gebhart/patrepeval huggingface dataset:
Hamiltonian gadgets with reduced resource requirements (2015)

Application of the adiabatic model of quantum computation requires efficient encoding of the solution to computational problems into the lowest eigenstate of a Hamiltonian that supports universal adiabatic quantum computation. Experimental systems are typically limited to restricted forms of two-body interactions. Therefore, universal adiabatic quantum computation requires a method for approximating quantum many-body Hamiltonians up to arbitrary spectral error using at most two-body interactions. Hamiltonian gadgets, introduced around a decade ago, offer the only current means to address this requirement. Although the applications of Hamiltonian gadgets have steadily grown since their introduction, little progress has been made in overcoming the limitations of the gadgets themselves. In this experimentally motivated theoretical study, we introduce several gadgets which require significantly more realistic control parameters than similar gadgets in the literature. We employ analytical techniques which result in a reduction of the resource scaling as a function of spectral error for the commonly used subdivision, three- to two-body and $k$-body gadgets. Accordingly, our improvements reduce the resource requirements of all proofs and experimental proposals making use of these common gadgets. Next, we numerically optimize these gadgets to illustrate the tightness of our analytical bounds. Finally, we introduce a gadget that simulates a $YY$ interaction term using Hamiltonians containing only ${X,Z,XX,ZZ}$ terms. Apart from possible implications in a theoretical context, this work could also be useful for a first experimental implementation of these key building blocks by requiring less control precision without introducing extra ancillary qubits.
Supplementary Table S2 from Senescence Sensitivity of Breast Cancer Cells Is Defined by Positive Feedback Loop between CIP2A and E2F1 (2023)

&lt;p&gt;Supplementary Table S2 PDF file - 90K, Ingenuity transcription factor analysis of CIP2A depleted cells&lt;/p&gt;
Laser-Induced Breakdown Spectroscopy of High-Pressure Bulk Aqueous Solutions (2006)

Laser-induced breakdown spectroscopy (LIBS) is presented for detection of several Group I and II elements (e.g., Na, Ca, Li, and K), as well as Mn and CaOH, in bulk aqueous solution at pressures exceeding 2.76 x 10(7) Pa (276 bar). Preliminary investigations reveal only minor pressure effects on the emission intensity and line width for all elements examined. These effects are found to depend on detector timing and laser pulse energy. The results of these investigations have implications for potential applications of LIBS for in situ multi-elemental detection in deep-ocean environments.
Analysis of Radiative Heat Transfer in Complex Two-Dimensional Enclosures With Obstacles Using the Modified Discrete Ordinates Method (2001)

In this work, an extension of a modified discrete ordinates method recently proposed by other researchers is presented. It is intended to counter the ray effect inherent in this method. The media analyzed are absorbing, emitting and isotropically or anisotropically scattering and the enclosure geometry is arbitrary. Cases with obstructions are emphasized. The radiative intensity is broken into two parts: the wall-related intensity and the medium-related intensity. The former is treated separately by rigorous integration over the entire solid boundary. A new differencing scheme based on quadrangular grids is also proposed and used for the treatment of the medium-related intensity. Results confirm that the proposed method is a good general remedy for anomalies caused by the ray effect due to the geometry.
PEO–PPO Diblock Copolymers Protect Myoblasts from Hypo-Osmotic Stress In Vitro Dependent on Copolymer Size, Composition, and Architecture (2017)

Poloxamer 188, a triblock copolymer of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), protects cellular membranes from various stresses. Though numerous block copolymer variants exist, evaluation of alternative architecture, composition, and size has been minimal. Herein, cultured murine myoblasts are exposed to the stresses of hypotonic shock and isotonic recovery, and membrane integrity was evaluated by quantifying release of lactate dehydrogenase. Comparative evaluation of a systematic set of PEO-PPO diblock and PEO-PPO-PEO triblock copolymers demonstrates that the diblock architecture can be protective in vitro. Short PPO blocks hinder protection with >9 PPO units needed for protection at 150 μM and >16 units needed at 14 μM. Addition of a tert-butyl end group enhances protection at reduced concentration. When the end group and PPO length are fixed, increasing the PEO length improves protection. This systematic evaluation establishes a new in vitro screening tool for evaluating membrane-sealing amphiphiles and provides mechanistic insight to guide future copolymer design for membrane stabilization in vivo.
Identification of the Rdl mutation in laboratory and field strains of the cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) (2004)

In many insect species, resistance to cyclodiene insecticides is caused by amino acid substitutions at a single residue (A302) within the M2 transmembrane region of the gamma-aminobutyric acid (GABA) receptor sub-unit termed Rdl (resistance to dieldrin). These mutations (A302S and A302G) have also been shown to confer varying levels of cross-resistance to fipronil, a phenylpyrazole insecticide with a similar mode of action to cyclodienes. To investigate the possible occurrence of these mutations in the cat flea, Ctenocephalides felis (Bouché), a 176-bp fragment of the cat flea Rdl gene, encompassing the mutation site, was PCR amplified and sequenced from nine laboratory flea strains. The A302S mutation was found in eight of the nine strains analysed, although the relative frequency of the mutant allele varied between strains. Only one strain (R6) was found to be homozygous for the S302 allele in all the individuals tested, and this correlated with previous reports of low-level fipronil resistance in this strain. A PCR-based diagnostic assay, capable of screening individual fleas for this mutation, was developed and used to survey a range of fleas collected at random from veterinary clinics in the UK and USA. The A302S mutation was present at a high frequency in these domestic pet populations.
Candidate gene analysis of gastrointestinal stromal tumors and paragangliomas in patients with carneys triad. (2011)

e12018 Background: Carneys triad (CT) describes the association of paragangliomas (PGLs) with gastrointestinal stromal tumors (GISTs) and pulmonary chondromas (PCH). CT is unique compared to other multiple neoplasia syndromes in that it is an apparently sporadic condition affecting mainly young females. CT is not always complete, with approximately ¼ of patients having all three components, and ½ having only 2 of the three (PCH and GIST). A similar syndrome (the Carney-Stratakis syndrome) is characterized by the familial association of GIST and PGL and can be inherited as an autosomal-dominant disorder due to mutations in SDHB,-C, and –D. The association of three rare tumors is strongly suggestive of a genetic disorder, yet no gene has been linked to CT. Using a novel CGH method, SOMATICS, chromosome 1p losses were determined to be frequent in both PGLs and GISTs from CT patients. Recent data implicate ARID1A as a tumor-suppressor gene frequently disrupted in ovarian clear-cell and endometrioid carcinomas. Using a candidate gene-based approach, we sequenced tumor suppressor genes in GISTs and PGLs from patients with CT. Methods: Gene candidacy was determined either by genome location (ARID1A 1p35.3), or potentially oncogenic pathway-defects in mitochondrial complex II activity (SDHAF1). Coding regions and exon-intron boundaries for ARID1A and SDHAF1 were PCR-amplified and sequenced using the Sanger method on tumor DNA from 13 patients with CT (7 paragangliomas and 11 GISTs). Results: All DNA specimens were confirmed to be negative for mutations in SDHA, SDHB, SDHC, SDHD, KIT and PDGFRA. Sequencing analysis revealed only polymorphisms, but no somatic mutations in both ARID1A and SDHAF1. Conclusions: Although the loss of chromosome 1p is a frequent feature, the ARID1A tumor suppressor gene that is located in this region, does not seem to harbor sequence alterations. These data indicate that another gene (or genes) is probably responsible for the tumor genesis in patients with CT. Further research using next generation sequencing is ongoing in our institution.
The Acceleration of Nonformaldehyde Electroless Copper Plating (2002)

Nonformaldehyde, low pH (compared to highly alkaline bath) electroless copper plating has been investigated. Thiourea and its derivatives have been shown to increase the deposition rate of electroless copper plating solutions using HEDTA [N-(2-hydroxyethyl)ethylenediaminetriacetic acid trisodium salt hydrate] as the complexing agent and sodium hypophosphite as the reducing agent. A thiourea concentration of 1.0 ppm produced a fourfold increase in the deposition rate of copper from about 1 to 4 μm/h. The effect of thiourea on the electrochemical reactions, and the crystal structures and electrical properties of the copper deposits were examined. A small amount of thiourea, or its derivatives, in the electroless copper solution improves the catalytic activity of the copper surface for the oxidation of hypophosphite, resulting in a higher electroless deposition rate. The thiourea also increases the growth colony size of the copper deposits and improves its conductivity. A reaction mechanism is proposed to describe the function of the thiourea and its derivatives on the process. © 2002 The Electrochemical Society. All rights reserved.
Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase (2017)

Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth <i>Manduca sexta</i> and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from <i>Nostoc</i> sp. PCC 7120, <i>Shewanella oneidensis</i>, <i>Shewanella woodyi</i>, and <i>Clostridium botulinum</i>, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from <i>M. sexta</i> and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.
A smartphone connected software updating framework for IoT devices (2015)

This paper proposes a software framework and hardware architecture to exchange the binaries and profiles from smartphones to IoT devices and reprogram devices with smartphones. This scheme, when included in a system of smartphones interconnected with locally deployed IoT devices in wired or wireless manners, can be used to implement a practical updater.
The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions (2022)

The accurate prediction of binding affinity between protein and small molecules with free energy methods, particularly the difference in binding affinities via relative binding free energy calculations, has undergone a dramatic increase in use and impact over recent years. The improvements in methodology, hardware, and implementation can deliver results with less than 1 kcal/mol mean unsigned error between calculation and experiment. This is a remarkable achievement and beckons some reflection on the significance of calculation approaching the accuracy of experiment. In this article, we describe a statistical analysis of the implications of variance (standard deviation) of both experimental and calculated binding affinities with respect to the unknown true binding affinity. We reveal that plausible ratios of standard deviation in experiment and calculation can lead to unexpected outcomes for assessing the performance of predictions. The work extends beyond the case of binding free energies to other affinity or property prediction methods.
13. ARTHROSCOPIC ROTATOR CUFF REPAIR WITH ADDITION OF PLATELET RICH FIBRIN (PRF): FEASIBILITY STUDY AND ULTRASOUND ASSESSMENT OF TENDON-TROCHITER ZONE VASCULARIZATION (2011)

Purpose of the study: Platelet rich fibrin (PRF) favours proliferation of tenocytes and synthesis of extracellular matrix. The purpose of this study was to demonstrate the technical feasibility of adding a PRF envelope during arthroscopic rotator cuff repair to favour short-term vascularisation of the tendon-trochiter zone vascularization.

Material and method: Twenty patients aged over 55 years with a posterosuperior rotator cuff tear were included in this prospective randomized controlled study. The double strand technique was used for all patients. Patients were selected at random for insertion of a PRF envelope between the tendon and the trochiter. There were thus two groups of ten patients. The SSV, SST, VAS and Constant scores were noted. Vascularization was assessed with Power Doppler ultrasound at 6 weeks and 3 months by an independent operator unaware of the study group.

Results: There were no complications during or after the operations. Postoperatively, all patients increased their SSV, SST, VAS and Constant scores significantly. Vascularization of the tendon-trochiter zone, as assessed by Power Doppler, was significantly higher in the PRF group at 6 weeks. It was unchanged in the two groups at 3 months.

Discussion: Arthroscopic rotator cuff repair with adjunction of a PRF envelope is technically feasible and increases vascularizaton of the tendon-trochiter zone at 6 weeks.

Conclusion: PRF can improve the tendon healing rate for rotator cuff tears.
Von der Grundlagenforschung zum Blockbuster: die Entdeckung des Antiepileptikums Lyrica (2008)

Der krampflösende Wirkstoff (S)-(+)-3-Isobutyl-γ-aminobuttersäure ((S)-(+)-3-Isobutyl-GABA, Lyrica; siehe Formel) ging aus Grundlagenforschungen hervor, die einen unerwarteten Verlauf nahmen. Die Wirkung von Lyrica beruht nicht, wie ursprünglich überlegt wurde, auf der Aktivierung der L-Glutamindecarboxylase und dem Anstieg des hemmenden Neurotransmitters GABA; vielmehr antagonisiert es einen Calciumkanal, was die Freisetzung des exzitatorischen Neurotransmitters L-Glutamat hemmt. Der letztendliche Effekt ist der gleiche.
Integrated, asymmetric twin-waveguide ultrafast all-optical switch (2002)

We demonstrate the monolithic integration of a terahertz optical asymmetric demultiplexer (TOAD) in an asymmetric twin-waveguide structure operating at /spl lambda/=1.55 /spl mu/m wavelength. The device utilizes a Mach-Zehnder interferometer geometry with counter-propagating signal and control pulses. The device consists of etched waveguides and 3-dB multimode-interference couplers, with a semiconductor optical amplifier (SOA) integrated into each arm of the interferometer and coupled to the passive waveguides by low-loss tapered mode transformers. Signal switching is accomplished via nonlinear gain compression and phase shifts in the SOAs induced by a control pulse propagating in the direction opposite that of the signal. A single control pulse is split in the two arms to provide both ON and OFF operations of the switch, with the switching window of 10-15 ps determined by the relative displacement of the two SOAs. The device is fabricated in an InGaAsP-InP asymmetric twin-waveguide structure grown by gas-source molecular beam epitaxy.
Supplementary Video 10 from Endogenous Two-Photon Fluorescence Imaging Elucidates Metabolic Changes Related to Enhanced Glycolysis and Glutamine Consumption in Precancerous Epithelial Tissues (2023)

&lt;p&gt;AVI file - 1258KB, Representative 3D RENDERING E6 EETE.&lt;/p&gt;
Reduction in atrial fibrillation using <underline>c</underline> ircadian <underline>o</underline> verdrive <underline>p</underline> acing at 80 65.PPM (2001)

We report follow-up data on 11 patients with bradycardia and paroxysmal atrial fibrillation (PAF) who received dual chamber pacemakers during an episode of PAF. Implants were carried out between February 1999 and May 2000. All patients had a conventional indication for pacing. 10 patients had previously documented episodes of PAF. 6 patients were in AF and 4 in atrial flutter prior to implant. 1 patient developed AF during the procedure before atrial pacing parameters could be measured. In all cases the atrial lead position was accepted solely on the X-ray appearances provided satisfactory sensing of fibrillation or flutter could be achieved. Following pacing, spontaneous cardioversion to sinus rhythm occurred in 4 patients within 24 hours and in 1 patient within 7 days. 5 patients underwent successful DC cardioversion after stabilisation on anticoagulant treatment. 1 patient has remained in flutter/fibrillation since implantation, in 10 patients, satisfactory atrial pacing and sensing parameters have been measured in the pacemaker clinic on at least one occasion. To date. follow-up data are available on all 11 patients for 0-4 months after successful cardioversion to sinus or atrial paced rhythm (average 2 months). At the most recent review, 9 patients were in sinus or atrial paced rhythm, 2 apparently in permanent AF.
LTE Uplink CoMP Trial in a HetNet Deployment (2012)

Low power remote radio units (RRU:s) are identified as one of the key components to increase the capacity of cellular networks in dense areas with high traffic demands. When the traffic is clustered in hotspots they are also feasible to, combined with high power macro RRU:s, form a heterogeneous network (HetNet). The inherited centralized architecture with RRU:s opens for advanced coordination features between sites. One such promising coordination feature is uplink CoMP (Co-ordinated Multi Point). This paper shows results from a recent full scale CoMP trial on release 8 3GPP Long Term Evolution (LTE). It is demonstrated that best uplink reception (in a micro node) can be decoupled from best downlink transmission (from a macro node), enabling improved uplink bitrate with maintained downlink bitrate. Furthermore, with joint reception a significant uplink reception macro diversity gain is achieved. In the tested scenario on a 10 MHz band the total improvement is in the order of 6 Mbps in the macro-micro transition area.
Subgroups of Diffuse Large B-Cell Lymphoma (DLBCL) with Different Genomic Lesions and Clinical Course During Treatment with R-CHOP. (2009)

Abstract Abstract 3957 Poster Board III-893 BACKGROUND Despite recent therapeutic improvements, the clinical course of DLBCL still differs considerably among patients. Here, we present the final results of a study to identify distinct DLBCL subgroups in patients treated with R-CHOP. METHODS DNA from 166 frozen DLBCL samples (PMBL,HIV-related DLBCL, post-transplant DLBCL and Richter's Syndromes were excluded) was analyzed with Affymetrix Human Mapping 250K arrays. Affymetrix U133 PLUS 2.0 gene expression profiles (GEP) were available for 54 cases. An optimized non-negative matrix factorization (NMF) was used for unsupervised clustering. The impact of the recurrent lesions on OS, PFS and DFS was evaluated with the log-rank test followed by multiple test correction (MTC). RESULTS 20 lesions showed a statistical significant impact on OS. Only 8p23.1 loss maintained its significance after MTC and was associated with additional aberrations, such as 17p- and 15q-. Unsupervised clustering identified 5 clusters with distinct genetic profiles, clinical characteristics and outcome: 1 (61/166, 37%), 2 (22/166, 13%), 3 (5/166, 4%), 4 (29/166, 17%), 5 (7/166, 6%). Cluster 1 was characterized by a heterogeneous genomic profile, lacking the most recurrent lesions. When compared to cluster 2 and 4, there were more HCV infections (9/38, 24% vs 1/12, 8% and 0/20; p=0.014) and bone marrow involvement (16/57, 28% vs 1/19, 5% and 2/24, 8%; p=0.008). GEP and morphology data suggested that cluster 1 could represent DLBCL with a high content of infiltrating T-cells, partially explaining the low rate of aberrations. This cluster has characteristics similar to the “host response” cluster previously identified by Monti et al., 2005. The outcome was poor with a high relapse rate (13/49, 26%) and a 5-yr OS of 76%. Cluster 2 (1q+/3q+/6q-/17p-) had also a relatively poor OS 80%. Cluster 4 (7+/12+) had a good outcome with a 5-yr OS of 92%. Clusters 2 and 4 showed differences in the number of pts with a high IPI-score (9/16, 56% vs. 7/26, 27%; p=0.057) and in single IPI factors, CR-rate (17/22, 77% vs. 25/29, 86%) and relapse rate (5/17, 29% vs. 2/25, 8%; p= 0.068). Cluster 3 (6q-/9-/11q+) had a trend for a good outcome. Instead, cluster 5 (3q+/11q+/18q+/6q-/8p-/15q-/17p-) showed a poor outcome. Clusters 2 and 4 were similar to ABC and GCB, respectively. CONCLUSIONS ArrayCGH provides the capability to identify genetic features and clusters, associated with a different outcome in patients treated with R-CHOP. The 8p23.1 locus should be investigated further for a gene that may be important in the pathogenesis of DLBCL. Disclosures: No relevant conflicts of interest to declare.
Epithelial wound healing in the denervated cornea (1994)

We studied the epithelial healing of denervated corneas in New Zealand albino rabbits with their left trigeminal ganglia surgically amputated. On the 14th day after amputation, the corneas were keratectomized (in 8.5 mm diameter) and documentation of the healing process began. We calculated the epithelial healing rate using simple regression analysis. We observed a mean healing rate of 0.463 +/- 0.059 mm2/hr (mean +/- SE) in the denervated corneas, compared to 0.609 +/- 0.031 mm2/hr in the control corneas; a statistically significant difference of P < 0.001. We performed scanning electron microscopic observation (SEM) at three points; before keratectomy, 48 hrs after keratectomy, and 14 days after keratectomy. SEM observation revealed that, in contrast to the control corneas, the surface of the epithelial cells in denervated corneas appeared rough with numerous exfoliating cells observed. This indicates that the epithelial cells might attach only weakly to the floor in denervated corneas. Transmission electron microscopic observation (TEM) performed at 48 hrs and 14 days after keratectomy also supports this finding. For example, the intercellular space is widened and fewer desmosomes are observed in denervated corneas. Using immunohistochemistry, the surface of the wound bed was covered with fibronectin in a similar fashion to the control. In the late stage, the denervated corneas demonstrated spontaneous epithelial breakdown with 83% of them having persistent epithelial defects. Epithelial healing in the control corneas displayed no abnormal signs. On the 14th day after keratectomy, these eyes were enucleated for immunohistochemistry using bromodeoxyuridine (Brd U) to observe dividing cells.(ABSTRACT TRUNCATED AT 250 WORDS)