gebhart/patrepeval huggingface dataset:
Two-tiered keratinocyte assay: IL-18 production by NCTC2544 cells to determine the skin sensitizing capacity and an epidermal equivalent assay to determine sensitizer potency (2012)

At present, the identification of potentially sensitizing chemicals is carried out using animal models. However, it should be very important, both from ethical and economic point of view, to discriminate allergy and irritation events, and to classify sensitizers according to their potency, without the use of animals. The aim of the EU FP6 Integrated Project Sens-it-iv was to develop and optimize an integrated testing strategy consisting of in vitro, human cell based assays which will closely mimic sensitization mechanisms in vivo. These assays should be an alternative approach to the LLNA. The NCTC2544 IL-18 assay can be used to identify the sensitizing capacity of a chemical (NCTC assay, tier 1) while the Epidermal Equivalent potency assay is used to quantify the potency of the sensitizing agent (EE assay, tier 2). These assays combined, may offer an unique opportunity to provide an alternative method to the LLNA. Both assays are based on the use of human keratinocytes, which have been shown, over the last two decades, to play a key role in all phases of skin sensitization. First, 4 known chemicals were tested during a transferability study in which 6 laboratories participated. Three sensitizers (DNCB, resorcinol, PPD) and 1 non sensitizer (lactic acid) were tested in tier 1. DNCB (extreme) and resorcinol (moderate) were ranked according to their potency in tier 2. These assays were successfully transferred to laboratories that did not perform both assays previously. Second, the actual pre-validation was performed with 29 coded chemicals for tier 1 and 13 coded chemicals for tier 2. Currently, all chemicals have been tested and data is collected. After all data has been processed, evaluation of the proposed prediction model will be assessed.
Insights into Stereocomplexation of Poly(lactic acid) Materials: Evolution of Interaction between Enantiomeric Chains and Its Role in Conformational Transformation in Racemic Blends (2022)

Enantiomers alternately packed stereocomplex crystals (SC) compete with homochiral enantiomer-packed homocrystals (HC) during the crystallization of poly(lactic acid) (PLA) racemic blends. However, an intensive understanding of the structural evolution of enantiomeric chains in racemic blends remains challenging because of the narrow time window required for structural evolution. Here, we report the initial conformation evolution and concomitant interaction between the enantiomeric chains in the racemic melt over a wide temperature range using commercial fast-scan chip calorimetry. The results showed that, after cooling the racemic melt at 3,000 K/s, 103 helices always emerged first. The interaction between the enantiomeric chains appeared gradually and triggered the transformation of 103 helices into 31 helices. A comprehensive understanding of the role of the interaction between the enantiomeric chains during the conformation transformation not only provides a physical basis for studying the competition between SC and HC of PLA but also lays a theoretical foundation for the preparation of biodegradable engineering plastics.
GENO-30DISTINCT GENE EXPRESSION PROFILE THAT IS NOT A KNOWN SURVIVAL PREDICTOR IN TUMORS FROM LONG-TERM HIGH GRADE GLIOMA SURVIVORS TREATED WITH A RETROVIRAL REPLICATING VECTOR ENCODING YEAST CYTOSINE DEAMINASE (2015)

A dose escalating clinical study (NCT01985256) using a retroviral replicating vector (RRV), Toca 511, in combination with oral Toca FC (extended-release 5-fluorocytosine [5-FC]) is ongoing to evaluate safety and preliminary efficacy of this investigational therapy in patients with recurrent HGG. Toca 511 (vocimagene amiretrorepvec) encodes a yeast-derived, codon-optimized and heat-stabilized cytosine deaminase (CD) that converts 5-FC to the anti-cancer drug 5-FU in infected tumors. This virus replicates preferentially in malignant tissue and may have wide application in cancer therapies. In the study discussed here, Toca 511 is injected into resection cavity walls at time of tumor resection, and followed with multiple courses of Toca FC. RNA sequencing results in subject tumor samples reveal a unique gene expression profile associated with survival in Toca 511-treated subjects, which may be predictive. RNA expression profiles of resected tumors from 27 subjects were obtained via next-generation sequencing. Quality RNA sequencing results were obtained from two or three spatially distinct pieces of tumor from each subject. Expression profiles from separate regions of the same tumor were generally more similar to each other than to expression profiles of other subjects' tumors, but considerable heterogeneity was observed. A disproportionate number of the subjects that survived greater than one year displayed a unique expression subtype profile in multiple tumor samples that was distinct from normal brain and resembled samples isolated and analyzed in an orthogonal study from non-enhancing regions at the advancing edge of GBM tumors. Expression profiles that tracked with survival in the current study were not in general prognostic in orthogonal primary tumor datasets from TCGA and Rembrandt. These results suggest underlying molecular features and pathological stage of the tumor may help define the ability of Toca 511 and Toca FC therapy to prolong survival. Multivariate analysis using molecular and clinical factors will be presented.
Comparison of the Characteristics of Nanocrystalline Ferrite in Fe-0.89C Steels with Pearlite and Spheroidite Structure Produced by Ball Milling (2002)

Nanocrystalline ferrite formation by ball milling in Fe–0.89C steels with initial pearlite and spheroidite microstructures and their annealing behaviors have been studied through microstructural observation and microhardness measurement. It was found that nanocrystalline ferrite first forms near the surface of powders due to localized severe deformation. The microhardness of nanocrystalline ferrite regions is much higher than that of work-hardening regions. The dissolution of cementite was observed together with the nanocrystallization of ferrite. The nanocrystallization rate of pearlite powder is faster than that of spheroidite powder due to higher work-hardening rate and smaller cementite size. After long time ball milling, the equiaxed nanocrystalline ferrite with less than 10 nm grain size forms in the whole powders of both pearlite and spheroidite structures, and the cementite dissolves completely. By annealing the milled pearlite and spheroidite powders, recrystallization was observed in the work-hardening regions, while continuous grain growth was observed in the nanocrystalline ferrite region. After annealing, microhardness of the former nanocrystalline ferrite region is always higher than that of the former work-hardening region when compared at the same annealing condition. The grain growth rate of nanocrystalline ferrite produced from pearlite structure is lower than that of spheroidite structure due to the finer grains.
Binary Level-Set Shape Optimization Model and Algorithm for Volumetric Modulated Arc Therapy in Radiotherapy Treatment (2013)

We introduce, in this paper, a variational framework for the construction of improved treatment plans in volumetric modulated arc therapy for cancer treatment. This framework consists of a shape optimization component, from the molding of beam shapes, as well as strong constraints, from the equipment involved, on both beam shapes and intensities. We apply the binary level-set method, to handle complex shape topologies, and the fast sweeping method, to handle beam intensity constraints. The result is a fast, flow-based algorithm, in a simplified setting, that guarantees energy decrease. We include numerical simulations of clinical cases to demonstrate the efficacy of the approach.
PROTOPLAST ISOLATION AND CELL DIVISION IN THE AGAR‐PRODUCING SEAWEED <i>GRACILARIA</i> (RHODOPHYTA)<sup>1</sup> (1986)

ABSTRACT Methods were developed for the isolation of large numbers of healthy protoplasts from two species of the agarophyte Gracilaria; G. tikvahiae McLachlan and G. lemaneiformis (Bory) Weber‐van Bosse. This is the first report of protoplast isolation and cell division in a commercially important, phycocolloid‐producing red seaweed, as well as for a member of the Florideophycidae. The optimal enzyme composition for cell wall digestion and protoplast viability consisted of 3% Onozuka R‐10, 3% Macerozyme R‐10, 1% agarase and 0.5% Pectolyase Y‐ 23 dissolved in a 60% seawater osmoticum containing 1.0 M mannitol. The complete removal of the cell wall was confirmed by several different methods, including electron microscopic examination, and the absence of Calcofluor White (for cellulose) and TBO (for sulfated polysaccharide) staining. Spontaneous protoplast fusion was observed on several occasions. Protoplast viability was dependent upon the strain and age of the parent material, as well as the mannitol concentration of the enzyme osmoticum. Cell wall regeneration generally occurred in 2‐6 days; cell division in 5‐10 days. Protoplast‐produced cell masses up to the 16‐32 cell stage have been grown in culture. However, efforts to regenerate whole plants have been unsuccessful to date.
Instabilities of quadratic band crossing points (2011)

Using a functional renormalization-group approach, we study interaction-driven instabilities in quadratic band crossing point two-orbital models in two dimensions, extending a previous study of Sun et al. [Phys. Rev. Lett. 103, 046811 (2009)]. The wave-vector dependence of the Bloch eigenvectors of the free Hamiltonian causes interesting instabilities toward spin-nematic, quantum anomalous Hall, and quantum spin Hall states. In contrast with other known examples of interaction-driven topological insulators, in the system studied here, the quantum spin Hall state occurs at arbitrarily small interaction strength and for rather simple intraorbital and interorbital repulsions.
Is Epinephrine Safe for Infant Digit Excision? A Retrospective Review of 402 Polydactyly Excisions in Patients Younger than 6 Months (2019)

Therapeutic, IV.
Anti-Biofouling Nanoporous Gold Electrodes for Biochemical Sensor Applications (2014)

Within the scope of traumatic brain injury research, the implications of radical oxygen species (ROS) have been a primary interest. The ability to monitor these species cannot only provide a window into the progression of resultant pathology but also assist in therapeutic intervention by detailing the associated ROS insult experienced by the afflicted patient. Formation of protein plaques and aggregates is also associated with traumatic brain injury. These can form a passivation layer on the sensor’s surface leading to bio-fouling, thus limiting or even nullifying the sensitivity. The nano-scale ‘roughness’ of our nanoporous gold (NPG) electrode augments the effective surface area for conduction and is found resistant to bio-fouling. Likely, the proteins are excluded from entering pores due to the constriction of pore sizes, which significantly reduces the sites for protein deposition. NPG and plain gold electrode (PG) were tested in bovine serum albumin and beta amyloid to assess relative biofouling resistivity. The cyclic voltammetry (CV) from BSA incubation shows promise for NPG while PG experiences rapid surface saturation and loss of sensitivity (fig.1). CV was also performed in phosphate buffered saline (PBS) with a well-known redox couple of potassium hexacyanoferrate (HCF). Comparison between the CV measures for each electrode shows the increased conductivity for NPG. The results implicate the dual benefits of using the NPG for electrodes for increased sensitivity and resistance to bio-fouling.
DDDR-14. YAP/TAZ TRANSCRIPTIONAL CO-ACTIVATORS DRIVE NEURO-GLIAL STEM/PROGENITOR CELL IDENTITY IN HIGH GRADE GLIOMAS (2022)

Abstract High-grade gliomas (HGGs), neoplasms derived from neuro-glial stem/progenitor cells, are the most common and lethal malignant primary brain tumors diagnosed in adults and children, with a median survival time of 14 months with current treatments. HGG tumorigenicity is often driven by genetic aberrations in receptor tyrosine kinases (RTKs), such as EGFR, and the Pi-3 kinase (PI3K) signaling pathway. Using Drosophila, mouse, and human HGG model systems of RTK-PI3K mutant HGGs, we identified the YAP and TAZ transcription co-activators, which regulate gene expression via TEAD co-factors, as key drivers of HGG tumorigenicity downstream of oncogenic RTK signaling. YAP and TAZ are highly expressed in RTK-mutant human HGG cells, and regulate TEAD-mediated transcription of several transcription factors, neurodevelopmental genes, and receptors, including the EGFR RTK, that together create a feedforward loop with RTKs to maintain a radial-glia-like stem/progenitor cell fate in HGG cells. Inhibition of YAP and TAZ in self-renewing stem-cell-like RTK mutant HGG cells can inhibit proliferation, block stem/progenitor cell fate, and elicit apoptosis. In particular, the benzoporphyrin derivative verteporfin, a disruptor of YAP/TAZ-TEAD mediated transcription, specifically induced apoptosis of cultured patient-derived HGG cells, suppressed expression of YAP/TAZ transcriptional targets, including RTKs, and conferred significant survival benefit in an orthotopic xenograft HGG model. Our efforts led us to initiate phase 0 and phase 1/2 clinical trials of Visudyne, an FDA-approved liposomal formulation of verteporfin, in which we have verified verteporfin uptake into tumor cells and are now testing the therapeutic efficacy of verteporfin in human patients. Finally, we have examined mechanisms of response and resistance to verteporfin, and we have evidence that stem-like HGG cells can escape the effects of YAP/TAZ inhibition by recapitulating neuro-glial developmental cell fate transitions. Together, our data indicate that targeting YAP/TAZ functionality is a promising therapeutic approach for HGG.
Characterization of Cryogenic Material Properties of 3-D-Printed Superconducting Niobium Using a 3-D Lumped Element Microwave Cavity (2020)

We present an experimental characterization of the electrical properties of 3-D-printed niobium. The study was performed by inserting a 3-D-printed Nb post inside an aluminum cylindrical cavity, forming a 3-D lumped element reentrant microwave cavity resonator. The resonator was cooled to temperatures below the critical temperature of niobium (9.25 K) and then aluminum (1.2 K) while measuring the quality factors of the electromagnetic resonances. This was then compared with finite element analysis of the cavity and a measurement of the same cavity with an aluminum post of similar dimensions and frequency, to extract the surface resistance of the niobium post. The 3-D-printed niobium exhibited a transition to the superconducting state below 9.25 K, as well as a surface resistance of 3.1 ± 0.54 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> Ω. This value was comparable to many samples of traditionally machined niobium previously studied without specialized surface treatment. Furthermore, this study demonstrates a simple new method for characterizing the material properties of a relatively small and geometrically simple sample of the superconductor, which could be easily applied to other materials, particularly 3-D-printed materials. Further research and development in additive manufacturing may see the application of 3-D-printed niobium in not only superconducting cavity designs but also in the innovative technology of the future.
Effective Subject Representation based on Multi-omics Disease Networks using Graph Embedding (2022)

The study of complex behavior of biological systems has become increasingly dependent on evolutionary network modeling. In particular, multi-omics networks capture interactions between biomolecules such as proteins and metabolites, providing a basis for predicting relationships between such biomolecules and various phenotypic traits of complex diseases. In this paper, we introduce an integrative framework that given a multi-omics network representing a cohort of subjects, learns expressive representations for network nodes, and combines the learned nodes representations with the biological profiles of individual subjects for enriched representation of the subjects. With extensive empirical evaluation using real-world multi-omics networks, we show that our proposed framework significantly outperforms existing and baseline methods in terms of subject representation accuracy, particularly when the multi-omics network representing the cohort is sparse and structured and therefore, more informative.
The Influence of Counterion Type and Temperature on Flory‐Huggins Binary Interaction Parameter in Polyelectrolyte Hydrogels (2009)

Abstract The Flory‐Huggins binary interaction parameter and its enthalpy and entropy parts were experimentally determined for polyelectrolyte hydrogels based on poly(acrylic) acid (PAAc) and poly(methacrylic) acid (PMAc) with various mono‐ and divalent counterions. It was shown that water is a poor solvent for acrylic and methacrylic polyelectrolyte hydrogels, as the binary interaction parameter is around 0.8 for mono‐ and 0.6 for divalent counterions. The type of counterion affects the enthalpy‐interaction parameter and according to its increase in PAAc gels, counterions can be placed in the following order: Li + &lt;Ca 2+ &lt;Mg 2+ &lt;TMA + &lt;Na + = K + . For most of the gels studied, the enthalpy interaction parameter was much lower than the entropy contribution. magnified image
Intraductal Papillary Mucinous Neoplasms With Associated Invasive Carcinoma of the Pancreas: Imaging Findings and Diagnostic Performance of MDCT for Prediction of Prognostic Factors (2013)

The purpose of this study was to assess the diagnostic accuracy of MDCT for determining the prognostic factors, including the T category, lymph node metastasis, tumor size, and perineural invasion, in surgically proven intraductal papillary mucinous neoplasms (IPMNs) with an associated invasive carcinoma (IPMC) and to investigate the imaging findings.Our study group consisted of 38 patients with surgically proven IPMC who underwent preoperative dynamic CT. Two radiologists retrospectively assessed the morphologic type of IPMN, size of the cyst, size of the main pancreatic duct, and presence or absence of mural nodules. The radiologists also assessed the T category, lymph node metastasis, and perineural invasion. They graded the perineural invasion using a 3-point scale as follows: 1, normal; 2, streaky and strandlike structure in fat tissue as well as a fine, reticular pattern; and 3, irregular masses adjacent to the lesions. Statistical analyses were performed using receiver operating characteristic analysis, the McNemar test, and Fisher exact test. Kappa statistics were used to determine interobserver agreement.The morphologic types of IPMC included the main-duct type (n=11, 29%), combined type (n=18, 47%), and branch-duct type (n=9, 24%). The diagnostic accuracy for the T category was 73.7% (n=28) and 68.4% (n=26) and for the lymph node metastasis was 68.4% (n=26) and 76.3% (n=29), respectively, for the two readers, with moderate interobserver agreement (κ=0.636 and 0.708). The areas under the receiver operating characteristic curve for perineural invasion were 0.868 and 0.821. The sensitivity, specificity, and positive predictive value were 100%, 71.4%, 55.5%, and 90%, 71.4%, 52.9%, respectively. Interobserver agreement was moderate (κ=0.659). The tumor size seen on CT was not statistically different from the tumor size determined on pathology (3.9±[SD] 2.7 cm vs 3.8±2.1 cm, p=0.582). The main duct size was 11.5+6.2 mm. Mural nodules were detected in 74% (n=28) of our study patients.CT might be useful for preoperatively evaluating the T category, lymph node metastasis, tumor size, and perineural invasion of IPMC. Main pancreatic duct dilatation and the presence of mural nodules are common findings of IPMC.
A three-gene predictor for early intrahepatic recurrence of hepatocellular carcinoma after curative hepatectomy (2008)

We previously developed a DNA microarray-based system that out-performs traditionally used clinical parameters for prediction of early intrahepatic recurrence (IHR) of hepatocellular carcinoma (HCC). Because DNA microarray is too expensive for daily clinical use, we used a quantitative real-time reverse transcription-polymerase chain reaction (QRT-PCR) to develop a lower-cost predictor for early IHR. From the 12 early IHR-related genes integrated in the previous predictor, we selected 6 genes whose levels showed the strongest association between data from the 2 distinct DNA microarray platforms with the same sample set. Expression of these 6 genes relative to that of GAPDH was measured by QRT-PCR in 82 HCCs. Of the 82 HCCs, 39 and 43 were assigned to training and independent test sets, respectively. By searching all combinations (n=2-6) of the 6 genes, we found an optimal combination of 3 genes (HLADRA, DDX17 and LAPTM5) that minimized the leave-one-out error for prediction of early IHR in the training set. The 3-gene predictor constructed with the Fisher linear classifier correctly predicted early IHR or non-recurrence in 35 (81.4%) of 43 HCCs in the independent test set and had a high positive predictive value of 72.7% and a high negative predictive value of 84.4%. Multivariate analysis with the stepwise logistic regression showed that the 3-gene predictor [F(x)<0] was an independent risk factor for early IHR (risk ratio, 13.6; p=0.006), indicating its potential as an easy-to-use predictor for accurate prediction of early IHR of HCC.
Assessment of the<i>Brettanomyces bruxellensis</i>metabolome during sulphur dioxide exposure (2013)

Brettanomyces bruxellensis displays a high degree of genotypic and phenotypic polymorphism and is the main yeast species involved in wine spoilage. The innate resistance of 108 B. bruxellensis strains to the antimicrobial agent SO2 used in winemaking was investigated. Nineteen strains (17.6%) were sensitive to SO2 , failing to grow at the lowest concentration tested (0.1 mg L(-1) molecular SO2). Twenty-nine strains (26.8%) grew at 0.1 mg L(-1), 42 strains (38.9%) grew at 0.2 mg L(-1) , and 16 strains (14.8%) were able to grow as high as 0.4 mg L(-1) mol. SO2. Two strains able to grow in the presence of 0.6 mg L(-1) mol. SO2 were further studied by GCMS-TOF analysis to define the metabolic response to SO2 treatment. Two hundred and fifty-three intracellular metabolites were detected. The main effect observed was a decrease in cytoplasmic levels of polyols and an increase in levels of some amino acids, alanine, glutamic acid, glycine, proline, 5-oxoproline, serine and valine, which were significantly accumulated in the presence of SO2. No alteration in the pentose phosphate pathway was observed, suggesting NADPH usage could be diverted to other pathways. Finally, a change in metabolites involved in the glycerophospholipid pathway (glycerol-3-phosphate and myo-inositol) was also found.