gebhart/patrepeval huggingface dataset:
NMR Analysis of the Hydrogen Bonding Interactions of the RNA-Binding Domains of the Drosophila Sex-Lethal Protein with Target RNA Fragments with Site-Specific [3-15N]Uridine Substitutions (1997)

It has been reported that a 183 residue fragment, consisting of the two RNA-binding domains (RBD1- RBD2) of the Drosophila melanogster Sex-lethal (Sxl) protein, strongly binds an oligonucleotide of the target RNA sequence (5'-GUUUUUUUUC-3') that regulates alternative splicing, and forms four or five hydrogen bonds with the imino groups of the RNA. In the present study, we used site-directed mutagenesis to improve the solubility of the didomain fragment of Sxl, and confirmed that this mutant fragment forms hydrogen bonds with the target RNA in the same manner as that of the wild-type fragment. The mutant fragment was shown to bind the cognate RNA sequences GUUUUUUUUC and AUUUUUUUUC more tightly than UUUUUUUUC. By using a [3-15N]uridine phosphoramidite, we synthesized a series of15N-labeled target RNAs, in which one of the uridine residues was specifically replaced by [3-15N]uridine. By observing the imino1H-15N coupling of the labeled uridine residue, we assigned all four of the hydrogen-bonded imino protons to U1, U2, U5 and U6, respectively, of the target RNA. The imino protons of U2 and U6 exhibited nuclear Overhauser effects with aliphatic protons of the protein. All these results indicate that the A/G, U1, U2, U5 and U6 residues in the target sequence of (G/A)UUUUUUUU are specifically recognized by the two RNA-binding domains of the Sxl protein.
Polymer-Supported Dendritic Phosphine Ligands (2007)

A series of polymer-supported dendritic phosphine ligands G1-3(X)TPP was prepared. Thus, for example, hydromethylpolystyrene was coupled with hydroxyisophthalate under Mitsunobu conditions and the resulting polymeric phthalate was reduced to give G1(O)OH. Through similar condensation-reduction sequence(s), G2 and G3(O)OH were obtained. Triphenylphosphino (TPP) groups were introduced via ester condensation of Gn(O)OH with diphenylphosphino­benzoic acid to give Gn(O)TPP. Gn(N)TPP and Gn(S)TPP were also prepared starting with bromomethyl­polystyrene.
Peripapillary choroidal thickness assessed using automated choroidal segmentation software in an Asian population (2015)

Using novel automated choroidal segmentation software, we provide reliable objective measurements of PPCT in a population-based setting. Shorter axial length, younger age, lower triglyceride levels and the presence of diabetes are the factors independently associated with thicker PPCT. These factors should be taken into consideration when interpreting Spectralis EDI SD-OCT-based PPCT measurements in clinics.
ChemInform Abstract: STEREOCHEMICAL CONTROL IN THE CONSTRUCTION OF VICINALLY SUBSTITUTED CYCLOPENTANES AND CYCLOHEXANES. INTRAMOLECULAR CONJUGATE ADDITION OF β‐KETOESTER ANIONS (1983)

Abstract Bei der Behandlung mit alkalischen Katalysatoren werden die ungesättigten Oxo‐Verbindungen (I) in Gemische isomerer Cyclisierungsprodukte (II) und (III) übergeführt und deren jeweilige Anteile in Relation zu den Reaktionsbedingungen bestimmt.
Cavity-enhanced emission from Germanium Vacancy centers in Diamond (2019)

The unique correlations in quantum systems, i.e. superposition and entanglement, enable quantum technologies to outperform classical technologies. Quantum networks is a quantum technology in fast development with many promising applications. An essential building block in a quantum network is the interface between matter nodes and quantum channels. A color center in diamond coupled to a micro-cavity is a promising route to achieve an eﬃcient interface. In this thesis we investigate the coupling of a single germanium vacancy (GeV) center to a Fabry-Pérot optical micro-cavity at room temperature. The Fabry-Pérot optical micro-cavity was formed by a macroscopic ﬂat mirror and a ﬁber-based concave microscopic mirror. The concave mirror was created on the end-facet of a ﬁber with short high power laser pulses from a CO2-laser. High qulity dielectric coating allowed us to achieve a ﬁnesse of 11,000 with a∼1 µm thin diamond membrane incorporated in the cavity. We achieved a cavity length of only a few µm and a small mode volume V = 2.7µm, which was essential for good coupling between the GeV center and the optical cavity mode. By studying the same GeV center in a confocal microscope setup, i.e. outside of the micro-cavity, and in the micro-cavity setup, we were able to measure an improved optical coherence of the GeV emission in the cavity. We determined an enhancement of the spectral density by a factor of ∼15. Furthermore, we determined the emission eﬃciency into the cavity mode β and compared it with the theoretical modelling. From the theoretical modelling, we predict the expected Purcell factor Fp = 200 for the zero phonon line in future experiments at cryogenic temperatures. Going to cryogenic temperatures is necessary to achieve eﬃcient spin-photon interfaces. This work provides valuable information for realizing eﬃcient spin-photon interfaces, which is critical for the practical implementation of a quantum network.
Properties of a Pseudomonas stutzeri outer membrane channel-forming protein (NosA) required for production of copper-containing N2O reductase (1989)

A protein (NosA) in the outer membrane of Pseudomonas stutzeri that is required for copper to be inserted into N2O reductase has been extracted and purified to homogeneity. The purified protein could form channels in black lipid bilayers. Like N2O reductase, NosA contained copper and was only made anaerobically. In contrast to N2O reductase, its synthesis was repressed by exogenous copper (but not by Mn, Co, Ni, Zn, or Fe). Also in contrast to N2O reductase, NosA homologs were not immunologically detectable in Pseudomonas aeruginosa, Pseudomonas mendocina, Pseudomonas alcaligenes, or other strains of P. stutzeri.
Characterization by serial deletion competition ELISAs of HIV-1 V3 loop epitopes recognized by monoclonal antibodies (1996)

Characterization of the sites recognized by antibody on the V3 loop of the envelope glycoprotein gp120 of HIV-1 was done by competition ELISAs on a series of four mouse mAbs, a human mAb and a human Fab. The solid-phase antigen consisted of biotin-YNKRK-RIHIGPGRAFYTTKN, a sequence from the center of the V3 loop of gp120MN, applied to streptavidin-coated wells. Competing antigens were two series of peptides with the HIV-1MN sequence each serially deleted at either the N or C terminus but kept constant at the other terminus. For each series, the amino acid at the deleting end needed to give a minimum KD was identified. The epitope was defined as the sequence including both of the identified amino acids as terminal amino acids. For the six antibodies reported, the epitope length ranged from seven to 14 amino acids. Use of a cyclic peptide as competing fluid-phase antigen suggested the influence of conformational constraints on presumed "linear" epitopes. The operationally-defined epitope was longer than the contact residues in one of two instances in which the X-ray crystallographic structure had been determined. The longer estimates of epitope length in the current study based on competition ELISAs with serial deletions suggest that non-contact residues are significant both in epitope definition and in functional applications including immunogen design.
Intelligent interactive image outlining using spline snakes (2002)

Outlining 2D shapes and image regions is often required in image manipulation and analysis. Most polygon and curve drawing tools in graphics do not use the knowledge of image intensities and its derivatives in guiding the outlining process, and hence are quite tedious and error prone. This paper presents a, fast interactive drawing tool based on a parametric spline formulation of snakes that exploits the underlying image intensities. Specifically, interactively specified contours are naturally attracted to strong image edges in the vicinity because spline snakes are designed to migrate to significant ridges in the gradient magnitude image. Furthermore, allowable stretching and bending can be controlled by minimizing explicitly the bending and stretching energies of the curve. Parameterization of spline snakes in terms of a limited number of control points yields a fast minimization solution thus enabling interactive rubber banding of the curve on the screen. This feedback allows users to quickly guide the snake on the desired path.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Dynamics Simulations of H2NSO2C6H4CONH(Gly)3OBn Bound to the Active Site of Human Carbonic Anhydrase II (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Dynamics Simulations of H2NSO2C6H4CONH(Gly)3OBn Bound to the Active Site of Human Carbonic Anhydrase IIDonovan N. Chin and George M. WhitesidesCite this: J. Am. Chem. Soc. 1995, 117, 23, 6153–6164Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/ja00128a001https://doi.org/10.1021/ja00128a001research-articleACS PublicationsRequest reuse permissionsArticle Views105Altmetric-Citations14LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
A Systematic Classification of Knowledge, Reasoning, and Context within the ARC Dataset (2018)

Michael Boratko, Harshit Padigela, Divyendra Mikkilineni, Pritish Yuvraj, Rajarshi Das, Andrew McCallum, Maria Chang, Achille Fokoue-Nkoutche, Pavan Kapanipathi, Nicholas Mattei, Ryan Musa, Kartik Talamadupula, Michael Witbrock. Proceedings of the Workshop on Machine Reading for Question Answering. 2018.
Protein Language Model for Prediction of Subcellular Localization of Protein Sequences from Gram-negative bacteria (ProtLM.SCL) (2022)

Abstract The prediction of bacterial protein Sub-Cellular Localization (SCL) is critical for antigen identification and reverse vaccinology, especially when determining protein localization in the lab is time consuming, expensive and not possible for all species. While PSORTb is one of the most widely used tool for predicting SCL, it has several limitations, including the tendency to label a large number of proteins as ‘Unknown’. To address these shortcomings, we present a protein language model capable of predicting the subcellular localization of a given protein (ProtLM.SCL) from gram-negative bacteria. By performing 10-fold cross validation on the PSORTb public data set, we demonstrate that ProtLM.SCL is more accurate and precise than PSORTb. When compared to empirically validated published data, our models also outperformed PSORTb, particularly when categorizing difficult occurrences.
Cognitive DF generalized order relay selection networks with interference from primary user (2015)

The generalized order relay selection scheme is efficient in situations where the opportunistic relaying scheme could fail. Such conditions include; the presence of imperfect channel-state-information (CSI) where the scheduling unit could fail in error in selecting the best relay among the available relays, the presence of outdated channel information (OCI) where the relay which was the best at the selection time instant could not be the best at the transmission time instant, and in situations where the best relay is busy in some scheduling duties in other parts of the network. Also, this scheme is efficient in situations where the best relay is busy in load balancing or scheduling duties in other parts of the network. In this paper, we introduce the generalized order relaying scheme for cognitive decode-and-forward (DF) relay networks and evaluate its performance in the presence of interference from primary user (PU) on the secondary user (SU). Closed-form and asymptotic expressions are derived for the outage probability in addition to deriving the diversity order and coding gain of the system. MonteCarlo simulations are given to verify the achieved results. Main findings illustrate that with fixed interference power, the diversity gain of the secondary system linearly decreases with decreasing the number of relays, and vice versa increases. Furthermore, the diversity gain linearly increases with decreasing the order of the selected relay, and vice versa decreases. Also, results show that the interference from the PU transmitter at the SU relays is more severe on the system performance compared to that at the SU destination.
Synthesis of Soluble Poly(thio-2,6-dimethyl-1,4-phenylene) by Oxidative Polymerization of Bis(3,5-dimethylphenyl) Disulfide (1992)

Abstract Poly(thio-2,6-dimethyl-1,4-phenylene) has been prepared by the oxidative polymerization of bis(3,5-dimethylphenyl) disulfide. The obtained polymer is amorphous and soluble in common organic solvents. The properties of the polymer are similar to those of poly(oxy-2,6-dimethyl-1,4-phenylene), rather than poly(thio-1,4-phenylene) (PPS). The polymer is obtained as a high molecular weight substance compared with other substituted or non-substituted PPS derivatives by the oxidative polymerization. The polymer containing a disulfide bond, whose structure was confirmed by the reduction of the polymer, acts as an initiator of radical polymerization.
Qualitative analysis of antibody–drug conjugates (ADCs): an experimental comparison of analytical techniques of cysteine-linked ADCs (2018)

Antibody-drug conjugates (ADCs) are an emerging type of biotherapeutics that utilize multiple tissue-specific antibodies combined with a range of linker designs to enable the transportation and selective release of cytotoxic drugs in close proximity to tumours. Consisting of antibodies conjugated to small drug molecules through a variety of linkers, ADCs are chemically complex analytes. Here we present a unique experimental comparison of four techniques for ADC analysis: hydrophobic interaction chromatography (HIC-UV/Vis), reversed phase liquid chromatography mass spectrometry (RPLC-MS), using either a QToF or an Orbitrap analyser, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Four different ADCs consisting of Trastuzumab, monomethyl auristatin E (MMAE) and a peptidic linker moiety differing in their respective stoichiometric ratios in regard to drug-to-antibody ratio (DAR) were used for the comparison. We found that the determined DAR from all techniques was comparable, while the accuracy of the molecular weights for the conjugated light and heavy chain differed more extensively. This indicates that the choice of a mass analyser is more crucial for determining the accurate weights of the light and heavy chains than to evaluate the DAR of a given batch. However, ambiguous DAR assignment in HIC-UV/Vis or bias for either the light or heavy chain fragments in the mass spectrometry-based techniques can influence the obtained average DAR value and the use of complementary techniques is advisable. Out of the four techniques evaluated, HIC-UV/Vis and MALDI required less time to obtain an average DAR value and would therefore be good for initial screenings in the early stages of the discovery phase of new ADCs.
Detection of conductivity voids and landmines using high frequency electromagnetic induction (2016)

Electromagnetic induction (EMI) instruments have been traditionally used to detect high electric conductivity discrete targets such as metal unexploded ordnance (UXO). The frequencies used for this EMI regime have typically been less than 100 kHz. To detect intermediate conductivity objects like carbon fiber, even less conductive saturated salts, and even voids embedded in conducting soils, higher frequencies up to the low megahertz range are required in order to capture characteristic relaxation responses. In this context, nonconducting lastic landmines can be considered a void plus small metallic parts such as the firing pin. To predict EMI phenomena at frequencies up to 15MHz, we modeled the response of conducting and nonconducting targets using the the Method of Auxiliary Sources. Our high-frequency electromagnetic induction (HFEMI) instrument is able to acquire EMI data at frequencies up to that same high limit. Modeled and measured characteristic relaxation signatures compare favorably and indicate new sensing possibilities in a variety of scenarios including the detection of voids and landmines.
P115 Real-world experience of peri-operative treatments on surgical complications after Ileo-caecal resection in Crohn’s disease (2020)

Abstract Background The current recommendations remain vague as to whether biologics are safe or deleterious when surgery is contemplated in patients with Crohn’s disease (CD). Conflicting data do not enable to adopt a definitive position on the time to surgery. The aims of this study were to evaluate the impact of perioperative treatments on the rate of surgical complications and to report surgical recurrence rate of CD after ileo-caecal (IC) resection. Methods This was a retrospective monocentric cohort study of consecutive CD patients who underwent IC resection between 1996 and 2018. An ethical committee has been approved (P2019/376). The overall rate of surgical complications was evaluated within 30 days after surgery. The effect of pre- and postoperative treatments was assessed on overall morbidity, general and infectious complications, anastomotic leakage and risk factors. Statistical analyses were performed using SPSS. Results Demographic data of the 165 CD patients who underwent a primary IC resection are presented in Table 1. The median age at time of the first IC resection was 35 years (IQR 24–44) while the median follow-up was 6.1 years (IQR 1–11). The overall rate of complications was 18% including 8.7% and 3.3% patients with infectious complications and anastomotic leakage, respectively. No risk factors have been found to be associated with surgical complications. In particular, immunosuppressants and biologics did not increase the risk of surgical complications. Twenty-four per cent of patients (n = 39/160) needed a second IC resection due to stenosis at the anastomosis site in 69.2% of cases (n = 27/39). Surgical recurrence was found to increase linearly over time with a second surgery after a median follow-up of 8 years (IQR 2–12). Anti-TNF used as post-operative treatment had a protective role on surgical recurrence in multivariable regression with odd ration (OR) of 0.15, p = 0.001 (Table 2). Conclusion Prevalence of complications after an IC resection in CD patients was of 18% in this retrospective monocentric cohort. No risk factors were found to be associated with surgical complications. Anti-TNF seems to have a protective role on surgical recurrence.
Near-Field Beamforming for STAR-RIS Networks (2023)

Recently, simultaneously transmitting and reflecting reconfigurable intelligent surfaces (STAR-RISs) have received significant research interest. The employment of large STAR-RIS and high-frequency signaling inevitably make the near-field propagation dominant in wireless communications. In this work, a STAR-RIS aided near-field multiple-input multiple-multiple (MIMO) communication framework is proposed. A weighted sum rate maximization problem for the joint optimization of the active beamforming at the base station (BS) and the transmission/reflection-coefficients (TRCs) at the STAR-RIS is formulated. The non-convex problem is solved by a block coordinate descent (BCD)-based algorithm. In particular, under given STAR-RIS TRCs, the optimal active beamforming matrices are obtained by solving a convex quadratically constrained quadratic program. For given active beamforming matrices, two algorithms are suggested for optimizing the STAR-RIS TRCs: a penalty-based iterative (PEN) algorithm and an element-wise iterative (ELE) algorithm. The latter algorithm is conceived for STAR-RISs with a large number of elements. Numerical results illustrate that: i) near-field beamforming for STAR-RIS aided MIMO communications significantly improves the achieved weighted sum rate compared with far-field beamforming; ii) the near-field channels facilitated by the STAR-RIS provide enhanced degrees-of-freedom and accessibility for the multi-user MIMO system; and iii) the BCD-PEN algorithm achieves better performance than the BCD-ELE algorithm, while the latter has a significantly lower computational complexity.
Separation of Latex Particles According to Size by Continuous Electrophoresis (1973)

(1973). Separation of Latex Particles According to Size by Continuous Electrophoresis. Separation and Purification Methods: Vol. 2, No. 1, pp. 153-198.
Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry (2007)

Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.
Computer-aided optimization of DC/DC converters for automotive applications (2003)

This paper investigates computer-aided optimization of DC/DC converters, with a focus on converters for dual-voltage automotive electrical systems. A new CAD optimization approach based on Monte Carlo search methods is introduced which allows the design space to be rapidly explored in an automated fashion and the most optimal designs and design approaches to be identified. The optimization approach also allows the effects of variations in design specifications on the cost, weight, and volume of an optimized converter to be readily determined. A prototype converter designed using this optimization procedure is evaluated and compared to a converter designed by conventional means.
Mechanism of methaemoglobin breakdown by the lysine-specific gingipain of the periodontal pathogen Porphyromonas gingivalis (2008)

Abstract The R- and K-gingipain proteases of Porphyromonas gingivalis are involved in proteolysis of haemoglobin from which the defensive dimeric haem pigment is formed. Whilst oxyhaemoglobin is refractory towards K-gingipain, methaemoglobin is rapidly degraded. Ligation of methaemoglobin with N3-, which effectively blocks haem dissociation from the protein, prevented haemoglobin breakdown. Haem-free globin was rapidly degraded by K-gingipain. These data emphasise the need for haemoglobin oxidation which encourages haem dissociation and makes the haem-free globin susceptible to proteolytic attack.
Evaluation of Proximal Junctional Kyphosis in Adolescent Idiopathic Scoliosis Following Pedicle Screw, Hook, or Hybrid Instrumentation (2010)

Adjacent level proximal kyphosis was significantly increased with pedicle screws, but the clinical significance of this is unclear. A potential solution is the substitution of hooks at the upper-instrumented vertebrae, but further investigation is required.