gebhart/patrepeval huggingface dataset:
A Cross-Disciplinary Outlook of Directions and Challenges in Industrial Electronics (2022)

How to build a sustainable society in view of industrial electronics has been discussed from energy, information and communication technologies, cyber-physical systems (CPSs), and other viewpoints. This paper presents a cross-disciplinary view that integrates the fields of human factors, professional education, electronic systems on chip, resilience and security for industrial applications, technology ethics and society, and standards. After explaining the efforts and challenges in these fields, this paper shows a methodology for cross-disciplinary technology that integrates the technical committees in Cluster 4, Industrial Electronics Society. A project, which was launched in March 2020, implements a &#x2018;Proof of Concept&#x2019; trial of the methodology.
Winter Meeting. Abstracts of the 211th Meeting of the Pathological Society of Great Britain & Ireland, 22–23 January 2019, London (2019)

Pathological diagnosis of brain tumours has become increasingly dependent on the molecular characteristics of each case. In the 2016 WHO CNS Tumour Classification, key molecular changes were formally incorporated as defining features of some diagnostic entities for the first time. Designations such as Diffuse midline glioma, H3K27M mutant and Medulloblastoma, SHH activated, TP53 mutated embody this new diagnostic reality. While the incorporation of molecular data allows for greater precision, issues with implementing the current classification scheme on a day to day basis, as well as accounting for the rapid ongoing changes in molecular understanding, pose significant challenges. The goal of this presentation is to summarize these recent changes, to review emerging disruptive technologies such as methylation profile based tumour classification, and to introduce new international efforts such as the cIMPACT-NOW consortium which seek to provide ongoing guidance.
Photon count imaging using an extremely small capacitor and a high-precision low-noise quantizer (2003)

This paper presents a method of low light imaging using an extremely small capacitor for charge detection in a CMOS image sensor and a high-precision low-noise analog-to-digital converter. A condition for photon counting is that the charge-to-voltage conversion gain is much higher than the root mean square (rms) random noise of the readout circuits. The other condition is that the quantization step of the A/D converter is chosen to be the same as the conversion gain or the amplified conversion gain if the pixel output is further amplified. Simulation results show that if the rms random noise is reduced to one-sixth of the conversion gain, the 10 times digital integration without the noise increase is possible. This means that even if a very small charge detection capacitor and a relative small power supply voltage are used, a sufficient dynamic range can be achieved by the digital integration without noise increase.
Inter-homologue repair in fertilized human eggs? (2017)

Many human diseases have an underlying genetic component. The development and application of methods to prevent the inheritance of damaging mutations through the human germline could have significant health benefits, and currently include preimplantation genetic diagnosis and carrier screening. Ma et al. take this a step further by attempting to remove a disease mutation from the human germline through gene editing 1 . They assert the following advances: (i) the correction of a pathogenic gene mutation responsible for hypertrophic cardiomyopathy in human embryos using CRISPR-Cas9 and (ii) the avoidance of mosaicism in edited embryos. In the case of correction, the authors conclude that repair using the homologous chromosome was as or more frequent than mutagenic nonhomologous end-joining (NHEJ). Their conclusion is significant, if validated, because such a “self-repair” mechanism would allow gene correction without the introduction of a repair template. While the authors’ analyses relied on the failure to detect mutant alleles, here we suggest approaches to provide direct evidence for inter-homologue recombination and discuss other events consistent with the data. We also review the biological constraints on inter-homologue recombination in the early embryo.
HybridSDF: Combining Deep Implicit Shapes and Geometric Primitives for 3D Shape Representation and Manipulation (2022)

Deep implicit surfaces excel at modeling generic shapes but do not always capture the regularities present in manufactured objects, which is something simple geometric primitives are particularly good at. In this paper, we propose a representation combining latent and explicit parameters that can be decoded into a set of deep implicit and geometric shapes that are consistent with each other. As a result, we can effectively model both complex and highly regular shapes that coexist in manufactured objects. This enables our approach to manipulate 3D shapes in an efficient and precise manner.
Frequency effects in protoplast dielectrophoresis (1986)

Abstract Pea protoplast dielectrophoretic coefficients were measured in AC fields of different frequencies applied between concentric cylindrical metal electrodes, outer and inner radii, 0.24 mm and 1 mm, respectively. The values for 0.5 M mannitol solutions are: (6.0, 1.0, 5.6, 16.0 and 17.8) X 10 −24 Fm 2 at frequencies 0.05, 0.1, 0.6, 1 and 8 MHz, respectively. The specific polarizabilities (dielectrophoretic coefficients per unit volume of the protoplasts) are: (5.0, 0.7, 4.0, 12.0 and 13.0) X 10 −10 Fm −1 , respectively. Below 10 kHz dielectrophoretic effects were not observed. Cell rotation was observed in the frequency range from 1 kHz to 10 kHz. These results may be of use in cell separation and electrofusion in scientific research and technology.
High-speed visible light communication systems (2013)

This article presents recent achievements and trends in high-speed indoor visible light communication (VLC) research. We address potential applications and future visions for the VLC technology, where transport of information is “piggybacked” on the original lighting function of LED-based lamps. To mature this technology and transfer it into practice, our recent research is focused on real-time implementation and trials. For the first time, a bidirectional real-time VLC prototype achieving data rates of up to 500 Mb/s is presented. This system paves the way for future real world applications. Finally, we discuss the remaining technical challenges as well as the research outlook in the field of high-speed VLC systems.
Delay guaranteed bandwidth allocation for real-time video delivery (2004)

Variable bit rate (VBR) video traffic exhibits high burstiness and long range dependence properties, which, in conjunction with the stringent quality of service (QoS) requirements, pose a great challenge in transporting video traffic over a communication network. The authors propose a QoS guaranteed bandwidth allocation for a given resource utilisation. Simulation and analytical results demonstrate that this scheme provides guaranteed delay and achieves high bandwidth utilisation.
NetVista: Growing an Internet solution for schools (1998)

NetVista™ is an integrated suite of clients and servers supporting Internet access for students and teachers in kindergarten through 12th-grade schools. Developed by a small team of IBM researchers, NetVista is a prime example of using an object-oriented framework to support user-centered design and to accommodate Internet-paced changes in network infrastructure, functionality, and user expectations. In this paper, we describe salient aspects of NetVista's design and development and its evolution from research project to product. In particular, we discuss the factors supporting a sustained focus on end users over the life of the project, the object-oriented framework underlying NetVista, and the role of this framework in accommodating both evolutionary and radical changes to the design of the user interface and the underlying technical infrastructure.
Two Genes Required for Cell Fusion During Yeast Conjugation: Evidence for a Pheromone-Induced Surface Protein (1987)

We characterized two genes, FUS1 and FUS2, which are required for fusion of Saccharomyces cerevisiae cells during conjugation. Mutations in these genes lead to an interruption of the mating process at a point just before cytoplasmic fusion; the partition dividing the mating pair remains undissolved several hours after the cells have initially formed a stable "prezygote." Fusion is only moderately impaired when the two parents together harbor one or two mutant fus genes, and it is severely compromised only when three or all four fus genes are inactivated. Cloning of FUS1 and FUS2 revealed that they share some functional homology; FUS1 on a high-copy number plasmid can partially suppress a fus2 mutant, and vice versa. FUS1 remains essentially unexpressed in vegetative cells, but is strongly induced by incubation of haploid cells with the appropriate mating pheromone. Immunofluorescence microscopy of alpha factor-induced a cells harboring a fus1-LACZ fusion showed the fusion protein to be localized at the cell surface, concentrated at one end of the cell (the shmoo tip). FUS1 maps near HIS4, and the intervening region (including BIK1, a gene required for nuclear fusion) was sequenced along with FUS1. The sequence of FUS1 revealed the presence of three copies of a hexamer (TGAAAC) conserved in the 5' noncoding regions of other pheromone-inducible genes. The deduced FUS1 protein sequence exhibits a striking concentration of serines and threonines at the amino terminus (46%; 33 of 71), followed by a 25-amino acid hydrophobic stretch and a predominantly hydrophilic carboxy terminus, which contains several potential N-glycosylation sites (Asn-X-Ser/Thr). This sequence suggests that FUS1 encodes a membrane-anchored glycoprotein with both N- and O-linked sugars.
Utilizing Electronic Health Records to Predict Acute Kidney Injury Risk and Outcomes: Workgroup Statements from the 15th ADQI Consensus Conference (2016)

The data contained within the electronic health record (EHR) is "big" from the standpoint of volume, velocity, and variety. These circumstances and the pervasive trend towards EHR adoption have sparked interest in applying big data predictive analytic techniques to EHR data. Acute kidney injury (AKI) is a condition well suited to prediction and risk forecasting; not only does the consensus definition for AKI allow temporal anchoring of events, but no treatments exist once AKI develops, underscoring the importance of early identification and prevention. The Acute Dialysis Quality Initiative (ADQI) convened a group of key opinion leaders and stakeholders to consider how best to approach AKI research and care in the "Big Data" era. This manuscript addresses the core elements of AKI risk prediction and outlines potential pathways and processes. We describe AKI prediction targets, feature selection, model development, and data display.
Adenovirus mediated gene transfer to skeletal muscle (2002)

Transfer of therapeutic genes into muscle tissue has promise for the treatment of a variety of muscular dystrophies. Various vectors have been used to deliver genes to skeletal muscle but their application has faced several major limitations including: (1) the lack of transgene persistence caused by the immune rejection of transduced myofibers and/or vector toxicity, and (2) the maturation dependence of viral transduction. While the immunorejection and/or cytotoxic problems are being overcome with the development of new vectors, maturation-dependent viral transduction is still a major hurdle in gene transfer to skeletal muscle. Poor adenoviral transduction in mature myofibers has been attributed to: (1) the extracellular matrix of mature myofibers may form a physical barrier and prevent the passage of large viral particles; (2) viral receptors are down-regulated with muscle maturation; and (3) loss of myoblasts with muscle maturation, which serve as intermediaries in the viral transduction. In this review, we will focus on recent developments in overcoming those hurdles of gene therapy in skeletal muscle, especially to adenovirus (Ad), including: (1) new mutant vectors lacking all viral genes to decrease immunogenicity, and hence, improve persistence of transgene expression in muscle in vivo; (2) using tissue specific promoters to evade immunorejection; (3) permeabilization of the extracellular matrix; (4) modifying the viral receptors in mature myofibers; and (5) myoblast or muscle stem cell mediated ex vivo gene transfer.
Glial Cell Reactions in Neurodegenerative Diseases Pathophysiology and Therapeutic Interventions (1998)

A variety of proteins known to be involved in inflammatory processes are associated with lesions in chronic neurodegenerative disorders such as Alzheimer disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). This is particularly true of AD, in which inflammatory reactions are believed to be important contributors to the neuronal loss. Inflammatory proteins associated with AD include complement proteins, complement inhibitors, acute-phase reactants, inflammatory cytokines, proteases, and protease inhibitors. Studies of cultured human astro-cytes and microglia obtained from postmortem brain have established that almost all of these proteins are produced by one or the other of these two cell types. Human neurons also produce many inflammatory proteins and their inhibitors, creating complex interactions. Accumulations of amyloid, extracellular tangles, or Lewy bodies apparently act as irritants, causing the activation of complement, the initiation of reactive changes in microglia, and the release of potentially neurotoxic products such as the membrane attack complex, oxygen free radicals, and excess glutamate. A number of epidemiologic studies indicate that populations taking anti-inflammatory drugs have a sharply reduced prevalence of AD. One small clinical trial with indo-methacin showed arrest of the disease over a 6-month period. Therapeutic intervention in key inflammatory processes holds great promise for the amelioration of AD and possibly other neurodegenerative disorders.
Reducing teaching hours, increasing wellbeing? (2020)

Dear EditorWe recently read a case study by Choi-Lundberg et al. (2020) and were particularly drawn by the observation that a 14% reduction in teaching hours produced minimal impact on students’ ex...
Molecular Lesions Of Signalling Pathway Genes In Indolent B-Cell Lymphoproliferations Mimicking Splenic Marginal Zone Lymphoma (2013)

Abstract Background Almost 60% cases of splenic marginal zone lymphoma (SMZL) cases harbor molecular lesions affecting signalling pathways involved in normal marginal zone (MZ) differentiation, including the NOTCH pathway, the NF-kB pathway, the toll-like receptor (TLR) pathway and the B-cell receptor (BCR) pathway. However, little is known with regard to these lesions in other indolent B-cell lymphoproliferative disorders mimicking SMZL. Methods Candidate gene mutations (NOTCH2, NOTCH1, BIRC3, TNFAIP3, TRAF3, IKBKB, MYD88, CD79A, CD79B, CARD11) were investigated in 60 indolent B-cell lymphoproliferative disorders, including nodal marginal zone lymphoma (NMZL=33), monoclonal B-cell lymphocytosis showing a MZL-like phenotype (MZL-like MBL=16), and variant hairy cell leukemia (vHCL=11). In all cases, tumor representation was &gt;50% in order to allow the detection of clonal lesions. All cases lacked the BRAF V600E mutation as assessed by AS-PCR. Results Overall, the genetics of NMZL and MZL-like MBL was consistent with that of SMZL, suggesting the involvement of a common oncogenic pathway in these disorders. Among NMZL, 51% (17/33) of cases were characterized by mutually exclusive genetic lesions affecting MZ differentiation genes, including NOTCH2 stabilizing mutations in 24% (8/33) of cases, TNFAIP3 disrupting mutations in 12% (4/33), MYD88 activating mutations in 12% (4/33), and NOTCH1, TRAF3 and BIRC3 mutations in 3% (1/33) of cases each. Among MZL-like MBL, 37% (6/16) of cases harbored mutually exclusive lesions of MZ genes, including MYD88 mutations in 25% (4/16) of cases, NOTCH2 mutations in 12% (2/16), and TNFAIP3 and CD79B mutations in 6% (1/16) of cases each. On the contrary, all cases (n=11) of vHCL lacked mutations of NOTCH, NF-kB, TLR or BCR genes, suggesting that none of these signaling pathways plays a relevant role in this disease. Among NMZL, MYD88 mutations were enriched among cases harboring an IgM type monoclonal component (3/4, 75% vs 1/18, 5%, p=.010) and showing cytological clues of plasma cell differentiation of lymph node tumor cells (3/6, 50% vs 0/9; p=.040). NOTCH2 mutations did not correlate with any pathologic feature (i.e. lymph node pattern of infiltration, presence of monocytoid B cells, immunoglobulin gene usage or mutation status). Among MZL-like MBL, neither MYD88 mutations nor NOTCH2 mutations correlated with specific clinico-pathologic features (i.e. presence of an IgM type monoclonal component, intrasinusoidal bone marrow infiltration, plasma cell differentiation). Conclusions These data suggest that: i) SMZL, NMZL and MZL-like MBL share a similar genotype and are all promoted by the same molecular deregulation of MZ differentiation genes; and ii) vHCL stands as a genetically different entity among indolent B-cell lymphoproliferations. These data might help to refine the differential diagnosis of indolent B-cell lymphoproliferations mimicking SMZL. Disclosures: No relevant conflicts of interest to declare.
Abstract 5531: A bioluminescent cell viability assay optimized for 3D microtissues. (2013)

Abstract It has been well demonstrated that the morphology, gene expression, and overall biological response of cells assessed in 3-dimensional (3D) culture models are frequently more physiologically relevant than that of cells studied in standard 2D culture formats. In spite of rapidly growing interest, one hindrance to the use of 3D models for drug discovery and other research efforts is the lack of convenient and effective assays explicitly validated for application to 3D microtissues. Here we report on a bioluminescent ATP-detection assay comprised of both an improved formulation and an optimized protocol specifically designed to measure the viability of cells grown in 3D culture. The ability of the 3D-optimized reagent to effectively lyse cells from throughout the full thickness of 3D microtissues, including cancer cell spheroids, was clearly demonstrated by use of confocal laser fluorescent microscopy in conjunction with a fluorogenic, membrane-impermeant DNA-binding dye. Importantly, the assay's ability to accurately report the ATP content, and therefore viability, of various 3D microtissues (including a range of cancer cell line spheroids) was demonstrated by comparison to a trichloroacetic acid ATP extraction method. In scaffold-free as well as scaffold-dependent 3D models, recovery and detection of greater than 80% of ATP present was routinely observed. In contrast, another frequently used ATP-detection assay was found to have greatly reduced lytic and ATP detection properties (&amp;lt;50% recovery). This new, homogeneous 3D-assay format requires minimal sample manipulation, a brief incubation period (generally less than 30 min), and exhibits excellent sensitivity. It should be amenable to both low- and high-throughput applications and accurately report drug sensitivities of cells assayed in both 2D and 3D culture models. Citation Format: Michael P. Valley, Chad Zimprich, James J. Cali, Dan F. Lazar. A bioluminescent cell viability assay optimized for 3D microtissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5531. doi:10.1158/1538-7445.AM2013-5531
Multi-Variate High-Order Attacks of Shuffled Tables Recomputation. (2015)

Abstract. Masking schemes based on tables recomputation are classi-cal countermeasures against high-order side-channel attacks. Still, they are known to be attackable at order d in the case the masking involves d shares. In this work, we mathematically show that an attack of order strictly greater than d can be more successful than an attack at order d. To do so, we leverage the idea presented by Tunstall, Whitnall and Oswald at FSE 2013: we exhibit attacks which exploit the multiple leak-ages linked to one mask during the recomputation of tables. Specifically, regarding first-order table recomputation, improved by a shuffled execu-tion, we show that there is a window of opportunity, in terms of noise variance, where a novel highly multivariate third-order attack is more ef-ficient than a classical bivariate second-order attack. Moreover, we show on the example of the high-order secure table computation presented by Coron at EUROCRYPT 2014 that the window of opportunity enlarges linearly with the security order d.
Assays, Surrogates, and Alternative Technologies for a TB Lead Identification Program Targeting DNA Gyrase ATPase (2014)

Mycobacterium tuberculosis (Mtb) DNA gyrase ATPase was the target of a tuberculosis drug discovery program. The low specific activity of the Mtb ATPase prompted the use of Mycobacterium smegmatis (Msm) enzyme as a surrogate for lead generation, since it had 20-fold higher activity. Addition of GyrA or DNA did not significantly increase the activity of the Msm GyrB ATPase, and an assay was developed using GyrB alone. Inhibition of the Msm ATPase correlated well with inhibition of Mtb DNA gyrase supercoiling across three chemical scaffolds, justifying its use. As the IC50 of compounds approached the enzyme concentration, surrogate assays were used to estimate potencies (e.g., the shift in thermal melt of Mtb GyrB, which correlated well with IC(50)s >10 nM). Analysis using the Morrison equation enabled determination of K(i)(app)s in the sub-nanomolar range. Surface plasmon resonance was used to confirm these IC(50)s and measure the K ds of binding, but a fragment of Mtb GyrB had to be used. Across three scaffolds, the dissociation half life, t1/2, of the inhibitor-target complex was ≤ 8 min. This toolkit of assays was developed to track the potency of enzyme inhibition and guide the chemistry for progression of compounds in a lead identification program.