gebhart/patrepeval huggingface dataset:
A Bioresistant Nitroxide Spin Label for In‐Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies (2017)

Approaching protein structural dynamics and protein-protein interactions in the cellular environment is a fundamental challenge. Owing to its absolute sensitivity and to its selectivity to paramagnetic species, site-directed spin labeling (SDSL) combined with electron paramagnetic resonance (EPR) has the potential to evolve into an efficient method to follow conformational changes in proteins directly inside cells. Until now, the use of nitroxide-based spin labels for in-cell studies has represented a major hurdle because of their short persistence in the cellular context. The design and synthesis of the first maleimido-proxyl-based spin label (M-TETPO) resistant towards reduction and being efficient to probe protein dynamics by continuous wave and pulsed EPR is presented. In particular, the extended lifetime of M-TETPO enabled the study of structural features of a chaperone in the absence and presence of its binding partner at endogenous concentration directly inside cells.
Even Delta-Matroids and the Complexity of Planar Boolean CSPs (2018)

The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvořák and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable . It properly includes classes that were known to be tractable before, namely, co-independent , compact , local , linear , and binary , with the following caveat: We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n × n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.
Activity-dependent lateral inhibition signals for synaptic competition (2019)

SUMMARY In developing brains, activity-dependent remodeling facilitates the formation of precise neuronal connectivity. Synaptic competition is known to facilitate synapse elimination; however, it has remained unknown how different synapses compete to each other within a postsynaptic cell. Here we investigate how a mitral cell in the olfactory bulb prunes all but one primary dendrite during the developmental remodeling process. We find that spontaneous activity generated within the olfactory bulb is essential. We show that strong glutamatergic inputs to one dendrite trigger branch-specific changes in RhoA activity to facilitate the pruning of the remaining dendrites: NMDAR-dependent local signals suppress RhoA to protect it from pruning; however, the subsequent neuronal depolarization induces neuron-wide activation of RhoA to prune non-protected dendrites. NMDAR-RhoA signals are also essential for the synaptic competition in the barrel cortex. Our results demonstrate a general principle whereby activity-dependent lateral inhibition across synapses establishes a discrete receptive field of a neuron.
Low level laser (light) therapy and photobiomodulation: the path forward (2015)

Low level laser (light) therapy (LLLT) also known as photobiomodulation (PBM) therapy has been practiced for almost fifty years, and hundreds of positive clinical trials and thousands of laboratory studies have been published. Despite these impressive accomplishments LLLT has still not reached the stage of acceptance by mainstream medicine. The reasons for this were discussed at a recent Optical Society of America (OSA) Incubator meeting in Washington DC in 2014. Uncertainty about mechanisms was highlighted, and this paper will describe the current thinking. To drive LLLT towards mainstream medicine, we need better guidelines with standardized protocols and consistent parameters. Studies should be published in higher impact scientific and medical journals. Companies should avoid false promises and deceptive marketing, and physicians should receive a clearly defined return on investment with insurance reimbursement.
AMP-Activated Protein Kinase Is Involved in Endothelial NO Synthase Activation in Response to Shear Stress (2006)

Our results suggest that shear stress activates AMPK in ECs, which contributes to elevated eNOS activity and subsequent NO production. Hence, AMPK, in addition to serving as an energy sensor, also plays an important role in regulating vascular tone.
Why Does Hip Arthroscopy Fail? Indications and PEARLS for Revision Success (2020)

The surgical treatment of femoroacetabular impingement has been shown to have successful early and mid-term clinical outcomes. Despite these favorable clinical outcomes that have been published in the literature, there is a subgroup of patients that present with continued or recurrent symptoms after surgical treatment. Not only has there been an increase in the number of hip arthroscopy procedures, but also there has been a corresponding increase in the number of revision hip arthroscopy and hip preservation surgeries. Previous studies have reported residual deformity to be the most common reason for revision hip arthroscopy. However, chondral, labral, and capsular considerations also are important when addressing patients not only in the primary but also, the revision setting. In this review, we outline the evaluation and treatment of the patient that presents with continued hip and groin pain after undergoing a hip.
Specific core-shell approaches and related properties in nanostructured ferroelectric ceramics (2018)

Interfaces are a major issue when designing ferroelectric nanostructured materials with tailored properties. In a context of integration and multifunctionality in the field of electronics, several strategies have been developed to control the microstructure and defect chemistry of interfaces that strongly impact the macroscopic properties. The suitability of the core-shell approaches that allow a subtle tuning of interface phenomena at different scales has been widely demonstrated. We focus here on the flexibility of the core-shell approach devoted to the processing of nanostructured ferroelectric composites. Our strategy relies on the use of advanced synthesis processes to design ferroelectric grains coated with shells of different nature, morphology and crystallinity. Typical examples will be reviewed with a specific attention on their impact on both microstructure and dielectric properties. Our approach, based also on the use of fast sintering technique, provides a guidance to design 3D bulk nanostructured ferroelectrics while controlling and/or exploiting size, interface and defects chemistry. The contribution of specific spectroscopies to probe interfacial chemistry and defects is underlined. The high density of interfaces in core-shell materials is obviously an advantage to target additional functionality such as magneto-electric coupling. This is illustrated in 3D composites and one dimensional nanostructures that coaxially combine electric and magnetic materials. The core-shell approach described here could be transferred to a much broader range of materials covering many functionalities provided a deeper understanding of the interfaces at the atomic scale is achieved and a further development of low temperature processing is reached.
Network-based Translation of GWAS Findings to Pathobiology and Drug Repurposing for Alzheimer’s Disease (2020)

Abstract Genome-wide association studies (GWAS) have identified numerous susceptibility loci for Alzheimer’s disease (AD). However, utilizing GWAS to identify high-confidence AD risk genes (ARGs) that can guide development of new therapeutics for patients suffering from AD has heretofore not been successful. To address this critical problem in the field, we have developed a genotype-informed, network-based methodology that interrogates pathogenesis to identify new therapeutics. When applied to AD, this approach integrates GWAS findings, multi-omics data from brain samples of AD patients and preclinical AD models, drug-target networks, and the human protein-protein interactome, along with large-scale patient database validation and in vitro mechanistic observations in human microglia cells. Through this approach, we identified 103 ARGs validated by various levels of pathobiological evidence in AD. Via network-based prediction and population-based validation, we then showed that pioglitazone usage is significantly associated with decreased risk of AD (hazard ratio (HR) = 0.895, 95% confidence interval [CI] 0.841-0.951, P = 3.97 × 10 −4 ) in a retrospective case-control validation. Pioglitazone is a peroxisome proliferator-activated receptor agonist used to treat type 2 diabetes, and propensity score matching cohort studies confirmed its association with reduced risk of AD in comparison to glipizide (HR =0.921, 95% CI 0.861-0.983, P = 0.0146), an insulin secretagogue that is also used to treat type 2 diabetes. In vitro experiments showed that pioglitazone downregulated glycogen synthase kinase 3 beta (GSK3β) and cyclin-dependent kinase (CDK5) in human microglia cells, supporting a possible mechanism-of-action for its beneficial effect in AD. In summary, we present an integrated, network-based methodology to rapidly translate GWAS findings and multi-omics data to genotype-informed therapeutic discovery in AD.
A five-year follow-up study on the pathological changes of gastric mucosa after H. pylori eradication. (2003)

H. pylori eradication results in remarkable reduction in the severity and activity of chronic gastritis, marked resolution of intestinal metaplasia in the antrum. On the other hand, continuous H. pylori infection leads to progressive aggravation of atrophy and intestinal metaplasia.
Transcript profiling of hairy vetch ( Vicia villosa Roth) identified interesting genes for seed dormancy (2023)

Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
Evaluation of Glycosylated FlpA and SodB as Subunit Vaccines Against Campylobacter jejuni Colonisation in Chickens (2020)

<i>Campylobacter jejuni</i> is the leading bacterial cause of human gastroenteritis worldwide and the handling or consumption of contaminated poultry meat is the key source of infection. <i>C. jejuni</i> proteins FlpA and SodB and glycoconjugates containing the <i>C. jejuni N</i>-glycan have been separately reported to be partially protective vaccines in chickens. In this study, two novel glycoproteins generated by protein glycan coupling technology-G-FlpA and G-SodB (with two and three <i>N</i>-glycosylation sites, respectively)-were evaluated for efficacy against intestinal colonisation of chickens by <i>C. jejuni</i> strain M1 relative to their unglycosylated variants. Two independent trials of the same design were performed with either a high challenge dose of 10<sup>7</sup> colony-forming units (CFU) or a minimum challenge dose of 10<sup>2</sup> CFU of <i>C. jejuni</i> M1. While antigen-specific serum IgY was detected in both trials, no reduction in caecal colonisation by <i>C. jejuni</i> M1 was observed and glycosylation of vaccine antigens had no effect on the outcome. Our data highlight inconsistencies in the outcome of <i>C. jejuni</i> vaccination trials that may reflect antigen-, challenge strain-, vaccine administration-, adjuvant- and chicken line-specific differences from previously published studies. Refinement of glycoconjugate vaccines by increasing glycosylation levels or using highly immunogenic protein carriers could improve their efficacy.
Variable impedance actuators: Moving the robots of tomorrow (2012)

Most of today's robots have rigid structures and actuators requiring complex software control algorithms and sophisticated sensor systems in order to behave in a compliant and safe way adapted to contact with unknown environments and humans. By studying and constructing variable impedance actuators and their control, we contribute to the development of actuation units which can match the intrinsic safety, motion performance and energy efficiency of biological systems and in particular the human. As such, this may lead to a new generation of robots that can co-exist and co-operate with people and get closer to the human manipulation and locomotion performance than is possible with current robots.
ChemInform Abstract: Palladium‐Catalyzed Hiyama Couplings of α‐Silylenoates and α‐Silylenamides. (2012)

Abstract The reactions allow efficient formation of various stereodefined trisubstituted alkenes.
Solving Symmetric Diagonally-Dominant Systems by Preconditioning (2003)

In this paper we design support-tree preconditioners for n × n matrices with m nonzeros that are symmetric and diagonally-dominant with a nonnegative diagonal (SDD matrix). This reduces to designing such a preconditioner for a Laplacian matrix, A, which can be interpreted as an undirected nonnegatively-weighted graph, G with n vertices and m edges. Preconditioners accelerate the convergence of iterative methods for solving linear systems, and our preconditioner allows us to analyze the convergence of a particular algorithm, due to Gremban and Miller, called support-tree conjugate gradient (STCG). An advantage of support-tree preconditioners is that STCG parallelizes well. We show that STCG equipped with our preconditioner requires O(m log 2 n · � dilexp(G)) work and O(m) space to solve the system Ax = b, where dilexp(G) is an edge-expansion-based upper bound on the diameter of G. Existing bounds depend only on the size of the matrix (graph), hence our bound is incomparable. For instance, if G is a bounded-degree expander graph with uniform edge weights, dilexp(G) = O(log 2 n), and the work is O(n log 3 n). This is currently the best known bound for Laplacians of expander graphs. We show that dilexp(G) is always at most n, hence our bound is at most O(m √ n log 2 n) for any Laplacian (or SDD) matrix. For sufficiently dense systems, when m = Ω(n 1.61), this bound offers the best known work guarantee of any linear-space method. The main technical contributions of this paper include (i) adapting a recent result of Räcke to designing support-tree preconditioners, (ii) extending a power dissipation approach for bounding support numbers of preconditioners, and (iii) applying the methods used in Leighton and Rao’s approximate max-flow min-cut theorem to the “asymmetric” product flows the arise in Räcke’s construction.
Automatic Mouse Embryo Brain Ventricle & Body Segmentation and Mutant Classification From Ultrasound Data Using Deep Learning (2019)

High-frequency ultrasound (HFU) is well suited for imaging embryonic mice in vivo because it is non-invasive and real-time. Manual segmentation of the brain ventricles (BVs) and whole body from 3D HFU images is time-consuming and requires specialized training. This paper presents a deep-learning-based segmentation pipeline which automates several time-consuming, repetitive tasks currently performed to study genetic mutations in developing mouse embryos. Namely, the pipeline accurately segments the BV and body regions in 3D HFU images of mouse embryos, despite significant challenges due to position and shape variation of the embryos, as well as imaging artifacts. Based on the BV segmentation, a 3D convolutional neural network (CNN) is further trained to detect embryos with the Engrailed-1 (En1) mutation. The algorithms achieve 0.896 and 0.925 Dice Similarity Coefficient (DSC) for BV and body segmentation, respectively, and 95.8% accuracy on mutant classification. Through gradient based interrogation and visualization of the trained classifier, it is demonstrated that the model focuses on the morphological structures known to be affected by the En1 mutation.
ChemInform Abstract: Rh(III)‐Catalyzed Synthesis of 1‐Substituted Isoquinolinium Salts via a C—H Bond Activation Reaction of Ketimines with Alkynes. (2014)

Abstract Ruthenium complexes can also be employed as catalysts.
Role of DNA minor groove alkylation and DNA cross-linking in the cytotoxicity of polybenzamide mustards. (2000)

Interstrand DNA cross-links have been considered essential to the activity of current clinical DNA-alkylating antitumour drugs, which generally alkylate in the major groove. However, the relationship between cross-linking adducts located in the minor groove of DNA with cytotoxicity and antitumour activity has not been extensively investigated. Previous studies have shown that cross-linking ability is not correlated with cytotoxicity in a novel series of polybenzamide-linked nitrogen mustard compounds which alkylate DNA at adenines in the minor groove. In the present study the nature of these cross-linking adducts was explored for a related pair of compounds which are both highly effective cross-linkers but which differ in antitumour potential. Both of these drugs effectively interact with adenines in the minor groove, although their sequence specificity differs. However, the cross-linking event was not inhibited by pre-treatment with Hoechst 33258, although this pre-treatment effectively prevented adenine alkylation. The primary cross-links detected may thus represent guanine N7 alkylations in the major groove. Whether minor groove cross-linking adducts can be formed is uncertain, since the effect of background guanine N7 alkylation may complicate analysis. The cytotoxicity of the polybenzamides may therefore be related to other factors such as their interaction with cellular repair systems.
High-power multi-megahertz source of waveform-stabilized few-cycle light (2015)

Waveform-stabilized laser pulses have revolutionized the exploration of the electronic structure and dynamics of matter by serving as the technological basis for frequency-comb and attosecond spectroscopy. Their primary sources, mode-locked titanium-doped sapphire lasers and erbium/ytterbium-doped fibre lasers, deliver pulses with several nanojoules energy, which is insufficient for many important applications. Here we present the waveform-stabilized light source that is scalable to microjoule energy levels at the full (megahertz) repetition rate of the laser oscillator. A diode-pumped Kerr-lens-mode-locked Yb:YAG thin-disk laser combined with extracavity pulse compression yields waveform-stabilized few-cycle pulses (7.7 fs, 2.2 cycles) with a pulse energy of 0.15 μJ and an average power of 6 W. The demonstrated concept is scalable to pulse energies of several microjoules and near-gigawatt peak powers. The generation of attosecond pulses at the full repetition rate of the oscillator comes into reach. The presented system could serve as a primary source for frequency combs in the mid infrared and vacuum UV with unprecedented high power levels.
Randomised comparison between adrenaline injection alone and adrenaline injection plus heat probe treatment for actively bleeding ulcers (1997)

The addition of heat probe treatment after endoscopic adrenaline injection confers an advantage in ulcers with spurting haemorrhage.
Rolled monopole with bandstop function for UWB applications (2006)

In this paper, the rolled fat monopole antenna with bandstop function for UWB systems is proposed. The proposed antenna has the omnidirectional patterns in azimuth and very small size. It covers 3.1~10.6 GHz band for VSWR < 2, using the rolled monopole structure. The proposed antenna has wide bandwidth and bandstop function of 5 GHz WLAN band limited by IEEE802.11a and HIPERLAN/2. To achieve these two characteristics of wide bandwidth and bandstop, the fat monopole and lambda/4 slits are used, respectively. From the measured results, it is observed that wide bandwidth from 3.1 to 10.6 GHz for the VSWR<2 is achieved, while 5 ~ 6 GHz WLAN band is band-notched.
The Importance of the NP: VP35 Ratio in Ebola Virus Nucleocapsid Formation (2011)

Ebola virus VP35 is a cofactor of the viral RNA polymerase complex and, together with NP and VP24, is an essential component for nucleocapsid formation. In the present study, we examined the interactions between VP35 and NP and found that VP35 interacts with helical NP-RNA complexes through the C-terminus of NP. We also found that coexpression of excess VP35 with NP reduced the yields of NP-RNA complexes purified by CsCl gradient ultracentrifugation and inhibited the formation of the NP-induced inclusion bodies that typically form in Ebola virus-infected cells. These findings suggest that the NP to VP35 ratio is important in the Ebola virus replication cycle and advance our knowledge of nucleocapsid morphogenesis.
A long-wavelength, annular In0.53Ga0.47As p-i-n photodetector (1982)

We describe a novel, annular In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> As p-in photodiode sensitive to λ = 1.7 µm for use as a fiber tap or front-face laser monitor. The diode has a 150 µm diameter, straight-walled hole through the diode cross-section formed by photochemical etching. The hole is concentric with the 430 µm diameter mesa. A dark current of I = 90 nA at 5 V and a breakdown voltage of 33 V indicate that the hole formation process does not result in significant degradation of the device operating characteristics. Measurements of photoresponse as a function of position across the diode surface give further evidence that the hole does not effect overall device performance.
A 4.5mW/Gb/s 6.4Gb/s 22+1-lane source-synchronous link rx core with optional cleanup PLL in 65nm CMOS (2010)

Source synchronous links are often used in server systems for multi-lane high-speed serial applications such as connecting CPU to CPU, to memory, or to bridge chips due to their inherent tracking of correlated jitter [1]. This paper presents a low-power compact differential source synchronous receiver PHY comprised of 22 data lanes and 1 clock lane. This receiver, plus a corresponding transmitter and impedance calibration macro, support multiple differential and ground terminated link standards at 4.8 to 6.4Gb/s, such as Intel QPI 1.0 and IBM proprietary memory links.
Cocaine and morphine in cancer patients with chronic pain (1984)

Kaiko, R. F.; Kanner, R.; Foley, K. M.; Wallenstein, S. L.; Canel, A.; Anderson, C.; Rogers, A. G.; Houde, R. W. Author Information