gebhart/patrepeval huggingface dataset:
On the Dimensionality of Sleep-EEG Data (1995)

Sleep-EEG data of 16 healthy subjects, classified according to the Rechtschaffen and Kales criteria, were taken to determine the correlation exponent (CE) or dimensionality (D2) of the data using the Corex program. We tested the applicability of this program to the analysis of sleep-EEG data changing systematically the embedding dimension (ED), the time lag (tau), the number of involved pairs of vectors and the EEG segment by split half. We could confirm the results of other authors according to which the complexity of the EEG signal decreases from stage 'awake, eyes closed' to sleep stages 1, 2, 3 and 4. The differences between the various sleep stages were significant. Stage REM could be differentiated from every stage but stage 1. The most important finding of our study was that the absolute value of the dimensionality depends on almost all the parameters tested: with increasing tau up to tau = 200 the CE increases, which means a 1.56-second shift. A higher number of pairs is needed when the signal is more complex. The ED is selected well between 6 and 11, that means reasonably higher or close to the dimensionalities for that purpose as presented in the literature. Different segments of one sleep stage in 1 subject led to different CE values, thus demonstrating that the EEG signal is not stationary over a segment of 2 min time. Although using chaos mathematics seems to be a useful tool in analyzing EEG data to explore their complexity, we could demonstrate the urgent need of calibrations and conventions to be able to interpret the absolute values.
Detection of autoreactive CD4 T cells using major histocompatibility complex class II dextramers (2011)

The data suggest that MHC dextramers are useful tools to track the generation and functionalities of self-reactive CD4 cells in various experimental systems.
Molecular evolution of the homeodomain family of transcription factors (2001)

The homeodomain family of transcription factors plays a fundamental role in a diverse set of functions that include body plan specification, pattern formation and cell fate determination during metazoan development. Members of this family are characterized by a helix-turn-helix DNA-binding motif known as the homeodomain. Homeodomain proteins regulate various cellular processes by specifically binding to the transcriptional control region of a target gene. These proteins have been conserved across a diverse range of species, from yeast to human. A number of inherited human disorders are caused by mutations in homeodomain-containing proteins. In this study, we present an evolutionary classification of 129 human homeodomain proteins. Phylogenetic analysis of these proteins, whose sequences were aligned based on the three-dimensional structure of the homeodomain, was performed using a distance matrix approach. The homeodomain proteins segregate into six distinct classes, and this classification is consistent with the known functional and structural characteristics of these proteins. An ancestral sequence signature that accurately describes the unique sequence characteristics of each of these classes has been derived. The phylogenetic analysis, coupled with the chromosomal localization of these genes, provides powerful clues as to how each of these classes arose from the ancestral homeodomain.
A screen for fast evolving genes from  <i>Drosophila</i> (1997)

In an attempt to quantify the rates of protein sequence divergence in Drosophila, we have devised a screen to differentiate between slow and fast evolving genes. We find that over one-third of randomly drawn cDNAs from a Drosophila melanogaster library do not cross-hybridize with Drosophila virilis DNA, indicating that they evolve with a very high rate. To determine the evolutionary characteristics of such protein sequences, we sequenced their homologs from a more closely related species (Drosophila yakuba). The amino acid substitution rates among these cDNAs are among the fastest known and several are only about 2-fold lower than the corresponding values for silent substitutions. An analysis of within-species polymorphisms for one of these sequences reveals an exceptionally high number of polymorphic amino acid positions, indicating that the protein is not under strong negative selection. We conclude that the Drosophila genome harbors a substantial proportion of genes with a very high divergence rate.
Carbonyl Insertions into Metal-Nitrogen Bonds of Group 4 Dialkylamido Complexes. X-ray Structure of Cp*(Me2N)2Ti[O(Me2N)C]W(CO)5 (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbonyl Insertions into Metal-Nitrogen Bonds of Group 4 Dialkylamido Complexes. X-ray Structure of Cp*(Me2N)2Ti[O(Me2N)C]W(CO)5Mikhail Galakhov, Avelino Martin, Miguel Mena, Federico Palacios, Carlos Yelamos, and Paul R. RaithbyCite this: Organometallics 1995, 14, 1, 131–136Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://doi.org/10.1021/om00001a022RIGHTS & PERMISSIONSArticle Views114Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (797 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Poster For Nips Publication: Protein Interface Prediction Using Graph Convolutional Networks (2017)

This poster was presented at the 2017 NIPS conference at Long Beach, CA. It accompanies the identically named paper. Paper: https://papers.nips.cc/paper/7231-protein-interface-prediction-using-graph-convolutional-networks Code: https://github.com/fouticus/pipgcn Data: https://zenodo.org/record/1127774
Inclusion of Higher Order Terms for Small-Signal (Modal) Analysis: Committee Report—Task Force on Assessing the Need to Include Higher Order Terms for Small-Signal (Modal) Analysis (2005)

This paper summarizes the work done by the Task Force on Assessing the Need to Include Higher Order Terms for Small-Signal (Modal) Analysis. This Task Force was created by the Power System Dynamic Performance Committee to investigate the need to include higher order terms for small signal (modal) analysis. The focus of the work reported here is on establishing and documenting the practical significance of these terms in stability analysis using the method of Normal Forms. Special emphasis was placed on determining and describing conditions when higher order terms need to be included to accurately describe modal interactions. Test cases were developed on a standard test system to demonstrate the application of appropriate indices to detect the occurrence of nonlinear interaction and hence the need for higher order terms in stability analyzes. The use of the higher order terms in the site selection for a damping controller is also documented.
The Effect of Iron on the Primary Root Elongation of Arabidopsis during Phosphate Deficiency   (2008)

Root architecture differences have been linked to the survival of plants on phosphate (P)-deficient soils, as well as to the improved yields of P-efficient crop cultivars. To understand how these differences arise, we have studied the root architectures of P-deficient Arabidopsis (Arabidopsis thaliana Columbia-0) plants. A striking aspect of the root architecture of these plants is that their primary root elongation is inhibited when grown on P-deficient medium. Here, we present evidence suggesting that this inhibition is a result of iron (Fe) toxicity. When the Fe concentration in P-deficient medium is reduced, we observe elongation of the primary root without an increase in P availability or a corresponding change in the expression of P deficiency-regulated genes. Recovery of the primary root elongation is associated with larger plant weights, improved ability to take up P from the medium, and increased tissue P content. This suggests that manipulating Fe availability to a plant could be a valuable strategy for improving a plant's ability to tolerate P deficiency.
P0 of Beet Western Yellows Virus Is a Suppressor of Posttranscriptional Gene Silencing (2002)

Higher plants employ a homology-dependent RNA-degradation system known as posttranscriptional gene silencing (PTGS) as a defense against virus infection. Several plant viruses are known to encode proteins that can suppress PTGS. Here we show that P0 of beet western yellows virus (BWYV) displays strong silencing suppressor activity in a transient expression assay based upon its ability to inhibit PTGS of green fluorescent protein (GFP) when expressed in agro-infiltrated leaves of Nicotiana benthamiana containing a GFP transgene. PTGS suppressor activity was also observed for the P0s of two other poleroviruses, cucurbit aphid-borne yellows virus and potato leafroll virus. P0 is encoded by the 5'-proximal gene in BWYV RNA but does not accumulate to detectable levels when expressed from the genome-length RNA during infection. The low accumulation of P0 and the resulting low PTGS suppressor activity are in part a consequence of the suboptimal translation initiation context of the P0 start codon in viral RNA, although other factors, probably related to the viral replication process, also play a role. A mutation to optimize the P0 translation initiation efficiency in BWYV RNA was not stable during virus multiplication in planta. Instead, the P0 initiation codon in the progeny was frequently replaced by a less efficient initiation codon such as ACG, GTG, or ATA, indicating that there is selection against overexpression of P0 from the viral genome.
Discovery of Inverse Agonists for the Liver Receptor Homologue-1 (LRH1;NR5A2) (2011)

NR5A2 (Liver receptor homologue-1; LRH1) belongs to the four-member NR5A, or Ftz-F1, subfamily V of nuclear receptors. Murine LRH1 was originally identified due to its sequence homology to Drosophila Fushi tarazu factor-1. Orthologs were subsequently identified in other species including rat, chicken, horse, zebrafish and human. LRH1, and its closest family member steroidogenic factor-1 (SF-1, NR5A1), bind to identical DNA consensus sequences (response elements; REs) and both are able to bind phospholipids in their ligand binding domains (LBDs). LRH1 was shown to regulate expression of Cyp19 (aromatase), suggesting LRH1 as a target for inverse agonists for the treatment of ER-positive breast cancers. Interestingly, recently it was shown that LRH1 promotes motility and invasiveness in both ER-positive and ER-negative breast cancer cells (MDA-MB-231), with remodeling of the actin cytoskeleton and E-cadherin processing observed with LRH1 over-expression. These findings suggest that inhibition of LRH1 activity should be useful in attenuating both migration and invasion in ER-positive and ER-negative breast cancers. In addition to LRH1’s role in cholesterol metabolism and bile acid homeostasis, the receptor can impact expression of markers of acute phase response (APR) to tissue injury. Thus, we endeavored to identify potent and selective LRH1 inverse agonists which may provide new approaches for the treatment of cancer and to blunt APR. We pursued a Center-based Initiative with transfection studies testing the ability of various chemical scaffolds to inhibit LRH-1-mediated activation of the Cyp19-Aromatase-luciferase and the StAR-luciferase reporter, followed by counterscreening against SF-1 and VP16, as well as studies examining the effect of compounds on LRH-1 modulation of the APR markers haptoglobin and serum amyloid A1 and A4 (SAA1 and SAA4). Combined, the studies led to identification of two novel LRH-1 inverse agonist probe compounds ML179 (PubChem CID 45100448) and ML180 (PubChem CID 3238389) with potent activity in breast cancer cells. In reporter assays ML179 and ML180 had potency IC50 values of 320nM and 3.7 μM and maximum efficacy of 40% and 64% repression, respectively. It is unclear at this stage if maximum repression is more important than potency; thus two probes were declared that differ from each other in terms of potency and efficacy. Further optimization is focused on improving both potency and efficacy. Also, it is likely that the selectivity of these probe compounds versus SF1 is cell context-and promoter-dependent. The mechanism of action of these probes will require much more detailed studies which are currently underway.
Nanocontainer‐Based Anticorrosive Coatings: Effect of the Container Size on the Self‐Healing Performance (2013)

Abstract Organic coatings based on inhibitor loaded inorganic containers for smart corrosion inhibition are presented. The overall coating performance is strongly influenced by the containers as well as their inhibitor capacity, compatibility with the coating matrix, and size. The important effect of container size is described for the first time in this work by investigating two types of mesoporous silica containers of different diameters: 80 and 700 nm. The coating physical properties (thickness and adhesion) are comparable for both container types. In contrast, the coating barrier properties are strongly influenced by the container size as assessed with electrochemical impedance spectroscopy (EIS). The incorporation of bigger containers reduces the coating resistance by a factor of two. Surprisingly, despite the similar amounts (20 wt%) of loaded inhibitor (2‐mercaptobenzothiazole), different active inhibition ability is detected with the scanning vibrating electrode technique (SVET). Therefore, it is found that coatings with smaller containers exhibit better self‐healing performance.
Applicability of Frequency Selective Surfaces to Enhance Mobile Network Coverage in Future Energy-Efficient Built Environments (2015)

Modern houses and constructions use energy efficient building materials, like metal shielding and energy saving windows, to improve the thermal insulation and efficiency. However, such energy efficient building materials not only block the thermal radiation but also substantially increase the building penetration losses of the radio signals, forming thus a challenging problem in mobile cellular networks where majority of network elements are still located outdoors while more and more of the mobile data use takes place indoors. In this article, the use of frequency selective surface (FSS) is studied as one potential means to reduce the penetration loss while still maintaining high thermal insulation of the buildings. FSS structures build on a combination of either conducting patches or apertures in a thin conducting sheet arranged periodically in one or two dimensional array, and can be etched on the metal coating of energy saving windows that behave as electromagnetic filter. Thus, such energy saving windows incorporating FSS structures can potentially allow transmission of radio signals while still essentially retaining its major thermal insulation properties. The aim of this paper is to investigate the applicability of such FSS structures in realworld scenarios with actual field measurements in real mobile networks. First, double square-loop FSS structure which is transparent to GSM 900MHz and UMTS/HSPA 2100MHz frequency bands is developed and analyzed. The developed FSS structure is then fabricated using aluminum foil and tested and measured in both laboratory conditions as well as in real mobile networks and real buildings. In the mobile network measurements, the developed FSS prototype shows substantial improvements of the indoor signal strengths, in the order of 8-13 dB for GSM 900MHz band and 2-5 dB for UMTS/HSPA 2100MHz frequency band, compared to the uniform metal coating. This indicates that FSS structures can provide useful and feasible means to enhance the indoor signal levels in future energy efficient built environments, and thus substantially enhance the indoor coverage and capacity of wireless networks.
Effect of Damage Removal Treatment after Trench Etching on the Reliability of Trench MOSFET (2013)

Guaranteeing the reliability of gate oxides is one of the most important topics to realize regarding the SiC power MOSFET. In the case of trench MOSFET, since the gate oxides are formed on the trench sidewall, the damage and roughness on the trench sidewall can affect the lifetime of the gate oxides. Generally speaking, damage removal treatment is processed after trench dry etching in most cases. In Si processes, sacrificial oxidation, H 2 anneal and CDE (Chemical Dry Etching) are adopted commonly. In the case of SiC processes, sacrificial oxidation, H 2 anneal, and SiH 4 /Ar anneal have been reported. Neverthless CDE which applied to SiC trench MOSFET has few precedents. We clarified the effect of CDE as a damage removal process. CDE has the effect of flattening the trench sidewall, and CDE makes the lifetime of gate oxides improve. CDE is an effective process for the reliability of SiC trench MOSFET.
In vitro Interactions of Endometrial Stromal and Epithelial Cells in Matrigel: Reorganization of the Extracellular Matrix (1994)

Fragments of human endometrial glands and dispersed endometrial stromal cells were cultured together in a thick layer of reconstituted basement membrane (Matrigel). Epithelial cells kept their glandular morphology whereas stromal cells grew into round clusters of mainly fusiform cells. Transmission electron micrographs showed collagen fibers between stromal cells as well as in surrounding extracellular matrix after 2.5 weeks. A well-defined basement membrane was found when epithelial and stromal cells were in close proximity to each other. Beneath the lamina densa there was a loose network of collagen fibers or a dense fibrillar network arranged parallel to the cell layers. Epithelial cells showed hemidesmosomes at their basal surface where they were close to stromal cells.
Treatment Enables High-TDS Water Use as Base Fluid for Hydraulic Fracturing (2013)

Technology Update The beneficial use of produced water is receiving great attention in the oil and gas industry. As oil and gas are produced, large quantities of water containing high amounts of total dissolved solids (TDS) are produced in the process. Most of the high-saline produced water is reinjected into disposal wells. Reclaiming produced water as the base fluid for hydraulic fracturing not only helps to alleviate the industry’s dependence on fresh water, but also lowers the overall cost of the fracturing treatment. Contents of Produced Water Produced water usually comprises the formation water and the injected fluids from previous treatments. It can contain hydrocarbons, high levels of TDS, suspended solids, and residual production chemicals. The use of produced water for hydraulic fracturing has many advantages, such as reduction in disposal of produced water, reduction of freshwater consumption during completion and production operations, and realization of economic benefits by the operator. If produced water is gathered at or near the production site and a minimal treatment is applied in hydraulic fracturing fluids, recycling and reuse programs may become economically and environmentally beneficial. As hydraulic fracturing in shale plays continues to require large amounts of fresh water for oilfield operations (i.e., 4 to 6 million gallons per well in some cases), reusing produced water reduces freshwater consumption. With increased restrictions on water availability from subsurface or surface sources, fresh water is becoming more difficult to obtain. In some basins, the use of produced water in oil and gas drilling and slick-water-based fracturing treatments has been explored. Typically, these applications use water with low TDS levels. Little work has been done on the use of produced water with high TDS levels (&gt;200,000 ppm) in fracturing fluids designed with linear or crosslinked gel bases. Treating High-TDS Water To reuse high-TDS produced water effectively in crosslinked gel-based hydraulic fracturing fluids, the water must first be treated. The treatment need not generate potable or fresh water, as some oil and gas industry water treatments do. The goal of the treatment is to remove only minerals that hinder the development of the crosslinked fluid or that cause scale buildup in the well. One effective form of produced water treatment is electrocoagulation (EC).
OSTEOSYNTHESIS OF THE CERVICAL SPINE WITH AN ANTERIOR PLATE (1995)

Osteosynthesis with an anterior plate is indicated for stabilization of the cervical spine. It is used for reconstruction of the vertebral body following corpectomy and for cervical instability due to fractures, fracture-dislocations, and post-laminectomy. In these situations, a well-keyed anterior graft or posterior fusion alone may be inadequate to attain stability. The authors retrospectively review 25 cases of osteosynthesis of the cervical spine using the AO H-plate. All the patients were stable enough postoperatively to allow early mobilization with a cervicothoracic orthosis. Average follow up was 31.2 months. All the grafts fused; however, complications occurred in 36% of the cases. The majority of these complications did not affect the long-term clinical result. This method involves potential risks to the spinal cord, esophagus, carotid structures, and laryngeal nerve. It should therefore be used in carefully selected cases.
Charge-based chemical sensors: a neuromorphic approach with chemoreceptive neuron MOS (C/sub V/MOS) transistors (2003)

A novel chemoreceptive neuron MOS (C/spl nu/MOS) transistor with an extended floating-gate structure has been designed with several individual features that significantly facilitate system integration of chemical sensing. We have fabricated C/spl nu/MOS transistors with generic molecular receptive areas and have characterized them with various fluids. We use an insulating polymer layer to provide physical and electrical isolation for sample fluid delivery. Experimental results from these devices have demonstrated both high sensitivity via current differentiation and large dynamic range from threshold voltage shifts in sensing both polar and electrolytic liquids. We have established electrochemical models for both steady-state and transient analyses. Our preliminary measurement results have confirmed the basic design and operations of these devices, which show potential for developing silicon olfactory and gustatory units that are fully compatible with current CMOS technology.