gebhart/patrepeval huggingface dataset:
UHPLC‐ESI‐QqTOF‐MS/MS characterization of minor chlorogenic acids in roasted Coffea arabica from different geographical origin (2018)

Chlorogenic acids are relevant coffee quality markers, taste, and aroma precursors as well as important bioactive compounds. A number of mono-acyl, di-acyl, and tri-acyl quinic acid isomers were found in green coffee beans, being mono-caffeoyl, mono-feruloyl, mono-p-coumaroyl, and di-caffeoylquinic acid isomers considered as quantitatively major compounds. Roasting process increases the chemical complexity of coffee by inducing the formation of a number of lactones (quinides), shikimates, and other chlorogenic acids derivatives. So far, little attention has been paid in characterizing minor chlorogenic acids and derivatives in roasted Coffea arabica, also known as Arabica. In the present work, roasted C. arabica samples from different geographical origins (Brazil, Colombia, Costa Rica, Ethiopia, Guatemala, and India) were characterized by UHPLC-ESI-QqTOF-MS/MS. Several minor chlorogenic acid isomers were identified. In particular, HR-MS/MS provided putative identification of four dimethoxycinnamoyl-quinic acid derivatives, such as 4-dimethoxycinnamoylquinic acid, 4-dimethoxycinnamoyl-3-caffeoylquinic acid, 3-dimethoxycinnamoyl-4-feruloylquinic acid, 4-dimethoxycinnamoyl-5-feruloylquinic acid, and two caffeoyl, feruloyl quinic acid derivatives (3-caffeoyl-4-feruloylquinic acid and 3-feruloyl-4-caffeoylquinic acid). To our knowledge, these compounds were found in roasted Arabica coffee for the first time, and their presence is independent on the different geographical origins examined.
Introduction to the Special Section on the 2021 IEEE International Solid-State Circuits Conference (ISSCC) (2021)

This Special Section of the IEEE Journal of Solid-State Circuits is dedicated to a collection of the best articles selected from the 2021 IEEE International Solid-State Circuits Conference (ISSCC) that took place on February 13–22, 2021, in San Francisco, CA, USA. This Special Section covers articles from the Wireline, Digital Circuits, Digital Architectures and Systems (DASs), Machine Learning and AI, and Memory Committees.
The Performance Effects of Squeeze Film Stiffness on Non-Resonate Interferometric Inertial Sensors (2007)

This paper studies the nonlinear effects of squeeze film stiffening on the performance of a high resolution MEMS nonresonant inertial sensor. It is shown that these effects introduce a surprising dynamic response that extends the operational frequency range of the devices by retarding the resonate response. In addition, this performance advantage will occur without the traditional gain trade-off associated with linear systems of this type. A method is introduced to experimentally characterize the squeeze film stiffness of a passive inertial sensor through the resonant characterization of a Fabry-Pe´rot interferometric accelerometer under reduced pressure. Such passive devices are uniquely suited for the study of squeeze films and, due to the dependence of both the sensitivity and bandwidth on the device structural stiffness, variation of the stiffness with frequency must be considered to accurately predict sensor performance. The characterization confirms established analytical squeeze film stiffness theory in the continuous gas regime for conditions of Knudsen numbers less then one. As the Knudsen number equal to one is approached, it is shown that ideal kinetic gas theory and continuous squeeze film theory converge yielding a simplified stiffness estimate under the resonant response under reduced pressure. These analytical results are used to predict the performance gains due to the nonlinear, frequency dependent total stiffness of the sensor during non-resonant operation.
Entry Force and Intra-abdominal Pressure Associated With Six Laparoscopic Trocar-Cannula Systems (1999)

In Brief Objective In trocar-cannula systems, increased entry force could result in loss of operator control, a potential cause of serious visceral and vascular injuries. We developed a system to measure entry force and intraperitoneal pressure to evaluate and compare trocar-cannula systems. Methods Six laparoscopic trocar-cannula systems of similar diameter (12 mm) were tested (two pyramidal, two cutting-dilating, and two blunt conical) using a white swine model. All six systems were inserted into each of 12 subjects with location designated by random allotment (72 insertions). During each insertion, intraperitoneal pressure and entry force were measured using a system consisting of a gas-gas transducer, a 50-lb load cell, and a multichannel data acquisition board. Mean entry force and intraperitoneal pressure were compared using mixed-model analysis of variance. Results Mean entry force measurements were as follows: pyramidal 9.01 lb and 13.48 lb, cutting-dilating 9.94 lb and 16.46 lb, and blunt conical 19.15 lb and 31.91 lb. Intraperitoneal pressure changes generally reflected measured entry force. Conclusion The system successfully measured both entry force and resultant intraperitoneal pressure. Pyramidal trocar-cannula systems required the lowest force for entry. These differences in entry force have potential clinical implications related to the risk of visceral and vascular injury. Intraperitoneal pressure measurement could be used as a surrogate for insertional force measurement. A system designed to evaluate insertional force of laparoscopic trocar-cannula systems found that pyramidal-tipped trocars required the lowest insertional force.
Radioanalytical Chemistry for Automated Nuclear Waste Process Monitoring (2004)

This research program is directed toward rapid, sensitive, and selective determination of beta- and alpha-emitting radionuclides such as 99Tc, 90Sr, and trans-uranium (TRU) elements in low-activity waste (LAW) processing streams. The overall technical approach is based on automated radiochemical measurement principles, which entails integration of sample treatment and separation chemistries and radiometric detection within a single functional analytical instrument. Nuclear waste process streams are particularly challenging for rapid analytical methods due to the complex, high-ionic-strength, caustic brine sample matrix, the presence of interfering radionuclides, and the variable and uncertain speciation of the radionuclides of interest. As a result, matrix modification, speciation control, and separation chemistries are required for use in automated process analyzers. Significant knowledge gaps exist relative to the design of chemistries for such analyzers so that radionuclides can be quantitatively and rapidly separated and analyzed in solutions derived from low-activity waste processing operations. This research is addressing these knowledge gaps in the area of separation science, nuclear detection, and analytical chemistry and instrumentation.
Coupling between parallel dark spatial soliton waveguides (1993)

Dark spatial solitons are able to guide light in a self-defocusing Kerr-type medium by inducement of a refractive-index profile equivalent to a dielectric waveguide. We derive the coupling coefficients between two parallel dark soliton waveguides and investigate the coupling length as a function of various dark soliton and guided-wave parameters.
Macrophages modulate bacterial persistence and gastric pathology during Helicobacter pylori infection (INC4P.346) (2015)

Abstract Based on preliminary data suggesting that macrophages are critical regulators of Helicobacter pylori colonization and gastric pathology, we investigated how macrophage phenotypes shape the outcome of infection and persistence. The loss of PPARγ in the myeloid compartment favors a 5 to 10-fold decrease in bacterial loads at the expense of more severe gastric lesions. PPARγ-deficient macrophages present altered control of transcription factors such as NFκB, which results in a pro-inflammatory phenotype. Stomach lamina propria analyses at weeks 0 to 4 post-infection revealed increased levels of CD11b+ F4/80hi CD64+ CR3CR1+ macrophages in WT mice, while PPARγKO mice failed to expand and maintain such population. Macrophage depletion using clodronate liposomes resulted in a significant reduction of gastric H. pylori in WT mice, thus abrogating the differences in bacterial loads observed between WT and PPARγKO mice. In vitro co-culture of H. pylori with bone marrow derived macrophages showed that either PPARγ loss or pharmacological blockade enhances bactericidal activity, which is associated to significant differential expression of chil1, etv5, iigp1, ptger4, sqle, osm, hspa2 and rptoros levels as revealed by global transcriptome analyses. Hence, macrophages facilitate H. pylori infection by 1) serving as bacterial reservoirs and allowing intracellular replication, and 2) favoring a gastric regulatory response that favors persistence.
Fluorination, and Tunneling across Molecular Junctions (2015)

This paper describes the influence of the substitution of fluorine for hydrogen on the rate of charge transport by hole tunneling through junctions of the form Ag(TS)O2C(CH2)n(CF2)(m)T//Ga2O3/EGaIn, where T is methyl (CH3) or trifluoromethyl (CF3). Alkanoate-based self-assembled monolayers (SAMs) having perfluorinated groups (R(F)) show current densities that are lower (by factors of 20-30) than those of the homologous hydrocarbons (R(H)), while the attenuation factors of the simplified Simmons equation for methylene (β = (1.05 ± 0.02)n(CH2)(-1)) and difluoromethylene (β = (1.15 ± 0.02)n(CF2)(-1)) are similar (although the value for (CF2)n is statistically significantly larger). A comparative study focusing on the terminal fluorine substituents in SAMs of ω-tolyl- and -phenyl-alkanoates suggests that the C-F//Ga2O3 interface is responsible for the lower tunneling currents for CF3. The decrease in the rate of charge transport in SAMs with R(F) groups (relative to homologous R(H) groups) is plausibly due to an increase in the height of the tunneling barrier at the T//Ga2O3 interface, and/or to weak van der Waals interactions at that interface.
Adenovirus Serotype 5-Vectored Foot-And-Mouth Disease Subunit Vaccines: The First Decade (2009)

The results of the first decade of the development of a replication-defective human adenovirus serotype 5 (Ad5) containing the capsid- and 3C protease-coding regions of foot-and-mouth disease (FMD) virus as a vaccine candidate are presented. In proof-of-concept studies, it was demonstrated that a single inoculation with this vaccine vector containing the capsid of FMD virus A24 Cruzeiro protected both swine and cattle following homologous challenge by direct inoculation 1 week postvaccination. We have expanded these studies in cattle with larger numbers of animals and by testing the vaccine in direct-contact challenge studies, including its ability to prevent FMD virus shedding and transmission. Furthermore, we have developed manufacturing protocols to allow the scalable production of these FMD molecular vaccine products for US Department of Agriculture licensure approval and availability for inclusion in the US National Veterinary Stockpile. We have also constructed and initiated cattle efficacy testing of Ad5 vectors containing the capsid-coding regions from other FMD virus serotypes and subtypes, as well as initiated studies to improve FMD molecular vaccine potency.
Synthesis of novel polymeric colorants (2003)

There are several structural types of polymeric dyes (polydyes) that have been synthesised as colorants for thermoplastic materials, particularly polyesters. This paper reviews three synthetic methods used to prepare polydyes. In method 1, anthraquinone polysulphonamide polydyes were prepared by reacting anthraquinonedisulphonyl chlorides with diamines in the presence of a base. Polymethine polydyes were prepared in method 2 by reacting bis‐aldehydes containing two linked aromatic aldehyde moieties with a bis‐(active methylene) component under Knoevenagel reaction conditions. In the final method, a variety of polymer types were synthesised by reacting acidic dyes containing two acidic groups with glycol sulphonates in the presence of a base. Most of the polydyes were evaluated as colorants for polyesters, by melt blending and extruding, followed by the preparation of films for further testing of properties such as fastness to light. The primary emphasis of this paper is to discuss the synthetic methods involved and to present the various types of structure that have been investigated.
Novel Structured Reporting Systems for Theranostic Radiotracers (2019)

Standardized reporting is more and more routinely implemented in clinical practice, and such structured reports have a major impact on a large variety of medical fields, such as laboratory medicine, pathology, and, recently, radiology. Notably, the field of nuclear medicine is constantly evolving as novel radiotracers for numerous clinical applications are developed. Thus, framework systems for standardized reporting in this field may increase clinical acceptance of new radiotracers, allow for inter- and intracenter comparisons for quality assurance, and be used in global multicenter studies to ensure comparable results and enable efficient data abstraction. In the last couple of years, several standardized framework systems for PET radiotracers with potential theranostic applications have been proposed. These include systems for prostate-specific membrane antigen-targeted PET agents to diagnose and treat prostate cancer, and systems for somatostatin receptor-targeted PET agents to diagnose and treat neuroendocrine neoplasia. In the present review, the framework systems for these 2 types of cancer will be briefly introduced, followed by an overview of their advantages and limitations. In addition, potential applications will be defined, approaches to validate such concepts will be proposed, and future perspectives will be discussed.
Employers With Metabolic Syndrome and Increased Depression/Anxiety Severity Profit Most From Structured Exercise Intervention for Work Ability and Quality of Life. (2020)

ClinicalTrials.gov, identifier NCT03293264.
A Multi-Modal AI-Driven Cohort Selection Tool to Predict Suboptimal Non-Responders to Aflibercept Loading-Phase for Neovascular Age-Related Macular Degeneration: PRECISE Study Report 1 (2023)

Patients diagnosed with exudative neovascular age-related macular degeneration are commonly treated with anti-vascular endothelial growth factor (anti-VEGF) agents. However, response to treatment is heterogeneous, without a clinical explanation. Predicting suboptimal response at baseline will enable more efficient clinical trial designs for novel, future interventions and facilitate individualised therapies. In this multicentre study, we trained a multi-modal artificial intelligence (AI) system to identify suboptimal responders to the loading-phase of the anti-VEGF agent aflibercept from baseline characteristics. We collected clinical features and optical coherence tomography scans from 1720 eyes of 1612 patients between 2019 and 2021. We evaluated our AI system as a patient selection method by emulating hypothetical clinical trials of different sizes based on our test set. Our method detected up to 57.6% more suboptimal responders than random selection, and up to 24.2% more than any alternative selection criteria tested. Applying this method to the entry process of candidates into randomised controlled trials may contribute to the success of such trials and further inform personalised care.
Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature (2021)

Information overload is a prevalent challenge in many high-value domains. A prominent case in point is the explosion of the biomedical literature on COVID-19, which swelled to hundreds of thousands of papers in a matter of months. In general, biomedical literature expands by two papers every minute, totalling over a million new papers every year. Search in the biomedical realm, and many other vertical domains is challenging due to the scarcity of direct supervision from click logs. Self-supervised learning has emerged as a promising direction to overcome the annotation bottleneck. We propose a general approach for vertical search based on domain-specific pretraining and present a case study for the biomedical domain. Despite being substantially simpler and not using any relevance labels for training or development, our method performs comparably or better than the best systems in the official TREC-COVID evaluation, a COVID-related biomedical search competition. Using distributed computing in modern cloud infrastructure, our system can scale to tens of millions of articles on PubMed and has been deployed as Microsoft Biomedical Search, a new search experience for biomedical literature: https://aka.ms/biomedsearch.
DNMT3Bin vitroknocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation (2016)

Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway.Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
Put Them Out to Pasture? What Are Old Granule Cells Good for, Anyway…? (2010)

In this issue, Alme and colleagues propose a novel hypothesis that young adult-born neurons represent the functional population of the dentate gyrus, and that old granule cells "retire" from relevance. Here, we present several implications of this interesting theory for the function of both neurogenesis and the dentate gyrus.
The Photo-Fries Rearrangement and Its Use in Polymeric Imaging Systems (1985)

The photo-Fries rearrangement which was first reported (1,2) in the early 1960's has some potential in the design of photoresist materials since it involves the transformation of molecules such as phenolic esters into free phenols, thereby providing a route to selective image development by differential dissolution. Initial interest in the photo-Fries rearrangement of aromatic polyesters was mainly due to the fact the reaction is accompanied by the formation of o-hydroxy aromatic compounds which possess great photostability. This interesting property of the rearranged products can be used to design polymers containing photostabilizing ortho-hydroxy aromatic groups (3-6); the photostabilizing action of such compounds has been recently reviewed (7-8). Scheme 1 shows the reaction which occurs when an aromatic polyester such as [I] is subjected to UV irradiation (5). The polymer first undergoes main-chain cleavage with subsequent rearrangement to polymer [II] which is photostable and can be used as a thin coating to
Visibility of fiducial markers used for image‐guided radiation therapy on optical coherence tomography for registration with CT: An esophageal phantom study (2017)

We studied the visibility of eight types of commercially available fiducial markers at different depths on OCT using dedicated esophageal phantoms. All tested fiducial markers were visible at depths ≤3.0 mm and most, but not all, clinically implanted markers were at a depth accessible to OCT. Consequently, the use of fiducial markers as a reference for OCT to CT registration is feasible.
Shape Data Operations for VSB LB Data Conversion Using CAD Tools (1989)

For fast electron beam (EB) data conversion, an improved system of hierarchical process has been constructed. Several functions have been added to hierarchically perform shape data operations with increased efficiency. The added functions aim to cut redundant checks in oversizing, to reduce shape data expansion in array data handling and to speed cell overlap checks. These functions were implemented on a computer-aided design (CAD) system utilizing software tools available on it. The new system was applied to the variable shaped beam (VSB) EB data conversion and demonstrated to have better performance. A 16 Kbit SRAM design, conventionally degenerated near a flat level process, was successfully processed in a hierarchical manner, and performance gains of 1.6 to 3.1 were obtained.
Surrogate modeling for Bayesian optimization beyond a single Gaussian process (2022)

Bayesian optimization (BO) has well-documented merits for optimizing black-box functions with an expensive evaluation cost. Such functions emerge in applications as diverse as hyperparameter tuning, drug discovery, and robotics. BO hinges on a Bayesian surrogate model to sequentially select query points so as to balance exploration with exploitation of the search space. Most existing works rely on a single Gaussian process (GP) based surrogate model, where the kernel function form is typically preselected using domain knowledge. To bypass such a design process, this paper leverages an ensemble (E) of GPs to adaptively select the surrogate model fit on-the-fly, yielding a GP mixture posterior with enhanced expressiveness for the sought function. Acquisition of the next evaluation input using this EGP-based function posterior is then enabled by Thompson sampling (TS) that requires no additional design parameters. To endow function sampling with scalability, random feature-based kernel approximation is leveraged per GP model. The novel EGP-TS readily accommodates parallel operation. To further establish convergence of the proposed EGP-TS to the global optimum, analysis is conducted based on the notion of Bayesian regret for both sequential and parallel settings. Tests on synthetic functions and real-world applications showcase the merits of the proposed method.