosis upon the Pharmacokinetics of Methohexital (1991)

DUVALDESTIN, P.; CHAUVIN, M.; LEBRAULT, C.; BERTRAND, F.; KAROLAK, F. TAMSIER; FARINOTTI, R. Author Information
A Need for Consistency in Behavioral Phenotyping for ASD: Analysis of the Valproic Acid Model (2021)

Autism spectrum disorder (ASD) is a highly prevalent and impairing neurodevelopmental disorder that affects 1 : 54 persons. Over the last several decades, the reported incidence of ASD in the US has increased potentially due to increased awareness and improved diagnostic measurement. Although ASD prevalence is increasing, the etiology of ASD remains relatively unknown. To better understand the neurological basis of ASD, rodent models of ASD have been developed for research. Currently, there is not a standardized set of behavioral tests to quantify ASD-like behavior in rodents. The goal of this review is to present an overview of the methodologies used to analyze ASD-like behaviors in rodents, focusing on the valproic acid (VPA) model, and illustrate inconsistencies between different approaches. Despite that the <i>in utero</i> VPA rodent model for ASD is widely used and extensively characterized, behaviors vary substantially between different researchers. Moving forward, consistency in behavioral method analytics would benefit progress in evaluating interventions for all models of ASD and help to uncover unique qualities underlying mechanisms causing ASD signs and symptoms.
Selective enhancement of blue electroluminescence from GaN:Tm (2003)

Selective enhancement of electroluminescent emission from high-energy transitions in Tm-doped GaN has been observed to be a strong function of GaN growth temperature. GaN:Tm thin films have been grown by molecular beam epitaxy at temperatures from 100 to 700 °C. At low growth temperatures (100–200 °C) the low energy (infrared-801 nm) transition dominates, while at higher growth temperatures (400–700 °C) the high energy (blue-477 nm) transition dominates. For films grown at low temperatures the main emission excitation mechanism is impact excitation, while for films grown at higher temperatures (⩾600 °C) the main excitation mechanism appears to be lattice impact ionization followed by energy transfer to Tm ions.