gebhart/patrepeval huggingface dataset:
Clinical and genetic studies on 12 preaxial polydactyly families and refinement of the localisation of the gene responsible to a 1.9 cM region on chromosome 7q36 (1999)

Polydactyly is the most frequently observed congenital hand malformation with a prevalence between 5 and 19 per 10000 live births. It can occur as an isolated disorder, in association with other hand/foot malformations, or as a part of a syndrome, and is usually inherited as an autosomal dominant trait. According to its anatomical location, polydactyly can be generally subdivided into pre- and postaxial forms. Recently, a gene responsible for preaxial polydactyly types II and III, as well as complex polysyndactyly, has been localised to chromosome 7q36. In order to facilitate the search for the underlying genetic defect, we ascertained 12 additional families of different ethnic origin affected with preaxial polydactyly. Eleven of the kindreds investigated could be linked to chromosome 7q36, enabling us to refine the critical region for the preaxial polydactyly gene to a region of 1.9 cM. Our findings also indicate that radial and tibial dysplasia/aplasia can be associated with preaxial polydactyly on chromosome 7q36. Combining our results with other studies suggests that all non-syndromic preaxial polydactylies associated with triphalangism of the thumb are caused by a single genetic locus, but that there is genetic heterogeneity for preaxial polydactyly associated with duplications of biphalangeal thumbs. Comparison of the phenotypic and genetic findings of different forms of preaxial polydactyly is an important step in analysing and understanding the aetiology and pathogenesis of these limb malformations.
Detection of Microregional Hypoxia in Mouse Cerebral Cortex by Two-photon Imaging of Endogenous NADH Fluorescence (2012)

The brain's ability to function at high levels of metabolic demand depends on continuous oxygen supply through blood flow and tissue oxygen diffusion. Here we present a visualized experimental and methodological protocol to directly visualize microregional tissue hypoxia and to infer perivascular oxygen gradients in the mouse cortex. It is based on the non-linear relationship between nicotinamide adenine dinucleotide (NADH) endogenous fluorescence intensity and oxygen partial pressure in the tissue, where observed tissue NADH fluorescence abruptly increases at tissue oxygen levels below 10 mmHg1. We use two-photon excitation at 740 nm which allows for concurrent excitation of intrinsic NADH tissue fluorescence and blood plasma contrasted with Texas-Red dextran. The advantages of this method over existing approaches include the following: it takes advantage of an intrinsic tissue signal and can be performed using standard two-photon in vivo imaging equipment; it permits continuous monitoring in the whole field of view with a depth resolution of ~50 μm. We demonstrate that brain tissue areas furthest from cerebral blood vessels correspond to vulnerable watershed areas which are the first to become functionally hypoxic following a decline in vascular oxygen supply. This method allows one to image microregional cortical oxygenation and is therefore useful for examining the role of inadequate or restricted tissue oxygen supply in neurovascular diseases and stroke.
Regulation of cytokine production in the human thymus: epidermal growth factor and transforming growth factor alpha regulate mRNA levels of interleukin 1 alpha (IL-1 alpha), IL-1 beta, and IL-6 in human thymic epithelial cells at a post-transcriptional level. (1991)

Human thymic epithelial (TE) cells produce interleukin 1 alpha (IL-1 alpha), IL-1 beta, and IL-6, cytokines that are important for thymocyte proliferation. The mRNAs for these cytokines are short-lived and are inducible by multiple stimuli. Thus, the steady-state levels for IL-1 and IL-6 mRNAs are critical in establishing the final cytokine protein levels. In this study we have evaluated the effect of epidermal growth factor (EGF), a growth factor for TE cells, and its homologue transforming growth factor alpha (TGF-alpha), on primary cultures of normal human TE cells for the levels of IL-1 alpha, IL-1 beta, IL-6, and TGF-alpha mRNA. We showed that TE cells expressed EGF receptors (EGF-R) in vitro and in vivo, and that treatment of TE cells with EGF or TGF-alpha increased IL-1 and IL-6 biological activity and mRNA levels for IL-1 alpha, IL-1 beta, and IL-6. Neither EGF nor TGF-alpha increased transcription rates of IL-1 alpha, IL-1 beta, and IL-6 genes, but rather both EGF and TGF-alpha increased cytokine mRNA stability. By indirect immunofluorescence assay, TGF-alpha was localized in medullary TE cells and thymic Hassall's bodies while EGF-R was localized to TE cells throughout the thymus. Thus, TGF-alpha and EGF are critical regulatory molecules for production of TE cell-derived cytokines within the thymus and may function as key modulators of human T cell development in vivo.
Impact of intensive venous sampling on characterization of pulsatile GH release (1987)

The effect of sampling intensity on quantitative properties of pulsatile growth hormone (GH) release was tested using an objective, statistically based pulse detection algorithm (Cluster). Seven normal young men had blood withdrawn at 5-min intervals for 24 h. The number of GH peaks/24 h (mean +/- SE) detected in the 5-min series (5.93 +/- 0.66) was significantly greater than the number of peaks documented in the constituent 10-min (3.45 +/- 0.28), 15-min (2.79 +/- 0.31), 20-min (2.86 +/- 0.64), 30-min (2.5 +/- 0.36), 45-min (2.21 +/- 0.21), and 60-min (1.93 +/- 0.23) series. The increased number of peaks detected with 5-min sampling reflected high-frequency pulsatile GH release occurring within the major GH secretory episodes. Both the mean widths and areas associated with peaks identified in the 5-min series were smaller than those documented with less intensive sampling. Peak amplitude did not change with sampling intensity. These data suggest that the major secretory episodes of GH release in normal young men encompass high-frequency GH secretory activity. That these high-frequency GH secretory events have not previously been described probably reflects the relatively infrequent sampling paradigms (e.g., every 20-30 min) commonly used in the past.
Technological Challenges In the Development of AHS (1998)

Abstract The objective of an Automated Highway System (AHS) is to enhance user comfort, convenience and safety with vehicle and highway automation. In a broad sense vehicle and highway automation has been an ongoing process with many improvements in vehicles and infrastructure introduced over the years, such as vehicle cruise control and roadway traffic signal sequence control. In a narrower definition, the introduction of vehicle and highway automation will reduce the role of drivers to various degrees. The development of an AHS is likely to be controversial for many years and will have far-reaching ripple effects. The AHS is very influential since it relates closely to the daily lives of people. Although it may become only an optional type of transportation, the success of the AHS development can cause significant changes in the way people travel. In this paper, we discuss the technical aspects of vehicle and highway automation for an AHS and will try to identify the critical challenges to bring an AHS into reality. Although the concepts of an AHS are still being debated and the implementation of a national AHS is not imminent, it is timely and beneficial to examine the technological elements, to explore the current limitations and to identify the hurdles yet to overcome.
Demonstrating the Anatomical Expression of Two Genes in the Garden Pea (1980)

Research Article| April 01 1980 Demonstrating the Anatomical Expression of Two Genes in the Garden Pea James A. Hawk, James A. Hawk Search for other works by this author on: This Site PubMed Google Scholar Thompson D. Pizzolato Thompson D. Pizzolato Search for other works by this author on: This Site PubMed Google Scholar The American Biology Teacher (1980) 42 (4): 238–239. https://doi.org/10.2307/4446909 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation James A. Hawk, Thompson D. Pizzolato; Demonstrating the Anatomical Expression of Two Genes in the Garden Pea. The American Biology Teacher 1 April 1980; 42 (4): 238–239. doi: https://doi.org/10.2307/4446909 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe American Biology Teacher Search This content is only available via PDF. Copyright 1980 The National Association of Biology Teachers Article PDF first page preview Close Modal You do not currently have access to this content.
Metamaterial Based Terahertz Detector (2011)

We present a metamaterial based terahertz (THz) detector. The detector design, which combines metamaterials and MEMs, is frequency selective, and we have fabricated and tested detectors at 95 GHz and 693 GHz with noise equivalent powers of 1.13 × 10-8 W/√Hz and 2.96 × 10-8 W/√Hz and responsivities of 16,500 V/W and 6,800 V/W, respectively. These values were achieved at room temperature and pressure.
Adrenocortical Causes of Hypertension (2011)

Primary aldosteronism is the most common cause of secondary hypertension. In the past, screening for primary aldosteronism was offered only in patients with hypertension associated with hypokalemia. Recent studies showed that hypokalemia is seen in only 25% of the patients with primary aldosteronism, which has increased the prevalence of primary aldosteronism to 10-15% of all cases with new onset hypertension.
Supporting early development of advanced high-performance logic with synchrotron orbital radiation lithography: a feasibility evaluation (1994)

The synchrotron x ray lithography (XRL) project described was conducted as a learning and feasibility vehicle for gate level lithography in support of IBM's most advanced CMOS logic programs. An electrically probable multilevel lithography test site was developed and characterized to exercise critical design, mask manufacture, alignment, exposure, and metrology issues in the 150 - 350 nm linewidth range. A fully capped silicided polysilicon gate stack was chosen for the electrical measurements in order to develop and demonstrate the XRL and related reactive ion etch process on a realistic, product-like substrate. This paper addresses test site design issues, elaborates on the mask manufacturing process, and presents SEM and electrical data from wafers processed at IBM's Advanced Semiconductor Technology Center. The data presented demonstrate the feasibility of supporting early device development and process integration with XRL and highlight the need for high resolution, defect free, proximity corrected masks to fully exploit the capabilities of x ray lithography.
DeepTensor: Low-Rank Tensor Decomposition with Deep Network Priors (2022)

DeepTensor is a computationally efficient framework for low-rank decomposition of matrices and tensors using deep generative networks. We decompose a tensor as the product of low-rank tensor factors (e.g., a matrix as the outer product of two vectors), where each low-rank tensor is generated by a deep network (DN) that is trained in a self-supervised manner to minimize the mean-squared approximation error. Our key observation is that the implicit regularization inherent in DNs enables them to capture nonlinear signal structures (e.g., manifolds) that are out of the reach of classical linear methods like the singular value decomposition (SVD) and principal component analysis (PCA). Furthermore, in contrast to the SVD and PCA, whose performance deteriorates when the tensor's entries deviate from additive white Gaussian noise, we demonstrate that the performance of DeepTensor is robust to a wide range of distributions. We validate that DeepTensor is a robust and computationally efficient drop-in replacement for the SVD, PCA, nonnegative matrix factorization (NMF), and similar decompositions by exploring a range of real-world applications, including hyperspectral image denoising, 3D MRI tomography, and image classification. In particular, DeepTensor offers a 6dB signal-to-noise ratio improvement over standard denoising methods for signals corrupted by Poisson noise and learns to decompose 3D tensors 60 times faster than a single DN equipped with 3D convolutions.
Spatial modulation of free-electron wavepackets by shaping ultrafast plasmonic excitations (2020)

By engineering the boundary conditions of plasmonic excitations, we present a novel method for electron wavefront shaping utilizing the ultrafast interaction of femtosecond free- electron and laser pulses in plasmonic samples.
A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification (2019)

We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca<sup>2+</sup>) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm<sup>-1</sup>) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
Vision Transformers for Computational Histopathology (2023)

Computational histopathology is focused on the automatic analysis of rich phenotypic information contained in gigabyte whole slide images, aiming at providing cancer patients with more accurate diagnosis, prognosis, and treatment recommendations. Nowadays deep learning is the mainstream methodological choice in computational histopathology. Transformer, as the latest technological advance in deep learning, learns feature representations and global dependencies based on self-attention mechanisms, which is increasingly gaining prevalence in this field. This article presents a comprehensive review of state-of-the-art vision transformers that have been explored in histopathological image analysis for classification, segmentation, and survival risk regression applications. We first overview preliminary concepts and components built into vision transformers. Various recent applications including whole slide image classification, histological tissue component segmentation, and survival outcome prediction with tailored transformer architectures are then discussed. We finally discuss key challenges revolving around the use of vision transformers and envisioned future perspectives. We hope that this review could provide an elaborate guideline for readers to explore vision transformers in computational histopathology, such that more advanced techniques assisting in the precise diagnosis and treatment of cancer patients could be developed.
TMPRSS6 Inhibition with a Monoclonal Antibody Improves Red Blood Cell Health and Reduces Hepatic Iron Loading in Mouse Models of Iron Overload Diseases (2022)

Beta-thalassemia is a genetic disorder arising from loss of function mutations in the beta-globin gene, leading to ineffective erythropoiesis and organ iron overload. The latter contributes to liver fibrosis, type-2 diabetes, cancer, and cardiac toxicities. The major cause of increased iron loading is the reduced hepcidin levels because of the ineffective erythropoiesis. Iron is regulated by the hormone hepcidin. The BMP6-HJV signaling axis induces hepcidin expression via SMAD1/5 activation and the serine-protease TMPRSS6 is a negative regulator of HJV. Individuals with loss-of-function mutations in the TMPRSS6 gene have high levels of circulating hepcidin resulting in iron-restricted/iron-deficiency anemia. Thus, blocking TMPRSS6 may be a viable strategy to elevate hepcidin and reduce iron levels in beta-thalassemia or hereditary hemochromatosis. We generated a monoclonal antibody (REGN7999) that inhibits TMPRSS6 activity hence preventing HJV cleavage. This in turn accentuates BMP6-HJV signaling, consequently increasing serum hepcidin. In the Hbbth3/+ mouse model of beta-thalassemia, treatment with REGN7999 (10 mg/kg, s.c., weekly for 8 weeks) led to a significant reduction in liver iron (~50% reduction compared to the isotype treated group) and improved red blood cell health as determined by Annexin V staining, intracellular oxidative stress, and measurement of red blood cell turnover. This effect on red blood cells was reflected by a longer running distance of Hbbth3/+ mice during forced exercise and a reduction in serum lactate production. Our data shows, that targeting TMPRSS6 has significant advantages over current treatments, such as Luspatercept, an ACVR2b receptor trap or iron chelation. These therapeutics target either red blood cell formation (Luspatercept) or iron loading (iron chelators), but not both. Hence, blockade of TMPRSS6 seems a good addition to current therapeutics. In addition, we tested REGN7999 in HFE-/-mice, a mouse model of hereditary hemochromatosis. After 8 weeks treatment, liver iron from HFE-/- mice was significantly reduced in these animals. Taken together, inhibition of TMPRSS6 is an advantageous strategy in different iron overload diseases.
Free-breathing 3D stack-of-radial MRI quantification of liver fat and R2* in adults with fatty liver disease (2021)

To investigate the agreement, intra-session repeatability, and inter-reader agreement of liver proton-density fat fraction (PDFF) and R2* quantification using free-breathing 3D stack-of-radial MRI, with and without self-gated motion compensation, compared to reference breath-hold techniques in subjects with fatty liver disease (FLD). In this institutional review board-approved prospective study, thirty-eight adults with FLD and/or iron overload (24 male, 58 ± 12 years) were imaged at 3T using free-breathing stack-of-radial MRI, breath-hold 3D Cartesian MRI, and breath-hold single-voxel MR spectroscopy (SVS). Each sequence was acquired twice in random order. To assess agreement compared to reference breath-hold techniques, the dependency of liver PDFF and/or R2* quantification on the sequence, radial sampling factor, and radial self-gating temporal resolution was assessed by calculating the Bayesian mean difference (MDB) of the posteriors. Intra-session repeatability and inter-reader agreement (two independent readers) were assessed by the coefficient of repeatability (CR) and intraclass correlation coefficient (ICC), respectively. Thirty-five participants (21 male, 57 ± 12 years) were included for analysis. Both free-breathing radial MRI techniques (with and without self-gating) achieved ICC ≥ 0.92 for quantifying PDFF and R2*, and quantified PDFF with MDB < 1.2% compared to breath-hold techniques. Free-breathing radial MRI required self-gating to accurately quantify R2* (MDB < 10s−1 with self-gating; MDB < 50s−1 without self-gating). The radial sampling factor affected PDFF and R2* quantification while the radial self-gating temporal resolution only affected R2* quantification. Repeated self-gated free-breathing radial MRI scans achieved CR < 3% and CR < 27 s−1 for PDFF and R2*, respectively. A free-breathing stack-of-radial MRI technique with self-gating demonstrated agreement, repeatability, and inter-reader agreement compared to reference breath-hold techniques for quantification of liver PDFF and R2* in adults with FLD.
Improvements of Bayesian Matting (2007)

Previous studies demonstrated an enhancing effect of granulocyte-macrophage colony-stimulating-factor (GM-CSF) on natural cytotoxicity. It was the aim of this study to investigate if CD56(+) natural-killer (NK) cells are responsible for the increased natural cytotoxicity after GM-CSF treatment. NK-cells were incubated with or without GM-CSF and Interferon-alpha (IFN-alpha) at various concentrations. NK-activity was determined by their ability to lyse NK-sensitive tumor cells (K562) and by cell surface expression of activation markers (CD25 and CD69). In our experimental setting incubation of CD56(+) NK-cells with GM-CSF did not significantly alter NK-cell mediated cytotoxicity or the expression of activation markers. In contrast, pre-treatment with IFN-alpha, a well known stimulant of NK-activity enhanced cytotoxicity by 69.2%+/-13.2%, P<0.05, effector/target cell ratio (E/T) 10:1 and by 43.3%+/-17.3%, P<0.05, E/T 20:1 and increased the expression of CD69 and CD25. Our results suggest that GM-CSF treatment alone cannot enhance natural cytotoxicity mediated by CD56(+) NK-cells in vitro.
Enhanced Specific Heat of Sodium Acetate Trihydrate by In-Situ Nanostructure Synthesis (2018)

Recent studies have shown that doping nanoparticles (NPs) into a molten salt eutectic can induce salt molecules to form a stelliform nanostructure that can enhance the effective heat capacity of the mixture. This phenomenon can result from a unique characteristic of a eutectic molten salt system, which can self-form a nanostructure on a nanoscale solid surface. Hence, such an enhancement was only observed in a molten salt eutectic. Similarly, a stelliform nanostructure can be artificially synthesized and dispersed in other liquids. Mixing polar-ended molecules with a NP in a medium can induce the polar-ended molecules ionically bonded to a NP to form a stelliform nanostructure. Hence, this may enhance the effective heat capacity of the mixture. In this study, we disperse various NPs and polar-ended materials into a sodium acetate trihydrate (SAT) at different ratios to explore the effect of NP type and concentration as well as polar-ended materials and their concentrations on the resultant heat capacity of SAT. The result shows that the specific heat capacity was the highest with silica NP at 1% concentration of weight and polar-ended material at 4% concentration.
SensMiLi: Absolutes Wegmess-System aus einer diffraktiven q-nären Pseudo-Zufalls-Sequenz (2012)

Zusammenfassung Es wird ein neuartiges Prinzip für ein optisch absolut codiertes Wegmess-System vorgestellt, das auf der Beugung von Licht beruht. Optimiert für die Integration in Miniatur-Linearmotoren soll es diese zu hochdynamischen, mikrometergenauen Bewegungen in Reinräumen befähigen. Zum ersten Mal wird gezeigt wie q -näre Pseudo-Zufalls-Sequenzen durch optische Beugung codiert werden können und so u. a. Verbesserungen bzgl. Code-Effizienz, Integrationsfähigkeit und Robustheit ermöglichen.