gebhart/patrepeval huggingface dataset:
The landscape of genomic alterations across childhood cancers (2018)

Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
Bit Cost Scalable (BiCS) technology for future ultra high density memories (2013)

We proposed Bit Cost Scalable (BiCS) technology in 2007 as a three-dimensional memory for the future ultra high density storage devices, which extremely reduce the bit costs by vertically stacking memory arrays with punch and plug process. We've applied it to just NAND flash, which is BiCS Flash memory, and established the mass production technology. Moreover, we can apply the BiCS technology to various memories. The critical issues and the comparison among various 3D NAND Flash-type memories are to be discussed, as well.
Aberrant Expression of Connexin 26 Is Associated with Lung Metastasis of Colorectal Cancer (2008)

These findings suggest that aberrant expression of Cx26 plays an essential role in lung metastasis. Thus, Cx26 is a promising therapeutic target, particularly for CRC patients who develop lung metastasis.
Minimum Void Size and 3-Parameter Lognormal Distribution for EM Failures in Cu Interconnects (2006)

Broad failure time distributions were observed for line depletion electromigration in Cu interconnects for various structures without sufficient liner contact and via redundancy. The root cause for this behavior was identified as the sensitivity of failure times to the void size, shape and location. Application of the traditional 2-parameter lognormal distribution model to corresponding stress data often results in very pessimistic EM lifetime projections. A 3-parameter lognormal distribution was found not only to fit the experimental data better, especially for the early portion of the failure time distributions, but also to generate more accurate lifetime projections for void-size-limited EM. Given the nature of EM wear-out, deeper consideration indicates that a 3-parameter lognormal distribution has a sounder physical basis than a 2-parameter lognormal distribution. The new parameter introduced in the model, the minimum failure time (X <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0 </sub> ), scales with via size over several technology generations, further validating the minimum void size explanation
Surgical delivery of drug releasing poly(lactic-co-glycolic acid)/poly(ethylene glycol) paste with in vivo effects against glioblastoma (2014)

Chemotherapy loaded PLGA/PEG paste seems to be a promising technology capable of delivering active drugs into partially resected tumours. The preliminary results of this study suggest efficacy with no toxicity and will lead to larger scale efficacy studies in orthotopic glioblastoma models.
Global Profiling of Reactive Oxygen and Nitrogen Species in Biological Systems (2011)

Herein we describe a high-throughput fluorescence and HPLC-based methodology for global profiling of reactive oxygen and nitrogen species (ROS/RNS) in biological systems. The combined use of HPLC and fluorescence detection is key to successful implementation and validation of this methodology. Included here are methods to specifically detect and quantitate the products formed from interaction between the ROS/RNS species and the fluorogenic probes, as follows: superoxide using hydroethidine, peroxynitrite using boronate-based probes, nitric oxide-derived nitrosating species with 4,5-diaminofluorescein, and hydrogen peroxide and other oxidants using 10-acetyl-3,7-dihydroxyphenoxazine (Amplex® Red) with and without horseradish peroxidase, respectively. In this study, we demonstrate real-time monitoring of ROS/RNS in activated macrophages using high-throughput fluorescence and HPLC methods. This global profiling approach, simultaneous detection of multiple ROS/RNS products of fluorescent probes, developed in this study will be useful in unraveling the complex role of ROS/RNS in redox regulation, cell signaling, and cellular oxidative processes and in high-throughput screening of anti-inflammatory antioxidants.
Photonic crystal nanocavity with a Q factor exceeding eleven million (2017)

Photonic crystal nanocavities that simultaneously possess small modal volumes and high quality (Q) factors have opened up novel research areas in photonics during this decade. Here, we present an important key for the increase of Q factors to ranges beyond ten million. A systematic investigation on photon lifetimes of air-bridge-type heterostructure nanocavities fabricated from silicon on insulator (SOI) substrates indicated the importance of cleaning the bottom side (buried oxide side) of the nanaocavites. Repeated thermal oxidation and an oxide removal process applied after the removal of the buried oxide layer underneath the nanocavities realized an experimental Q factor greater than eleven million, which is the highest experimental Q ever recorded. The results provide important information not only for Si PC nanocavities but also for general Si nanophotonic devices and photonic electronic convergence systems.
Synthesis of thyroid hormone analogues. Part 2. Oxidative coupling approach to SK&F L-94901 (1988)

A synthesis of L-3,5-dibromo-3′-[(6-oxo-l,6-dihydropyridazin-3-yl)methyl]thyronine-SK&F L-94901 (1), a novel, selective and potent thyromimetic – is described. The key step in this synthesis involves the formation of a hindered diaryl ether moiety. This paper describes an approach via oxidative coupling of the hindered phenols (2) and (3). Some by-products and impurities generated during the synthesis are discussed briefly.
Predictive Analytics for Business Processes in Service Management (2015)

Underlying business processes in service management are people intensive and collaborative by nature. We are observing an emerging trend in the service management applications, moving away from rigid process orchestration to leveraging collaboration. Such solutions allow staffers to define their own customized, ad-hoc step flow consisting of the sequence of the activities necessary to handle a service component. These ad-hoc steps introduce uncertainty to the successful completion of a service request. When there is uncertainty, predictive guidance about future outcomes could provide value to the workers handling a time-sensitive service delivery component. Predicting the future outcomes using machine-learning techniques requires effective representation of the process execution traces. This is challenging when process model includes parallel execution flows or repeated executions of some activities. In this chapter, we describe algorithms for training machine learning models when the execution paths include parallel flows and when some activities are repeatedly executed.
Ennoblement of Type 316L Coupled with Dissimilar Metal in Chlorinated Seawater (2001)

Abstract This paper describes the case of localized corrosion of type 316L thermo-wells installed in a seawater cooling system of a power plant. Susceptibility to localized corrosion of type 316L in biocide-treated seawater service is discussed with respect to dissimilar metal coupling with titanium. Titanium ennobled in chlorinated seawater has shifted the corrosion potential of type 316L to its pitting potential. A shock dosage has ennobled titanium remarkably while low concentration of chlorine has not increased the potential of titanium. The ennobled potential of titanium induced by such shock dosage has been maintained even the chlorine level was lowered to as low as 1.6 ppm. In order to prevent ennoblement of titanium condenser tubes after a shock dosage, interruption of continuous chlorination is required to prevent localized corrosion of type 316L.
Machine Learning-Based Edge Placement Error Analysis and Optimization: A Systematic Review (2022)

As the semiconductor manufacturing process is moving towards the 3 nm node, there is a crucial need to reduce the edge placement error (EPE) to ensure proper functioning of the integrated circuit (IC) devices. EPE is the most important metric that quantify the fidelity of fabricated patterns in multi-patterning processes, and it is the combination of overlay errors and critical dimension (CD) errors. Recent advances in machine learning have enabled many new possibilities to improve the performance and efficiency of EPE optimization techniques. In this paper, we conducted a survey of recent research work that applied machine learning/ deep learning techniques for the purposes of enhancing virtual overlay metrology, reducing overlay error, and improving mask optimization methods for EPE reduction. Thorough discussions about the objectives, datasets, input features, models, key findings, and limitations are provided. In general, the results of the review work show a great potential of machine learning techniques in aiding the improvement of EPE in the field of semiconductor manufacturing.
A Case Study: Construction of Bucket Foundations for Jackup Ships (2013)

Jackup ships are built to transport wind turbines foundation between offshore logistics center and the installation site. It require sufficiently stable seabed next to quay walls. Otherwise jackup processes may reduce the stability of the quay wall and remained footprints of the legs could induce unsafe jackup procedures in the future. Foundations have been planned to improve the strength of seabed in front of the quay wall. The numerical analyses of the penetration/extraction processes of the legs into/out of the foundations were presented in OMAE2011-49928 to study the bearing capacity of two foundation designs (open-ended cylinder and bucket foundation). In consequence of the numerical studies, the bucket foundation was selected and was improved by reduction the height of the foundations and adjust the inclination of the inner wall to reduce the construction costs. Four bucket foundations have been built in Bremerhaven, Germany. This paper provided of a resume of design, construction and set-up process. The penetration and extraction processes of the jackup legs were tested the results were compared with the numerical predictions.
Styrene oxide as a stereochemical probe for the mechanism of aralkylation at different sites on guanosine (1988)

The stereochemistry at the alpha-carbon atom of the styrene moiety in styrene oxide-guanosine products was established, and the stereochemical consequences of reaction of optically active styrene oxide with guanosine were investigated. Inversion of stereochemistry in products at the alpha-carbon of styrene oxide decreased in the sequence 7- much greater than N2- greater than O6-substituted guanosines. These findings show that an extensively ionized substrate is needed for reaction at the exocyclic N2 and O6 sites on guanosine but that the reactive intermediate is not an ideal planar trigonal carbonium ion. This follows because inversion exceeds retention in both of the exocyclic substituted products.
Sports hip injuries: assessment and management. (2013)

Over the past 10 years, the understanding, assessment, and management of hip pain and injuries in the athlete have improved. Traditionally, the evaluation of hip pain and injuries was limited to obvious disorders, such as hip arthritis and fractures, or disorders that were previously considered to be simply soft-tissue strains and contusions, such as groin pulls, hip pointers, and bursitis. Two parallel tracks of progress have improved understanding of the complexities of hip joint athletic injuries and the biomechanical basis of early hip disease. In the field of sports medicine, improved diagnostic skills now allow better interpretation of debilitating intra-articular hip disorders and their effects on core performance. In the field of hip preservation, there has been an evolution in understanding the effects of biomechanical mismatches between the femoral head and the acetabulum on the development of early hip damage, injury, and arthritis. The integration of these two parallel fields has accelerated the understanding of the importance of hip biomechanics and early hip injury in human performance and function.
Detecting changes in a semi-structured business process through spectral graph analysis (2011)

Semi-structured business processes are emerging at a rapid pace in industries such as government, insurance, banking and healthcare. The workflows underlying these case-oriented processes are non-deterministic. They are mostly driven by human decision making and content status and they may change frequently depending on factors such as economic conditions, legislative policy changes and technological upgrades. This paper describes a method to detect changes in a running business process by conducting spectral graph analysis of sets of execution traces of the process. This method is beneficial because it does not require mining a process model of the business process, and is consequently independent of any assumptions about the nature of the business process. This makes it particularly applicable to case-oriented semi-structured business processes whose lifecycle is not fully driven by a formal process model. In this paper we present our algorithm for computing graph spectra from business process execution traces, and discuss some initial promising results, as well as exciting ideas generated by this research for future work.
Pectic Galactan Polysaccharide‐Based Gene Delivery System for Targeting Neuroinflammation (2021)

Abstract Treating neuroinflammation‐related injuries and disorders through manipulation of neuroinflammation functions is being heralded as a new therapeutic strategy. In this study, a novel pectic galactan (PG) polysaccharide based gene therapy approach is developed for targeting reactive gliosis in neuroinflammation. Galectin‐3 (Gal‐3) is a cell protein with a high affinity to β‐galactoside sugars and is highly expressed in reactive gliosis. Since PG carries galactans, it can target reactive gliosis via specific carbohydrate interaction between galactan and Gal‐3 on the cell membrane, and therefore can be utilized as a carrier for delivering genes to these cells. The carrier is synthesized by modifying quaternary ammonium groups on the PG. The resulting quaternized PG (QPG) is found to form complexes with plasmid DNA with a mean diameter of 100 nm and have the characteristics required for targeted gene therapy. The complexes efficiently condense large amounts of plasmid per particle and successfully bind to Gal‐3. The in vivo study shows that the complexes are biocompatible and safe for administration and can selectively transfect reactive glial cells of an induced cortical lesion. The results confirm that this PG‐based delivery system is a promising platform for targeting Gal‐3 overexpressing neuroinflammation cells for treating neuroinflammation‐related injuries and neurodegenerative diseases.
Synthesis of a novel amphiphilic porphyrin carrying water-soluble polyether side chains of controlled chain length. Formation of a cofacial molecular assembly in aqueous media (1988)

A novel amphiphilic porphyrin carrying poly(oxyethylene) side chains of controlled chain length was obtained by polymerization of epoxyethane initiated by an aluminium porphyrin [(5,10,15,20-tetraphenylporphyrinato)-aluminium chloride] in the presence of a porphyrin with phenolic substituents [5,10,15,20-tetrakis(4′-hydroxyphenyl)porphyrin], and was found to form cofacial aggregates spontaneously in aqueous media.
Protease inhibitors α1‐antitrypsin and ilomastat are not ototoxic in the chinchilla (2003)

Protease inhibitors that are currently under study in animal models and humans for the treatment of inflammatory diseases that are related to imbalances between protease and protease inhibitor have no significant toxic effect on the inner ear of chinchillas. These findings support the safety of further clinical trials using these inhibitors to treat middle ear inflammation.
Electrical Properties of the Near-Surface Earth (2020)

The electrical properties of the near-surface Earth depend on the chemical properties of the fluids filling pores, grain size, the geometry of the interconnected pore network and mineralogy of the solids. We first describe how electrical resistivity depends on the ionic composition of an electrolyte. We next discuss the controls on the resistivity of a porous medium. We start with Archie’s laws and summarize the development of the parallel conduction model used to incorporate surface conduction at the solid–fluid interface. We describe how the induced polarization (IP) effect in the case of a non-electronically conducting matrix is incorporated into the parallel conduction model through a complex surface conductivity. Models to describe the frequency dependence of resistivity in terms of a distribution of polarization length-scales, e.g. grain sizes or pore sizes, are reviewed. We discuss models to describe the mechanisms causing the large polarization enhancement observed in the presence of electronically conducting minerals and show how IP parameters are, in this case, related to the volume and size of the electronically conducting particles. We finish by considering the role of contaminants in modifying electrical properties of near surface materials and briefly consider the possibility of non-linear effects in measurements.
Erratum: Increased neutrophil-lymphocyte ratio is a poor prognostic factor in patients with primary operable as well as inoperable pancreatic cancer (2013)

Correction to: British Journal of Cancer (2013) 109, 416–421. doi:10.1038/bjc.2013.332 Owing to an error during final correction and data submission to PubMed, two of the author names (AL Ress and W AlZoughbi) were incorrectly presented in PubMed and on the BJC website upon publication in Volume 109, Issue 2 of the Journal.
ADMoE: Anomaly Detection with Mixture-of-Experts from Noisy Labels (2022)

Existing works on anomaly detection (AD) rely on clean labels from human annotators that are expensive to acquire in practice. In this work, we propose a method to leverage weak/noisy labels (e.g., risk scores generated by machine rules for detecting malware) that are cheaper to obtain for anomaly detection. Specifically, we propose ADMoE, the first framework for anomaly detection algorithms to learn from noisy labels. In a nutshell, ADMoE leverages mixture-of-experts (MoE) architecture to encourage specialized and scalable learning from multiple noisy sources. It captures the similarities among noisy labels by sharing most model parameters, while encouraging specialization by building "expert" sub-networks. To further juice out the signals from noisy labels, ADMoE uses them as input features to facilitate expert learning. Extensive results on eight datasets (including a proprietary enterprise security dataset) demonstrate the effectiveness of ADMoE, where it brings up to 34% performance improvement over not using it. Also, it outperforms a total of 13 leading baselines with equivalent network parameters and FLOPS. Notably, ADMoE is model-agnostic to enable any neural network-based detection methods to handle noisy labels, where we showcase its results on both multiple-layer perceptron (MLP) and the leading AD method DeepSAD.
Evaluation of invariant models for dolphin photo-identification (2002)

Individual identification of dolphins is of much interest to marine mammologists. Natural markings and notches on the trailing edge of the dorsal fin provide an almost unique signature within a study population for individual recognition. The dorsal fin is an almost rigid, planar object, and, as a result, the problem boils down to planar curve matching. Invariants under three groups of similarity, affine and projective transformations are examined in this paper. Three families of differential, algebraic and semi-differential invariants are studied and evaluated for their applicability and performance in dolphin identification from photographs. It is observed that, under practical conditions, for smooth quasi-rigid curves like the trailing edge of the dorsal fin, curvature-based matching methods outperform almost all of the other techniques which offer a higher level of invariance.
Differential processing of osteopontin transcripts in rat kidney- and osteoblast-derived cell lines. (1992)

Using immunoprecipitation and tryptic peptide microsequencing we confirmed the identity of normal rat kidney (NRK) cell-secreted 69-kDa major phosphoprotein as osteopontin (OP). We then immunoselected a 1.4-kilobase pair (kb) OP cDNA from a lambda gt11 library prepared from Kirsten sarcoma virus-transformed NRK (KNRK) cellular mRNA, using rabbit anti-69-kDa OP serum. Sequence analysis of this cDNA revealed the presence of a 52-nucleotide-long insert in the 5'-noncoding region, which was absent in OP cDNA cloned from the cDNA library of ROS 17/2.8 rat osteosarcoma cells. The insert sequence is flanked by putative intron splice junctions and is located 15-nucleotide upstream of the translational initiation site. An insert-specific 30-mer oligonucleotide probe hybridized to a single 1.5-kb RNA species from both NRK and KNRK cells, but not from ROS 17/2.8 cells. However, Southern analysis showed the presence of this insert sequence in the genomic DNA of both NRK and ROS 17/2.8 cells. Furthermore, PCR amplification of the insert-containing region using genomic DNAs from both NRK and ROS 17/2.8 cells gave products of identical size and sequence. Since OP is a single copy gene, these data provide strong evidence for differential cell type-specific processing of OP transcripts. In addition, we demonstrate that, in contrast to most transformed cells, levels of OP expression are significantly reduced in KNRK cells as compared to NRK cells.
Serologic and molecular characterization of a human monoclonal rheumatoid factor derived from rheumatoid synovial cells (1990)

Molecular characterization of rheumatoid factors (RF) in rheumatoid arthritis (RA) has been hampered because of their polyclonality. To overcome this problem, we generated monoclonal RF-secreting hybridomas from rheumatoid synovial cells. Among the RF-secreting hybridomas, HAF10 secreted an IgM-RF that was monospecific for human IgG. It bound well to IgG1 and IgG2, but not to IgG3 and IgG4. Sequence analysis of its heavy and light chains showed that it contained a VH1 heavy chain and a V lambda light chain that did not belong to any known lambda light chain subgroup, and therefore, probably represented a new lambda subgroup. These results indicated that both the heavy and light chains of a monoclonal IgM-RF from rheumatoid synovial cells were quite different from the reported variable region sequences of several monoclonal RF derived mainly from patients with mixed cryoglobulinemia. Further studies of additional monoclonal RF from RA patients are warranted to define precisely their genetic basis and to further our understanding of the immunopathology of RA.