gebhart/patrepeval huggingface dataset:
Detection of long repeat expansions from PCR-free whole-genome sequence data (2016)

Abstract Identifying large repeat expansions such as those that cause amyotrophic lateral sclerosis (ALS) and Fragile X syndrome is challenging for short-read (100-150 bp) whole genome sequencing (WGS) data. A solution to this problem is an important step towards integrating WGS into precision medicine. We have developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3,001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Taking the RP-PCR calls as the ground truth, our WGS-based method identified pathogenic repeat expansions with 98.1% sensitivity and 99.7% specificity. Further inspection identified that all 11 conflicts were resolved as errors in the original RP-PCR results. Compared against this updated result, ExpansionHunter correctly classified all (212/212) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2,786/2,789) of the wild type samples were correctly classified as wild type by this method with the remaining two identified as possible expansions. We further applied our algorithm to a set of 144 samples where every sample had one of eight different pathogenic repeat expansions including examples associated with fragile X syndrome, Friedreich’s ataxia and Huntington’s disease and correctly flagged all of the known repeat expansions. Finally, we tested the accuracy of our method for short repeats by comparing our genotypes with results from 860 samples sized using fragment length analysis and determined that our calls were &gt;95% accurate. ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.
Radio Sensing with Large Intelligent Surface for 6G (2023)

This paper leverages the potential of Large Intelligent Surfaces (LIS) for radio sensing in 6G wireless networks. By taking advantage of arbitrary communication signals occurring in the scenario, we apply direct processing to the output signal from the LIS to obtain a radio map that describes the physical presence of passive devices (scatterers, humans) which act as virtual sources due to the communication signal reflections. We then assess the usage of machine learning and computer vision methods including clustering, template matching and component labeling to extract meaningful information from these radio maps. As an exemplary use case, we evaluate this method for passive multi-human detection in an indoor setting. The results show that the presented method has high application potential as we are able to detect around 98% of humans passively even in quite unfavorable Signal-to-Noise Ratio (SNR) conditions.
Symposium: Masters in Otolaryngology—Update in Rhinology (2003)

Abstract The past few years have witnessed several noteworthy advances in the field of rhinology in general and in the treatment of chronic sinusitis in particular. Many of these advances can be classified into three major trends: technology, techniques, and tissue eosinophilia.
Geometry Dependence of Total-Dose Effects in Bulk FinFETs (2014)

<?Pub Dtl=""?> The total ionizing dose (TID) response of bulk FinFETs is investigated for various geometry variations, such as fin width, channel length, and fin pitch. The buildup of oxide-trapped charge in the shallow trench isolation turns on a parasitic transistor, leading to increased leakage current (higher <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${{I}_{{\rm OFF}}}$</tex></formula> .) The TID-induced degradation increases with decreasing fin width. Transistors with longer channels degrade less than those with shorter channels. Transistors with large fin pitch degrade more, compared to those with narrow fin pitch. TCAD simulations are used to analyze the buildup of trapped charge in the trench isolation oxide and its impact on the increase in leakage current. The strong influence of charge in the STI in narrow-fin transistors induces a parasitic leakage current path between the source and the drain, while in wide-fin devices, for the same amount of trapped charge in the isolation oxide, the subsurface leakage path is less effective.
Improved functionalization of oleic acid-coated iron oxide nanoparticles for biomedical applications (2012)

Superparamagnetic iron oxide nanoparticles can provide multiple benefits for biomedical applications in aqueous environments such as magnetic separation or magnetic resonance imaging. To increase the colloidal stability and allow subsequent reactions, the introduction of hydrophilic functional groups onto the particles' surface is essential. During this process, the original coating is exchanged by preferably covalently bonded ligands such as trialkoxysilanes. The duration of the silane exchange reaction, which commonly takes more than 24 h, is an important drawback for this approach. In this paper, we present a novel method, which introduces ultrasonication as an energy source to dramatically accelerate this process, resulting in high-quality water-dispersible nanoparticles around 10 nm in size. To prove the generic character, different functional groups were introduced on the surface including polyethylene glycol chains, carboxylic acid, amine, and thiol groups. Their colloidal stability in various aqueous buffer solutions as well as human plasma and serum was investigated to allow implementation in biomedical and sensing applications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11051-012-1100-5) contains supplementary material, which is available to authorized users.
ChemInform Abstract: Silaheterocycles. Part 35. Carbon=Carbon Hydrogenation of Silicon‐Functionalized Silaheterocycles. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Turkey Behavior Identification System with a GUI Using Deep Learning and Video Analytics (2021)

In this paper, we propose a video analytics system to identify the behavior of turkeys. Turkey behavior provides evidence to assess turkey welfare, which can be negatively impacted by uncomfortable ambient temperature and various diseases. In particular, healthy and sick turkeys behave differently in terms of the duration and frequency of activities such as eating, drinking, preening, and aggressive interactions. Our system incorporates recent advances in object detection and tracking to automate the process of identifying and analyzing turkey behavior captured by commercial grade cameras. We combine deep-learning and traditional image processing methods to address challenges in this practical agricultural problem. Our system also includes a web-based user interface to create visualization of automated analysis results. Together, we provide an improved tool for turkey researchers to assess turkey welfare without the time-consuming and labor-intensive manual inspection.
Chiral recognition of N<sup>α</sup>‐protected amino acids and derivatives in non‐covalently molecularly imprinted polymers (1994)

Highly crosslinked synthetic polymers, selective for various N alpha-protected amino acids and derivatives, were prepared by non-covalent molecular imprinting. Methacrylic acid and ethylene glycol dimethacrylate were copolymerized in the presence of the print molecules, which were subsequently extracted from the polymers. The recognition of the polymers for the print molecules and molecules of similar structures was investigated by using the polymers as stationary phases in HPLC. The functional groups of the print molecules interact via hydrogen bonds with the positioned carboxyls of the polymer. It was shown that the N alpha-protecting group, the C alpha-protecting group and the amino acid side chain are also recognized by the binding sites in the polymer.
Characterization of an HLA‐B62 variant (B*1538) exhibiting an additional B52 serologic reactivity (1997)

Antigens bearing the B62 serologic specificity are a heterogeneous group being encoded by at least 10 alleles and are widespread in most populations including the Korean population (10.5%). This study characterized a new allele encoding a B62 molecule with extra B52 serologic reactivity from a Korean family and unrelated individuals. Based on the DNA sequence, it appears that the single nucleotide substitution at codon 171 (TAC-->CAC), resulting in an amino acid change from tyrosine to histidine, is responsible for creating the extra reactivity. B*1538 was confirmed by PCR-SSP using a primer annealing to codon 171 in two additional unrelated individuals also exhibiting the same serologic reaction pattern. The haplotype associated with the novel allele, A31-B*1538-Bw6-Cw3-DRB1*1101-DRB3*02-DQB1*0301, was identified in the family members and two unrelated individuals. The novel B*1538 allele and its associated haplotype adds to the HLA diversity in this population.
Quantum Transport in the Charge-Density-Wave State of the Quasi Two-Dimensional Bronzes(PO<sub>2</sub>)<sub>4</sub>(WO<sub>3</sub>)<sub>2m</sub> (m = 4, 6) (1995)

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Analysis by Single-Gene Reassortment Demonstrates that the 1918 Influenza Virus Is Functionally Compatible with a Low-Pathogenicity Avian Influenza Virus in Mice (2012)

The 1918-1919 "Spanish" influenza pandemic is estimated to have caused 50 million deaths worldwide. Understanding the origin, virulence, and pathogenic properties of past pandemic influenza viruses, including the 1918 virus, is crucial for current public health preparedness and future pandemic planning. The origin of the 1918 pandemic virus has not been resolved, but its coding sequences are very like those of avian influenza virus. The proteins encoded by the 1918 virus differ from typical low-pathogenicity avian influenza viruses at only a small number of amino acids in each open reading frame. In this study, a series of chimeric 1918 influenza viruses were created in which each of the eight 1918 pandemic virus gene segments was replaced individually with the corresponding gene segment of a prototypical low-pathogenicity avian influenza (LPAI) H1N1 virus in order to investigate functional compatibility of the 1918 virus genome with gene segments from an LPAI virus and to identify gene segments and mutations important for mammalian adaptation. This set of eight "7:1" chimeric viruses was compared to the parental 1918 and LPAI H1N1 viruses in intranasally infected mice. Seven of the 1918 LPAI 7:1 chimeric viruses replicated and caused disease equivalent to the fully reconstructed 1918 virus. Only the chimeric 1918 virus containing the avian influenza PB2 gene segment was attenuated in mice. This attenuation could be corrected by the single E627K amino acid change, further confirming the importance of this change in mammalian adaptation and mouse pathogenicity. While the mechanisms of influenza virus host switch, and particularly mammalian host adaptation are still only partly understood, these data suggest that the 1918 virus, whatever its origin, is very similar to avian influenza virus.
Analysis and Control of a Body-Attached Spring-Mass Runner Based on Central Pivot Point Approach (2020)

The Spring-Loaded Inverted Pendulum (SLIP) template and its extensions have long been used as benchmark models for analyzing the dynamics of legged systems in biology and robotics. The fundamental SLIP model is composed of single point mass attached to the ground (during stance phase) via an ideal lossless spring. Many researchers introduced various extensions to this fundamental model, such as damping & torque actuation, to handle critical physical phenomena that are unavoidable in real systems. Another crucial missing concept in SLIP template is the effect of the upper body in humans and humanoid robotic systems on the closed-loop system dynamics. Even though the SLIP template can effectively capture COM behavior, it cannot provide a framework for describing fullbody stabilization and control. In this paper, we present a new control policy called the Central Pivot Point (CPP) for the body attached spring-mass runners. In the stance phase, CPP directs ground reaction forces through the center of mass and cancels the torque created by these forces on the body. In this way, the CPP model makes it possible to develop different controllers for both the body's rotational and euclidean dynamics. Firstly, we analyze the characteristics and stability of the periodic solutions of the CPP model. Then, we develop a PD controller for pitch dynamics and an LQR (Linear Quadratic Regulator) for gait level apex to apex discrete dynamics to stabilize the system's periodic solutions. We compute the basin of attraction of the proposed control scheme and show examples of how the model behaves under disturbances. The results show that the purposed model and associated control policy could be beneficial in the design and control of humanoid robotic systems.
Initial Results of First <i>In Vivo</i> Imaging of Bladder Lesions Using a High-Resolution Confocal Microendoscope (2020)

<b><i>Purpose:</i></b> Conventional cystoscopy plays an important role in detection of bladder cancer; however, it is difficult to differentiate benign and neoplastic lesions based on cystoscopic appearance alone. Advanced microscopic modalities, such as confocal laser endomicroscopy and optical coherence tomography, have been shown to provide critical histopathologic information to help identify neoplastic bladder lesions in real time, but their availability and clinical adoption are limited due to a high cost. In this study, we present the first use of a novel and low-cost ($ <5000) confocal high-resolution microendoscope (confocal HRME) for <i>in vivo</i> imaging of bladder lesions. <b><i>Materials and Methods:</i></b> In a cohort of 15 patients undergoing white light cystoscopy as part of their standard of care, high-resolution images of proflavine-stained bladder lesions were acquired <i>in vivo</i> using the confocal HRME. Based on these images, we evaluated the ability of the confocal HRME to visualize uroepithelium with subcellular resolution and high contrast. Furthermore, we analyzed the cellular architecture and staining patterns of benign and neoplastic bladder lesions in confocal HRME images and compared results to that of standard cystoscopy and histopathology. <b><i>Results:</i></b><i>In vivo</i> imaging in the pilot study demonstrates that the confocal HRME resolved subcellular structures of bladder uroepithelium with high contrast. In a wide range of clinical conditions from normal bladder wall to benign and neoplastic lesions, confocal HRME images revealed important diagnostic features that correlated to histopathology. <b><i>Conclusions:</i></b> The confocal HRME provides an affordable, portable, and easy-to-use tool to allow real-time and high-contrast subcellular characterization of bladder lesions, well suited for bladder cancer detection in community and resource-constrained settings. The ClinicalTrials.gov Identifier: NCT02340650.
Giant internal carotid artery aneurysms and porcelain aorta in an elderly patient with Marfan syndrome (2022)

Marfan syndrome (MFS) an inherited disorder caused by <i>FBN1</i> gene variants, is well known to cause lethal aortic aneurysm and dissections at a relatively young age. Here, we report giant internal carotid artery aneurysms (ICAAs) and porcelain aorta in an elderly patient with MFS.
Both Sertoli and Peritubular Cells Respond to Androgens with Increased Expression of an Androgen Response Element Reporter1 (1994)

To explore the ability of androgens to affect gene expression in Sertoli and peritubular cells in vitro, constitutively expressed pSV2-Luc and a regulated reporter containing an androgen response element (MMTV-Luc) were transiently transfected into these cells. Reporter expression was markedly affected by cell density and maturational age. Mibolerone-stimulated MMTV-Luc expression increased in Sertoli cells with animal age between 15 and 25 days, consistent with the developmental increase in androgen receptor concentration, but was not markedly age-dependent in peritubular cells. The antiandrogen hydroxyflutamide inhibited stimulation of MMTV-Luc expression by 1 and 10 nM testosterone in both Sertoli and peritubular cells, consistent with an androgen receptor-mediated event. In contrast, dexamethasone at 1 and 10 nM elicited no effect in Sertoli cells, but stimulated MMTV-Luc expression in peritubular cells. In this study, the androgen receptor/glucocorticoid receptor ratio was 2.4 and 0.06 in Sertoli and peritubular cells, respectively. Cotransfection of Sertoli and peritubular cells with a plasmid expressing the rat androgen receptor further increased the androgen-stimulated expression of MMTV-Luc. These data demonstrate the functionality of the androgen receptors in both Sertoli and peritubular cells in culture. Receptor expression appears to be a limiting factor in the response. The data are consistent with potential roles for both Sertoli and peritubular cells in androgen-mediated transcriptional events in the testis.
Retrieval of material parameters for uniaxial metamaterials (2015)

We present a general method for retrieving the effective tensorial permittivity of uniaxially anisotropic metamaterials. By relaxing the usually imposed constraint of assuming nonmagnetic metal/dielectric metamaterials, we also retrieve the effective permeability tensor and show that multilayer hyperbolic metamaterials exhibit a strong and broadband diamagnetic response in the visible regime. The method provides the means for designing magnetically anisotropic metamaterials for studying magnetic topological transitions in the visible regime. We obtain orientation-independent effective material parameters, which are distinguishable from mere wave parameters. We analytically validate this method for $\mathrm{Ag}/\mathrm{Si}{\mathrm{O}}_{2}$ planar metamaterials with a varying number of layers and filling fractions and compare to the results from effective medium theory and Bloch theory.
A Timer for analyzing temporally dynamic changes in transcription during differentiation in vivo (2017)

Abstract Understanding the mechanisms of cellular differentiation is challenging because differentiation is initiated by signaling pathways that drive temporally dynamic processes, which are difficult to analyse in vivo. We establish a new Tool, Timer-of-cell-kinetics-and-activity (Tocky [toki], time in Japanese). Tocky uses the Fluorescent Timer protein, which spontaneously shifts its emission spectrum from blue-to-red, in combination with computer algorithms to reveal the dynamics of differentiation in vivo. Using a transcriptional target of T cell receptor (TCR)-signaling, we establish Nr4a3-Tocky to follow downstream effects of TCR signaling. Nr4a3-Tocky reveals the temporal sequence of events during regulatory T cell (Treg) differentiation and shows that persistent TCR signals occur during Treg generation. Remarkably, antigen-specific T cells at the site of autoimmune inflammation also show persistent TCR signaling. In addition, by generating Foxp3-Tocky, we reveal the in vivo dynamics of demethylation of the Foxp3 gene. Thus, Tocky is a Tool for cell biologists to address previously inaccessible questions by directly revealing dynamic processes in vivo. Summary The authors establish a new Tool, Timer-of-cell-kinetics-and-activity (Tocky) revealing the temporal dynamics of cellular activation and differentiation in vivo. The tool analyses the temporal sequence of molecular processes during cellular differentiation and identifies cells that receive persistent signals in vivo.
Ultra-selective defect-free interfacially polymerized molecular sieve thin-film composite membranes for H<sub>2</sub> purification (2017)

Ultrathin, defect-free thin-film polyamide composite membranes developed for H<sub>2</sub>/CO<sub>2</sub> separation exhibit mixed-gas performance far exceeding all state-of-the-art polymeric membranes.
A database for evaluating the quality of experience in light field applications (2016)

Light fields captured by a new generation of digital photo cameras are processed in order to render different representation of the same scene. Evaluating the quality of experience in light field imaging applications requires publicly available databases in order to allow the research community to fairly compare the obtained results. This paper presents an open access database of light field images and corresponding views rendered at several refocusing and perspective changes.
Androgen deprivation and other treatments for advanced prostate cancer. (2001)

Among the issues discussed at this year's meeting on prostate cancer in Vail, Colorado, were several that specifically relate to the patient with advanced disease. Dr. E. David Crawford addressed the issue of the timing of hormone therapy, specifically reviewing several important trials that give a glimpse at the potential outcome of aggressive treatment in stage D1.5. The efficacy of antiandrogens, flutamide, bicalutamide, and nilutamide, when combined with chemical or surgical castration, was reviewed. Dr. Arturo Mendoza-Valdes reviewed the rationale behind intermittent (versus continuous) total androgen blockade, especially as related to quality of life. Dr. Paul Miller gave an update on the role of bisphosphonates as adjuvant therapy for prostate cancer. Also discussed was an important new agent for androgen deprivation, Abarelix, a sustained-release GnRH antagonist with low histamine-releasing potential which avoids testosterone and other hormone surge and flare.
Adjuvant Chemotherapy in Older Women with Early-Stage Breast Cancer (2009)

Standard adjuvant chemotherapy is superior to capecitabine in patients with early-stage breast cancer who are 65 years of age or older. (ClinicalTrials.gov number, NCT00024102.)
FADD-deficient T Cells Exhibit a Disaccord in Regulation of the Cell Cycle Machinery (2001)

FADD is an adapter protein that was originally isolated as a transducer of apoptotic signals for death domain-containing receptors. However, FADD-deficient mice are embryonic lethal and FADD(-/-) T cells developed from FADD(-/-) embryonic stem cells in the RAG-1(-/-) hosts lack the full potential to proliferate when stimulated through their T-cell receptor complex, suggesting that FADD protein might play a dualistic role in mediating not only cell death signaling but other non-apoptotic cellular pathways as well. Here we show that a substantial number of freshly isolated FADD(-/-) peripheral T cells are cycling but are defective in their co-stimulatory response when stimulated. Analysis of several cell cycle proteins shows normal down-regulation of p27 inhibitor but increased levels of p21, decreased levels of cyclin D2, and constitutive activation of several cyclin-dependent kinases in activated T cells. These data suggest that FADD is involved in the regulation of cell cycle machinery in T lymphocytes.
Toward Realization of Long-Range Wireless-Powered Sensor Networks (2019)

As the era of Internet of Things (IoT) emerges, powering massive IoT devices becomes a great challenge in need of immediate attention. This challenge can be resolved by radio frequency (RF) wireless power transfer (WPT) technology that remotely supplies power to a distant sensor device. In this article, we discuss the issues arising in designing wireless-powered sensor networks (WPSNs). We have built a prototype WPSN testbed with a large-scale antenna array. By demonstrating that a sensor node can perpetually operate up to the distance of 50 meters with self-powering, we validate the potential of turning the WPSN concept into reality.