gebhart/patrepeval huggingface dataset:
Probing scattering resonances of Vogel’s spirals with the Green’s matrix spectral method (2016)

Using the rigorous Green's function spectral method, we systematically investigate the scattering resonances of different types of Vogel spiral arrays of point-like scatterers. By computing the distributions of eigenvalues of the Green's matrix and the corresponding eigenvectors, we obtain important physical information on the spatial nature of the optical modes, their lifetimes and spatial patterns, at small computational cost and for large-scale systems. Finally, we show that this method can be extended to the study of three-dimensional Vogel aperiodic metamaterials and aperiodic photonic structures that may exhibit a richer spectrum of localized resonances of direct relevance to the engineering of novel optical light sources and sensing devices.
Dasatinib (BMS-354825) Selectively Induces Apoptosis in Lung Cancer Cells Dependent on Epidermal Growth Factor Receptor Signaling for Survival (2006)

Mutations of the epidermal growth factor receptor (EGFR) selectively activate Akt and signal transducer and activator of transcription (STAT) pathways that are important in lung cancer cell survival. Src family kinases can cooperate with receptor tyrosine kinases to signal through downstream molecules, such as phosphatidylinositol 3-kinase/PTEN/Akt and STATs. Based on the importance of EGFR signaling in lung cancer, the known cooperation between EGFR and Src proteins, and evidence of elevated Src activity in human lung cancers, we evaluated the effectiveness of a novel orally bioavailable Src inhibitor dasatinib (BMS-324825) in lung cancer cell lines with defined EGFR status. Here, we show that cell fate (death versus growth arrest) in lung cancer cells exposed to dasatinib is dependent on EGFR status. In cells with EGFR mutation that are dependent on EGFR for survival, dasatinib reduces cell viability through the induction of apoptosis while having minimal apoptotic effect on cell lines with wild-type (WT) EGFR. The induction of apoptosis in these EGFR-mutant cell lines corresponds to down-regulation of activated Akt and STAT3 survival proteins. In cell lines with WT or resistant EGFR mutation that are not sensitive to EGFR inhibition, dasatinib induces a G(1) cell cycle arrest with associated changes in cyclin D and p27 proteins, inhibits activated FAK, and prevents tumor cell invasion. Our results show that dasatinib could be effective therapy for patients with lung cancers through disruption of cell growth, survival, and tumor invasion. Our results suggest EGFR status is important in deciding cell fate in response to dasatinib.
ER−/PR+/HER2− breast cancer type shows the highest proliferative activity among all other combined phenotypes and is more common in young patients: Experience with 6643 breast cancer cases (2019)

The characterization of breast cancer according to its proliferative activity and the expression of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor-2 is a laboratory routine that has been adopted worldwide for prognostic and therapeutic purposes. By combining data on the expression of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor-2, it is possible to obtain 8 tumor patterns categorized as triple-negative, nonluminal (i.e. positive for human epidermal growth factor receptor-2 with four subtypes) and luminal (negative for human epidermal growth factor receptor-2 and positive for estrogen receptor and/or progesterone receptor with three subtypes) tumors. In general, luminal tumors are associated with a higher degree of tumor differentiation and have more favorable clinical outcomes. One of the subtypes of luminal tumors has an ER-/PR+ profile. This is a rather rare tumor subtype that behaves aggressively. The aim of this work was to analyse the proliferative activity of the eight tumor subgroups to verify if the ER-/PR+ type has a higher proliferative activity than the other subtypes, which might be correlated with its more aggressive behavior. To accomplish this, we examined estrogen receptor, progesterone receptor, human epidermal growth factor receptor-2 and Ki67 data from 6643 cases of breast cancer. We found that the tumor type that was positive for only the progesterone receptor and negative for both the estrogen receptor and human epidermal growth factor receptor-2 (1.3% of all cases) had a proliferative activity that was consistently much higher than those of the other luminal subtypes.
Multiplex Sets for the Amplification of Polymorphic Short Tandem Repeat Loci — Silver Stain and Fluorescence Detection (1996)

Multiplex PCR amplification systems were developed using well-characterized, polymorphic short tandem repeat (STR) loci. Eight loci utilized in the multiplex amplifications included HUMCSF1PO, HUMTPOX, HUMTH01, HUMVWFA31, HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL. From this list, three or four non-overlapping loci were simultaneously amplified, separated by denaturing polyacrylamide gel electrophoresis and visualized using silver stain or fluorescence detection. The multiplex PCR amplification systems offer a non-isotopic method for rapid, simple and accurate analysis of STR loci. This high-throughput method for DNA identification has immediate and valuable application in forensic analysis, paternity determination, tissue culture strain identification and bone marrow transplantation studies.
Goffman Turned to Me and Said With Some Surprise, “You like doing fieldwork?” (2007)

Dr. Ruth Horowitz, Professor of Sociology at the New York University, wrote this memoir at the invitation of Dmitri Shalin and gave her approval for posting the present version in the Erving Goffman Archives.
Ploidy Level Determinations in Buffalograss Clones and Populations (1998)

Buffalograss [ Buchloë dactyloides (Nutt.) Engelm.] is the subject of breeding programs for turfgrass use because of its drought and heat tolerance, low growing habit, and low management input. Three ploidy levels are known to exist ( x = n = 10), but plants at each level are nearly morphologically indistinguishable. In this paper, flow cytometry was evaluated as a means of determining ploidy levels of 31 buffalograss clones and 34 seeded populations. Six clones were analyzed for nuclear DNA base‐pair composition by flow cytometry. Based on DNA contents, buffalograss clones can be grouped into four sets corresponding to chromosome number or ploidy level. Mean DNA contents were 0.93, 1.80, 2.15, and 2.63 pg DNA/nucleus for diploid, tetraploid, pentaploid, and hexaploids, respectively. Chromosome numbers explained most of the DNA content variation as shown by the strong linear relationship between DNA content and chromosome number. Cultivar 315 is a pentaploid and is the first report of a pentaploid among buffalograss. Seeded populations analyzed include those exclusively tetraploid, mixture of tetraploid through hexaploid, and those exclusively hexaploid. Aneuploids between pentaploid and hexaploid levels were noted. No differences were observed between pioidy levels or genders with regard to base‐pair composition.
SoCLog: A real-time, automatically generated logging and profiling mechanism for FPGA-based Systems On Chip (2016)

Recent advances in FPGA technology and the proliferation of High Level Synthesis (HLS) tools makes it possible to implement complex System on Chip (SoC) designs that realize complete applications in a single FPGA device. To be able to exploit the large performance vs. area search space of such modern FPGA-based SoCs, system architects must have the appropriate performance analysis tools to evaluate-preferably at runtime-the computational requirements and the data flow of such a system to determine potential performance bottlenecks when running realistic workloads. In this paper we introduce SoCLog, a framework that automatically enhances the platform architecture with additional hardware components used to generate activity logs when the base SoC architecture executes an application. This real-time information can be analyzed by the system designer to expose performance bottlenecks not only on aggregate, but also at clock cycle granularity thus revealing potential design inefficiencies when there is burst of activity in the system. We evaluate our framework with a number of SoC designs to show that such a logging information can be valuable for the design of a complex SoC in a modern FPGA with minimal area overhead.
Salivary interleukin‐6 in the detection of oral cancer and precancer (2015)

The increase in salivary IL-6 in leukoplakia and OSCC might point out its local production by the tumor cells. The difference in its levels between these two lesions might indicate the progression of precancer to cancer. Further longitudinal studies with increased sample size are needed to substantiate the utility of salivary IL-6 as diagnostic or prognostic marker for oral cancer and precancer.
MFN2, a new gene responsible for mitochondrial DNA depletion (2012)

Sir, we read with great interest the paper by Rouzier et al. (2012) reporting a novel dominant MFN2 missense mutation (c.629A>T, p.D210V) in a large family displaying an optic atrophy ‘plus’ phenotype. Importantly, the authors identified MFN2 as a new gene implicated in mitochondrial DNA instability as they found multiple mitochondrial DNA deletions in skeletal muscle of two adult patients. Moreover, they have shown that mitochondrial fusion is necessary to repair stress-induced damage to mitochondrial DNA.

Here, we report a child with an early-onset progressive multi-systemic disorder and carrying a novel MFN2 missense mutation responsible for mitochondrial DNA depletion in skeletal muscle.

This girl was the second child of healthy unrelated parents, born after an uneventful pregnancy. Her birth weight was 2700 g [−2 standard deviations (SD)], her length 45.5 cm (−2 SD) and her head circumference 35 cm (mean). At the age of 6 months she was examined because of developmental delay with hypotonia, decreased rate of growth in head circumference (−2 SD), failure to thrive and severe gastro-oesophageal reflux. Brain MRI, EEG, brainstem auditory evoked potentials, metabolic and genetic investigations were all normal. At 3 years of age, the patient could only stand up when aided and had no language acquisition although her level of understanding seemed good as did her social interaction and behaviour. Drooling, abnormal ocular pursuit, ataxia, dysmetria, areflexia, weakness of limbs and near permanent abnormal movements appeared progressively thereafter. EMG disclosed an axonal sensorimotor neuropathy. At 5 years of age, brainstem auditory evoked potentials revealed hearing loss on the right side and the amplitude of visual evoked responses was decreased while the electroretinogram was normal. Complementary aetiological explorations were negative. Orthopaedic …
Efficient sequential sampling strategies for environmental monitoring (1992)

Assessments of resources at risk to anthropogenic pollution require extensive environmental monitoring. In addition, such assessments are required to have a long‐term monitoring component in order to evaluate not only the status but also the trend of the resources at risk to ecological stresses. There is a need to identify statistical methodologies that would provide effective and cost‐saving environmental monitoring designs, since such monitoring surveys are very expensive. In this paper the purely sequential, accelerated sequential, and three‐stage procedures are evaluated as effective fixed‐precision sampling procedures for environmental monitoring. Current monitoring designs utilize a sampling methodology where each resource is assigned a population inclusion probability, with the intent of describing the distribution of the whole population of resources at risk to anthropogenic environmental stresses. This study assumes that existing designs accurately describe the population distribution. A simultaneous fixed‐precision estimation procedure is developed as an efficient method of estimating practically relevant percentiles of the cumulative distribution function, using water quality data from the Eastern Lake Survey as a lake population distribution. Accelerated sequential and three‐stage procedures are shown to be better alternatives to the purely sequential procedure, requiring fewer sampling operations without any substantial loss of efficiency. Depending upon the precision required, all procedures showed potential reductions in sample size by as much as 60%. These types of designs for environmental monitoring are expected to be advantageous in national monitoring efforts directed toward the assessment of the status and trends of various ecological indicators.
Influence of Electrolyte Modulus on the Local Current Density at a Dendrite Tip on a Lithium Metal Electrode (2016)

Understanding and controlling the electrochemical deposition of lithium is imperative for the safe use of rechargeable batteries with a lithium metal anode. Solid block copolymer electrolyte membranes are known to enhance the stability of lithium metal anodes by mechanically suppressing the formation of lithium protrusions during battery charging. Time-resolved hard X-ray microtomography was used to monitor the internal structure of a symmetric lithium-polymer cell during galvanostatic polarization. The microtomography images were used to determine the local rate of lithium deposition, i.e. local current density, in the vicinity of a lithium globule growing through the electrolyte. Measurements of electrolyte displacement enabled estimation of local stresses in the electrolyte. At early times, the current density was maximized at the globule tip, as expected from simple current distribution arguments. At later times, the current density was maximized at the globule perimeter. We show that this phenomenon is related to the local stress fields that arise as the electrolyte is deformed. The local current density, normalized for the radius of curvature, decreases with increasing compressive stresses at the lithium-polymer interface. To our knowledge, our study provides the first direct measurement showing the influence of local mechanical stresses on the deposition kinetics at lithium metal electrodes.
Long-term quality assessment and monitoring of light microscope performance through accessible and reliable protocols, tools and metrics (2021)

Abstract Reliable, reproducible and comparable results are what biology requires from microscopy. To achieve that level of confidence, monitoring the stability of the microscope performance over time with standardized quality testing routines is essential for mining quantitative data. Three levels of microscope quality control procedures should be considered: i) usage of accessible and affordable tools and samples, ii) execution of easy and fast, preferably automatized, acquisition protocols, iii) analysis of data in the most automated way possible with adequate metrics for long-term monitoring. In this paper, we test the acquisition protocols on the mainly used microscope techniques (wide-field, spinning disk and confocal microscopy) with simple quality control tools. Seven protocols specify metrics on measuring the lateral and axial resolution (Point-Spread Function) of the system, field flatness, chromatic aberrations and co-registration, illumination power monitoring and stability, stage drift and positioning repeatability and finally temporal and spatial noise sources of camera detectors. We designed an ImageJ/FiJi java plugin named MetroloJ_QC to incorporate the identified metrics and automatize the data processing for the analysis. After processing and comparing the data of microscopes from more than ten imaging facilities, we test the robustness of the metrics and the protocols by determining experimental limit values. Our results give a first extensive characterization of the quality control procedures of a light microscope, with an automated data processing and experimental limit values that can be used by core facility staff and researchers to monitor the microscope performance over time.
Pharmacologically Induced Heart Failure for the Evaluation of Circulatory Assistance (1996)

For the evaluation of the hemodynamic interaction between the natural heart and an assist device, a reversible pharmacological model based on the channel blocker Verapamil under hyperkalemia, was developed for deterioration of left ventricular function. Four calves weighing 70-90 kg underwent standard implantation for left atrioaortal assist (BioMedicus, BP-80), pump anesthesia (oxygen/isoflurane [1%]; 8 mg/kg of BW/h keta-mine), and of ventricular demand pacing at 120 bpm. Left atrial pressure (LAP), ventricular pressure (LVP), aortic pressure (AoP), pulmonary arterial (Qpulm) pressures, and graft flow (Qgraft) were monitored. The hemodynamic effects of anesthetic overdose (2% Isoflurane) were compared with those of Verapamil (Isoptin: 0.2 mg/kg BW/h 5 mmol/kg of BW/h of KC1) medication. Both regimens caused a decrease in AoP to ≤50%. For Isoflurane, a slight reduction in cardiac output (CO) of 10% at a nearly constant LAP and a strong decrease of the peripheral resistance (Rperi) of 35% could be seen where Isoptin caused a significant reduction in CO of 40% at an increased LAP (+ 25%) and changes in Rperi of <10%. Because the vascular tonus remains nearly constant, the hemodynamic effects are controllable and reversible (antagonized with calcium chloride); thus we conclude that Verapamil administration under hyperkalemia conditions is a proper model for mimicking congestive heart failure with low systemic side effects.
Prognostic factors of recurrent disease in upper urinary tract urothelial cancer after radical nephroureterectomy: Subanalysis of the multi‐institutional national database of the Japanese Urological Association (2015)

Despite several limitations, our analysis suggests that pathological tumor stage, lymph node status, lymphovascular invasion, infiltrative growth pattern and age represent important prognostic variables after radical nephroureterectomy in Japanese patients with upper urinary tract urothelial cancer. This information could be potentially used to select patients for adjuvant systemic therapy.
Detecting head and neck lymph node metastases with white light reflectance spectroscopy; a pilot study (2021)

This proof of principle study is a first step in the development of an SFR spectroscopy technique to detect LN metastases in real time. A next step towards this goal is replicating these results in LNs with smaller metastases and in a larger cohort of patients. This future study will combine SFR spectroscopy with fine-needle aspiration, using the same needle, to perform preoperative in vivo measurements.
Mechanical testing of fixation techniques for scaffold‐based tissue‐engineered grafts (2007)

Full-thickness defects in articular cartilage can be functionally restored by autologous chondrocyte implantation (ACI). In past years, numerous types of scaffolds for tissue-engineered cartilage implants have been developed and thoroughly characterized. However, the fixation stability of the implants has been rarely investigated despite its well-known importance for successful therapy. In this study, we have mechanically tested the fixation stability of four commonly used biomaterials for ACI attached by four different fixation techniques (unfixed, fibrin glue, chondral suture, and transosseous suture) in situ. Scaffolds based on polyglycolic acid (PGA) and polyglycolic acid and poly-L-lactic acid (PGLA), collagen membranes, and a gel-like matrix material were fixed within rectangular full-thickness cartilage defects of 10 x 15 mm(2) and loaded in tension until failure. Fibrin glue fixation of PGLA-scaffolds withstood a load of 2.18 6 +/- 0.47 N, chondral sutured PGA-scaffolds of 26.29 6 +/- 1.55 N, and transosseous fixed PGA-scaffolds of 38.18 6 +/- 9.53 N. The PGA-scaffold could be loaded highest until failure for all fixation techniques compared to the PGLA-scaffold and collagen membrane. Our findings serve as basis for selecting the most suitable fixation technique for scaffold-based tissue-engineered grafts according to the expected in vivo loads.
Learning Meta-Representations of One-shot Relations for Temporal Knowledge Graph Link Prediction (2023)

Few-shot relational learning for static knowledge graphs (KGs) has drawn greater interest in recent years, while few-shot learning for temporal knowledge graphs (TKGs) has hardly been studied. Compared to KGs, TKGs contain rich temporal information, thus requiring temporal reasoning techniques for modeling. This poses a greater challenge in learning few-shot relations in the temporal context. In this paper, we follow the previous work that focuses on few-shot relational learning on static KGs and extend two fundamental TKG reasoning tasks, i.e., interpolated and extrapolated link prediction, to the one-shot setting. We propose four new large-scale benchmark datasets and develop a TKG reasoning model for learning one-shot relations in TKGs. Experimental results show that our model can achieve superior performance on all datasets in both TKG link prediction tasks.
Supplementary Figure 2 from Biological Roles of the Delta Family Notch Ligand Dll4 in Tumor and Endothelial Cells in Ovarian Cancer (2023)

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An Overview of Westinghouse Realistic Large Break LOCA Evaluation Model (2008)

Since the 1988 amendment of the 10 CFR 50.46 rule in 1988, Westinghouse has been developing and applying realistic or best-estimate methods to perform LOCA safety analyses. A realistic analysis requires the execution of various realistic LOCA transient simulations where the effect of both model and input uncertainties are ranged and propagated throughout the transients. The outcome is typically a range of results with associated probabilities. The thermal/hydraulic code is the engine of the methodology but a procedure is developed to assess the code and determine its biases and uncertainties. In addition, inputs to the simulation are also affected by uncertainty and these uncertainties are incorporated into the process. Several approaches have been proposed and applied in the industry in the framework of best-estimate methods. Most of the implementations, including Westinghouse, follow the Code Scaling, Applicability and Uncertainty (CSAU) methodology. Westinghouse methodology is based on the use of the WCOBRA/TRAC thermal-hydraulic code. The paper starts with an overview of the regulations and its interpretation in the context of realistic analysis. The CSAU roadmap is reviewed in the context of its implementation in the Westinghouse evaluation model. An overview of the code (WCOBRA/TRAC) and methodology is provided. Finally, the recent evolution to nonparametric statistics in the current edition of the W methodology is discussed. Sample results of a typical large break LOCA analysis for a PWR are provided.