gebhart/patrepeval huggingface dataset:
Ultra-Deep Sequencing of Mouse Mitochondrial DNA: Mutational Patterns and Their Origins (2011)

Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.
Artificial intelligence (AI) to enhance breast cancer screening: protocol for population-based cohort study of cancer detection (2022)

This study has ethical approval from the Women and Newborn Health Service Ethics Committee (EC00350) and the Curtin University Human Research Ethics Committee (HRE2020-0316). Findings will be published in peer-reviewed journals and presented at national and international conferences. Results will also be disseminated to stakeholders in Australian breast cancer screening programmes and policy makers in population screening.
How Big Data Analytics Enables Service Innovation: Materiality, Affordance, and the Individualization of Service (2018)

The article reports on an exploratory, multisite case study of four organizations from the insurance, banking, telecommunications, and e-commerce industries that implemented big data analytics (BDA) technologies to provide individualized service to their customers. Grounded in our analysis of these four cases, a theoretical model is developed that explains how the flexible and reprogrammable nature of BDA technologies provides features of sourcing, storage, event recognition and prediction, behavior recognition and prediction, rule-based actions, and visualization that afford (1) service automation and (2) BDA-enabled human-material service practices. The model highlights how material agency (in the case of service automation) and the interplay of human and material agencies (in the case of human-material service practices) enable service individualization, as organizations draw on a service-dominant logic. The article contributes to the literature on digitally enabled service innovation by highlighting how BDA technologies are generative digital technologies that provide a key organizational resource for service innovation. We discuss implications for research and practice.
Analysis of CD1 molecules on haematological malignancies of myeloid and lymphoid origin. I. Cell surface antigen expression. (1991)

One hundred and ninety well-characterized acute and chronic leukaemias were studied for the expression of CD1a antigen by indirect immunofluorescence (IIF). CD1a was detected on 28 per cent of mature B cell lymphoproliferative disorders, 26 per cent of acute non-lymphoblastic leukaemias (ANLL), 21 per cent of chronic granulocytic leukaemias in blast crisis (CML-BC), 53 percent of T acute lymphocytic leukaemias (T-ALL) and in only one out of 35 common acute lymphoblastic leukaemias (c-ALL). In some cases the expression of the CD1a antigen on the surface of leukaemic cells showed a spontaneous fluctuation after a short period of incubation in vitro. CD1b and CD1c molecules were also detected on B cells and acute non-lymphoblastic leukaemias. The presence of CD1 antigens was confirmed using a dot blot assay (DBA) on the lysate of leukaemic cells.
Methods of Evaluating and Mitigating NVH when Operating an Engine in Dynamic Skip Fire (2014)

<div class="section abstract"><div class="htmlview paragraph">Cylinder deactivation is a technology seeing increased automotive deployment in light of more demanding fuel economy and emissions requirements. Examples of current production systems include GM's Active Fuel Management and Chrysler's Multi-Displacement System, both of which provide one fixed level of deactivation. Dynamic Skip Fire (DSF), in which the number of fired cylinders is continuously varied to match the torque demand, offers significantly increased fuel savings over a wider operating range than the current production systems. One of the biggest challenges in implementing cylinder deactivation is developing strategies to provide acceptable Noise, Vibration and Harshness (NVH); this paper discusses those challenges and the methodologies developed. This work covers theoretical root causes; proposed metrics to quantify the NVH level; algorithmic and physical mitigation methods; and both subjective and objective evaluation results.</div></div>
Inhibition of BTK and ITK with Ibrutinib Is Effective in the Prevention of Chronic Graft-versus-Host Disease in Mice (2015)

Bruton's Tyrosine Kinase (BTK) and IL-2 Inducible T-cell Kinase (ITK) are enzymes responsible for the phosphorylation and activation of downstream effectors in the B-cell receptor (BCR) signaling and T cell receptor (TCR) signaling pathways, respectively. Ibrutinib is an FDA-approved potent inhibitor of both BTK and ITK that impairs B-cell and T-cell function. CD4 T cells and B cells are essential for the induction of chronic graft-versus-host disease (cGVHD). We evaluated these targets by testing the ability of Ibrutinib to prevent or ameliorate cGVHD, which is one of the major complications for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). We found that Ibrutinib significantly alleviated cGVHD across four different mouse models, accompanied by increased long-term survival and reduced clinical score. The clinical improvements in Ibrutinib-treated recipients were associated with decreased serum-autoantibodies, costimulatory molecule activation, B-cell proliferation, and glomerulonephritis compared to vehicle controls. Ibrutinib was also able to alleviate the clinical manifestations in acute GVHD (aGVHD), where the recipients were given grafts with or without B cells, suggesting that an inhibitory effect of Ibrutinib on T cells contributes to a reduction in both aGVHD and cGVHD pathogenesis. An effective prophylactic regimen is still lacking to both reduce the incidence and severity of human cGVHD following allo-HSCT. Our study shows that Ibrutinib is an effective prophylaxis against several mouse models of cGVHD with minimal toxicity and could be a promising strategy to combat human cGVHD clinically.
Mutants of<i>Listeria monocytogenes</i>Defective in In Vitro Invasion and Cell-to-Cell Spreading Still Invade and Proliferate in Hepatocytes of Neutropenic Mice (2000)

Listeria monocytogenes mutants defective in the actA gene, the plcB gene, and the inlA and inlB genes were less virulent when injected intravenously into BALB/c mice. The growth of these strains as well as of the virulent wild-type strains was increased by treating mice with a neutrophil-specific depleting monoclonal antibody, RB6-8C5. Histologic examination of the livers of the treated animals showed intrahepatocytic proliferation of the listeriae in all cases. Our data show that more than one pathway exists that allows L. monocytogenes to invade parenchymal cells. One pathway most likely involves the actA and plcB gene products, and a second one probably involves the internalins.
Constant-resistance filters with diplexer architecture for S-band applications (2019)

Constant-resistance filters are a class of absorptive filters that ideally present no reflection to the incoming signal of any frequency while their transfer function can be designed to exhibit low-pass, high-pass or band-pass characteristics. There is a variety of architectures employed to accomplish this function and such filters are used for terminating the output stages of amplifiers and mixers. In this work, we discuss the design of low-pass reflectionless filters employing a diplexer architecture with the intent to separating the useful signal (low-pass) from the higher harmonics which will be terminated externally to the filter.
PhotoFOAF: A Community Building Service driven by Socially-Aware Mobile Imaging (2006)

Mobile digital photography has become a ubiquitous service: nowadays, nearly every mobile phone is equipped with a camera. This results in huge collections of pictures that are hard to structure and has lead to problems in saving, managing and exchanging digital pictures. PhotoFOAF presents a new approach to mobile imaging, exploiting the social context of a picture as an important part of the metadata. We present an approach that allows users to insert social metadata in pictures while capturing them. The resulting collections of captured pictures can be managed, searched and exchanged more easily by taking benefit of the personal social relevance of a picture. PhotoFOAF implements an end-to-end process to accomplish this and it exploits, enhances and stimulates social relationships between users during all the different steps
Photoluminescence and Electroluminescence from a Hybrid of Lumogen Red in Nanoporous-Silica (2008)

In this paper white electroluminescence from a lumogen red-doped nanoporous silica matrix is presented. The matrix was prepared using a sol-gel process, and lumogen red--a perylene derivative--was doped at a number of concentrations. The photoluminescence and electroluminescence of the lumogen red-doped nanoporous-silica composite were investigated in detail. The structures, surface morphology, and optical properties of the nanoporous silica composites were investigated. The average pore size of the nanoporous-silica matrix was approximately 5 nm. The absorption spectra of the lumogen red in the nanoporous-silica matrix were broader than those from solution specimens. The photoluminescence of the lumogen red-doped nanoporous-silica matrix depended strongly on the excitation wavelengths. When excited at relatively longer wavelengths, e.g., 467 nm, the emissions peaked at constant positions (approximately 608 nm) for all cases, except a small shift to the red from its solution 601 nm. However, if excited at a shorter wavelength in the range of 200-400 nm, additional blue emissions were observed, which were particularly strong and suggested defect centers of the nanoporous-silica matrix. The electroluminescence from a single-layered sandwich device consisting of the lumogen red-doped nanoporous-silica was interesting. When driving with an AC electric field, electroluminescence spectra covered a whole spectral range, consisting of the red emission from lumogen red and the blue and green emission from the nanoporous silica matrix. In this way, we actually achieved a white electroluminescence from this hybrid organic and silica device with a color coordinate, CIE [x, y] = [0.30, 0.35] at a driving electric field of 3.0 x 10(6) V/cm. This was a first attempt to investigate electroluminescence from an organic dye-doped nanoporous silica matrix.
Ecologic Correlations of Selected Food Groups With Disease Incidence and Mortality in Switzerland (2013)

Ecologic associations between food availability and disease vary considerably on the basis of whether mortality or incidence rates are used in the analysis. Great care is thus necessary when interpreting our results.
Repositioning therapeutic cancer vaccines in the dawning era of potent immune interventions (2013)

Based on lessons learned with various immune interventions, this review aims to provide a constructive framework for repositioning therapeutic cancer vaccination. Intensive research throughout the past decade has identified key hurdles interfering with the efficacy of cancer vaccines. The vaccination concept still holds promise if positioned appropriately in minimal residual disease and select early disease stage cancer indications. However, in advanced cancer, it must be integrated with complementary immune interventions to ensure reconstruction of a functional immune repertoire and simultaneous blockade of immune inhibiting mechanisms. Vaccination could render complex and integrative immune interventions simpler, safer and more effective. The near future will witness an explosion of activities in the cancer immunotherapy arena, witnessing a rational repositioning of vaccines rather than their extinction.
Expression of tumor necrosis factor by different tumor cell lines results either in tumor suppression or augmented metastasis. (1993)

Tumor necrosis factor (TNF) produced by tumor cells after gene transfer can effectively suppress the growth of locally growing tumors. We wanted to test the effects of "local" TNF on the growth of a highly metastatic cell line. Therefore, a recombinant retrovirus allowing expression of the TNF gene by the beta-actin promotor has been constructed and used to infect the two tumor cell lines EB and ESB, which grow as solid tumor or metastasize, respectively. Expression of TNF by EB cells resulted in their rapid and dose-dependent rejection. In sharp contrast, mice injected with ESB cells producing similar amounts of TNF showed no signs of tumor suppression, but rather had reduced survival rates that correlated with enhanced hepatic metastases. The accelerated formation of liver metastases by ESB TNF cells could be reversed by an anti-TNF mAb. These results demonstrate the opposite effects TNF may have on tumor growth: suppression of a locally growing tumor and promotion of metastasis formation.
Markerless garment capture (2008)

A lot of research has recently focused on the problem of capturing the geometry and motion of garments. Such work usually relies on special markers printed on the fabric to establish temporally coherent correspondences between points on the garment's surface at different times. Unfortunately, this approach is tedious and prevents the capture of off-the-shelf clothing made from interesting fabrics. In this paper, we describe a marker-free approach to capturing garment motion that avoids these downsides. We establish temporally coherent parameterizations between incomplete geometries that we extract at each timestep with a multiview stereo algorithm. We then fill holes in the geometry using a template. This approach, for the first time, allows us to capture the geometry and motion of unpatterned, off-the-shelf garments made from a range of different fabrics.
A Holistic Approach to Delirium at the End of Life (2016)

Delirium at the end of life causes significant distress for patients, family and caregivers and its multi-factorial etiology makes management of this symptom challenging. Built around a case discussion of a delirious patient with terminal cancer at the end of life, a framework is proposed to aid healthcare teams tackle this problem holistically.
Localized FIB delayering on advanced process technologies (2014)

Good control over beam and chemistry conditions are required to enable uniform delayering of advanced process technologies in the FIB. The introduction of newer, thinner and more beam sensitive materials have made delayering more complicated. We shall introduce a new chemistry for device delayering and present results from both Ga and Xe ion beams showing its improvement over existing chemistries.
[Occupational contact allergy to feverfew Tanacetum parthenium (L.) Schultz-Bip.; Asteraceae]. (1981)

Allergic Contact Dermatitis due to Feverfew Tanacetum parathenium, Asteraceae. After breeding and selling a new ornamental form of feverfew (Tanacetum parthenium (L.) Schulz-Bip. = Chrysanthemum parthenium (L.) Bernh.), sold the flower markets under the misleading name, "chamomile", a 40 year old female florist developed after a half year handling recurrent dermatitis of the face, neck, hands and forearms. Epicutaneous tests revealed positive reactions to 10 species of the Compositae family, including chrysanthemums, aster Gaillardia. Arnica and truc chamomile. However, the strongests results were seen with petals and leaves of feverfew. Renewed strong reactions to parthenolid, the main sesquiterpene lactonic constitutent of European feverfew demonstrated that this compound was the responsible contact allergen. The sensitizing capacity of parthenolid has been shown in previous investigations in guina pigs. Furthermore, cross-reactionsto parthenolid were frequently observed in chrysanthemum sensitive persons. Mexican samples of feverfew contain the eudesmanolid santamarin and traces of other sesquiterpene lactones, but parthenolid is lacking. Further studies are needed to clarify the sensitizing potency of this related compound.
DEVELOPMENT OF NOVEL MUSCLE-SPECIFIC ADENO-ASSOCIATED VIRAL VECTOR CONSTRUCTS FOR GENE THERAPY OF DUCHENNE MUSCULAR DYSTROPHY (2014)

To investigate efficacy of synthetic SPc5-12 promoter expression in skeletal and heart muscles and compare its activity with that of MYODI and MYLK2 muscle specific promoters. We hypothesized that we could achieve efficient, safe and global cardiac and muscle gene transfer in mice following a single intravenous injection of scAAV-SPc5-12-luc2 vector. We reported relatively robust levels of luciferase expression in the heart and moderate levels in the skeletal muscles in particular the tibialis and gastrocnemius which are representative of fast twitch muscle fibers. No significant luciferase expression was observed in other tissues such as liver, lung, spleen and brain. The result of the luciferase expression quantified as (photons/sec/cm2/steridian) in the individual dissected organs were similar to the optical imaging results observed of the whole mice. This study report for the first time that the SPc5-12 promoter delivered by AAV9 serotype is robust and muscle specific.
Formation and stability of alternate-stranded triplex formed with alpha,beta-chimeric oligoDNA (2002)

Chimeric oligoDNAs composed of alpha-anomeric oligonucleotide and beta-anomeric oligonucleotide with modified nucleobases and/or phosphodiester backbone are synthesized and their ability to form alternate-stranded triple helix with dsDNA was examined. Substitution of normal phosphodiester linkages with phosphorothioate linkages resulted in the prominent destabilization of the alternate-stranded triplex. Meanwhile, the introduction of cationic molecule or intercalative molecule at certain positions of the modified DNA was effective to increase the stability of the triplexes.
Dynamics of keyhole and molten pool in laser welding (1998)

In laser and electron-beam welding, a deep cavity called a keyhole or beam hole is formed in the weld pool due to the intense recoil pressure of evaporation. The formation of the keyhole leads to a deep penetration weld with a high aspect ratio and this is the most advantageous feature of welding by high-energy-density beams. However, a hole drilled in a liquid is primarily unstable by its nature and the instability of the keyhole also causes the formation of porosity or cavities in the weld metal. In particular, the porosity formation is one of the serious problems in very high-power laser welding, but its mechanism has not been well understood. The authors have conducted systematic studies on observation of keyhole as well as weld pool dynamics and their related phenomena to reveal the mechanism of porosity formation and its suppression methods. The article will describe the real-time observation of keyhole and plume behaviors in the pulsed and continuous-wave laser welding by high-speed optical and x-ray transmission methods, the cavity formation process and its suppression measures.
PDE10A: A Striatum-Enriched, Dual-Substrate Phosphodiesterase (2006)

The mechanisms for transcriptional regulation of PDE10A expression in striatum and hippocampus remain to be determined. Lack of restriction of rotation for this conserved glutamine residue has also been proposed to account for dual substrate specificity in other Phosphodiesterase. The behavioral effects of PDE10A inhibition are reminiscent of those of dopamine D2 receptor antagonists. The high level of PDE10A expression in striatal medium spiny neurons suggests that a principal physiological function of the enzyme is in the regulation of cyclic nucleotide signaling within these neurons. PDE10A protein is also expressed at lower levels in a number of other neuronal populations, consistent with the presence of low levels of PDE10A mRNA. Initial surveys using Northern blot and dot blot analyses indicated that PDE10A mRNA is highly expressed only in brain and testis. Numerous splice variants derived from the single PDE10A gene have been identified in human, mouse, and rat.
Challenges in Disentangling Independent Factors of Variation (2017)

We study the problem of building models that disentangle independent factors of variation. Such models could be used to encode features that can efficiently be used for classification and to transfer attributes between different images in image synthesis. As data we use a weakly labeled training set. Our weak labels indicate what single factor has changed between two data samples, although the relative value of the change is unknown. This labeling is of particular interest as it may be readily available without annotation costs. To make use of weak labels we introduce an autoencoder model and train it through constraints on image pairs and triplets. We formally prove that without additional knowledge there is no guarantee that two images with the same factor of variation will be mapped to the same feature. We call this issue the reference ambiguity. Moreover, we show the role of the feature dimensionality and adversarial training. We demonstrate experimentally that the proposed model can successfully transfer attributes on several datasets, but show also cases when the reference ambiguity occurs.
Broad new OS research: challenges and opportunities (2005)

Contemporary software systems are beset by prob-lems that create challenges and opportunities for broad new OS research. To illustrate, we describe five areas where broad OS research could significantly improve the current user experience. These areas are depend-ability, security, system configuration, system exten-sion, and multi-processor programming. In each area we explore how contemporary systems fall short. Where we have thought of possible solutions, we offer directions for future research. Finally, we describe Singularity, a research project at Microsoft Research that is building a new operating system to explore four of these challenges. Singularity incorporates three specific design decisions in order to increase system dependability and improve system se-curity, configuration, and extension. These design de-cisions include the adoption of an abstract instruction set as part of the system binary interface, a unified ex-tension architecture for both the OS and applications, and a first-class application abstraction. 1.