gebhart/patrepeval huggingface dataset:
Detecting Single Photons Using Capacitive Coupling of Single Quantum Dots (2018)

Capturing single photons through light–matter interactions is a fascinating and important topic for both fundamental research and practical applications. The light–matter interaction enables the transfer of the energy of a single photon (∼1 eV) to a bound electron, making it free to move either in the crystal lattice or in the vacuum. In conventional single photon detectors (e.g., avalanche photodiodes), this free electron triggers a carrier multiplication process which amplifies the ultraweak signal to a detectable level. Despite their popularity, the timing jitter of these conventional detectors is limited to tens of picoseconds, mainly attributed to a finite velocity of carriers drifting through the detectors. Here we propose a new type of single photon detector where a quantum dot, embedded in a single-electron transistor like device structure, traps a photogenerated charge and gives rise to a sizable voltage signal (∼7 mV per electron or hole by simulation) on a nearby sense probe through capacitive coupling (with a capacitance ∼ aF). Possible working modes of the proposed detector are theoretically examined. Owing to a small lateral dimension of the quantum dot, detailed analyses reveal that the intrinsic timing jitter of the proposed detector is in the femtosecond to subpicosecond range, and the intrinsic dark count rate is negligible up to moderately high temperatures. These figures of merit are orders of magnitude superior to those of the state-of-the-art single photon detectors work in the same spectral range, making the proposed detector promising for timing-sensitive and quantum information applications.
Consequences of the electronic tuning of latent ruthenium-based olefin metathesis catalysts on their reactivity (2015)

Two ruthenium olefin metathesis initiators featuring electronically modified quinoline-based chelating carbene ligands are introduced. Their reactivity in RCM and ROMP reactions was tested and the results were compared to those obtained with the parent unsubstituted compound. The studied complexes are very stable at high temperatures up to 140 °C. The placement of an electron-withdrawing functionality translates into an enhanced activity in RCM. While electronically modified precatalysts, which exist predominantly in the trans-dichloro configuration, gave mostly the RCM and a minor amount of the cycloisomerization product, the unmodified congener, which preferentially exists as its cis-dichloro isomer, shows a switched reactivity. The position of the equilibrium between the cis- and the trans-dichloro species was found to be the crucial factor governing the reactivity of the complexes.
EduClust - A Visualization Application for Teaching Clustering Algorithms (2019)

We present EduClust, a visualization application for teaching clustering algorithms. EduClust is an online application that combines visualizations, interactions, and animations to facilitate the understanding and teaching of clustering steps, parameters, and procedures. Traditional classroom settings aim for cognitive processes like remembering and understanding. We designed EduClust for expanded educational objectives like applying and evaluating. Educators can use the tool in class to show the effect of different clustering parameters on various datasets while animating through each algorithm's steps, but also use the tool to prepare traditional teaching material quickly by exporting animations and images. Students, on the other hand, benefit from the ability to compare and contrast the influence of clustering parameters on different datasets, while seeing technical details such as pseudocode and step-by-step explanations.
Task based Cholesky decomposition on Xeon Phi architectures using OpenMP (2018)

The increasing number of computational cores in modern many-core processors, as represented by the Intel Xeon Phi architectures, has created the need for an open-source, high performance and scalable task-based dense linear algebra package that can efficiently use this type of many-core hardware. In this paper, we examined the design modifications necessary when porting PLASMA, a task-based dense linear algebra library, run effectively on two generations of Intel's Xeon Phi architecture, known as knights corner (KNC) and knights landing (KNL). First, we modified PLASMA's tiled Cholesky decomposition to use OpenMP tasks for its scheduling mechanism to enable Xeon Phi compatibility. We then compared the performance of our modified code to that of the original dynamic scheduler running on an Intel Xeon Sandy Bridge CPU. Finally, we looked at the performance of the OpenMP tiled Cholesky decomposition on knights corner and knights landing processors. We detail the optimisations required to obtain performance on these platforms and compare with the highly tuned Intel MKL math library.
Cytomorphological studies in relation to powdery mildew resistance in ber (Zizhyphus mauritiana Lamk.) (2002)

Pattern of morphological and cytological variation in relation to powdery mildew resistance In 80 germplasm accessions of ber (Zizhyphus mauritiana Lamk.) is reported. Metroglyph and index score analyses showed wide morphological variation in the germplasm. Eight distinct groups were recognized on the basis of variation in 23 morphological and fruit characters however, within group variations were of a low order. Meiotic studies revealed an array of forms ranging from diploid to triploid, tetra, penta and octaploid types. Our study suggested that the groupings based on morphological attributes have cytological foundation and a few diploid accessions and an octaploid genotype formed the basic source of immunity/resistance for powdery mildew disease.
Real-time aerial images based mask inspection, die-to-wafer image inspection (2006)

The concept of defect printability, i.e., mask error enhancement factor (MEEF), should be integrated into mask defect inspection procedures, and thus avoid the huge burden of defect detection algorithm development. It is necessary to simplify the difficult task of defining defect size which is caused by nonlinear transfer of killer defects, and which is strongly dependent on defect types. One solution to the problem is to incorporate defect printability study using aerial image based inspection into the existing mask inspection system. This paper shows how the measured mask pattern images obtained from mask inspection system are transformed into wafer-like images by simulation-based software. It is important that wafer-like images (WI) from measured mask images are created within a reasonable calculation time and the result has sufficient accuracy. The paper also introduces calculation of aerial images using perturbation approach and demonstrates the possibility of D-to-WI inspection. The paper points out that the technique of generating wafer-like image from measured mask pattern is well established for attenuated PSMs and Cr binary masks.
Genetics of Follicular Lymphoma Transformation (2014)

Follicular lymphoma (FL) is an indolent disease, but 30%-40% of cases undergo histologic transformation to an aggressive malignancy, typically represented by diffuse large B cell lymphoma (DLBCL). The pathogenesis of this process remains largely unknown. Using whole-exome sequencing and copy-number analysis, we show here that the dominant clone of FL and transformed FL (tFL) arise by divergent evolution from a common mutated precursor through the acquisition of distinct genetic events. Mutations in epigenetic modifiers and antiapoptotic genes are introduced early in the common precursor, whereas tFL is specifically associated with alterations deregulating cell-cycle progression and DNA damage responses (CDKN2A/B, MYC, and TP53) as well as aberrant somatic hypermutation. The genomic profile of tFL shares similarities with that of germinal center B cell-type de novo DLBCL but also displays unique combinations of altered genes with diagnostic and therapeutic implications.
Late renal allograft failure secondary to thrombotic microangiopathy-human immunodeficiency virus nephropathy. (1994)

The case of a renal transplant recipient with a known history of iv drug abuse but unknown human immunodeficiency virus (HIV) status who presents after having a stable renal allograft function for 4 yr, with acute/subacute advanced renal failure, nephrotic syndrome, and hypertension, as well as clinical and histologic findings of thrombotic microangiopathy, is reported. He was subsequently found to have a positive serology for HIV-1 with a low CD4 count but no clinical manifestations of the acquired immunodeficiency syndrome. He was treated conservatively with zidovudine (AZT). The patient never regained graft function and was ultimately discharged from the hospital on maintenance dialytic therapy. This is, to our knowledge, the first report of thrombotic microangiopathy in an HIV-1-infected patient presenting late in the course as acute/subacute renal allograft failure.
RAPID CELL CYCLE ANALYSIS BY MEASUREMENT OF THE RADIOACTIVITY PER CELL IN A NARROW WINDOW IN S PHASE (RCSi) (1977)

A new rapid method for the cell cycle analysis of asynchronously growing cells is presented. The new method is an alternative to the more time consuming and subjective fraction of labeled mitoses (FLM) method. Like the FLM method, all cells in the S phase of the cell cycle are marked by pulse labeling with a radioactive DNA precursor. The subsequent progress of the cohort of cells thus labeled is monitored through a narrow window in the cell cycle. The window is defined by a narrow range of DNA contents corresponding to cells in mid-S phase and is designated Si. The cellular DNA content is measured by flow cytometry and the cells in the window Si are selected by electronic cell sorting. The radioactivity per cell in Si (RCSi) is determined by liquid scintillation counting. The duration of S phase and of the total cycle and the dispersions therein are determined from the oscillation of the RCSi values with time. The complete cell cycle analysis can be accomplished in as little as 1 day following the collection of samples. Exponentially growing Chinese hamster ovary (CHO) cells were analyzed according to the RCSi method and the FLM method. It is demonstrated that the two techniques give essentially the same results.
The effect of Glucagon-Like Peptide-1 Receptor Blockade on glucagon-induced stimulation of insulin secretion (2022)

&lt;p&gt;Data from transgenic rodent models suggest that glucagon acts as an insulin secretagogue by signalling through the Glucagon-Like Peptide-1 Receptor (GLP1R) present on β-cells. However, its net contribution to physiologic insulin secretion in humans is unknown. To address this question, we studied non-diabetic individuals in 2 separate experiments. Each subject was studied on 2 occasions in random order. In the first experiment, during a hyperglycemic clamp, glucagon was infused at 0.4ng/kg/min, increasing by 0.2ng/kg/min every hour for 5 hours. On one day exendin-9,39 (300pmol/kg/min) was infused to block GLP1R, while on the other saline was infused. The insulin secretion rate (ISR) was calculated by nonparametric deconvolution from plasma concentrations of C-peptide. Endogenous glucose production (EGP) and glucose disappearance (Rd) were measured using the tracer-dilution technique. Glucagon concentrations, by design, did not differ between study days. Integrated ISR was lower during exendin-9,39 infusion (213 ± 26 vs. 191 ± 22 nmol per 5 hr, saline vs. exendin-9,39 respectively, &lt;em&gt;p&lt;/em&gt; = 0.02). In the separate experiment, exendin-9,39 infusion, compared to saline infusion, also decreased the β-cell secretory response to a 1mg glucagon bolus. These data show that in non-diabetic humans, glucagon partially stimulates the β-cell through GLP1R. &lt;/p&gt;
Advances in polymeric Cartesian polarizing beamsplitters and light engines employing them (2007)

3M Polarization Beam Splitter (PBS) technology has been shown to be the most light efficient solution to the needs of LCOS projection. It also provides very high contrast and extremely uniform dark states without the use of lead in the glass prisms. We report on recent improvements in contrast performance, increased understanding of the effects of pupil shape and size on contrast, effects of temperature on optical performance, and improved photostability. We also suggest new light-engine architectures employing the 3M PBSs with associated light budget analyses.
Data from Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The high fatality-to-case ratio of ovarian cancer is directly related to platinum resistance. Exportin-1 (XPO1) is a nuclear exporter that mediates nuclear export of multiple tumor suppressors. We investigated possible clinicopathologic correlations of XPO1 expression levels and evaluated the efficacy of XPO1 inhibition as a therapeutic strategy in platinum-sensitive and -resistant ovarian cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; XPO1 expression levels were analyzed to define clinicopathologic correlates using both TCGA/GEO datasets and tissue microarrays (TMA). The effect of XPO1 inhibition, using the small-molecule inhibitors KPT-185 and KPT-330 (selinexor) alone or in combination with a platinum agent on cell viability, apoptosis, and the transcriptome was tested in immortalized and patient-derived ovarian cancer cell lines (PDCL) and platinum-resistant mice (PDX). Seven patients with late-stage, recurrent, and heavily pretreated ovarian cancer were treated with an oral XPO1 inhibitor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; XPO1 RNA overexpression and protein nuclear localization were correlated with decreased survival and platinum resistance in ovarian cancer. Targeted XPO1 inhibition decreased cell viability and synergistically restored platinum sensitivity in both immortalized ovarian cancer cells and PDCL. The XPO1 inhibitor–mediated apoptosis occurred through both p53-dependent and p53-independent signaling pathways. Selinexor treatment, alone and in combination with platinum, markedly decreased tumor growth and prolonged survival in platinum-resistant PDX and mice. In selinexor-treated patients, tumor growth was halted in 3 of 5 patients, including one with a partial response, and was safely tolerated by all.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Taken together, these results provide evidence that XPO1 inhibition represents a new therapeutic strategy for overcoming platinum resistance in women with ovarian cancer. &lt;i&gt;Clin Cancer Res; 23(6); 1552–63. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Memory Efficient Experience Replay for Streaming Learning (2019)

In supervised machine learning, an agent is typically trained once and then deployed. While this works well for static settings, robots often operate in changing environments and must quickly learn new things from data streams. In this paradigm, known as streaming learning, a learner is trained online, in a single pass, from a data stream that cannot be assumed to be independent and identically distributed (iid). Streaming learning will cause conventional deep neural networks (DNNs) to fail for two reasons: 1) they need multiple passes through the entire dataset; and 2) non-iid data will cause catastrophic forgetting. An old fix to both of these issues is rehearsal. To learn a new example, rehearsal mixes it with previous examples, and then this mixture is used to update the DNN. Full rehearsal is slow and memory intensive because it stores all previously observed examples, and its effectiveness for preventing catastrophic forgetting has not been studied in modern DNNs. Here, we describe the ExStream algorithm for memory efficient rehearsal and compare it to alternatives. We find that full rehearsal can eliminate catastrophic forgetting in a variety of streaming learning settings, with ExStream performing well using far less memory and computation.
Supplementary Information from Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy (2023)

&lt;p&gt;Supplementary Methods, Figures, Table Legends Supplementary Figure 1: Representative Hematoxylin and Eosin stained photomicrographs of prostatectomy specimens demonstrating the effects of neoadjuvant chemohormonal therapy. Supplementary Figure 2: Quality metrics for targeted DNA sequencing of FFPE biopsy and RP specimens. Supplementary Figure 3: Somatic mutations detected pre- and post-treatment through targeted DNA sequencing. Supplementary Figure 4: Differences in the number and allelic frequency of somatic mutations between treated and untreated specimens. Supplementary Figure 5: Persistence of TP53 mutations in post-treated radical prostatectomy (RP) specimens. Supplementary Figure 6: Representative copy number plots from targeted sequencing of diagnostic biopsies and RP specimens from the untreated arm. Supplementary Figure 7: Pearson's correlation comparing the Nanostring platform (x axis) and RNA-seq (y axis) performed in 13 matched cases. Supplementary Figure 8: Scatterplots showing Pearson correlation between Nanostring data obtained from matched FFPE and fresh/frozen tissue in 7 patients. Supplementary Figure 9: Gene expression of PTEN (y axis) relative to genomic status (PTEN deletion or wild type (WT). Supplementary Figure 10: Left: Correlation of TMPRSS2-ERG fusion transcript expression (x axis) and ERG gene expression (y axis). Right: ERG expression vs. TMPRSS2-ERG fusion status with positive defined as normalized count&gt; 50. Supplementary Figure 11: Principal component analysis plotted using the Biological Coefficient of Variation (BCV) distance as part of the edgeR package. Supplementary Figure 12: Unsupervised analysis of expression of all genes within the panel in radical prostatectomies from treated (green) and untreated (yellow) arms. Red= high expression; blue= low expression.&lt;/p&gt;
NIMG-12. DSC-MRI PERFUSION IMAGING IN UNTREATED BRAIN METASTASES USING THE CONSENSUS ACQUISITION PROTOCOL: A MULTI-SITE BENCHMARK STUDY (2022)

Abstract INTRODUCTION DSC-MRI perfusion methods are commonly used to evaluate both primary and metastatic brain cancer with the creation of maps of relative cerebral blood volume (rCBV). Recently, guidelines were established to ensure a standard DSC-MRI acquisition protocol that reduces inter-site variability. The purpose of this study was to initiate the determination of rCBV benchmark values using the DSC-MRI consensus protocol in treatment-naïve brain metastases. METHODS Patients from three sites with treatment-naïve, contrast-enhancing brain metastases on MRI were considered for inclusion in this retrospective study. The MRIs included pre- and post-contrast T1w(T1+C) images obtained after administration of gadolinium-based contrast agent (GBCA) (0.1 mmol/kg), which serves as the recommended preload for the DSC-MRI data collection. A 2nd GBCA dose (0.1 mmol/kg) was administered 40-60sec after the collection of baseline GRE-EPI images using recommended settings (FA=60o, TE/TR=30ms/1100-1250ms) for 120s. Calibrated pre/post T1w difference maps (dT1) were used for delineation of enhancing lesion, and standardized (calibrated) rCBV (sRCBV) created. Mean sRCBV for metastases were compared to normal appearing white matter (NAWM) and treatment-naive glioblastoma (GBM) from a previous study. Pairwise comparisons were performed using the Mann-Whitney nonparametric test. RESULTS N=52 patients with primary histology of lung (n=27); breast (n=6); skin (n=7); gastrointestinal (GI: n=3) and genitourinary (GU: n=9) cancers were included in comparison to GBM (n=31). The mean sRCBV for all metastases (1.77+/-1.05) is significantly lower (p=0.0003) than for GBM (2.67+/-1.34) but with both statistically greater (p&amp;lt; 0.0001) than NAWM (0.706+/-0.163). Individually, lung (1.47+/- 0.61), breast (2.275+/-0.87), skin (2.10+/-1.22), GI (1.91+/- 0.64) and GU (2.01+/-0.63) mean sRCBV are statistically greater than for NAWM. CONCLUSION Using the consensus DSC-MRI acquisition protocol confirms use of sRCBV to identify biologically active, treatment-naive brain metastases setting benchmark values for future applications.
Direct Assay of Enzymes in Heme Biosynthesis for the Detection of Porphyrias by Tandem Mass Spectrometry. Porphobilinogen Deaminase (2008)

We report a new assay of human porphobilinogen deaminase (PBGD). Deficiency in this enzyme activity causes acute intermittent porphyria, the most common disorder of heme biosynthesis. The assay involves incubation of blood erythrocyte lysate with porphobilinogen, the natural PBGD substrate. Two subsequent enzymes in the heme biosynthetic pathway, uroporphyrinogen III synthase and uroporphyrinogen decarboxylase, are deactivated by heating so that their activity does not interfere with the PBGD assay. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) is used to monitor the production of uroporphyrinogen I and thus measure the PGBD activity. A simple and efficient workup using liquid-liquid extraction with >90% product recovery was employed to avoid separation by liquid chromatography. The assays show good reproducibility (+/-3.3%) and linear dependence of the uroporphyrinogen I formation on incubation time and protein amount. The Km of PGBD for porphobilinogen was measured as 11.2 +/- 0.5 microM with Vmax of 0.0041 +/- 0.0002 microM/(min.mg of hemoglobin). The coefficient of variation of PBGD activity among several unaffected individuals (12%) is significantly lower than the decrease due to acute intermittent porphyria (50%).
Intraoperative Ultrasonography as a Guidance for Dividing Bile Duct During Laparoscopic Living Donor Hepatectomy (2019)

BACKGROUND The purpose of this study was to investigate the feasibility of using intraoperative ultrasonography as a guidance in dividing bile duct during laparoscopic donor hepatectomy. MATERIAL AND METHODS Cases of living liver donors who underwent laparoscopic living donor hepatectomy from May 2013 to December 2017 were reviewed. Operative and postoperative data were compared between donors with intraoperative ultrasonography and donors with intraoperative cholangiography. For analyzing whether bile duct division was performed successfully, anatomical type and number of bile duct openings were reviewed. When the number of bile ducts were achieved as expected, it was considered "successful". RESULTS Intraoperative cholangiography was used in 67 donors (62.6%) while intraoperative ultrasonography was used in 36 donors (33.6%). Mean operation time was 405.0±76.2 minutes versus 275.1±37.5 minutes, P<0.001, respectively, and was longer in donors who had a cholangiography. There was no difference in the success rate of bile duct division between donors who had a cholangiography (92.5%) and donors who had an ultrasonography (88.9%, P=0.716). The mean hospital stay after operation was longer in donors who had a cholangiography (11.6±4.3 days versus 9.0±2.7 days, P<0.001). There was no difference in biliary complication rate between donors who had a cholangiography (11.9%) and donors who had an ultrasonography (8.3%, P=0.743). CONCLUSIONS Intraoperative ultrasonography can be used safely in dividing bile duct during laparoscopic living donor hepatectomy with similar outcomes to intraoperative cholangiography.