gebhart/patrepeval huggingface dataset:
Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort Study (2022)

The interplay between the sex-specific differences in tumor metabolome and colorectal cancer (CRC) prognosis has never been studied and represents an opportunity to improve patient outcomes. This study examines the link between tumor metabolome and prognosis by sex for CRC patients. Using untargeted metabolomics analysis, abundances of 91 metabolites were obtained from primary tumor tissues from 197 patients (N = 95 females, N = 102 males) after surgical colectomy for stage I-III CRC. Cox Proportional hazard (PH) regression models estimated the associations between tumor metabolome and 5-year overall survival (OS) and recurrence-free survival (RFS), and their interactions with sex. Eleven metabolites had significant sex differences in their associations with 5-year OS, and five metabolites for 5-year RFS. The metabolites asparagine and serine had sex interactions for both OS and RFS. Furthermore, in the asparagine synthetase (ASNS)-catalyzed asparagine synthesis pathway, asparagine was associated with substantially poorer OS (HR (95% CI): 6.39 (1.78-22.91)) and RFS (HR (95% CI): 4.36 (1.39-13.68)) for female patients only. Similar prognostic disadvantages in females were seen in lysophospholipid and polyamine synthesis. Unique metabolite profiles indicated that increased asparagine synthesis was associated with poorer prognosis for females only, providing insight into precision medicine for CRC treatment stratified by sex.
Thermal Decomposition Behavior of Graphite anodes for Lithium Ion Batteries (2001)

The thermal decomposition reactions of lithium-intercalated graphite electrodes with the electrolyte solution have been investigated by DSC measurements. Three exothermic reaction peaks appeared in the DSC curves around 130°C (peak 1), 260°C (peak 2) and 300°C (peak 3), respectively. The total amount of generated exothermic heat increased linearly with the amount of intercalated lithium, not depending on specific surface area of graphite powder. The increase of specific surface area reduced temperatures of peak 2 and peak 3, and magnified the amount of heat generated at peak 1. The increase of specific surface area is considered to accelerate the thermal decomposition reactions of lithium-intercalated graphite with the electrolyte solution and reaction at peak 1, which was associated with passivation film formation. The reaction around 130°C has been investigated by GC and FT-IR measurements. Li2CO3 was produced on the graphite surface and CO2 gas was evolved during lithium-intercalated graphite heating at 130°C. It was supposed that lithium alkyl carbonate was created on the graphite surface at first and lithium alkyl carbonate was decomposed immediately to Li2CO3, which was more stable.
Temporal perturbations in sonic hedgehog signaling elicit the spectrum of holoprosencephaly phenotypes (2004)

One of the most perplexing questions in clinical genetics is why patients with identical gene mutations oftentimes exhibit radically different clinical features. This inconsistency between genotype and phenotype is illustrated in the malformation spectrum of holoprosencephaly (HPE). Family members carrying identical mutations in sonic hedgehog (SHH) can exhibit a variety of facial features ranging from cyclopia to subtle midline asymmetries. Such intrafamilial variability may arise from environmental factors acting in conjunction with gene mutations that collectively reduce SHH activity below a critical threshold. We undertook a series of experiments to test the hypothesis that modifying the activity of the SHH signaling pathway at discrete periods of embryonic development could account for the phenotypic spectrum of HPE. Exposing avian embryos to cyclopamine during critical periods of craniofacial development recreated a continuum of HPE-related defects. The craniofacial malformations included hypotelorism, midfacial hypoplasia, and facial clefting and were not the result of excessive crest cell apoptosis. Rather, they resulted from molecular reprogramming of an organizing center whose activity controls outgrowth and patterning of the mid and upper face. Collectively, these data reveal one mechanism by which the variable expressivity of a disorder such as HPE can be produced through temporal disruption of a single molecular pathway.
Empirical Mode Decomposition and Monogenic Signal-Based Approach for Quantification of Myocardial Infarction From MR Images (2018)

Quantification of myocardial infarction on late Gadolinium enhancement cardiovascular magnetic resonance (LGE-CMR) images into heterogeneous infarct periphery (or gray zone) and infarct core plays an important role in cardiac diagnosis, especially in identifying patients at high risk of cardiovascular mortality. However, quantification task is challenging due to noise corrupted in cardiac MR images, the contrast variation, and limited resolution of images. In this study, we propose a novel approach for automatic myocardial infarction quantification, termed DEMPOT, which consists of three key parts: Decomposition of image into intrinsic modes, monogenic phase performing on combined dominant modes, and multilevel Otsu thresholding on the phase. In particular, inspired by the Hilbert-Huang transform, we perform the multidimensional ensemble empirical mode decomposition and 2-D generalization of the Hilbert transform known as the Riesz transform on the MR image to obtain the monogenic phase that is robust to noise and contrast variation. Then, a two-stage algorithm using multilevel Otsu thresholding is accomplished on the monogenic phase to automatically quantify the myocardium into healthy, gray zone, and infarct core regions. Experiments on LGE-CMR images with myocardial infarction from 82 patients show the superior performance of the proposed approach in terms of reproducibility, robustness, and effectiveness.
Haemodynamic flow abnormalities in bicuspid aortic valve disease improve with aortic valve replacement (2015)

Background Bicuspid aortic valve disease (BAV) is associated with dilatation of the proximal aorta and abnormal flow patterns, particularly increased helical flow and changes in the aortic wall shear stress. These altered flow patterns may be partly responsible for the aortic dilation, though the aetiology is still unclear. Aortic valve replacement can modify the flow pattern in the proximal aorta (potentially to normal) and could thus have an effect on future aortic dilation. In this study, we aimed to assess the effect of different types of aortic valve replacement (AVR) on aortic flow patterns. Methods We prospectively enrolled 69 participants: 23 BAV patients with prior AVR (10 mechanical, 6 bioprosthetic, 7 Ross procedure), 23 BAV patients with a native aortic valve and 23 healthy volunteers. All underwent 4D flow cardiovascular magnetic resonance. Results The majority of patients with mechanical AVR or Ross showed a normalised flow pattern (70% and 57% respectively) with near normal rotational flow values (7.4±3.9 and 11.0±12.0mm 2 /s respectively; normal range -5 to +11 mm 2 /s); and reduced in-plane wall shear stress compared to native BAV (0.13±0.18N/m 2 for mechanical AVR vs. 0.37±0.26N/m 2 for native BAV, p<0.05). In contrast, all subjects with bioprosthetic AVR showed abnormal flow patterns (mainly marked right-handed helical flow), with similar rotational flow values to native
PerfuPul—A Versatile Perfusable Platform to Assess Permeability and Barrier Function of Air Exposed Pulmonary Epithelia (2021)

Complex <i>in vitro</i> models, especially those based on human cells and tissues, may successfully reduce or even replace animal models within pre-clinical development of orally inhaled drug products. Microfluidic lung-on-chips are regarded as especially promising models since they allow the culture of lung specific cell types under physiological stimuli including perfusion and air-liquid interface (ALI) conditions within a precisely controlled <i>in vitro</i> environment. Currently, though, such models are not available to a broad user community given their need for sophisticated microfabrication techniques. They further require systematic comparison to well-based filter supports, in analogy to traditional Transwells®. We here present a versatile perfusable platform that combines the advantages of well-based filter supports with the benefits of perfusion, to assess barrier permeability of and aerosol deposition on ALI cultured pulmonary epithelial cells. The platform as well as the required technical accessories can be reproduced <i>via</i> a detailed step-by-step protocol and implemented in typical bio-/pharmaceutical laboratories without specific expertise in microfabrication methods nor the need to buy costly specialized equipment. Calu-3 cells cultured under liquid covered conditions (LCC) inside the platform showed similar development of transepithelial electrical resistance (TEER) over a period of 14 days as cells cultured on a traditional Transwell<sup>®</sup>. By using a customized deposition chamber, fluorescein sodium was nebulized <i>via</i> a clinically relevant Aerogen<sup>®</sup> Solo nebulizer onto Calu-3 cells cultured under ALI conditions within the platform. This not only allowed to analyze the transport of fluorescein sodium after ALI deposition under perfusion, but also to compare it to transport under traditional static conditions.
Towards Monitoring-Oriented Programming (2003)

With the explosion of software size, checking conformance of implementation to specification becomes an increasingly important but also hard problem. Current practice based on ad-hoc testing does not provide correctness guarantees, while highly confident traditional formal methods like model checking and theorem proving are still too expensive to become common practice. In this paper we present a paradigm for combining formal specification with implementation, called monitoring-oriented programming (MoP), providing a light-weighted formal method to check conformance of implementation to specification at runtime. System requirements are expressed using formal specifications given as annotations inserted at various user selected places in programs. Efficient monitoring code using the same target language as the implementation is then automatically generated during a pre-compilation stage. The generated code has the same effect as a logical checking of requirements and can be used in any context, in particular to trigger user defined actions, when requirements are violated. Our proposal is language- and logic- independent, and we argue that it smoothly integrates other interesting system development paradigms, such as design by contract and aspect oriented programming. A prototype has been implemented for Java, which currently supports requirements expressed using past time and future time linear temporal logics, as well as extended regular expressions.
Targeting the leukemia cell metabolism by the CPT1a inhibition: functional preclinical effects in leukemias (2015)

Cancer cells are characterized by perturbations of their metabolic processes. Recent observations demonstrated that the fatty acid oxidation (FAO) pathway may represent an alternative carbon source for anabolic processes in different tumors, therefore appearing particularly promising for therapeutic purposes. Because the carnitine palmitoyl transferase 1a (CPT1a) is a protein that catalyzes the rate-limiting step of FAO, here we investigated the in vitro antileukemic activity of the novel CPT1a inhibitor ST1326 on leukemia cell lines and primary cells obtained from patients with hematologic malignancies. By real-time metabolic analysis, we documented that ST1326 inhibited FAO in leukemia cell lines associated with a dose- and time-dependent cell growth arrest, mitochondrial damage, and apoptosis induction. Data obtained on primary hematopoietic malignant cells confirmed the FAO inhibition and cytotoxic activity of ST1326, particularly on acute myeloid leukemia cells. These data suggest that leukemia treatment may be carried out by targeting metabolic processes.
Machine Learning Constructives and Local Searches for the Travelling Salesman Problem (2021)

The ML-Constructive heuristic is a recently presented method and the first hybrid method capable of scaling up to real scale traveling salesman problems. It combines machine learning techniques and classic optimization techniques. In this paper we present improvements to the computational weight of the original deep learning model. In addition, as simpler models reduce the execution time, the possibility of adding a local-search phase is explored to further improve performance. Experimental results corroborate the quality of the proposed improvements.
Longitudinal development of thalamic and internal capsule microstructure in autism spectrum disorder (2017)

Microstructure of the thalamus, a key sensory and motor brain area, appears to develop differently in individuals with autism spectrum disorder (ASD). Microstructure is important because it informs us of the density and organization of different brain tissues. During childhood, thalamic microstructure was distinct in the ASD group compared to the typically developing group. However, these group differences appeared to narrow with age, suggesting that the thalamus continues to dynamically change in ASD into adulthood.
A Frequency-Shift Method to Measure Shear-Wave Attenuation in Soft Tissues (2016)

In vivo quantification of shear-wave attenuation in soft tissues may help to better understand human tissue rheology and lead to new diagnostic strategies. Attenuation is difficult to measure in acoustic radiation force elastography because the shear-wave amplitude decreases due to a combination of diffraction and viscous attenuation. Diffraction correction requires assuming a cylindrical wavefront and an isotropic propagation medium, which may not be the case in some applications. In this paper, the frequency-shift method, used in ultrasound imaging and seismology, was adapted for shear-wave attenuation measurement in elastography. This method is not sensitive to diffraction effects. For a linear frequency dependence of the attenuation, a closed-form relation was obtained between the decrease in the peak frequency of the gamma-distributed wave amplitude spectrum and the attenuation coefficient of the propagation medium. The proposed method was tested against a plane-wave reference method in homogeneous agar-gelatin phantoms with 0%, 10%, and 20% oil concentrations, and hence different attenuations of 0.117, 0.202, and 0.292 [Formula: see text]/Hz, respectively. Applicability to biological tissues was demonstrated with two ex vivo porcine liver samples (0.79 and 1.35 [Formula: see text]/Hz) and an in vivo human muscle, measured along (0.43 [Formula: see text]/Hz) and across (1.77 [Formula: see text]/Hz) the tissue fibers. In all cases, the data supported the assumptions of a gamma-distributed spectrum for the source and linear frequency attenuation for the tissue. This method provides tissue attenuation, which is relevant diagnostic information to model viscosity, in addition to shear-wave velocity used to assess elasticity. Data processing is simple and could be performed automatically in real time for clinical applications.
A 249-Mpixel/s HEVC Video-Decoder Chip for 4K Ultra-HD Applications (2013)

High Efficiency Video Coding, the latest video standard, uses larger and variable-sized coding units and longer interpolation filters than H.264/AVC to better exploit redundancy in video signals. These algorithmic techniques enable a 50% decrease in bitrate at the cost of computational complexity, external memory bandwidth, and, for ASIC implementations, on-chip SRAM of the video codec. This paper describes architectural optimizations for an HEVC video decoder chip. The chip uses a two-stage subpipelining scheme to reduce on-chip SRAM by 56 kbytes-a 32% reduction. A high-throughput read-only cache combined with DRAM-latency-aware memory mapping reduces DRAM bandwidth by 67%. The chip is built for HEVC Working Draft 4 Low Complexity configuration and occupies 1.77 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 40-nm CMOS. It performs 4K Ultra HD 30-fps video decoding at 200 MHz while consuming 1.19 nJ/pixel of normalized system power.
International prognostic score for asymptomatic early-stage chronic lymphocytic leukemia (2020)

Most patients with chronic lymphocytic leukemia (CLL) are diagnosed with early-stage disease and managed with active surveillance. The individual course of patients with early-stage CLL is heterogeneous, and their probability of needing treatment is hardly anticipated at diagnosis. We aimed at developing an international prognostic score to predict time to first treatment (TTFT) in patients with CLL with early, asymptomatic disease (International Prognostic Score for Early-stage CLL [IPS-E]). Individual patient data from 11 international cohorts of patients with early-stage CLL (n = 4933) were analyzed to build and validate the prognostic score. Three covariates were consistently and independently correlated with TTFT: unmutated immunoglobulin heavy variable gene (IGHV), absolute lymphocyte count higher than 15 × 109/L, and presence of palpable lymph nodes. The IPS-E was the sum of the covariates (1 point each), and separated low-risk (score 0), intermediate-risk (score 1), and high-risk (score 2-3) patients showing a distinct TTFT. The score accuracy was validated in 9 cohorts staged by the Binet system and 1 cohort staged by the Rai system. The C-index was 0.74 in the training series and 0.70 in the aggregate of validation series. By meta-analysis of the training and validation cohorts, the 5-year cumulative risk for treatment start was 8.4%, 28.4%, and 61.2% among low-risk, intermediate-risk, and high-risk patients, respectively. The IPS-E is a simple and robust prognostic model that predicts the likelihood of treatment requirement in patients with early-stage CLL. The IPS-E can be useful in clinical management and in the design of early intervention clinical trials.
Diastereospecific synthesis of cis- and trans-2,3-dimethyl-1,4-thiamorpholines (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiastereospecific synthesis of cis- and trans-2,3-dimethyl-1,4-thiamorpholinesMaria Teresa Gallego , Ernesto Brunet , Jose Luis Garcia Ruano , and Ernest L. Eliel Cite this: J. Chem. Educ. 1991, 68, 6, 517Publication Date (Print):June 1, 1991Publication History Received3 August 2009Published online1 June 1991Published inissue 1 June 1991https://doi.org/10.1021/ed068p517RIGHTS & PERMISSIONSArticle Views133Altmetric-Citations2LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
ChemInform Abstract: Highly Diastereoselective Diels‐Alder Reaction of Optically Active 2‐(p‐Tolylsulfinyl)‐2‐cycloalkenones with Cyclopentadiene. (1990)

Abstract The p‐tolylsulfinylcycloalkenones (I) react with cyclopentadiene (II) to form the Diels‐Alder adducts (III) and (IV) in ratios depending on the Lewis acid catalysts employed.
Molecular Evaluation of Fluoroquinolone Resistance in Serial Mycobacterium tuberculosis Isolates from Individuals Diagnosed with Multidrug-Resistant Tuberculosis (2020)

Fluoroquinolones (FQ) are crucial components of multidrug-resistant tuberculosis (MDR TB) treatment. Differing levels of resistance are associated with specific mutations within the <u>q</u>uinolone-<u>r</u>esistance-<u>d</u>etermining <u>r</u>egion (QRDR) of <i>gyrA</i> We sequenced the QRDR from serial isolates of MDR TB patients in the Preserving Effective TB Treatment Study (PETTS) with baseline FQ resistance (FQ<sup>R</sup>) or acquired FQ resistance (FQ<sup>ACQR</sup>) using an Ion Torrent Personal Genome Machine (PGM) to a depth of 10,000× and reported single nucleotide polymorphisms in ≥1% of reads. FQ<sup>R</sup> isolates harbored 15 distinct alleles with 1.3 (maximum = 6) on average per isolate. Eighteen alleles were identified in FQ<sup>ACQR</sup> isolates with an average of 1.6 (maximum = 9) per isolate. Isolates from 78% of FQ<sup>ACQR</sup> individuals had mutant alleles identified within 6 months of treatment initiation. Asp94Gly was the predominant allele in the initial FQ-resistant isolates followed by Ala90Val. Seventy-seven percent (36/47) of FQ<sup>ACQR</sup> group patients had isolates with FQ resistance alleles prior to changes to the FQ component of their treatment. Unlike the individuals treated initially with other FQs, none of the 21 individuals treated initially with levofloxacin developed genotypic or phenotypic FQ resistance, although country of residence was likely a contributing factor since 69% of these individuals were from a single country. Initial detection of phenotypic resistance and genotypic resistance occurred simultaneously for most; however, phenotypic resistance occurred earlier in isolates harboring mixtures of alleles of very low abundance (<1% of reads), whereas genotypic resistance often occurred earlier for alleles associated with low-level resistance. Understanding factors influencing acquisition and evolution of FQ resistance could reveal strategies for improved treatment success.
Towards coherent optical control of a single hole spin: Rabi rotation of a trion conditional on the spin state of the hole (2009)

A hole spin is a potential solid-state q-bit, that may be more robust against nuclear spin induced dephasing than an electron spin. Here we propose and demonstrate the sequential preparation, control and detection of a single hole spin trapped on a self-assembled InGaAs/GaAs quantum dot. The dot is embedded in a photodiode structure under an applied electric-field. Fast, triggered, initialization of a hole spin is achieved by creating a spin-polarized electron-hole pair with a picosecond laser pulse, and in an applied electric-field, waiting for the electron to tunnel leaving a spin-polarized hole. Detection of the hole spin with picosecond time resolution is achieved a second picosecond laser pulse to probe the positive trion transition, where a trion is created conditional on the hole spin to be detected as a change in photocurrent. Finally, using this setup we observe a Rabi rotation of the hole-trion transition that is conditional on the hole spin, which for a pulse-area of $2π$ can be used to impart a phase-shift of $π$ between the hole spin states, a non-general manipulation of the hole spin.
Efficacy and Safety of Isopropanolic Black Cohosh Extract for Climacteric Symptoms (2005)

This isopropanolic extract of black cohosh root stock is effective in relieving climacteric symptoms, especially in early climacteric women.