gebhart/patrepeval huggingface dataset:
Nonsecretory α-Chain Disease with Immunoproliferative Smallintestinal Disease (1989)

HEAVY-CHAIN diseases in humans, which have been described for the three main classes of immunoglobulins, are B-cell disorders in which proliferating cells produce truncated monoclonal heavy chains that lack associated light chains.1 The abnormal proteins have deletions of part or all of the variable region and of one or two constant domains, usually CH1. The normal sequence resumes at a position corresponding to the beginning of an exon.2 The heavy chains are synthesized as abnormally short chains.3 , 4 Recent studies in a few cases of μ–heavy-chain and γ-heavy-chain diseases have shown that the messenger RNA (mRNA) was short and . . .
Dehydration of Glucose to 5‐Hydroxymethylfurfural Using Nb‐doped Tungstite (2016)

Dehydration of glucose to 5-hydroxymethylfurfural (HMF) remains a significant problem in the context of the valorization of lignocellulosic biomass. Hydrolysis of WCl6 and NbCl5 leads to precipitation of Nb-containing tungstite (WO3 ⋅H2 O) at low Nb content and mixtures of tungstite and niobic acid at higher Nb content. Tungstite is a promising catalyst for the dehydration of glucose to HMF. Compared with Nb2 O5 , fewer by-products are formed because of the low Brønsted acidity of the (mixed) oxides. In water, an optimum yield of HMF was obtained for Nb-W oxides with low Nb content owing to balanced Lewis and Brønsted acidity. In THF/water, the strong Lewis acidity and weak Brønsted acidity caused the reaction to proceed through isomerization to fructose and dehydration of fructose to a partially dehydrated intermediate, which was identified by LC-ESI-MS. The addition of HCl to the reaction mixture resulted in rapid dehydration of this intermediate to HMF. The HMF yield obtained in this way was approximately 56 % for all tungstite catalysts. Density functional theory calculations show that the Lewis acid centers on the tungstite surface can isomerize glucose into fructose. Substitution of W by Nb lowers the overall activation barrier for glucose isomerization by stabilizing the deprotonated glucose adsorbate.
Fluid dynamics of flow through microscale lattice structures formed from self‐propagating photopolymer waveguides (2010)

Abstract The fluid dynamics of flow through microscale lattice structures is characterized for different unit cell sizes, flow angles, and flow rates. The structures consist of an octahedral‐type periodic unit cell, which is formed from an interconnected pattern of self‐propagating photopolymer waveguides. The periodic unit cell of each sample has a node‐to‐node spacing between 800 and 2400 μm and a truss member diameter between 148 and 277 μm. Water is directed through the microscale lattice structures, and the resulting pressure drop is investigated for two different flow angles and superficial flow rates between 0.5 and 4.8 L/min. Finite element analysis is used to determine pressure drop in the laminar flow regime. The results are used to develop a correlation describing friction factor as a function of flow direction, geometric characteristics, and Reynolds number. This work enables control of the fluid dynamics in microarchitected multifunctional truss materials through design and superficial flow angle. © 2010 American Institute of Chemical Engineers AIChE J, 2011
A SYNOPTIC CLIMATOLOGY OF TORNADOES IN VIRGINIA (1997)

Although tornadoes are microscale meteorological features, their occurrence is linked to the larger synoptic-scale environment. Most conceptual models of synoptic situations that give rise to tornadoes are based on conditions prevalent in the Great Plains of the United States. However, tornadoes develop in many different synoptic environments, particularly when they form beyond the boundaries of “Tornado Alley.” Tornado occurrences in the state of Virginia are identified from 1951 through 1992. Using upper air data for the nearest site and observation time, a synoptic classification is produced via application of principal components analysis and cluster analysis. The five resulting synoptic classes each exhibit distinctive thermodynamic and flow conditions that serve as air-mass paradigms for tornado occurrence in Virginia. The groups include thermodynamic/northwest flow air masses, a mixed thermodynamic/dynamic category, a polar front jet situation, cool season midlatitude cyclone events, and Great Plains type tornadic air masses. A sixth type, tornadoes spawned by tropical systems, is defined separately. A variety of indices have been developed by forecasters to provide information about the likelihood of severe weather and tornadic activity. The lifted index, K-index, Showalter index, SWEAT, Totals index, and a wind shear index are calculated for each tornado event. Analysis of variance indicates that most of these indices are statistically different between synoptic classes. These results suggest that the synoptic-scale mechanisms responsible for tornado occurrence in the mid-Atlantic states are quite variable. Enhanced predictive capability could be gained by considering the prevailing synoptic conditions associated with individual storms. [Key words: synoptic climatology, tornadoes, Virginia, classification, severe weather.]
LRADNN: High-throughput and energy-efficient Deep Neural Network accelerator using Low Rank Approximation (2016)

In this work, we propose an energy-efficient hardware accelerator for Deep Neural Network (DNN) using Low Rank Approximation (LRADNN). Using this scheme, inactive neurons in each layer of the DNN are dynamically identified and the corresponding computations are then bypassed. Accordingly, both the memory accesses and the arithmetic operations associated with these inactive neurons can be saved. Therefore, compared to the architectures using the direct feed-forward algorithm, LRADNN can achieve a higher throughput as well as a lower energy consumption with negligible prediction accuracy loss (within 0.1%). We implement and synthesize the proposed accelerator using TSMC 65nm technology. From the experimental results, a 31% to 53% energy reduction together with a 22% to 43% throughput increase can be achieved.
Life Beyond Kinases: Structure-Based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors (2012)

Of great interest in recent years has been computationally predicting the novel polypharmacology of drug molecules. Here, we applied an "induced-fit" protocol to improve the homology models of 5-HT(2A) receptor, and we assessed the quality of these models in retrospective virtual screening. Subsequently, we computationally screened the FDA approved drug molecules against the best induced-fit 5-HT(2A) models and chose six top scoring hits for experimental assays. Surprisingly, one well-known kinase inhibitor, sorafenib, has shown unexpected promiscuous 5-HTRs binding affinities, K(i) = 1959, 56, and 417 nM against 5-HT(2A), 5-HT(2B), and 5-HT(2C), respectively. Our preliminary SAR exploration supports the predicted binding mode and further suggests sorafenib to be a novel lead compound for 5HTR ligand discovery. Although it has been well-known that sorafenib produces anticancer effects through targeting multiple kinases, carefully designed experimental studies are desirable to fully understand whether its "off-target" 5-HTR binding activities contribute to its therapeutic efficacy or otherwise undesirable side effects.
Photobleaching effects in organic thin film sensing probes (2012)

The phenomenon of photobleaching of fluorescence indicators in organic thin films is presented. The study is performed on the fluorescein methacrylate indicator immobilized in an acrylate matrix. A LED based interrogation setup has been realized to evaluate the effects of photobleaching. The experimental results show as stability and drift of the fluorescence signal induced by photobleaching are the most critical aspects in sensing applications.
An Approximate Maximum Likelihood Time Synchronization Algorithm for\n Zero-padded OFDM in Channels with Impulsive Gaussian Noise (2020)

In wireless communication systems, Orthogonal Frequency-Division Multiplexing\n(OFDM) includes variants using either a cyclic prefix (CP) or a zero padding\n(ZP) as the guard interval to avoid inter-symbol interference. OFDM is ideally\nsuited to deal with frequency-selective channels and additive white Gaussian\nnoise (AWGN); however, its performance may be dramatically degraded in the\npresence of impulse noise. While the ZP variants of OFDM exhibit lower bit\nerror rate (BER)and higher energy efficiency compared to their CP\ncounterparts,they demand strict time synchronization, which is challenging in\nthe absence of pilot and CP. Moreover, on the contrary to AWGN, impulse noise\nseverely corrupts data. In this paper, a new low-complexity timing offset (TO)\nestimator for ZP-OFDM for practical impulsive-noise environments is proposed,\nwhere relies on the second-other statistics of the multipath fading channel and\nnoise. Performance comparison with existing TO estimators demonstrates either a\nsuperior performance in terms of lock-in probability or a significantly lower\ncomplexity over a wide range of signal-to-noise ratio (SNR) for various\npractical scenarios.\n
Phase-contrast x-ray imaging for nondestructive evaluation of materials (2006)

Phase-contrast x-ray imaging has been studied intensively in the past, mainly with applications to low density biological materials. In this work experimental and theoretical aspects of phase-contrast microfocus x-ray imaging of structural materials (metals and polymers) are considered. The diffraction field in an object from a point x-ray source is simulated and the effects of geometrical and material parameters on the x-ray phase-contrast image are obtained. It is shown that higher-order terms should be retained in the asymptotic expansion of the Green function in the image plane to accurately image discontinuities in structural materials. Experimental phase-contrast images of small defects are obtained with a 5μm microfocal x-ray source and compared with those from computer simulation as a function of geometrical magnification and photon energy. The phase-contrast x-ray imaging provides enhanced image contrast and improved edge definition and is important for further development of nondestructive evaluation of structural materials.
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription (2015)

Our results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction.
Chitosan Oligosaccharide Prevents Afatinib-Induced Barrier Disruption and Chloride Secretion through Modulation of AMPK, PI3K/AKT, and ERK Signaling in T84 Cells (2022)

Diarrhea is an important adverse effect of epidermal growth factor receptor-tyrosine kinase inhibitors, especially afatinib. Novel antidiarrheal agents are needed to reduce epidermal growth factor receptor-tyrosine kinase inhibitor-associated diarrhea to improve the quality of life and treatment outcome in cancer patients. This study aimed to investigate the anti-diarrheal activity of chitosan oligosaccharide against afatinib-induced barrier disruption and chloride secretion in human intestinal epithelial cells (T84 cells). Chitosan oligosaccharide (100 μg/mL) prevented afatinib-induced barrier disruption determined by changes in transepithelial electrical resistance and FITC-dextran flux in the T84 cell monolayers. In addition, chitosan oligosaccharide prevented afatinib-induced potentiation of cAMP-induced chloride secretion measured by short-circuit current analyses in the T84 cell monolayers. Chitosan oligosaccharide induced the activation of AMPK, a positive regulator of epithelial tight junction and a negative regulator of cAMP-induced chloride secretion. Moreover, chitosan oligosaccharide partially reversed afatinib-induced AKT inhibition without affecting afatinib-induced ERK inhibition via AMPK-independent mechanisms. Collectively, this study reveals that chitosan oligosaccharide prevents the afatinib-induced diarrheal activities in T84 cells via both AMPK-dependent and AMPK-independent mechanisms. Chitosan oligosaccharide represents a promising natural polymer-derived compound for further development of treatment for afatinib-associated diarrheas.
296-OR: Submicron Ultrasound Contrast Agents as Therapeutic Delivery Vehicles in Type 1 Diabetes (2023)

Type 1 diabetes (T1D) is characterized by immune-mediated destruction of insulin-producing beta cells resulting in severe hyperglycemia if untreated. Prior work has shown that islet microvasculature becomes hyperpermeable during presymptomatic T1D, allowing for ‘nanobubble (NB)’ submicron ultrasound contrast agents to accumulate in immune-infiltrated islets, which can be quantified using ultrasound contrast. We investigated the utility of these lipid-shelled NBs as peptide delivery vehicles to provide islet-targeted delivery, for acoustically driven therapeutic release and where therapeutic delivery can be visualized in real-time with ultrasound. We developed this platform to enhance efficacy of insulin peptide mimotopes, which can promote the expansion of anti-inflammatory regulatory T cells (Tregs) and prevent T1D in mice. We modified insulin B:9-23 peptides with a palmitoyl fatty acid tail to incorporate in the NB lipid shell. NBs accumulated specifically in NOD islets and not in other abdominal organs or NOD-SCID (control) islets (p &amp;lt; 0.0001). We found that palmitoylation enhanced peptide retention in NBs (p &amp;lt; 0.001) and is essential for delivery to NOD islets (p &amp;lt; 0.0001), where the extent of peptide delivery correlates with extent of insulitis (p &amp;lt; 0.05). Peptide incorporation did not affect NB echogenicity (in vitro and in vivo), ability to burst, and size distribution. Palmitoylation and incorporation in NBs does not affect the ability for peptide-pulsed antigen presenting cells to stimulate insulin-reactive T cells in vitro (p &amp;lt; 0.0001). Finally, NOD mice treated with peptide-NBs had a higher proportion of Tregs amongst insulin-reactive CD4+ T cells in islets, as compared to mice treated with NBs or peptide alone (p &amp;lt; 0.05). This serves as an important proof-of-principle for the usage of NBs for targeted peptide delivery and has the potential to improve therapeutic intervention in T1D. Disclosure M.Ciccaglione: None. K.Mcdaniel: None. A.W.Michels: Stock/Shareholder; Immnomolecular Therapeutics. A.A.Exner: None. R.K.Benninger: None. Funding National Institute of Diabetes and Digestive and Kidney Diseases (R01DK102950, R01DK106412, P30DK116073, T32DK120520); National Center for Advancing Translational Sciences (TL1TR002533); JDRF (1-INO-2017-435-A-N); University of Colorado
Thrombospondin in human glomerulopathies. A marker of inflammation and early fibrosis. (1994)

Extensive damage is thought to occur to endothelial cells in renal vasculitis and other glomerulopathies. The state of inflammation of these endothelial cells was investigated through the use of a panel of monoclonal antibodies (MAb) directed against thrombospondin (TSP), von Willebrand factor (vWF), integrins (alpha IIb beta 3, alpha v beta 3), CD36, and classical markers of inflammation (P-selectin, E-selectin, ICAM-1, VCAM). Results show that the anti-TSP MAb (LYP10) stains large areas of interstitium in focal sclerosis, vasculitis, membranous glomerulonephritis (GN), and diabetic GN but does not in normal kidney. In contrast, very limited areas are stained by LYP10 in minimal change nephropathy and Berger's disease. On paraffin-embedded specimens these areas stained by LYP10 appear edematous and early fibrous. Up-regulation of vWF and ICAM-1 is matched by an increased binding of LYP10 to the interstitium. In addition, fibrous crescents in injured glomeruli are stained by LYP10. This study reports for the first time an increased TSP secretion in glomerulopathies. Such TSP secretion may be part of physiological adaptive changes associated with inflammation and early fibrosis.
Drug-resistant tuberculosis: etiology, management and prevention. (1994)

Drug-resistant Mycobacterium tuberculosis inevitably arises from inadequate or inappropriate drug taking or drug prescribing, effectively resulting in monotherapy. This may occur in the patient being treated (acquired resistance) or in a patient who has been infected by another patient with drug resistant tuberculosis (primary resistance). There is some evidence that multidrug-resistant tuberculosis, ie, resistance to both isoniazid and rifampin, is increasing in the United States and in other countries where unsupervised treatment with rifampin has been common. Human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS), although not causing drug-resistant tuberculosis, have certainly magnified the problem, especially in New York City. Treatment of drug-resistant tuberculosis must be based on results of drug susceptibility studies. Patients with isolated isoniazid-resistant tuberculosis respond well to modified short-course therapy with rifampin, ethambutol, and pyrazinamide. Multidrug-resistant disease is more difficult to treat, although most patients will respond to regimens of second-line drugs if the infecting organisms are susceptible to these agents. Drug-resistant tuberculosis can be prevented by accurate identification of patients with newly diagnosed tuberculosis who may be at increased risk of primary drug resistance, the administration of an appropriate treatment regimen to all newly diagnosed patients, the application of fully supervised therapy during at least the initial phase of treatment, the use of combination preparations of drugs, and the proper management of failure and relapse cases.
Differentially expressed protein markers in human submandibular and sublingual secretions (2004)

Proteome analysis of secretions from individual salivary glands is important for understanding the health of the oral cavity and pathogenesis of certain diseases. However, cross-contamination of submandibular (SM) and sublingual (SL) glandular secretions can occur. The close anatomic relationship of the SM and SL ductal orifices can lead to such contamination. Additionally, these glands may share common ducts. To insure the purity of SM/SL secretions for proteomic analysis, it is important to develop unique biomarkers which could be used to verify the integrity of the individual glandular saliva. In this study, a proteomics approach based on mass spectrometry and gel electrophoresis techniques was utilized to identify and verify a set of proteins (cystatin C, calgranulin B and MUC5B mucin), which are differentially expressed in SM/SL secretions. SM/SL fluids were obtained from nine healthy subjects. Cystatin C was found to be an SM-selective protein as it was found in all SM fluids but not detected in two SL fluids. MUC5B mucin and calgranulin B, on the other hand, were found to be SL-selective proteins. All SL samples contained MUC5B mucin, whereas MUC5B mucin was not detected in four SM samples. Eight of the SL samples contained calgranulin B; however, calgranulin B was absent in eight SM samples. This set of protein markers, especially calgranulin B, can be used to determine the purity of SM/SL samples, and therefore identify potential individuals who do not exhibit cross-contaminated SM/SL secretions, an important requirement for subsequent proteome analysis of pure SM and SL secretions.
Robust adaptive geometric tracking controls on SO(3) with an application to the attitude dynamics of a quadrotor UAV (2011)

This paper provides new results for a robust adaptive tracking control of the attitude dynamics of a rigid body. Both of the attitude dynamics and the proposed control system are globally expressed on the special orthogonal group, to avoid complexities and ambiguities associated with other attitude representations such as Euler angles or quaternions. By designing an adaptive law for the inertia matrix of a rigid body, the proposed control system can asymptotically follow an attitude command without the knowledge of the inertia matrix, and it is extended to guarantee boundedness of tracking errors in the presence of unstructured disturbances. These are illustrated by numerical examples and experiments for the attitude dynamics of a quadrotor UAV.
Isolation and Analysis of the Enzymatic Properties of Thermophilic Fungi from Compost (2014)

To the best of our knowledge, this is the first report on thermophilic fungi isolated in Korea. Three species of thermophiles were isolated from compost and were identified as Myriococcum thermophilum, Thermoascus aurantiacus, and Thermomyces lanuginosus. They can grow at temperatures above 50℃ and produce high levels of cellulolytic and xylanolytic enzymes at high temperatures. Notably, the considerable thermostability of the endo-glucanase produced by T. aurantiacus has made the fungus an attractive source of industrial enzymes.
An Experimental Device to Record Infant Head Movements (1981)

putting the baby's head in a light and moving head cap with an electrical potentiometer located on the cap. Head movements are translated into an electrical signal which is amplified and registered by a polygraph recorder. This method is generally used to study either head-turning movements along the longitudinal axis when the baby is lying down (Bernuth & Prechtl 1969; Casaer 1979; Papousek 1961) or horizontal rotations of the head when the infant is sitting in a semivertical position (Trevarthen & Tursky 1969; Tronick & Clanton 1971). The second method, proposed by Delucia and Bullinger (1976) and used in newborns by Bullinger (1977) employs a rather simple photoelectrical device: a light-detection system with a two-cell position so that the ambient light, altered by the infant's head displacements, differentially affects these cells.
Histoplasmosis clinically imitating cutaneous malignancy (2008)

Disseminated histoplasmosis can have a varied presentation when it affects the skin. Presentation mimicking a cutaneous neoplasm is an uncommon manifestation. We present the case of an 86-year-old man presenting with a cutaneous lesion clinically suspicious for malignancy that was ultimately determined to be his first clinical manifestation of disseminated histoplasmosis after biopsy for histopathologic analysis. Microscopically, the lesion was a nodule with an eroded epidermis overlying a dense dermal inflammatory process. The infiltrate was characterized by numerous epithelioid histiocytes admixed with acute and chronic inflammation. On closer inspection, numerous 2-4 mum intracellular spores surrounded by a clear halo were identified. The organisms were highlighted with periodic acid schiff (PAS) stain. We present this case to highlight a unique presentation of disseminated histoplasmosis. Although this presentation is uncommon, it serves as a reminder that histopathologic confirmation of clinical diagnoses is important before undertaking more invasive procedures such as excision.