gebhart/patrepeval huggingface dataset:
Color Change of the Snapper ( Pagrus auratus ) and Gurnard ( Chelidonichthys kumu ) Skin and Eyes during Storage: Effect of Light Polarization and Contact with Ice (2014)

Ten gurnard and 10 snapper were stored on ice. One side always contacted the ice; the other side was always exposed to air. At different intervals for up to 12 d, the fish were placed in a light box, and the images of both sides were taken using polarized and nonpolarized illumination. Image analysis resulted in average L*, a*, and b* values of skin, and average L* values of the eyes. The skin L* value of gurnard changed significantly over time while that of snapper was substantially constant. The a* and b* values of both fish decreased over time. The L* values of eyes were significantly lower for polarized images, and significantly lower for the side of fish exposed to air only. This may be a concern in quality evaluation methods such as QIM. The difference of colors between the polarized and nonpolarized images was calculated to quantify the reflection off the surface of fish. For accurate measurement of surface color and eye color, use of polarized light is recommended.
Shiga Toxin–Producing Escherichia coli in Wheat Grains: Detection and Isolation by Polymerase Chain Reaction and Culture Methods (2021)

Shiga toxin-producing <i>Escherichia coli</i> (STEC) are major foodborne pathogens and seven serogroups, O26, O45, O103, O111, O121, O145, and O157, often called top-7 STEC, account for the majority of the STEC-associated human illnesses in the United States. Two Shiga toxins, Shiga toxins 1 and 2, encoded by <i>stx</i>1 and <i>stx</i>2 genes, are major virulence factors that are involved in STEC infections. Foodborne STEC infections have been linked to a variety of foods of both animal and plant origin, including products derived from cereal grains. In recent years, a few STEC outbreaks have been linked to contaminated wheat flour. The microbiological quality of the wheat grains is a major contributor to the safety of wheat flour. The objective of the study was to utilize polymerase chain reaction (PCR)- and culture-based methods to detect and isolate STEC in wheat grains. Wheat grain samples (<i>n</i> = 625), collected from different regions of the United States, were enriched in modified buffered peptone water with pyruvate (mBPWp) or <i>E. coli</i> (EC) broth, and they were then subjected to PCR- and culture-based methods to detect and isolate STEC. Wheat grains enriched in EC broth yielded more samples positive for <i>stx</i> genes (1.6% vs. 0.32%) and STEC serogroups (5.8% vs. 2.4%) than mBPWp. The four serogroups of top-7 detected and isolated were O26, O45, O103, and O157 and none of the isolates was positive for the Shiga toxin genes. A total of five isolates that carried the <i>stx</i>2 gene were isolated and identified as serogroups O8 (0.6%) and O130 (0.2%). The EC broth was a better medium to enrich wheat grains than mBPWp for the detection and isolation of STEC. The overall prevalence of virulence genes and STEC serogroups in wheat grains was low. The <i>stx</i>2-positive serogroups isolated, O8 and O130, are not major STEC pathogens and have only been implicated in sporadic infections in animals and humans.
A 1.4 million element, full frame CCD image sensor with vertical overflow drain for anti-blooming and low color crosstalk (1987)

Blooming and color crosstalk must be greatly suppressed in solid-state image sensors for nearly all imaging applications. A vertical overflow drain has been developed for a 1.4 megapixel image sensor for blooming suppression and low color crosstalk. The overflow drain is formed using a uniform flat p-well. This paper describes the modeling, fabrication, and experimental data associated with implementing vertical overflow in this device.
Quantification of plasma lipids and apolipoproteins by use of proton NMR spectroscopy, multivariate and neural network analysis (2000)

New approaches for quantification of human blood plasma lipids and apolipoproteins are presented. One method is based on multivariate analysis of proton nuclear magnetic resonance spectra of human blood plasma. Although similar approaches have been developed previously, this is the first time principal component analysis (PCA) and partial least squares regression (PLS) have been applied to this particular task. Further, a large proportion of the subjects in this study were cancer patients undergoing treatment, which introduced a new dimension to the quantification of lipoprotein distributions. Calibration models for prediction of lipids and apolipoproteins were constructed by use of PLS, and blind samples were used to test the predictive ability. Comparison of the predicted vs observed data obtained by standard clinical chemical procedures gave good agreement; the correlation coefficient for total plasma triglyceride was 0.99, for total plasma cholesterol 0.98, for LDL cholesterol 0. 97, and for HDL cholesterol 0.88. These results are comparable with those obtained with other methods. The quantitative analysis of 14 components (including total cholesterol and total triglyceride) of human blood plasma was also undertaken using various neural network (NN) analyses of selected portions of the spectra. Conventional fully connected backpropagation neural network topologies were capable of providing excellent predictions for the majority of the variables, confirming and reinforcing literature related to this approach. However HDL triglycerides were poorly predicted, while intermediate-quality results were obtained for the LDL cholesterol, plasma apoA1 and LDL apoB variables. In these instances, applying significantly different neural network algorithms involving either general regression or polynomial neural networks in combination with genetic adaptive components for parameter optimisation made improved predictions.
Learning-Based Resource Allocation for Backscatter-Aided Vehicular Networks (2021)

Heterogeneous backscatter networks are emerging as a promising solution to address the proliferating coverage and capacity demands of next-generation vehicular networks. However, despite its rapid evolution and significance, the optimization aspect of such networks has been overlooked due to their complexity and scale. Motivated by this discrepancy in the literature, this work sheds light on a novel learning-based optimization framework for heterogeneous backscatter vehicular networks. More specifically, the article presents a resource allocation and user association scheme for large-scale heterogeneous backscatter vehicular networks by considering a collaboration centric spectrum sharing mechanism. In the considered network setup, multiple network service providers (NSPs) own the resources to serve several legacy and backscatter vehicular users in the network. For each NSP, the legacy vehicle user operates under the macro cell, whereas, the backscatter vehicle user operates under small private cells using leased spectrum resources. A joint power allocation, user association, and spectrum sharing problem has been formulated with an objective to maximize the utility of NSPs. In order to overcome challenges of high dimensionality and non-convexity, the problem is divided into two subproblems. Subsequently, a reinforcement learning and a supervised deep learning approach have been used to solve both subproblems in an efficient and effective manner. To evaluate the benefits of the proposed scheme, extensive simulation studies are conducted and a comparison is provided with benchmark techniques. The performance evaluation demonstrates the utility of the presented system architecture and learning-based optimization framework.
YXXM Motifs in the PDGF-β Receptor Serve Dual Roles as Phosphoinositide 3-Kinase Binding Motifs and Tyrosine-based Endocytic Sorting Signals (2003)

Phosphoinositide 3-kinases (PI 3-kinases) are important regulators of endocytic trafficking. Previous studies have shown that mutant human platelet-derived growth factor-beta receptors (PDGFR), which contain Phe in place of Tyr at the two p85/p110 PI 3-kinase binding sites (PDGFR-F/F), are defective for both p85 binding and ligand-stimulated degradation. This suggested that p85/p110 regulates PDGFR trafficking. However, more recent work has identified hVPS34, and not p85/p110, as the major PI 3-kinase regulating the movement of receptors through the endosomal system. To reconcile this discrepancy, we hypothesized that YXXM motifs in the PDGFR might play a second role as Tyr-based lysosomal sorting motifs (YXXPhi). To test this, we replaced both YXXM motifs with a motif from LAMP-1, YQTI. This mutant PDGFR (PDGFR-YQTI) still underwent PDGF-stimulated autophosphorylation but did not bind p85. In CHO cells, both wild-type and YQTI receptors showed PDGF-stimulated turnover, whereas F/F receptors did not. In addition, uptake and degradation of cell surface-labeled YXXM and YQTI receptors was fast relative to F/F receptors. We also constructed chimeras containing extracellular and membrane-spanning domains from CD25 (Tac) and cytoplasmic tails containing the YQTI motif, two YXXM motifs, or two mutant FXXM motifs. The YXXM and YQTI chimeras mediated lysosomal delivery of fluorescein isothiocyanate-labeled anti-CD25 antibodies, whereas the F/F chimera was defective. Thus, YQTI motifs can target PDGFR for degradation in the absence of p85/p110 binding, and the p85/p110 binding motifs from PDGFR are sufficient to target Tac chimeras to the lysosome. These data suggest that the YXXM motifs in the PDGFR serve two distinct functions: PI 3-kinase recruitment and lysosomal targeting.
Application and evaluation of knowledge graph embeddings in biomedical data (2021)

Linked data and bio-ontologies enabling knowledge representation, standardization, and dissemination are an integral part of developing biological and biomedical databases. That is, linked data and bio-ontologies are employed in databases to maintain data integrity, data organization, and to empower search capabilities. However, linked data and bio-ontologies are more recently being used to represent information as multi-relational heterogeneous graphs, "knowledge graphs". The reason being, entities and relations in the knowledge graph can be represented as embedding vectors in semantic space, and these embedding vectors have been used to predict relationships between entities. Such knowledge graph embedding methods provide a practical approach to data analytics and increase chances of building machine learning models with high prediction accuracy that can enhance decision support systems. Here, we present a comparative assessment and a standard benchmark for knowledge graph-based representation learning methods focused on the link prediction task for biological relations. We systematically investigated and compared state-of-the-art embedding methods based on the design settings used for training and evaluation. We further tested various strategies aimed at controlling the amount of information related to each relation in the knowledge graph and its effects on the final performance. We also assessed the quality of the knowledge graph features through clustering and visualization and employed several evaluation metrics to examine their uses and differences. Based on this systematic comparison and assessments, we identify and discuss the limitations of knowledge graph-based representation learning methods and suggest some guidelines for the development of more improved methods.
Growth of Azotobacter vinelandii UWD in Fish Peptone Medium and Simplified Extraction of Poly-β-Hydroxybutyrate (1993)

Azotobacter vinelandii UWD was grown in a fermentor with glucose medium with and without 0.1% fish peptone (FP) in batch and fed-batch cultures for the production of the natural bioplastic poly-beta-hydroxybutyrate (PHB). Strain UWD formed PHB five times faster than cell protein during growth in glucose and NH(4), but PHB synthesis stopped when NH(4) was depleted and nitrogen fixation started. When FP was added to the same medium, PHB accumulated 16 times faster than cell protein, which in turn was inhibited by 40%, and PHB synthesis was unaffected by NH(4) depletion. Thus, FP appeared to be used as a nitrogen source by these nitrogen-fixing cells, which permitted enhanced PHB synthesis, but it was not a general growth stimulator. The addition of FP to the medium led to the production of large, pleomorphic, osmotically sensitive cells that demonstrated impaired growth and partial lysis, with the leakage of DNA into the culture fluid, but these cells were still able to synthesize PHB at elevated rates and efficiency. When FP was continuously present in fed-batch culture, the yield in grams of polymer per gram of glucose consumed was calculated to range from 0.43 g/g, characteristic of nongrowing cells, to an unprecedented 0.65 g/g. Separation of an FP-free growth phase from an FP-containing growth phase in fed-batch culture resulted in better growth of these pleomorphic cells and good production of PHB (yield, 0.32 g/g). The fragility of these cells was exploited in a simple procedure for the extraction of high-molecular-weight PHB. The cells were treated with 1 N aqueous NH(3) (pH 11.4) at 45 degrees C for 10 min. This treatment removed about 10% of the non-PHB mass from the pellet, of which 60 to 77% was protein. The final product consisted of 94% PHB, 2% protein, and 4% nonprotein residual mass. The polymer molecular weight (1.7 x 10 to 2.0 x 10) and dispersity (1.0 to 1.9) were not significantly affected (P = 0.05) by this treatment. In addition, the NH(3) extraction waste could be recycled in the fermentation as a nitrogen source, but it did not promote PHB production like FP. A scheme for improved downstream extraction of PHB as well as the merits of using pleomorphic cells in the production of bioplastics is discussed.
CdTe photoluminescence: Comparison of solar-cell material with surface-modified single crystals (2005)

Low-temperature photoluminescence (PL) is used to study defect evolution during Cu diffusion into single-crystal CdTe under various atmospheres. PL reveals a zero-order phonon peak at 1.456 eV when Cu-coated CdTe is annealed at 400 °C in an oxidizing atmosphere, but not under other tested conditions. A similar peak is seen in polycrystalline thin-film CdTe samples, which are known to contain copper and oxygen impurities. First-principles band structure calculations determined the likely defect assignment as a transition between a Cui–OTe donor complex and the valence band.
Acquired resistance to imatinib and secondary KIT exon 13 mutation in gastrointestinal stromal tumour (2006)

Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the gastrointestinal tract. Most of them have an activating mutation of KIT or PDGFRalpha tyrosine-kinase receptors. Imatinib is a selective tyrosine-kinase inhibitor of ABL, KIT and PDGFR, and provides a clinical benefit in about 85% of patients with advanced GIST. Unfortunately, secondary resistance following initial responses occurs in most of the cases, and molecular mechanisms are poorly understood. We sequenced KIT and PGDFRalpha exons from one patient with GIST before and after the development of imatinib resistance. We identified, in addition to a primary mutation in exon 9, a secondary mutation in KIT exon 13 (first kinase domain) in the resistant sample. We demonstrate for the first time the feasibility of sequencing such samples removed by non-surgical biopsies during imatinib therapy. Such a approach, far less invasive than surgery and combined with sequencing, will likely help in better tailoring the treatment of advanced GISTs and understanding the mechanisms of resistance and response to imatinib.
Outcomes and patterns of failures after hypofractionated radiation therapy for intrahepatic cholangiocarcinoma. (2019)

e15609 Background: Locally advanced unresectable intrahepatic cholangiocarcinoma (IHCC) remains incurable. Prior data has shown the effectiveness of hypofractionated radiation therapy (HRT) with biological equivalent doses (BED) greater than 80.5 Gy in improving local control and survival for this patient population. This is an updated report of our IHCC experience with HRT in 15 or 25 fractions using a simultaneous integrated boost technique. Methods: A retrospective analysis of 63 patients (median age 64, range 29-87) diagnosed between 2007-2016 who received HRT was performed. RT dose ranged from 58-90 Gy in 15 fractions and 62.5-100 Gy in 25 fractions, translating to a median BED of 97.5 (range 78.1-144 Gy). Median primary tumor size at diagnosis was 7.8 cm (2.4-17cm). Forty-eight (76%) patients received gemcitabine-based therapy prior to HRT. Results: Median follow up was 31 months (4-110). The 2 year overall-survival (OS), local-progression-free-survival (LPFS), intrahepatic-distant-metastasis-free-survival (IH-DMFS) and extraheptic-distant-metastasis-free-survival (EH-DMFS) were 71% (95% CI 58-82), 67% (95% CI 50-80), 40% (95% CI 28-54) and 40% (95% CI 27-54) respectively. Pattern of failure analysis revealed 16 patients with local failure after HRT, of which only 5 (8% of total) progressed within the high iso-dose field line (BED &gt; 80.5). After HRT, 41 (65%) patients had intrahepatic metastasis that occurred outside the radiation field, and 34 (54%) patients developed extrahepatic metastasis. On multi-variate analysis, T-stage was an independent predictor of OS, LPFS, IH-DMFS, and EH-DMFS. Larger normal liver volume and 15 fraction treatments were independently associated with better LPFS and IH-MFS respectively. There were no significant HRT-related toxicities. Conclusions: HRT demonstrates safety and efficacy for durable local control and prolonged overall survival in patients with unresectable IHCC. Dominant modes of failure are outside the HRT field. Improvements in systemic therapies could further improve outcomes for this patient population.
Tracing Power With Circuit Theory (2019)

Power tracing is the task of disaggregating the power injection of a generator (or a load) into a sum of constituent components that can unambiguously be attributed to loads (generators) and losses. Applications of power tracing range the broad spectrum of: transmission services pricing, loss allocation in distribution networks, fixed-cost allocation, modelling bilateral transactions, and financial storage rights. This paper develops an analytical approach to power tracing leveraging elementary circuit laws. The method is rigorous from a system-theoretic vantage point, and it yields unambiguous results that are consistent with constitutive principles that describe the steady-state behaviour of power networks. Moreover, it can be implemented with limited computational burden, applies to networks with arbitrary topologies, and preserves the coupling between activeand reactive-power injections. Numerical experiments indicate that given a solved power-flow solution, disaggregations can be computed for a test system with 2383 buses, 327 generators, and 2056 loads in 4.34 s on a personal computer, hence establishing computational scalability. Furthermore, applications are demonstrated in distribution and transmission networks with case studies focused on quantifying the impact of distributed generation on loss allocation and extracting nodal contributions to bilateral transactions, respectively.
SecureNoC: A Learning-Enabled, High-Performance, Energy-Efficient, and Secure On-Chip Communication Framework Design (2021)

We propose SecureNoC, a learning-based framework to enhance NoC security against Hardware Trojan (HT) attacks while holistically improving performance and power. The proposed framework enhances NoC security with several architectural innovations, namely a per-router HT detector, multi-function bypass channels (MBCs), and a lightweight data encryption design. Specifically, the threat detector uses an artificial neural network for runtime HT detection with high accuracy. The MBCs consist of a router bypass route and reconfigurable channel buffers which can efficiently isolate malicious nodes and reduce power consumption. The proposed data encryption design adapts to diverse traffic patterns and dynamically deploys novel lightweight encryption techniques for desired security goals with improved latency. Additionally, to balance the trade-offs and handle the dynamic interactions of the proposed dynamic designs, a proactive deep-Q-learning (DQL) control policy is proposed to simultaneously provide optimized NoC security, performance, and power consumption. Simulation studies using PARSEC benchmarks show that the proposed SecureNoC achieves 36% higher HT detection accuracy over state-of-the-art NoC security techniques while reducing network latency by 39% and energy consumption by 46%.
Imprisonment of Resonance Radiation in Gases. II (1951)

This paper is a continuation of an earlier paper which treated the decay of resonance radiation in optically excited gases for the case of doppler-broadened radiation in plane-parallel enclosures. The treatment is here extended to a second type of enclosure geometry---infinite cylinders---and to a variety of spectral line shapes.
Biochemical mapping of the simian rotavirus SA11 genome (1983)

Biochemical mapping experiments of the simian rotavirus SA11 genome were performed to determine which double-stranded RNA segment coded for each of the viral polypeptides. Viral RNA transcripts were synthesized in vitro by using the endogenous viral RNA polymerase and fractionated by electrophoresis in acid-urea agarose gels. The fractionated transcripts were translated in two cell-free systems: micrococcal nuclease-treated reticulocyte lysates and wheat germ extracts. The polypeptide products were identified by polyacrylamide gel electrophoresis and partial peptide analysis and compared with polypeptides synthesized in infected cells or found in purified virus. The RNA segment that coded for each transcript was determined by hybridization of the fractionated transcripts to the double-stranded RNA genome and analysis of the hybrids by electrophoresis in polyacrylamide gels. Primary gene products were assigned for 10 of the rotavirus transcripts and 10 of the double-stranded RNA segments. The coding assignments are as follows: the inner-capsid polypeptides, VP1, VP2, and VP6, were assigned to segments 1, 2, and 6, respectively; the major outer-capsid polypeptides, VP3 and VP7, were assigned to segments 4 and 9, respectively; segments 5, 7, and 8 coded for nonstructural polypeptides with molecular weights of 53,000, 34,000, and 35,000, respectively; segment 10 coded for the 20,000-molecular-weight precursor to the 29,000-molecular-weight glycosylated nonstructural polypeptide; and segment 11 coded for a 26,000-molecular-weight polypeptide that may be the precursor to the minor outer-capsid polypeptide VP9. Several methods were used to determine the product of gene segment 3, and the problems associated with the identification of this gene product are discussed.
Induction Hardened Ductile Iron Camshafts (2002)

&lt;div class="htmlview paragraph"&gt;The General Motors L850 world engine uses an induction hardened, ductile iron, camshaft. Unlike most induction hardened camshafts that are machined first and then hardened, this camshaft is deep hardened first and then machined. Using this process, the beneficial compressive surface residual stresses are extremely high.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;During the development of the L850 camshaft, the casting process was optimized to produce material of sufficient quality to resist quench cracking during the hardening process and to resist mechanical cracking during the machining process. Retained austenite content, residual stress profiles, hardness, microstructure and chemical composition were all characterized and optimized.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper reviews the material and process development for this unique automotive application.&lt;/div&gt;