gebhart/patrepeval huggingface dataset:
On optimal multipath rate-adaptive routing (2010)

A centralized rate-adaptive routing algorithm is presented that, in contrast to the distributed ones available in the literature, achieves provable stability, optimalilty with respect to optional linear or quadratic objective functions, and feasibility in that it can accommodate any admissible traffic matrix in the network without violating link capacities. We recast the routing problem in the framework of constrained optimal control theory to obtain optimal state feedback routing controllers, and we present simulations confirming that our routing controllers are viable in small- and middle-sized networks.
Mechanism of the Facilitation of PC2 Maturation by 7B2: Involvement in ProPC2 Transport and Activation but Not Folding (1997)

Among the members of the prohormone convertase (PC) family, PC2 has a unique maturation pattern: it is retained in the ER for a comparatively long time and its propeptide is cleaved in the TGN/ secretory granules rather than in the ER. It is also unique by its association with the neuroendocrine protein 7B2. This interaction results in the facilitation of proPC2 maturation and in the production of activatable proPC2 from CHO cells. In the present study, we have investigated the mechanism of this interaction. ProPC2 binds 7B2 in the ER, but exits this compartment much more slowly than 7B2. We found that proPC2 was also slow to acquire the capacity to bind 7B2, whereas 7B2 could bind proPC2 rapidly after synthesis. This indicated that proPC2 folding was the limiting step in the formation of the complex. Indeed, sensitivity of native proPC2 to N-glycanase F digestion and inhibition of proPC2 folding supported the notion that 7B2 is not involved in the early steps of proPC2 folding, and that proPC2 must fold before binding 7B2. Under experimental conditions that prevent propeptide cleavage, 7B2 expression increased proPC2 transport to the Golgi. This increase exhibited the same kinetics as the facilitation of the removal of the propeptide. Finally, proPC2 activation could be reconstituted in Golgi- enriched subcellular fractions. In vitro, 7B2 was required for proPC2 activation at an acidic pH. Taken together, our results demonstrate that rather than promoting proPC2 folding, 7B2 acts as a helper protein involved in proPC2 transport and is required in the proPC2 activation process. We propose, therefore, that 7B2 stabilizes proPC2 in a conformation already competent for these two events.
From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide Conformations (2013)

Past experimental results and molecular dynamics simulations provide evidence that, under some conditions, electrospray ionization (ESI) of biomolecules produces ions that retain elements of solution phase structures. However, there is a dearth of information regarding the question raised by Breuker and McLafferty, "for how long, under what conditions, and to what extent, can solution structure be retained without solvent?" (Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18145). Here, we use cryogenic ion mobility-mass spectrometry to experimentally probe the structural evolution of the undecapeptide substance P (SP) during the final stages of ESI. The results reveal that anhydrous SP conformers originate from evaporation of cluster ions, specifically, [SP + 2H](2+) (H2O)n (n = 0 to ∼50) and [SP + 3H](3+) (H2O)n (n = 0 to ∼30), and that major structural changes do not occur during the evaporative process. In the case of [SP + 3H](3+), the results demonstrate that a compact dehydrated conformer population can be kinetically trapped on the time scale of several milliseconds, even when an extended gas phase conformation is energetically favorable.
Design of a 9 GHz Four-Beam Antenna Array Fed by a Butler Matrix (2021)

A 9 GHz four beam antenna array fed by a Butler matrix is designed, fabricated and measured. Two 4×4 Butler matrices are addressed and compared in this work: (1) with and (2) without crossovers. It has been shown that this latter presents the best performances in terms of losses and complexity. The fabricated prototype (without crossovers) connected to four patch antennas exhibits good performance and allows the forming of four orthogonal uniform beams (at −46°, + 16°, −18° and +45°) with an effective coverage of 91°.
Magneto-Luminescence Spectroscopy of Excitonic Transitions in Homoepitaxial GaN Layers (1999)

Excitonic optical properties of homoepitaxial GaN layers have been studied by means of magneto-luminescence spectroscopy. Under magnetic field perpendicular to the hexagonal c-axis, Zeeman splittings and diamagnetic shifts were observed for the luminescence lines due to the radiative recombination of excitons bound to neutral donors and acceptors. The effective g-factors for both the donor- and acceptor-bound excitons were estimated to be 2.02 and 2.47, respectively. The diamagnetic shift of the donor-bound exciton was found to be smaller than that of the acceptor-bound exciton.
Caged Phytohormones: From Chemical Inactivation to Controlled Physiological Response (2021)

Plant hormones, also called phytohormones, are small signaling molecules regulating a wide range of growth and developmental processes. These unique compounds respond to both external (light, temperature, water, nutrition, or pathogen attack) and internal factors (<i>e.g.</i>, age) and mediate signal transduction leading to gene expression with the aim of allowing plants to adapt to constantly changing environmental conditions. Within the regulation of biological processes, individual groups of phytohormones act mostly through a web of interconnected responses rather than linear pathways, making elucidation of their mode of action in living organisms quite challenging. To further progress with our knowledge, the development of novel tools for phytohormone research is required. Although plenty of small molecules targeting phytohormone metabolic or signaling pathways (agonists, antagonists, and inhibitors) and labeled or tagged (fluorescently, isotopically, or biotinylated) compounds have been produced, the control over them <i>in vivo</i> is lost at the time of their administration. Caged compounds, on the other hand, represent a new approach to the development of small organic substances for phytohormone research. The term "caged compounds" refers to light-sensitive probes with latent biological activity, where the active molecule can be freed using a light beam in a highly spatio/temporal-, amplitude-, or frequency-defined manner. This review summarizes the up-to-date development in the field of caged plant hormones. Research progress is arranged in chronological order for each phytohormone regardless of the cage compound formulation and bacterial/plant/animal cell applications. Several known drawbacks and possible directions for future research are highlighted.
AlGaN-based Intersubband Device Technology (2013)

Gallium nitride (GaN)-based technology has been successfully applied for: (1) high-electron-mobility transistors (HEMTs) that can withstand high critical electric fields (~3.5 MV/cm) and operate at high saturation velocity (3 × 107 cm/s), (2) efficient ultraviolet-visible light-emitting diodes, and, more recently, for (3) advanced near-infrared devices operating in the terahertz regime by utilizing intersubband levels in AlGaN/GaN superlattices (SLs), as described below.
Prediction of the structural interface between fibroblast growth factor23 and Burosumab using alanine scanning and molecular docking (2022)

Burosumab, an FGF23 targeting monoclonal antibody, was approved by the FDA in 2018 for use in children and adults with X-linked hypophosphatemia (or XLH). While several clinical studies have demonstrated the long-term safety and efficacy of Burosumab, the molecular basis of FGF23-Burosumab interaction which underpins its mechanism of action remains unknown. In this study, we employed molecular docking combined with alanine scanning of epitope and paratope to predict a model of FGF23-Burosumab interaction. Then, we used the model to understand the species-species cross-reactivity of Burosumab and to reverse engineer mouse FGF23 with 'back to human' mutations to bind Burosumab. Finally, we redesigned the CDRs with two mutations to engineer an affinity enhanced variant of the antibody. Our study provides insights into the FGF23-Burosumab interaction and demonstrates that alanine-scanning coupled with molecular docking can be used to optimize antibody candidates (e.g., structure-guided affinity maturation) for therapeutic use.
Accounting for Standard Errors of Vision-Specific Latent Trait in Regression Models (2014)

Patient-reported data, using Rasch analysis techniques, do not take into account the SE of latent trait in association analyses. The HB one-stage "joint-analysis" is a better approach, producing accurate effect size estimations and information about the independent association of exposure variables with vision-specific latent traits.
Evidence for the existence of associated lignin-carbohydrate polymers as revealed by carbon-13 CPMAS solid-state NMR spectroscopy (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEvidence for the existence of associated lignin-carbohydrate polymers as revealed by carbon-13 CPMAS solid-state NMR spectroscopyWalter V. Gerasimowicz, Kevin B. Hicks, and Philip E. PfefferCite this: Macromolecules 1984, 17, 12, 2597–2603Publication Date (Print):December 1, 1984Publication History Published online1 May 2002Published inissue 1 December 1984https://pubs.acs.org/doi/10.1021/ma00142a023https://doi.org/10.1021/ma00142a023research-articleACS PublicationsRequest reuse permissionsArticle Views238Altmetric-Citations41LEARN 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-Alertsclose Get e-Alerts
Prion protein codon 129 genotype prevalence is altered in primary progressive aphasia (2005)

The prion protein (PrP) is central to the prion diseases, although a role in other neurodegenerative diseases has been postulated. A common polymorphism (Met or Val) at codon 129 of the PrP gene (PRNP) features prominently in the risk and phenotype, of prion disease, and an abnormality in its distribution frequency may signal a role for PrP in other diseases. We conducted a case-control study to compare the PRNP codon 129 genotype distribution in Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and primary progressive aphasia (PPA), including 281 AD, 256 ALS, 39 PPA, and 415 healthy control subjects. Statistical analysis was applied to determine the presence or absence of disease-specific genotype associations. The distribution of codon 129 genotypes was similar among healthy control, AD, and ALS subjects, although the heterozygous state was significantly overrepresented (age-adjusted odds ratio, 8.47) in PPA, a rare condition of unknown cause. Although these findings do not entirely exclude a role for PrP in AD or ALS, they do not support the codon 129 genotype as a risk factor for either disease. However, the strong association between heterozygosity and PPA raises new questions about its cause and the role of PrP in other neurodegenerative diseases.
Tear miRNAs Identified in a Murine Model of Sjögren’s Syndrome as Potential Diagnostic Biomarkers and Indicators of Disease Mechanism (2022)

A panel of differentially expressed miRNAs were identified in tears of male NOD mice, with some preliminary validation in SS patients, including some never previously linked to SS. These may have potential utility as indicators of ocular symptoms of SS; evaluation of the pathways influenced by these dysregulated miRNAs may also provide further insights into SS pathogenesis.
Development and Scale-up of an Organocatalytic Enantioselective Process to Manufacture (S)-Pregabalin (2015)

Herein is reported the development of a new process to manufacture (S)-pregabalin. The method comprises six steps, run under the catalysis of a recyclable polymer bound phase transfer catalyst, and afforded (S)-pregabalin in overall 54% yield, starting from building blocks acetylacetone, isovaleraldehyde, and nitromethane.
Future developments and new research in genitourinary cancers. Perspectives (1987)

Significant advances in the therapy of genitourinary cancers have occurred, yet the challenge of metastatic disease in many of these tumors remains unsolved. The great success achieved in the treatment of testicular cancer has been in large part due to the development of effective systemic therapy. Effective treatment for metastatic transitional cell carcinoma is just beginning to be described. Advanced renal and prostatic carcinomas remain a major clinical problem with no effective curative therapy. Novel new approaches to systemic therapy developed on sound basic experimental principles are needed. Several potential approaches such as angiogenesis factor, interleukin II, lymphokine activated killer cells, and tumor necrosis factor are discussed.
Antioxidant Activities and Antitumor Screening of Extracts from Cranberry Fruit (Vaccinium macrocarpon) (2002)

Polyphenolic compounds in cranberries have been investigated to determine their role in protection against cardiovascular disease and some cancers. Extracts of whole fruit were assayed for radical-scavenging activity and tumor growth inhibition using seven tumor cell lines. Selective inhibition of K562 and HT-29 cells was observed from a methanolic extract in the range of 16-125 microg/mL. Radical-scavenging activity was greatest in an extract composed primarily of flavonol glycosides. Seven flavonol glycosides were isolated and purified from whole fruit for further evaluation; the anthocyanin cyanidin 3-galactoside was also purified for comparison with the flavonoids. Three flavonol monoglycosides were newly identified by (13)C NMR as myricetin 3-alpha-arabinofuranoside, quercetin 3-xyloside, and 3-methoxyquercetin 3-beta-galactoside (isorhamnetin); the other four isolated were the previously identified myricetin 3-beta-galactoside, quercetin 3-beta-galactoside, quercetin 3-alpha-arabinofuranoside, and quercetin 3-alpha-rhamnopyranoside. These compounds were evaluated for 1,1-diphenyl-2-picrylhydrazyl radical-scavenging activity and ability to inhibit low-density lipoprotein oxidation in vitro. Most of the flavonol glycosides showed antioxidant activity comparable or superior to that of vitamin E; cyanidin 3-galactoside showed activity superior to that of the flavonoids as well as vitamin E or Trolox in both antioxidant assays.
In vivo imaging identifies temporal signature of D1 and D2 medium spiny neurons in cocaine reward (2016)

The reinforcing and rewarding properties of cocaine are attributed to its ability to increase dopaminergic transmission in nucleus accumbens (NAc). This action reinforces drug taking and seeking and leads to potent and long-lasting associations between the rewarding effects of the drug and the cues associated with its availability. The inability to extinguish these associations is a key factor contributing to relapse. Dopamine produces these effects by controlling the activity of two subpopulations of NAc medium spiny neurons (MSNs) that are defined by their predominant expression of either dopamine D1 or D2 receptors. Previous work has demonstrated that optogenetically stimulating D1 MSNs promotes reward, whereas stimulating D2 MSNs produces aversion. However, we still lack a clear understanding of how the endogenous activity of these cell types is affected by cocaine and encodes information that drives drug-associated behaviors. Using fiber photometry calcium imaging we define D1 MSNs as the specific population of cells in NAc that encodes information about drug associations and elucidate the temporal profile with which D1 activity is increased to drive drug seeking in response to contextual cues. Chronic cocaine exposure dysregulates these D1 signals to both prevent extinction and facilitate reinstatement of drug seeking to drive relapse. Directly manipulating these D1 signals using designer receptors exclusively activated by designer drugs prevents contextual associations. Together, these data elucidate the responses of D1- and D2-type MSNs in NAc to acute cocaine and during the formation of context-reward associations and define how prior cocaine exposure selectively dysregulates D1 signaling to drive relapse.
Coating of Conducting and Insulating Threads with Porous MOF Particles through Langmuir-Blodgett Technique (2021)

The Langmuir-Blodgett (LB) method is a well-known deposition technique for the fabrication of ordered monolayer and multilayer thin films of nanomaterials onto different substrates that plays a critical role in the development of functional devices for various applications. This paper describes detailed studies about the best coating configuration for nanoparticles of a porous metal-organic framework (MOF) onto both insulating or conductive threads and nylon fiber. We design and fabricate customized polymethylmethacrylate sheets (PMMA) holders to deposit MOF layers onto the threads or fiber using the LB technique. Two different orientations, namely, horizontal and vertical, are used to deposit MIL-96(Al) monolayer films onto five different types of threads and nylon fiber. These studies show that LB film formation strongly depends on deposition orientation and the type of threads or fiber. Among all the samples tested, cotton thread and nylon fiber with vertical deposition show more homogenous monolayer coverage. In the case of conductive threads, the MOF particles tend to aggregate between the conductive thread's fibers instead of forming a continuous monolayer coating. Our results show a significant contribution in terms of MOF monolayer deposition onto single fiber and threads that will contribute to the fabrication of single fiber or thread-based devices in the future.
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis (2011)

Fusion of proteomics and metabolomics data is possible. The main issues of high-dimensionality and missing values are overcome. The outcome leads to higher accuracy in prediction and more exhaustive description of the disease profile. The biological interpretation of the involved variables validates our fusion approach.
Cardiomyopathic Etiology and SERCA2a Reverse Remodeling During Mechanical Support of the Failing Human Heart (2005)

Many hearts in end-stage, chronic failure (CHF) retain the capacity to reverse abnormal expression of genes regulating myocyte calcium cycling when supported with a left ventricular assist device (LVAD). In the present study, we determined whether LVAD-induced upregulation of the gene encoding for the key calcium cycling protein sarcoplasmic endoreticular calcium adenosine triphosphatase subtype 2a (SERCA2a) is influenced by the nature of underlying disease broadly characterized as ischemic (ICM) or idiopathic dilated (DCM) cardiomyopathy. Data from Northern blot analysis of SERCA2a messenger (m)RNA within 84 heart samples (50 CHF [23 DCM and 27 ICM] and 34 CHF+LVAD [18 DCM and 16 ICM]) were used for characterizing gene expression. In addition, measurements of the force-frequency relationship (FFR), a reflection of in vivo SERCA2a function, were obtained in myocardial trabeculae isolated from 75 hearts (51 CHF [29 DCM and 22 ICM] and 24 CHF+LVAD [10 DCM and 14 ICM]). SERCA2a mRNA demonstrated upregulation after LVAD that was not influenced by ICM or DCM. However, only in DCM hearts was the proportion of trabeculae exhibiting a normal FFR increased after LVAD. Thus, although upregulated SERCA2a gene expression after LVAD support is independent of myopathic origin, normalization of myocardial FFR, an index of SERCA2a function, is not. These data provide new insight into the process of cardiac "reverse molecular remodeling," and underscore potential differences in the impact of disease processes on posttranscriptional events.
Nutraceuticals Synergistically Promote Proliferation of Human Stem Cells (2006)

A viable alternative to stem cell transplantation is to design approaches that stimulate endogenous stem cells to promote healing and regenerative medicine. Many natural compounds have been shown to promote healing; however, the effects of these compounds on stem cells have not been investigated. We report here the effects of several natural compounds on the proliferation of human bone marrow and human CD34(+) and CD133(+) cells. A dose-related effect of blueberry, green tea, catechin, carnosine, and vitamin D(3) was observed on proliferation with human bone marrow as compared with human granulocyte-macrophage colony-stimulating factor (hGM-CSF). We further show that combinations of nutrients produce a synergistic effect to promote proliferation of human hematopoietic progenitors. This demonstrates that nutrients can act to promote healing via an interaction with stem cell populations.
Evaluation of a System for Automatic Detection of Diabetic Retinopathy From Color Fundus Photographs in a Large Population of Patients With Diabetes (2008)

We thank Olson et al. (1) for their close reading of our recent study (2), where we examined sensitivity and specificity of automated diabetic retinopathy detection and demonstrated an area under the receiver operating characteristic curve of 0.87. A limited, 500-patient sample of all 10,000 photographic exams was examined by multiple, masked experts. We felt uncomfortable recommending a system for clinical practice for which patient safety compared to an accepted (gold) standard could not be established, concluding that it should be tested against widely accepted clinical standards, if practical. We have recently presented studies of an improved algorithm on a new, larger dataset of 15,000 exams with an area under the curve of 0.90 …
Navigation in Total Hip Arthroplasty (2009)

Learning Objective Understand the assets, liabilities, and limitations of computer navigation in total hip arthroplasty
Comparative study of NOTES rectosigmoidectomy in a swine model: E-NOTES vs. P-NOTES (2011)

E-NOTES rectosigmoidectomy in the swine model is safe, but remains challenging for use in pelvic dissection. P-NOTES rectosigmoidectomy using TEM may be a promising tool for pelvic dissection, but the transgastric approach involves a high degree of risk.
Rücktitelbild: Controlling Internal Pore Sizes in Bicontinuous Polymeric Nanospheres (Angew. Chem. 8/2015) (2015)

Die innere Struktur komplexer polymerer Nanokügelchen wurde von S. J. Holder, N. A. J. M. Sommerdijk et al. in der Zuschrift auf S. 2487 ff. aufgeklärt. Die Autoren zeigen, dass die innere Struktur durch Anpassung des Molekulargewichts und des relativen hydrophilen Anteils der Kompositpolymere eingestellt werden kann. Dies ermöglicht die Verwendung solcher bikontinuierlichen Polymernanokügelchen z. B. als Vektoren für die gezielte Freisetzung von Gästen und als Template für die Synthese von anorganischen und Hybridmaterialien.