gebhart/patrepeval huggingface dataset:
The Thyrotropin Receptor Mutation Database: Update 2003 (2003)

In 1999 we have created a TSHR mutation database compiling TSHR mutations with their basic characteristics and associated clinical conditions (www.uni-leipzig.de/innere/tshr). Since then, more than 2887 users from 36 countries have logged into the TSHR mutation database and have contributed several valuable suggestions for further improvement of the database. We now present an updated and extended version of the TSHR database to which several novel features have been introduced: 1. detailed functional characteristics on all 65 mutations (43 activating and 22 inactivating mutations) reported to date, 2. 40 pedigrees with detailed information on molecular aspects, clinical courses and treatment options in patients with gain-of-function and loss-of-function germline TSHR mutations, 3. a first compilation of site-directed mutagenesis studies, 4. references with Medline links, 5. a user friendly search tool for specific database searches, user-specific database output and 6. an administrator tool for the submission of novel TSHR mutations. The TSHR mutation database is installed as one of the locus specific HUGO mutation databases. It is listed under index TSHR 603372 (http://ariel.ucs.unimelb.edu.au/~cotton/glsdbq.htm) and can be accessed via www.uni-leipzig.de/innere/tshr.
Transbronchoscopic 3D volumetric optical coherence tomography (OCT) imaging of airways (2011)

Introduction: OCT, a non-invasive optical modality capable of high-resolution cross-sectional imaging of tissue microanatomy, holds potential of “in-vivo” diagnostics of pathology. Development of miniature probes & laser sources have advanced real-time OCT imaging of small structure such as airway morphologies. Aim: To develop 3D volumetric OCT imaging of airways. Methods: IRB approved porcine protocol. Airways imaged with a 1300-nm swept-source OCT at a 40 kHz A-scan rate, placed within a1.3 mm catheter advanced through 2 mm bronchoscope channel. Axial & lateral resolution of the system is ∼7 μm and ∼20 μm in tissue, respectively. 3D volumetric imaging achieved by rotating the OCT catheter while pulling it back (similar to spiral CT), at an imaging speed of 10 frames/sec & helical rotation pitch of ∼100 μm. Results: 3rd to 7th generation airways imaged, spiral scanning data recorded, then processed. In addition to presentation as isolated axial slices, playback can present spiral imaging reformatted as 3D volumes plus virtual fly-through of airways. Conclusion/Clinical significance: Transbronchoscopic OCT imaging can generate high-res axial imaging of airway microstructures. Reconstruction of dataset generates dynamic 3D imaging. In-vivo temporal monitoring of pathologic events such as cancer progression or physiologic effects of bronchoconstriction in airway disease will advance diagnosis and management of lung diseases.
Gas to Particle Partitioning of Organic Acids in the Boreal Atmosphere (2019)

Gas to particle partitioning of carboxylic acids was investigated using a high-resolution chemical ionization time-of-flight mass spectrometer (HR–CI–ToF–MS) with the filter inlet for gases and aerosol (FIGAERO). Specifically, the partitioning coefficients of 640 components with unique molecular composition were calculated from an assumed linear relationship between [particle]/[gas] versus the mass of the organic fraction (Morg) according to Raoult’s law, i.e., equilibrium phase partitioning. We demonstrate that, using the full data set, most of the compounds do not follow a linear relationship. This is especially the case for low- and high-molecular-weight species. Using a subset of the data, with concurrent low sulfate ambient observations ([SO42– < 0.4 μg m–3), the relationship improved significantly and Ki could be derived from the slope of a linear regression to the data. The 100 species with the highest R2 (≥0.7) of this regression are presented. The restrictions during high sulfate conditions can be explained by changes in either the equilibrium conditions (e.g., the activity coeffient, γi) or uptake kinetics (mass transfer limitation). This study demonstrates that partitioning of compounds in the complex ambient atmosphere follows ideal Raoult’s law for some limited conditions and stresses the need for studies also in more polluted environments.
The HPV DNA virus hybrid capture assay: what is it--and where do we go from here? (2003)

The biotechnology that has made HPV DNA testing possible has the capacity to reduce the incidence of cervical carcinoma substantially, especially in the patients diagnosed with ambiguous low-grade lesions, such as ASC-US, on Pap smears. Reflex HPV DNA testing of thin layer preparations diagnosed as ASC-US, and in other certain instances as outlined by ASCCP, will play a major role in the management of abnormal cervical cytology. Other applications, such as possible primary screening, may in the future play a substantial role in cervical screening. These potential applications will require more in-depth study and research, and will ultimately have to stand the test of time.
Harnessing Multi-Source Data about Public Sentiments and Activities for Informed Design (2018)

The intelligence of Smart Cities (SC) is represented by its ability in collecting, managing, integrating, analyzing, and mining multi-source data for valuable insights. In order to harness multi-source data for an informed place design, this paper presents “Public Sentiments and Activities in Places” multi-source data analysis flow (PSAP) in an Informed Design Platform (IDP). In terms of key contributions, PSAP implements 1) an Interconnected Data Model (IDM) to manage multi-source data independently and integrally, 2) an efficient and effective data mining mechanism based on multi-dimension and multi-measure queries (MMQs), and 3) concurrent data processing cascades with Sentiments in Places Analysis Mechanism (SPAM) and Activities in Places Analysis Mechanism (APAM), to fuse social network data with other data on public sentiment and activity comprehensively. As proved by a holistic evaluation, both SPAM and APAM outperform compared methods. Specifically, SPAM improves its classification accuracy gradually and significantly from 72.37 to about 85 percent within nine crowd-calibration cycles, and APAM with an ensemble classifier achieves the highest precision of 92.13 percent, which is approximately 13 percent higher than the second best method. Finally, by applying MMQs on “Sentiment&Activity Linked Data”, various place design insights of our testbed are mined to improve its livability.
CZT virtual Frisch-grid detector: Principles and applications (2009)

Cadmium Zinc Telluride (CdZnTe or CZT) is a very attractive material for using as room-temperature semiconductor detectors, because it has a wide bandgap and a high atomic number. However, due to the material's poor hole mobility, several special techniques were developed to ensure its suitability for radiation detection. Among them, the virtual Frisch-grid CZT detector is an attractive option, having a simple configuration, yet delivering an outstanding spectral performance. The goal of our group in Brookhaven National Laboratory (BNL) is to improve the performance of Frisch-ring CZT detectors; most recently, that effort focused on the non-contacting Frisch-ring detector, allowing us to build an inexpensive, large-volume detector array with high energy-resolution and a large effective area. In this paper, the principles of virtual Frisch-grid detectors are described, especially BNL's innovative improvements. The potential applications of virtual Frisch-grid detectors are discussed, and as an example, a hand-held gamma-ray spectrometer using a CZT virtual Frisch-grid detector array is introduced, which is a self-contained device with a radiation detector, readout circuit, communication circuit, and high-voltage supply. It has good energy resolution of 1.4% (FWHM of 662-keV peak) with a total detection volume of ~20 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . Such a portable inexpensive device can be used widely in nonproliferation applications, non-destructive detection, radiation imaging, and for homeland security. Extended systems based on the same technology have potential applications in industrial- and nuclear-medical-imaging.
Abstract 2717: Brain Mammillary Body Volumes are Diminished in Heart Failure (2008)

Emotional and cognitive abnormalities, including memory deficits, are common in heart failure (HF). Mammillary bodies in the brain play essential roles in spatial and short-term memory processing, ...
L-MolGAN: An improved implicit generative model for large molecular graphs (2021)

Deep generative models are used to generate arbitrary molecular structures with the desired chemical properties. MolGAN is a renowned molecular generation models that uses generative adversarial networks (GANs) and reinforcement learning to generate molecular graphs in one shot. MolGAN can effectively generate a small molecular graph with nine or fewer heavy atoms. However, the graphs tend to become disconnected as the molecular size increase. This poses a challenge to drug discovery and material design, where large molecules are potentially inclusive. This study develops an improved MolGAN for large molecule generation (L-MolGAN). In this model, the connectivity of molecular graphs is evaluated by a depth-first search during the model training process. When a disconnected molecular graph is generated, L-MolGAN rewards the graph a zero score. This procedure decreases the number of disconnected graphs, and consequently increases the number of connected molecular graphs. The effectiveness of L-MolGAN is experimentally evaluated. The size and connectivity of the molecular graphs generated with data from the ZINC-250k molecular dataset are confirmed using MolGAN as the baseline model. The model is then optimized for a quantitative estimate of drug-likeness (QED) to generate drug-like molecules. The experimental results indicate that the connectivity measure of generated molecular graphs improved by 1.96 compared with the baseline model at a larger maximum molecular size of 20 atoms. The molecules generated by L-MolGAN are evaluated in terms of multiple chemical properties, QED, synthetic accessibility, and log octanol–water partition coefficient, which are important in drug design. This result confirms that L-MolGAN can generate various drug-like molecules despite being optimized for a single property, i.e., QED. This method will contribute to the efficient discovery of new molecules of larger sizes than those being generated with the existing method.
Critical slowing down as early warning for the onset and termination of depression (2013)

About 17% of humanity goes through an episode of major depression at some point in their lifetime. Despite the enormous societal costs of this incapacitating disorder, it is largely unknown how the likelihood of falling into a depressive episode can be assessed. Here, we show for a large group of healthy individuals and patients that the probability of an upcoming shift between a depressed and a normal state is related to elevated temporal autocorrelation, variance, and correlation between emotions in fluctuations of autorecorded emotions. These are indicators of the general phenomenon of critical slowing down, which is expected to occur when a system approaches a tipping point. Our results support the hypothesis that mood may have alternative stable states separated by tipping points, and suggest an approach for assessing the likelihood of transitions into and out of depression.
Blocking thin-film nonuniformities: Photovoltaic self-healing (2004)

An approach is developed to block the effects of lateral nonuniformities in thin-film semiconductor structures. The nonuniformity modulates the surface photovoltage distribution. When exposed to light and immersed in a proper electrolyte, this distribution will generate laterally nonuniform electrochemical reactions. Such treatments result in a nonuniform interfacial layer that balances the original nonuniformity. This approach has been implemented for CdTe/CdS photovoltaic devices, in which it improved the device efficiency from 1%–3% to 11%–12%.
Quintessence (2000)

A revolution is taking place in cosmology. New ideas are usurping traditional notions about the composition of the universe, the relationship between geometry and destiny, and Einstein's greatest blunder. As numerous observations and experiments reshape the field, many cosmologists are exploring the possibility that the vast majority of the energy in the universe is in the form of a hitherto undiscovered substance called "quintessence".
Optical anapoles (2019)

The anapole, a non-radiating charge-current configuration, was recently observed in a variety of artificial materials and nanostructures. We provide a brief overview of this rapidly developing field and discuss implications for spectroscopy, energy materials, electromagnetics, as well as quantum and nonlinear optics.
Ultrashort-Pulse Optically-Assisted Domain Engineering in Lithium Niobate (2006)

Ultrashort laser pulses (∼120–150 fs) of near-ultraviolet (305 nm) to near-infrared (800 nm) wavelengths have been used to optically-assist domain nucleation and growth in lithium niobate. Within illuminated areas, the electric field required for domain nucleation is reduced by up to 41% in undoped and up to 98% in 5-mol% Mg-doped congruently melting materials, allowing direct-writing of inverted domains with electric fields as small as 100 V mm− 1. A first step towards the formation of optically-defined periodically poled lithium niobate was achieved by illumination via a phase mask, demonstrated over small areas with a period of 5.25 microns.
Re: Allium™ TPS—A New Prostatic Stent for the Treatment of Patients with Benign Prostatic Obstruction: The First Report (2016)

No AccessJournal of UrologyAdult Urology1 Oct 2016Re: Allium™ TPS—A New Prostatic Stent for the Treatment of Patients with Benign Prostatic Obstruction: The First Report Jeffrey A. CadedduMD Jeffrey A. CadedduJeffrey A. Cadeddu More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.07.024AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Allium™ TPS—A New Prostatic Stent for the Treatment of Patients with Benign Prostatic Obstruction: The First Report." The Journal of Urology, 196(4), p. 1222 © 2016 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 196Issue 4October 2016Page: 1222 Advertisement Copyright & Permissions© 2016 by American Urological Association Education and Research, Inc.MetricsAuthor Information Jeffrey A. Cadeddu More articles by this author Expand All Advertisement PDF downloadLoading ...
LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator (2005)

The bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 is encoded by five genes (hoxEFUYH) which are transcribed as one unit. The transcription of the hox-operon is regulated by a promoter situated upstream of hoxE. The transcription start point was located at -168 by 5'Race. Several promoter probe vectors carrying different promoter fragments revealed two regions to be essential for the promoter activity. One is situated in the untranslated 5'leader region and the other is found -569 to -690 nucleotides upstream of the ATG. The region further upstream was shown to bind a protein. Even though an imperfect NtcA binding site was identified, NtcA did not bind to this region. The protein binding to the DNA was purified and found to be LexA by MALDI-TOF. The complete LexA and its DNA binding domain were overexpressed in Escherichia coli. Both were able to bind to two sites in the examined region in band-shift-assays. Accordingly, the hydrogenase activity of a LexA-depleted mutant was reduced. This is the first report on LexA acting not as a repressor but as a transcriptional activator. Furthermore, LexA is the first transcription factor identified so far for the expression of bidirectional hydrogenases in cyanobacteria.
Orientation of sugars bound to the principal C-type carbohydrate-recognition domain of the macrophage mannose receptor (1998)

The extracellular region of the macrophage mannose receptor, a protein involved in the innate immune response, contains eight C-type carbohydrate-recognition domains (CRDs). The fourth of these domains, CRD-4, is central to ligand binding by the receptor, and binds mannose, fucose and N-acetylglucosamine by direct ligation to Ca2+. Site-directed mutagenesis combined with NMR and molecular modelling have been used to determine the orientation of monosaccharides bound to CRD-4. Two resonances in the 1H NMR spectrum of CRD-4 that are perturbed on sugar binding are identified as a methyl proton from a leucine side chain in the core of the domain and the H-2 proton of a histidine close to the predicted sugar-binding site. The effects of mutagenesis of this histidine residue, a nearby isoleucine residue and a tyrosine residue previously shown to stack against sugars bound to CRD-4 show the absolute orientation of sugars in the binding site. N-Acetylglucosamine binds to CRD-4 of the mannose receptor in the orientation seen in crystal structures of the CRD of rat liver mannose-binding protein. Mannose binds to CRD-4 in the orientation seen in the CRD of rat serum mannose-binding protein and is rotated by 180 degrees relative to GlcNAc bound to CRD-4. Interaction of the O-methyl group and C-1 of alpha-methyl Fuc with the tyrosine residue accounts for the strong preference of CRD-4 for this anomer of fucose. Both anomers of fucose bind to CRD-4 in the orientation seen in rat liver mannose-binding protein.
Efficacy of the hexpolar configuration in localizing the activation of retinal ganglion cells under electrical stimulation (2012)

Retinal visual prostheses provide hope of restoring sight to patients suffering from retinal degeneration such as retinitis pigmentosa and age-related macular degeneration. Retinal prostheses are used to electrically stimulate residual neurons that are spared in these diseases, namely the retinal ganglion cells (RGCs), eliciting percepts of light termed 'phosphenes'. The elicitation of multiple phosphenes via an electrode array allows patterns to be produced, resulting in a rudimentary form of vision. For such patterns to be produced effectively, the prosthesis must generate well-defined phosphenes. To this end, the hexpolar configuration has been proposed as an alternative to the traditional monopolar or bipolar configurations. It utilizes six electrodes surrounding the stimulating electrode to serve as a combined return, or 'hex guard', purportedly localizing the activation to cells located within them. In this study, the efficacy of the hexpolar configuration in localizing activity was investigated by using patch-clamp electrophysiology to measure the activation thresholds of RGCs to electrical stimulation in isolated rabbit retina. Cells located outside the hex guard were found to have significantly higher relative hexpolar thresholds (>2 fold) as compared to cells located within the hex guard. This confirms the efficacy of the hexpolar configuration in localizing activity to within the hex guard. Furthermore, the effect of using cathodic-first versus anodic-first stimulation on hexpolar threshold and localization was investigated. No significant difference was observed between the two groups, in terms of lowering thresholds or improving localization.
Ribosomal incorporation of cyclic β-amino acids into peptides using in vitro translation (2020)

We demonstrate in vitro incorporation of cyclic β-amino acids into peptides by the ribosome through genetic code reprogramming. Further, we show that incorporation efficiency can be increased through the addition of elongation factor P.
Vitamin A and apoptosis in colonic tumor cells. (1997)

The mechanism by which vitamin A prevents or delays chemical carcinogenesis remains unclear. In addition to these antimutagenic and antiproliferative activities, vitamin A seems able to induce programmed cell death. In this study, we assess the suggested role of vitamin A on the in vitro apoptosis induction in a rat colonic tumor cell line. Several concentrations of retinyl palmitate were added in the culture media. We observed cell proliferation by measuring the (3H)thymidine incorporation, cell differentiation by measuring the intestinal alkaline phosphatase expression, and apoptosis induction by DNA fragmentation and morphological evolution of adherent and floating cells. The results show that vitamin A decreases (3H)thymidine incorporation after 1 day of treatment, induces alkaline phosphatase expression, and increases the number of cells falling in apoptosis. This report confirms the role of vitamin A on the induction of cell differentiation, on the inhibition of cell proliferation and shows the vitamin A capacity to induce apoptosis. These results could be attractive to prevent development of colon cancer by vitamin A supplemented diets.
Low-Power and Process Variation Tolerant Memories in sub-90nm Technologies (2006)

Inter-die and intra-die variation in process parameters increases parametric failures and leakage spread in nano-scale memories, leading to significant yield degradation. Design level optimization methods are not sufficient to address the leakage and parametric failures, particularly, under large variation. In this paper, we propose two post-silicon tuning techniques which can simultaneously reduce the leakage spread and improve parametric yield in memories. We show that, self- repairing and self-adaptive systems with post-silicon tuning are essential for designing low-power and robust memories in sub- 90 nm technologies.
A Survey of Usage Protocols of Syndromic Surveillance Systems by State Public Health Departments in the United States (2009)

The majority of states reported using syndromic surveillance systems, with greatest penetration in those at highest risk for a terrorist attack. Most states used multiple systems and had varied methods (central and local) of responding to alerts, indicating the need for detailed response protocols.
Molecular biology of Na+ absorption (1997)

Aldosterone controls the activity of the amiloride-sensitive epithelial Na+ channel located in the apical membrane of epithelial cells from the distal colon and kidney collecting duct. This channel is a key element in the antinatriuretic response to aldosterone. It consists of three homologous subunits, alpha-ENaC, beta-ENaC, and gamma-ENaC (for epithelial Na+ channel), which share significant identity with degenerins, a family of proteins found in the nematode Caenorhabditis elegans, and with ligand-gated cation channels, such as FaNaC [Phe-Met-Arg-Phe-NH2 (i.e., FMRF-amide) Na+ channel] or ASIC (acid-sensing ion channel), two neuronal ionotropic receptors for Phe-Met-Arg-Phe-NH2 and H+, respectively. All of these proteins contain a large extracellular loop located between two large hydrophobic domains. The NH2- and COOH-terminal domains are cytoplasmic and contain potential regulatory motifs. Gain-of-function mutations affecting beta-ENaC and gamma-ENaC genes can cause Liddle syndrome, a rare from of genetic hypertension. Loss-of-function mutations affecting alpha-ENaC or beta-ENaC genes can cause pseudohypoaldosteronism type 1. Steroids strongly increase beta-ENaC and gamma-ENaC transcription in rat distal colon. A different situation is observed in rat kidney, in which the large stimulation of ENaC activity is mainly via posttranslational mechanisms. In both tissues, aldosterone increases cell surface expression of the ENaC subunits.