gebhart/patrepeval huggingface dataset:
The Creolophins: A Family of Linear Triquinanes from Creolophus cirrhatus (Basidiomycete) (2007)

Abstract Complicatic acid and five novel linear triquinanes were isolated from mycelial cultures of Creolophus cirrhatus . The creolophins A, C, D, and E represent a novel type of highly oxidized triquinane sesquiterpenoids. Whereas those compounds with a secondary alcohol moiety in ring A are stable, the exomethylene ketone creolophin E ( 5 ) partly dimerized during workup to form the decacyclic 1,4‐dioxepin‐6‐one neocreolophin ( 6 ). Compounds 5 and 6 display cytotoxic activities against several tumor cell lines.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Reversible Tip-induced Structural Modifications in Scanning Tip Microscopy (1996)

Tip-induced structural modifications of the Si(100) surface in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) are investigated with first-principles total energy pseudopotential calculations. The atoms of the tungsten tip and the surface are fully relaxed according to the tip-surface interactions. At tip-surface distances relevant to STM measurements, the tip is found to significantly influence the dynamics of the surface atoms leading a new understanding of the microscopic STM measurement process. At smaller tip-surface distances, the tip-surface interactions can be used to directly manipulate the geometry of the surface atoms. At very low temperature, the theory predicts the existence of micromechanical hysteresis on an atomic scale which can be measured in low temperature AFM. The theory also leads to the discovery of a specific protocol of tip movements with implications towards a novel design for an ultra-high density memory storage device.
Intraductal Tissue Sampling Device Designed for the Biliary Tract (2021)

Clinical sampling of tissue that is read by a pathologist is currently the gold standard for making a disease diagnosis, but the few minimally invasive techniques available for small duct biopsies have low sensitivity, increasing the likelihood of false negative diagnoses. We propose a novel biopsy device designed to accurately sample tissue in a biliary stricture under fluoroscopy or endoscopic guidance. The device consists of thin blades organized around the circumference of a cylinder that are deployed into a cutting annulus capable of comprehensively sampling tissue from a stricture. A parametric study of the device performance was done using finite element analysis; this includes the blade deployment under combined axial compression and torsion followed by an axial 'cutting' step. The clinical feasibility of the device is determined by considering maximum deployment forces, the radial expansion achieved and the cutting stiffness. We find practical parameters for the device operation to be an overall length of 10 mm and a diameter of 3.5 mm for a [Formula: see text] blade thickness, which allow the device to be safely deployed with a force of 10N and achieve an expansion over 3x its original diameter. A model device was fabricated with these parameters and a [Formula: see text] thickness out of a NiTi superalloy and tested to validate the performance. The device showed strong agreement with an equivalent numerical model, reaching a peak force within 2% of that predicted numerically and fully recovering after compression to 20% of its length. <i><b>Clinical and Translational Impact Statement</b></i> -This pre-clinical research conceptually demonstrates a novel expandable device to biopsy tissue in narrow strictures during an ERCP procedure. It can greatly improve diagnostic tissue yield compared to existing methods.
Class III β‐tubulin, a marker of resistance to paclitaxel, is overexpressed in pancreatic ductal adenocarcinoma and intraepithelial neoplasia (2007)

TUBB3 is expressed in most pancreatic ductal adenocarcinomas, possibly accounting for the suboptimal response of these tumours to microtubule-stabilizing agents. Up-regulation of TUBB3 in PanIN lesions suggests that microtubule dysfunction is an early feature of this disease. TUBB3 immunohistochemistry could potentially help identify pancreatic cancer patients lacking TUBB3 expression who might benefit from taxane therapy.
ICA model order selection of task co-activation networks (2013)

Independent component analysis (ICA) has become a widely used method for extracting functional networks in the brain during rest and task. Historically, preferred ICA dimensionality has widely varied within the neuroimaging community, but typically varies between 20 and 100 components. This can be problematic when comparing results across multiple studies because of the impact ICA dimensionality has on the topology of its resultant components. Recent studies have demonstrated that ICA can be applied to peak activation coordinates archived in a large neuroimaging database (i.e., BrainMap Database) to yield whole-brain task-based co-activation networks. A strength of applying ICA to BrainMap data is that the vast amount of metadata in BrainMap can be used to quantitatively assess tasks and cognitive processes contributing to each component. In this study, we investigated the effect of model order on the distribution of functional properties across networks as a method for identifying the most informative decompositions of BrainMap-based ICA components. Our findings suggest dimensionality of 20 for low model order ICA to examine large-scale brain networks, and dimensionality of 70 to provide insight into how large-scale networks fractionate into sub-networks. We also provide a functional and organizational assessment of visual, motor, emotion, and interoceptive task co-activation networks as they fractionate from low to high model-orders.
Expression of neurturin, GDNF, and their receptors in the adult mouse CNS (1998)

Neurturin (NTN) and glial cell line-derived neurotrophic factor (GDNF) are the first two members of the GDNF family (GF) of neurotrophic factors. These two proteins are potent survival factors for several populations of central and peripheral neurons in mature and developing rodents. The receptor for these factors is a multicomponent complex that includes the RET (rearranged during transfection) tyrosine kinase receptor and one of two glycosyl phosphatidylinositol (GPI)-linked ligand-binding components called GDNF family receptor alphas (GFRalpha-1 and GFRalpha-2). We have used in situ hybridization to study the mRNA expression of NTN, GDNF, RET, GFRalpha-1, and GFRalpha-2 in the central nervous system (CNS) of adult mice. GF receptors are expressed in several areas in which neuronal populations known to respond to NTN and GDNF are located, including the ventral horn of the spinal cord and the compacta region of the substantia nigra. In addition, we have demonstrated receptor expression in other areas of the brain including the thalamus and hypothalamus. Neurons in these areas express GF receptors, and therefore, may respond to NTN or GDNF. NTN and GDNF are expressed in targets of neurons that express GF receptors. The pattern of GF factor and receptor expression in the adult brain suggests a role for these factors in maintaining neuronal circuits in the mature CNS.
Evidence for pair generation of anE’ center and a nonbridging oxygen-hole center in γ-ray-irradiated fluorine-doped low-OH synthetic silica glasses (1992)

We have examined effects of fluorine concentration on defect formation by \ensuremath{\gamma}-ray irradiation in low-OH synthetic silica glasses over the F concentration range 0--3 wt. %. Doping with 1 wt. % of fluorine eliminates effectively \ensuremath{\equiv}Si-Cl without causing formation of \ensuremath{\equiv}Si-Si\ensuremath{\equiv} and \ensuremath{\equiv}Si-H (all such structural units may be precursors of the E' center); and \ensuremath{\equiv}Si-F does not behave as the precursors of the E' center. At this doping level, the concentration of the E' center is minimized, and the concentration coincides with that of the nonbridging oxygen-hole center (NBOHC). We conclude that pair generation of the E' center and NBOHC from intrinsic \ensuremath{\equiv}Si-O-Si\ensuremath{\equiv} bonds is observed in the samples in which the precursor defects are suppressed by proper F doping.
Interdependence and information loss in multi-sensor systems (1999)

Often, information cues obtained by the sensors of the multi-sensor system are not completely independent. This is true since sensors operate in a close vicinity and are subjected to the same disturbances in the working environment. In some instances the observations made by the different sensors of the systems are somewhat redundant. For example, there is always a possibility that a certain degree of overlap among these observations exists, and, hence, the estimates may be based, at least in part, on the same data. This problem could become more pronounced in intelligent sensors, where sensors are expected to possess some overlapping inferring ability, which in many cases leads to the possibility that two sensors or more base their decisions on similar underlying assumptions, theories, or common methods of analysis. Dependence in this case is not informative and therefore should be properly modeled so that its effect can be eliminated. Ignoring or improperly modeling this dependence may result in less informative observations and therefore sensors will tend to overestimate the importance of information cues communicated to them by other sensors. Consequently, the sensors may be perceived as being more accurate than they actually are. This article presents an information theory model for capturing dependence in multi-sensory data. A data fusion algorithm which revolves around the proposed dependency model for minimizing the impact of dependence among sensors is also presented. ©1999 John Wiley & Sons, Inc.
P: 56 Evaluation of Cognitive Dysfunction in Animal Models and Relatability to Human Disease (2019)

ABSTRACT: Animal models are essential to investigate the mechanisms responsible for the cognitive and motor alterations in minimal or clinical hepatic encephalopathy (HE). The characterization of these mechanisms allows identifying new therapeutic targets which modulation may improve neurological function in patients. Animal models also allow testing if treatments directed to modulate these targets improve cognitive and motor function. These studies require evaluation of cognitive and motor function in animal models. It is important to understand which tests can be performed in rodents, which cognitive and motor aspects are evaluated by the tests and how they can be related to cognitive and motor dysfunction in the patients. The earliest alterations in patients with minimal HE (MHE) include attention deficits, psychomotor slowing, impairment of visuo-motor and bimanual coordination, of working memory, spatial memory, long-term memory, spatial orientation, verbal learning, concentration, balance and equilibrium, associated with increased falls. To understand the mechanisms involved in each type of cognitive and motor alteration in MHE the behavioral tests in animal models should be designed to evaluate these neurological alterations by procedures that maximize the translatability to the human situation and the utility to evaluate treatments to improve cognitive and motor impairment. Many functions are evaluated in humans using pencil or computerized tests such as number connection tests, repetition of series of words or numbers, naming colors, and other actions which can't be reproduced exactly in animal models. Functions such as verbal learning can't be evaluated in animal models. However, a good number of cognitive and motor processes impaired in patients with MHE may be evaluated in rodents using appropriate behavioral tests. For example, a combination of properly designed tests in the radial maze, Morris water maze, object recognition and object location allows evaluating with high sensitivity working memory, reference memory and distinguishing the spatial and non-spatial components of working and reference memory. These components are altered in rats with MHE and different mechanisms are involved in the impairment of different components. Also, there are pharmacological treatments that restore selectively working or reference memory and spatial or non-spatial learning and memory in rats with MHE. There are also appropriate test to assess some motor alterations: hypokinesia, fine motor coordination or balance. Studies based on proper use of animal models will accelerate the advance in understanding the mechanisms involved in MHE and will open new therapeutic approaches to improve quality of life and life span of the patients.
Influence of anti-TNF therapy on monocyte gene expression in rheumatoid arthritis (2003)

Heterogeneity and multifactoriality complicate diagnostics and our understanding of pathogenesis of rheumatoid arthritis (RA). The only accepted serologic parameter (rheumatoid factor [RF]) is not disease specific, nor are any of several novel RA autoantibodies. We aimed at identifying profiles instead of individual autoreactivities allowing for unambiguous prediction of RA. Selected RA autoantigens were tested by ELISA (RF and anti-cyclic citrullinated peptide [anti-CCP]) or Western blot (heavy-chain-binding protein [BiP], heterogeneous ribonucleoprotein particle A2 [RA33/ hnRNP A2], calpastatin and calreticulin). Antibody reactivities were assayed from serum samples of 149 RA patients and 132 patients with other rheumatic diseases and from synovial fluids (SF) (58 RA, 65 non-RA). No single autoreactivity was sufficient for unambiguous prediction of RA. Frequencies of multiparameter profiles consisting of 3, 4, 5 and 6 autoreactivites were determined. Fifteen six-parameter serum profiles were exclusively expressed in RA patients, representing a cumulative sensitivity of 59%. Twelve SF profiles were exclusively expressed in 64% of RA patients. The self-learning classification algorithm CLASSIF1 was capable of accurately predicting RA when these profiles were present. Data profile analysis of RF/CCP/BiP/calpastatin/calreticulin/RA33 provided specific discrimination of 64% of RA. Most importantly, RA specific profiles were observed in 64% of patients with early disease (<12 months). For the first time, the accurate prediction of the class RA has been achieved by the use of multiparametric autoreactivity profiles. Because of early expression in disease, these profiles make it possible to start a disease-modifying therapy long before irreversible bone and joint destruction may develop. Additional RA-specific profiles are required to cover the entire group of RA patients.
User-friendly power management algorithms (2009)

This article addresses the optimal choice of the waiting period (or timeout) that a device should respect before entering sleep mode, so as to optimize a tradeoff between power consumption and user impact. The optimal timeout is inferred by appropriate statistical modeling of the times between user requests. In a test approach, these times are supposed independent, and a constant optimal timeout is inferred accordingly. In a second approach, some dependency is introduced through a hidden Markov chain, which also models specific activity states, like business hours or night periods. This model leads to a statistical framework for computing adaptive optimal timeout values. Different strategies are assessed using real datasets, on the basis of the power consumption, user impact and the frequency of wrong decisions. 1
Results from the Randomized Controlled Trial Cyclical Lower Extremity Exercise (CYCLE) Trial for Parkinson’s disease (2018)

Parkinson’s disease (PD) is a neurodegenerative disease affecting approximately one million Americans. Our previous work suggested that forced exercise (FE), a mode of aerobic exercise in which voluntary exercise (VE) rate is augmented, results in global motor improvements. PURPOSE: The aim of this randomized clinical trial was to systematically evaluate the effects of voluntary and forced exercise on the motor symptoms of PD. METHODS: A total of 100 individuals with PD (age 63 ± 8 years, n = 38 females) were randomized into one of three groups: VE (n = 40), FE (n = 40), or no-exercise control (n = 20). The VE and FE groups exercised 3x/week for 8 weeks on a stationary semi-recumbent cycle ergometer in a target heart rate range of 60-80% of heart rate reserve. The FE group exercised on a stationary cycle with the assistance of a motor that augmented pedaling rate by 35% compared to their preferred exercise rate. The MDS-Unified Parkinson’s Disease Rating Scale (UPDRS) was used to characterize PD motor function. All clinical evaluations were completed while patients were ‘off’ antiparkinsonian medication (12 hr) at baseline, end of treatment (EOT), EOT+4 week and EOT+8 week. RESULTS: UPDRS-III scores significantly decreased from baseline to the EOT for both the VE and FE groups. The VE and FE groups demonstrated significant improvements in clinical ratings following exercise. The magnitude of improvement was 5.4 and 4.5 points for the VE and FE groups (p<0.001) at EOT. The significant decrease in UPDRS-III was maintained for the VE (-3.5) and FE (-3.2) during the EOT+8 week follow up. The control group exhibited a slight worsening, 2.2 increase, at EOT in clinical ratings. There were no significant differences between the VE and FE groups. CONCLUSION: Improvements in global motor performance following VE and FE interventions indicate high intensity aerobic exercise is likely enhancing central nervous function (CNS) which ameliorates basal ganglia dysfunction associated to PD. The clinical rating improvement in the FE and VE groups persisted eight weeks after ending treatment suggesting high intensity aerobic cycling may have potential in altering PD progression and efficacy as a complementary treatment to traditional approaches to PD.
Silicon-based highly-efficient fiber-to-waveguide coupler for high index contrast systems (2006)

A coupler to efficiently transfer broadband light from a single-mode optical fiber to a single-mode high-index contrast waveguide has been fabricated on a silicon substrate. We utilized a novel coupling scheme, with a vertically asymmetric design consisting of a stepwise parabolic graded index profile combined with a horizontal taper, to simultaneously confine light in both directions. Coupling efficiency has been measured as a function of the device dimensions. The optimal coupling efficiency is achieved for structures whose length equals the focal distance of the graded index and whose input width is close to the mode field diameter of the fiber. The fabricated structure is compact, robust and highly efficient, with an insertion loss of 2.2dB at 1550nm. The coupler exhibits less than 1dB variation in coupling efficiency in the measured spectral range from 1520nmto1620nm. The lowest insertion loss of 1.9dB is measured at 1540nm. The coupler design offers highly efficient coupling for single mode waveguides of core indices up to 2.2.
A method to site-specifically introduce methyllysine into proteins in E. coli (2010)

A mutant pyrrolysyl-tRNA synthetase/tRNA pair was used to genetically encode allylcarbamoyl methyllysine in bacteria. This amino acid can be converted to methyllysine with a ruthenium catalyst, providing a straightforward approach for site-specifically introducing methyllysine residues into proteins.
Red blood cell storage is associated with length of stay and renal complications after cardiac surgery (2011)

Our data support previous suggestions of an association between transfusion of older RBCs and poorer outcome in cardiac surgery patients. Randomized controlled trials are required to determine the true causal nature of any such association.
Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development (2023)

Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.
Optical Phase Modulators for MHz and GHz Modulation in Silicon-On-Insulator (SOI) (2004)

This paper reports the simulation of the direct current (dc), transient, and optical characteristics of low-loss single-mode optical phase modulators based on silicon-on-insulator (SOI) material. The devices operate by injecting free carriers to change the refractive index in the guiding region and have been modeled using the two-dimensional (2-D) device simulation package SILVACO and the optical simulator BeamPROP to determine their electrical and optical performance, respectively. These simulators have been employed to optimize the overlap between the injected free carriers in the intrinsic region and the propagating optical mode. Attention has been paid to both the steady state and transient properties of the device. In order to produce quantitative results, a particular p-i-n device geometry has been employed in the study, but the trends in the results are sufficiently general to be of help in the design of many modulator geometries. The specific example devices used are designed to support a single optical guided mode and are of approximately 1 mm in cross-sectional dimensions. The modeling results predict that the transient performance of the device is affected significantly by the contact width and the rib doping depth. Results presented encompass Gaussian and constant doping profiles in the n/sup +/ regions. The doping profile of the contacts has a tremendous effect on both the dc and transient performances. Phase modulators with drive currents as low as 0.5 mA and transient rise times of 0.3 ns and fall times of 0.12 ns are predicted. Following from these results, a realistic doping profile is proposed that surpasses the electrical results of the Gaussian and most of the constant doping profiles. The improvements in electrical device characteristics are at the expense of a slightly increased optical absorption loss. An alternative switching technique is also presented that could further improve the device speed.