gebhart/patrepeval huggingface dataset:
Signal spectrum analysis and period estimation by using delayed signal sampling (2001)

The paper describes a signal power spectrum analyzer and a signal period estimator whose bandwidth is not limited by the mean sampling time. The procedure relies on the evaluation of the input signal autocorrelation function in different delayed time instants, located at either equispaced or random time instants. To do this, a recursive random sampling process in the time domain was used in order to avoid any bandwidth limitation due to the sampling strategy in the evaluation of each autocorrelation function. The signal power spectrum as well as its period, provided that an approximate value of the fundamental frequency is known, can finally be evaluated. Some theoretical background and experimental work are reported in the paper for validating the performance of the method.
Prediction of the as Low as Diagnostically Acceptable CT Dose for Identification of the Inferior Alveolar Canal Using 3D Convolutional Neural Networks with Multi-Balancing Strategies (2023)

Ionizing radiation is necessary for diagnostic imaging and deciding the right radiation dose is extremely critical to obtain a decent quality image. However, increasing the dosage to improve the image quality has risks due to the potential harm from ionizing radiation. Thus, finding the optimal as low as diagnostically acceptable (ALADA) dosage is an open research problem that has yet to be tackled using artificial intelligence (AI) methods. This paper proposes a new multi-balancing 3D convolutional neural network methodology to build 3D multidetector computed tomography (MDCT) datasets and develop a 3D classifier model that can work properly with 3D CT scan images and balance itself over the heavy unbalanced multi-classes. The proposed models were exhaustively investigated through eighteen empirical experiments and three re-runs for clinical expert examination. As a result, it was possible to confirm that the proposed models improved the performance by an accuracy of 5% to 10% when compared to the baseline method. Furthermore, the resulting models were found to be consistent, and thus possibly applicable to different MDCT examinations and reconstruction techniques. The outcome of this paper can help radiologists to predict the suitability of CT dosages across different CT hardware devices and reconstruction algorithms. Moreover, the developed model is suitable for clinical application where the right dose needs to be predicted from numerous MDCT examinations using a certain MDCT device and reconstruction technique.
Abstract 3725: ABI1 regulates STAT3 transcription through a DNA binding activity (2023)

Abstract Prostate cancer (PCa) is characterized by the complexity of oncogenic signaling and heterogeneity of transcriptional landscapes. Adaptor protein ABI1 is a tumor suppressor in PCa, as evidenced by its loss or downregulation in high-grade and metastatic tumors. STAT3 activation is a hallmark of high-risk prostate tumors. ABI1 loss is associated with STAT3 activation leading to transcriptional reprogramming and epithelial-mesenchymal-transition (EMT) of prostate cancer cells (Nath, Li et al. Cell Commun Signal. 2019). EMT changes involve several homeobox transcription factors. The fact that ABI1 contains a homeobox homology region (HHR) suggests the possibility that it plays a role in EMT by directly regulating transcriptional activity by DNA binding. To examine this hypothesis, we set out to analyze ABI1-DNA binding. Structural NMR studies and in-vitro protein-DNA binding assays confirmed ABI1 binding to DNA regulated by alternative spliced ABI1 Exon 4 region located on the C-terminus of ABI1 HHR. RNA-sequencing data and PCa cell lines qPCR assays reveal the alternative ABI1 Exon 4 spliced-in is enriched in high Gleason-scored PCa samples. ABI1 and STAT3 co-regulate their nuclear vs. cytoplasm localization, and the subsequent functional studies using PCa lines expressing wild type or HHR Exon 4 deletion mutant of ABI1 demonstrated that HHR regulates the STAT3 DNA binding patterns, STAT3 mediated chromatin structure programming as well as its transcription activities. We propose that ABI1 is a critical regulator of STAT3 activity during prostate cancer progression. Citation Format: Xiang Li, Neeru Arya, Baylee A. Porter, Allysa P. Kemraj, Xuesen Dong, Dominique Frueh, Alaji Bah, Leszek Kotula. ABI1 regulates STAT3 transcription through a DNA binding activity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3725.
Learning the Structure of Generative Models without Labeled Data (2017)

Curating labeled training data has become the primary bottleneck in machine learning. Recent frameworks address this bottleneck with generative models to synthesize labels at scale from weak supervision sources. The generative model's dependency structure directly affects the quality of the estimated labels, but selecting a structure automatically without any labeled data is a distinct challenge. We propose a structure estimation method that maximizes the $\ell_1$-regularized marginal pseudolikelihood of the observed data. Our analysis shows that the amount of unlabeled data required to identify the true structure scales sublinearly in the number of possible dependencies for a broad class of models. Simulations show that our method is 100$\times$ faster than a maximum likelihood approach and selects $1/4$ as many extraneous dependencies. We also show that our method provides an average of 1.5 F1 points of improvement over existing, user-developed information extraction applications on real-world data such as PubMed journal abstracts.
Gene Delivery to the Mouse Brain with Adeno-Associated Virus (2004)

The efficient transduction of postmitotic cells by adeno-associated virus (AAV) makes it an excellent vector to deliver marker, functional, or therapeutic genes to the mammalian brain. An attractive feature of AAV is that all the viral-coding sequences are removed when engineering the recombinant genome, thereby limiting the extent of cell toxicity and immune response that are often associated with viral gene transcription. Of the seven described AAV serotypes, AAV serotype-2 (AAV2) is the most studied gene-transfer vehicle for in the mammalian brain. A feature of AAV2 transduction in the brain is that the vector remains confined to the injection site and predominately infects neurons rather than glia (2-8). The limited diffusion of AAV2 vectors is beneficial for controlled gene delivery. For instance, targeting therapeutic genes only to brain structures showing pathology would eliminate complications associated with vector diffusion and subsequent expression in healthy structures, and is an important consideration when designing treatment strategies for localized neurodegenerative diseases. The same is true for other experimental paradigms, such as investigating the function of genes in specific brain structures or using marker genes in tract-tracing experiments. Although AAV2 vectors were shown to remain predominately at the injection site, one study demonstrated that the vector itself may undergo axonal transport in inter-regional systems (9).
Roentgenological diagnosis of amebic colitis. (1986)

アメーバ性大腸炎の診断にはまず本症を疑う事が重要であり,また先行して施行されるX線検査でも本症と診断することがアメーバ性大腸炎の確診過程で極めて重要と思われる.そこで本院内科で経験したアメーバ性大腸炎8症例のX線所見を検討した結果,壁不整,横ヒダの肥厚,念珠状陰影,タコイボ様陰影,バリウムの付着不良の5所見がその基本的所見と思われる.内視鏡所見ではタコイボ隆起が主体でありX線所見とやや趣を異にしている,これは病変部では粘液が多く,またタコイボ隆起の頂上が出血していたり,分泌物が付着しているため病変が忠実に描出されなかったためと思われる.さらに粘膜浮腫の所見も加わりX線所見は多彩であったが,上述5所見に注目すればアメーバ性大腸炎のX線診断はほぼ可能である.また本症とX線所見で鑑別を要する大腸リンパ濾胞増殖症,大腸悪性リンパ腫,潰瘍性大腸炎とも鑑別可能と思われる.
Multi-Walled Carbon Nanotube Filled Conductive Elastomers: Materials and Application to Micro Transducers (2006)

We report a detailed study investigating the use of multi-walled carbon nanotube (MWNT) filled elastomers to enable sensitive and yet robust MEMS devices. This work is contrasted with previous work using carbon black filling, showing an 8-fold improvement in performance through the use of MWNT. The percolation behavior of MWNT in polydimethylsiloxane (PDMS) and polyurethane (PU) elastomers is presented. We have also developed and characterized two devices: (1) MWNT-based force sensitive resistors (FSRs), analogous to polymer piezoresistors; (2) robust collapsible capacitive tactile sensors using soft conductive elastomers.
Study of ArF resist material in terms of transparency and dry etch resistance. (1995)

We investigated the etch rates of various polymers etch rates,and found that alicyclic polymers show a good dry etch resistance in spite of the lack of the aromatic rings. On the basis of this finding we proposed a new ArF resist material which has good transparency and good dry etch resistance for use as a single layer resist.. The resist comprises an alicyclic copolymer of adamantyl methacrylate (AdMA) and 3-oxocyclohexyl methaclyrate (OCMA) and a triphenylsulphonium hexafuluoroantimonate as a photoacid generator (PAG). The transmittance of the 1.tm thick copolymer is about 70% at ArF wavelength. This high transparency ensures pattern imaging of the resist in ArF lithography. The dry etch resistance of the resist is also high and is comparable to that of Novolak resist. We obtained 0.17 m line and space patterns with this resist, using ArF excimer laser stepper.
Pseudoxanthoma Elasticum: A Streamlined, Ethnicity‐based Mutation Detection Strategy (2010)

Pseudoxanthoma elasticum (PXE), an autosomal recessive multisystem disorder, is caused by mutations in the ABCC6 gene, and approximately 300 distinct mutations representing >1000 mutant alleles have been disclosed thus far. Few population-based studies have reported mutational hotspots in some geographic areas. In this study, we attempted to correlate recurring mutations with the individuals' ethnic origin. Specifically, we plotted our international database of 70 families from distinct or mixed ethnic backgrounds against their mutations. The frequent p.R1141X mutation was distributed widely across Europe, while deletion of exons 23-29 (del23-29) was encountered in Northern Europe and in Northern Mediterranean countries. p.R1138W may be a marker for French descent, evidenced by its presence also in French Canadians. The splice site transition mutation 3736-1G→A was seen in the neighboring countries Greece and Turkey, whereas 2542 delG occurs only in the Japanese. Two mutations seem to be present worldwide without evidence of a founder effect, p.Q378X and p.R1339C, suggesting the presence of mutational hotspots. Knowledge of this distribution will allow us to streamline mutation screening through a targeted, stepwise approach when the ethnicity of a patient is known. This will facilitate the identification of individuals at risk, improving their care to prevent ophthalmological and vascular disease.
(283) Petal Color Changes in Carnation Plants Transformed with an Antisense DFR and a CHI Gene (2005)

To produce transgenic carnation plants expressing modified flower colors, cultivars of red-flowering carnation (`Desio' and `Garnet') were transformed with a antisense DFR gene encoding dihydroflavonol-4-reductase, and yellow-flowering carnations (`Pallas' and `Keumbyul') were introduced with a CHI gene encoding chalcone synthease isomerase. Explants of leaves, stems, and shoot tips were inoculated with Agrobacterium and grown overnight in induction broth supplemented with 0.2 m m acetosyringone. The cocultures of carnation explants were maintained in the light at 24 °C on one-half strength MS medium solidified with 0.3% Gelite and supplemented with 1.0 mg·L -1 BA for 10 days, and then were transferred to a selection medium containing 250 mg·L -1 cefotaxime/carbenicillin, 500 mg·L -1 kanamycin. They were subcultured every 2 weeks for over six times and regenerated. In `Garnet' and `Desio' carnation cultivars, a total of 146 plants was transformed with anti-sense DFR gene in pGA748/LBA4404. In yellow flowering cultivars `Pallas' and `Keumbyul', transformed with CHI gene in pGA748/LBA4404, 20 putative transformants obtained. The introduction of the transgenes were confirmed through PCR and flower color changes. Rates of phenotypic expression of the transgene, antisense DFR gene, vary among the transformants such as lighter pigmentation or chimeric discoloration, more prominently in outer petals of the flowers. Transgenic plants of chi gene bloomed flowers of lighter yellow petals in general. The most prominent phenotypic changes were discoloration of red strips on petals, which are typical characteristics of the cultivars.
Motion effects in proton treatments of hepatocellular carcinoma—4D robustly optimised pencil beam scanning plans versus double scattering plans (2018)

Pencil beam scanning (PBS) proton therapy enables better dose conformality for complex anatomical geometries than passive proton scattering techniques, but is more susceptible to organ motion. This becomes an issue when treating moving tumours in the thorax or abdomen. Novel four-dimensional treatment planning approaches have been developed to increase the robustness of PBS plans against motion. However, their efficacy still needs to be examined by means of 4D dynamically accumulated dose (4DDD) analyses. This study investigates the potential use of 4D robust optimisation to maintain sufficient target coverage in the presence of organ motion, while sparing surrounding healthy tissue, for hepatocellular carcinoma (HCC). The liver is particularly suited to study motion interplay effects since the treatment region exhibits smaller density gradients and more homogeneous tissue than targets in the thorax, making it less prone to range errors. A facility-specific beam time model, developed and experimentally validated previously, was used for the clinical evaluation. 4DDD analyses of eleven target volumes did not show a significant improvement of the target coverage using 4D robust optimisation, but a reduction of the dose to close-by organs at risk. Interplay effects were averaged out for the applied fractionation scheme of 15 fractions. Contrary to PBS, passive double scattering (DS) plans yielded homogeneous 4DDD dose distributions in a single fraction. But, in some cases, they exceeded organ at risk dose limits, which were only satisfied in PBS. The average normal liver dose could be decreased by almost 6% compared to non-robustly optimised PBS plans and by 16% compared to DS plans when implementing 4D robust optimisation. Except for some very small tumours with large motion amplitudes, 4D robustly optimised PBS plans were found to be clinically acceptable even without supplementary motion mitigation techniques.
Appearance and ionization potentials of ions produced by electron-impact on some phosphorus-fluorine compounds: the phosphorus-phosphorus bond dissociation energy in diphosphorus tetrafluoride (1974)

The ionization potentials of P2F4, PF3 PF2H and PF2I and the appearance potentials of the PF+2 ion from these species are reported. The ionization potential of the PF2˙ radical is estimated using approximations for the PF2—X (X = F, I and H) bond dissociation energies. The P—P bond dissociation energy in diphosphorus tetrafluoride is estimated as 57 ± 10 kcal mol–1.
Bioinformatics tools for genome-wide single nucleotide polymorphisms management and analyses: a review (2014)

Advances in modern genetics have brought a dramatic increase in the number of single nucleotide polymorphisms (SNPs), as well as the fast accumulating genotype data in public databases. In response, many bioinformatics tools are explored to manage and extract valuable information from such large datasets. Here, we firstly review the methodological strategies and introduce some well-established programs in management and analyses of SNP data. Then, possible challenges and development in this field are discussed. It hopes that these applied tools will greatly assist in exploring susceptibility for complex diseases.
Studies on the Mechanism Controlling Growth Hormone Release Induced by Chlorpromazine in the Anesthetized Rat (1975)

In intact urethane-anesthetized rats, plasma growth hormone (GH) levels were low but increased significantly following intravenous injection of chlorpromazine. Plasma GH levels were significantly elevated in rats with hypothalamic cuts such as complete deafferentiation, anterior cut and antero-lateral cut, whereas plasma GH levels in rats with posterior cut or postero-lateral cut were not significantly different from those in rats with sham-operation. Intravenous injection of chlorpromazine caused an increase of plasma GH in rats with any type of hypothalamic cut. However, the maximum increments of plasma GH following chlorpromazine were larger in rats with antero-lateral cut and smaller in rats with posterior cut than in rats with sham-operation. These results suggest that extrahypothalamic inhibiting and stimulating neurons influence the regulatory mechanism of rat GH secretion through anterior and posterior routes to the hypothalamus respectively.
Application and Network VNF migration in a MEC-enabled 5G Architecture (2018)

The upcoming fifth generation (5G) of mobile communications brings new paradigms, such as network slicing and automation, to the forefront. Cloud computing and network function virtualization (NFV) constitute two fundamental key enablers towards the implementation of these new paradigms. On the one hand, computational functionalities are no longer limited to distant servers, but they are coming closer to the end user through Multi-access Edge Computing (MEC) technology, thus creating a multi-tier cloud architecture in modern networks. On the other hand, going beyond the existing rigid architectures, NFV enables the flexible and on-the-fly creation and placement both of application and network functions, aiming at satisfying the diverse application requirements and optimizing the management of the heterogeneous (network, computational and storage) resources. In this paper, we discuss the challenges that arise in a MEC-enabled 5G architecture that supports the flexible placement/migration of network and application virtual network functions (VNFs), orchestrated by an NFV Orchestrator (NFVO) with admission management functionalities, able to manage on-the-fly the network functions and resources. Finally, we describe in detail a MEC-enabled testbed architecture that facilitates the development and testing of such solution in the context of 5G networks.
The Use of Fluorescent Proteins for Developing Cancer-Specific Target Imaging Probes (2012)

Target-specific imaging probes represent a promising tool in the molecular imaging of human cancer. Fluorescently-labeled target-specific probes are useful in imaging cancers because of their ability to bind a target receptor with high sensitivity and specificity. The development of probes relies upon preclinical testing to validate the sensitivity and specificity of these agents in animal models. However, this process involves both conventional histology and immunohistochemistry, which require large numbers of animals and samples with costly handling. In this chapter, we describe a novel validation tool that takes advantage of genetic engineering technology, whereby cell lines are transfected with genes that induce the target cell to produce fluorescent proteins with characteristic emission spectra, thus enabling their easy identification as cancer cells in vivo. Combined with multicolor fluorescence imaging, this can provide rapid validation of newly-developed exogenous probes that fluoresce at different wavelengths. For example, the plasmid containing the gene encoding red fluorescent protein (RFP) was transfected into cell lines previously developed to either express or not express specific cell surface receptors. Various antibody-based or ligand-based optical-contrast agents, with green fluorophores were developed to concurrently target cancer cells and validate their positive and negative controls, such as the β-D: -galactose receptor, HER1, and HER2 in a single animal/organ. Spectrally-resolved multicolor fluorescence imaging was used to detect separate fluorescence emission spectra from the exogenous green fluorophore and RFP. Here, we describe the use of "co-staining" (matching the exogenous fluorophore and the endogenous fluorescent protein to the positive control cell line) and "counter-staining" (matching the exogenous fluorophore to the positive control and the endogenous fluorescent protein to the negative control cell line) to validate the sensitivity and specificity of target-specific probes. Using these in vivo imaging techniques, we are able to determine the sensitivity and specificity of target-specific optical contrast agents in several distinct animal models of cancer in vivo, thus exemplifying the versatility of our technique, while reducing the number of animals needed to conduct these experiments.
TIA Fact Sheet (2012)

The Orange Cows project of the Vietnamese Victims of Agent Orange Trust started in 2007 and is aimed at improving smallholder farmers’ livelihoods by providing a breeding cow. A survey of the beneficiaries in four communes in Thua Thien-Hue province provided significant information on farming systems as well as an assessment of the progress of this project and its impact on households and communities.
Chemoprevention of Human Actinic Keratoses by Topical dl-α-tocopherol (2009)

Prior research shows that topical application of free, nonfatty acid-conjugated vitamin E (DL-alpha-tocopherol) prevents skin cancer in mice, as well as immunosuppression induced by UVB radiation. This study investigated the chemopreventive potential of DL-alpha-tocopherol in humans through monitoring surrogate end point biomarkers in sun-damaged skin. Contralateral arms of healthy human volunteers with actinic keratoses (AK) were randomly assigned to receive either 12.5% DL-alpha-tocopherol or placebo in a crème base for 6 months. Changes in number of AKs, levels of p53 protein expression, proliferating cell nuclear antigen, and polyamines were assessed along with skin and systemic vitamin E levels. Following treatment, plasma concentration levels of DL-alpha-tocopherol were unchanged, but skin levels were highly elevated (P < 0.001). Levels of p53 and proliferating cell nuclear antigen did not change significantly, whereas number of AKs declined insignificantly in both placebo and treatment arms. Regression models showed significant decreases in putrescine, spermidine, spermine, and total polyamine concentrations following treatment. Topically applied DL-alpha-tocopherol was substantially absorbed in skin, but the 6-month application did not significantly reduce numbers of preexisting AKs on moderately to severely sun-damaged forearms. Increases in polyamine synthesis are expected during tumor initiation and promotion; conversely, the significant reductions in polyamine levels resulting from the topical DL-alpha-tocopherol application are consistent with reductions in tumorigenesis potential. Topical tocopherol did not normalize established sun-induced lesions, but DL-alpha-tocopherol-induced reductions in polyamine metabolism are consistent with the inhibition of skin squamous cell carcinogenesis as seen in previous human trials and animal models.
Construction and Transfection of PCR Products Expressing siRNAs or shRNAs in Mammalian Cells (2004)

In mammalian cells, the RNA interference (RNAi) effect has been observed through expression of 21-23 base transcripts capable of forming duplexes, or via expression of short hairpin RNAs. Here, we describe a facile polymerase chain reaction (PCR)-based strategy for rapid synthesis and evaluation of small interfering RNAs (siRNA) expression units in mammalian cells. The siRNA expression constructs are constructed by PCR, and the PCR products are directly transfected into mammalian cells for functional testing. This method is fast and inexpensive, allowing several different siRNA gene candidates to be rapidly screened for efficacy.