gebhart/patrepeval huggingface dataset:
Optically Triggered Planarization of Boryl-Substituted Phenoxazine: Another Horizon of TADF Molecules and High-Performance OLEDs (2018)

We report the unprecedented dual properties of excited-state structural planarization and thermally activated delayed fluorescence (TADF) of 10-dimesitylboryl phenoxazine, i.e., PXZBM. Bearing a nonplanar phenoxazine moiety, PXZBM shows the lowest lying absorption onset at ∼390 nm in nonpolar solvents such as cyclohexane but reveals an anomalously large Stokes-shifted (∼14 500 cm<sup>-1</sup>) emission maximized at 595 nm. In sharp contrast, when a phenylene spacer is added between phenoxazine and dimesitylboryl moieties of PXZBM, the 10-(4-dimesitylborylphenyl)phenoxazine PXZPBM in cyclohexane reveals a much blue-shifted emission at 470 nm despite its red-shifted absorption maximized at 420 nm (cf. PXZBM). The emission of PXZBM further reveals solvent polarity dependence, being red-shifted from 595 nm in cyclohexane to 645 nm in CH<sub>2</sub>Cl<sub>2</sub>. For rationalization, the steric hindrance between phenoxazine and the dimesitylboryl unit in PXZBM caused a puckered arrangement of phenoxazine at the ground state. Upon electronic excitation, as supported by the femtosecond early relaxation dynamics, spectral-temporal evolution and energetics calculated along the reaction potential energy surfaces, the diminution of N → B electron transfer reduces π-conjugation and elongates the N-B bond length, inducing the fast phenoxazine planarization with a time constant of 890 ± 100 fs. The associated charge-transfer reaction from phenoxazine (donor) to dimesitylboryl unit (acceptor) results in a further red-shifted emission in polar solvents. In stark contrast, PXZPBM shows a planar phenoxazine and undergoes excited-state charge transfer only. Despite the distinct difference in excited-state relaxation dynamics, both PXZBM and PXZPBM exhibit efficient TADF capable of producing highly efficient orange and green organic light emitting diodes with peak efficiencies of 10.9% (30.3 cd A<sup>-1</sup> and 18.7 lm W<sup>-1</sup>) and 22.6% (67.7 cd A<sup>-1</sup> and 50.0 lm W<sup>-1</sup>).
Three New Triterpenoid Saponins from the Seeds ofVaccaria segetalis (2000)

Three new triterpenoid saponins, named segetoside G(1), H(2) and I(3), have been isolated from the seeds of Vaccaria segetalis. On the basis of chemical reaction and spectral data, their structures have been established as: 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-arabinofuranosyl (1-->3)]-beta-D-(4-O-acetyl)-fucopyranosyl-gypsogenin-3-O-beta-D-galactopyranosyl-(1-->2)-beta-D-(6-O-butyl ester)-glucuronopyranoside (1), 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-(5-O-acetyl)-arabinofuranosyl-(1-->3)]-beta-D-(4-O-acetyl)-fucopyranosyl-gypsogenin-3-O-beta-D-galactopyranosyl-(1-->2)-beta-D-glucuronopyranoside (2) and 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-(5-O-acetyl)-arabinofuranosyl-(1-->3)]-beta-D-(4-O-acetyl)-fucopyranosyl-quillaic acid-3-O-beta-D-galactopyranosyl-(1-->2)-beta-D-glucuronopyranoside (3).
Quantum Mechanical Calculations Suggest That Lignin Polymerization Is Kinetically Controlled (2019)

Lignin is an abundant biopolymer important for plant function while holding promise as a renewable source of valuable chemicals. Although the lignification process in plant cell walls has been long-studied, a comprehensive, mechanistic understanding on the molecular scale remains elusive. A better understanding of lignification will lead to improved atomistic models of the plant cell wall that could, in turn, inform effective strategies for biomass valorization. Here, using first-principles quantum chemical calculations, we show that a simple model of kinetically-controlled radical coupling broadly rationalizes qualitative experimental observations of lignin structure across a wide variety of biomass types, thus paving the way for predictive, first-principles models of lignification while highlighting the ability of computational chemistry to help illuminate complex biological processes.
Modulators of radiation-induced cardiopulmonary toxicities for non-small cell lung cancer: Integrated cytokines, single nucleotide variants, and HBP systems imaging (2022)

Radiation therapy (RT)-induced cardiopulmonary toxicities remain dose-limiting toxicities for patients receiving radiation dosages to the thorax, especially for lung cancer. Means of monitoring and predicting for those receiving RT or concurrent chemoradiation therapy before treatment begins in individual patients could benefit early intervention to prevent or minimize RT-induced side effects. Another aspect of an individual's susceptibility to the adverse effects of thoracic irradiation is the immune system as reflected by phenotypic factors (patterns of cytokine expressions), genotypic factors (single nucleotide variants SNVs; formerly single nucleotide polymorphisms [SNPs]), and aspects of quantitative cellular imaging. Levels of transcription, production, and functional activity of cytokines are often influenced by SNVs that affect coding regions in the promoter or regulatory regions of cytokine genes. SNVs can also lead to changes in the expression of the inflammatory cytokines, interferons, interleukins (IL-6, IL-17) and tumor necrosis factors (TNF-α) at the protein level. RT-induced cardiopulmonary toxicities could be quantified by the uptake of <sup>18</sup>F-fluorodeoxyglucose (FDG), however, FDG is a sensitive but not specific biomarker in differential diagnosis between inflammation/infection and tumor recurrence. FDG is suitable for initial diagnosis of predisposed tissue injuries in non-small cell lung cancer (NSCLC). <sup>99m</sup>Tc-ethylenedicysteine-glucosamine (<sup>99m</sup>Tc-EC-G) was able to measure tumor DNA proliferation and myocardial ischemia <i>via</i> hexosamine biosynthetic pathways (HBP). Thus, <sup>99m</sup>Tc-EC-G could be an alternative to FDG in the assessment of RT doses and select patients in HBP-directed targets for optimal outcomes. This article reviewed correlative analyses of pro-inflammatory cytokines, genotype SNVs, and cellular imaging to improve the diagnosis, prognosis, monitoring, and prediction of RT-induced cardiopulmonary toxicities in NSCLC.
Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin (2014)

Finegoldia magna is a Gram-positive anaerobic commensal of the human skin microbiota, but also known to act as an opportunistic pathogen. Two primary virulence factors of F. magna are the subtilisin-like extracellular serine protease SufA and the adhesive protein FAF. This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. FAF was found to be essential in the initial adherence of F. magna to human skin biopsies. In the upper layers of the epidermis FAF mediates adhesion through binding to galectin-7 - a keratinocyte cell marker. Once the bacteria moved deeper into the skin to the basement membrane layer, SufA was found to degrade collagen IV which forms the backbone structure of the basement membrane. It also degraded collagen V, whereby F. magna could reach deeper dermal tissue sites. In the dermis, FAF interacts with collagen V and fibrillin, which presumably helps the bacteria to establish infection in this area. The findings of this study paint a clear picture of how F. magna interacts with human skin and explain how it is such a successful opportunistic pathogen in chronic wounds and ulcers.
The genetics of programmed (apoptotic) cell death. (1995)

The genetic pathway for the activation and completion of programmed death of cells is as complex and well regulated as the pathway for cell proliferation. The identification of both the genetic elements in the signal transduction pathway involved with the initiation of programmed cell death, as well as the cellular machinery involved with DNA and cellular fragmentation into apoptotic bodies, is developing rapidly. Attempts at understanding how these elements are co-ordinated into a temporally discrete series of metabolic steps is only just beginning. This research not only will be fruitful from a basic science standpoint, but should also identify new approaches for cancer chemoprevention and therapy.
In-depth feasibility study of extreme ultraviolet damascene extension: Patterning, dielectric etch, and metallization (2022)

While semiconductor logic device nodes keep moving to N3 and beyond, the backend of line (BEOL) metal pitch is aggressively scaling to improve device performance and density. BEOL damascene extension refers to interconnect with a full metal pitch of 26–21 nm. The challenges of damascene extensions are profoundly critical due to an extreme ultraviolet (EUV) single exposure limit, dielectric etch, and metallization challenges. Multipatterning is required as well as more advanced low K dielectric etch. Severe line wiggling, bad via/contact hole open, and via/trench short issue can easily be observed. Cu resistance also contributes to most of the device’s R/C delay. Before transitioning to subtractive metal integrations, there is no doubt that multipatterning damascene extension plays an important role in bridging the gap between them. In this work, we provide an in-depth feasibility study on damascene extension focusing on EUV self-aligned double patterning with cut and block assembly for 24 nm pitch line and space. EUV double patterned self-aligned via is also validated for the dual damascene test. Both continuous wave and quasiatomic layer etch are developed to achieve a wiggling-free, bridge-free, and high metal hard mask selectivity process in TEL’s new generation capacitively coupled plasma etchers. Copper metallization is demonstrated in both via and trench of a 24 nm pitch. This report provides an important insight into damascene extension feasibility for high volume manufacturing.
Cellular Therapy for Disc Degeneration (2005)

Continued research is warranted to further define the optimal cell type, scaffolds, and adjuvants that will allow successful disc repair in human patients.
Development of tensile strength methodology for murine skin wound healing (2018)

In this study, a methodology was evaluated and improved to quickly measure the tensile strength of murine skin in a biomechanical assay for an incisional wound healing model. The aim was to streamline and enhance the wound model, skin specimen preparation, and tensile test so that large numbers of fresh tissue could be tested reliably and rapidly. Linear incisions of 25-mm length were made in the dorsal skin of mice along the spine and metallic staples were used to close the wound. After 20 days, the mice were sacrificed, and a square-shaped section of skin containing the linear incision was excised. Two metallic punches were fabricated and used to punch 15-mm long strips of skin of 2 mm width whose length was orthogonal to the direction of incision. The tensiometer configuration was modified to expedite tensile measurements on fresh skin, and load-to-failure was measured for each strip of skin from the cephalad to the caudal region. We evaluated sources of error in the animal model and the testing protocol and developed procedures to maximize speed and reproducibility in tensile strength measurements. This report provides guidance for efficient and reproducible tensile strength measurement of large numbers of skin specimens from freshly sacrificed animals. •Tattoo placement to identify the two ends of the healing incisional wound assisted in decreasing error in the position and orientation of tensile strips.•Custom-made punches to prepare skin strips for tensile testing helped conduct tensile tests of fresh tissue rapidly.•Alteration of the manual grips of the tensile tester enabled specimens to be gripped rapidly to significantly accelerate testing for each skin strip.
Rhinitis associated with asthma is distinct from rhinitis alone: The ARIA‐MeDALL hypothesis (2023)

Asthma, rhinitis, and atopic dermatitis (AD) are interrelated clinical phenotypes that partly overlap in the human interactome. The concept of "one-airway-one-disease," coined over 20 years ago, is a simplistic approach of the links between upper- and lower-airway allergic diseases. With new data, it is time to reassess the concept. This article reviews (i) the clinical observations that led to Allergic Rhinitis and its Impact on Asthma (ARIA), (ii) new insights into polysensitization and multimorbidity, (iii) advances in mHealth for novel phenotype definitions, (iv) confirmation in canonical epidemiologic studies, (v) genomic findings, (vi) treatment approaches, and (vii) novel concepts on the onset of rhinitis and multimorbidity. One recent concept, bringing together upper- and lower-airway allergic diseases with skin, gut, and neuropsychiatric multimorbidities, is the "Epithelial Barrier Hypothesis." This review determined that the "one-airway-one-disease" concept does not always hold true and that several phenotypes of disease can be defined. These phenotypes include an extreme "allergic" (asthma) phenotype combining asthma, rhinitis, and conjunctivitis. Rhinitis alone and rhinitis and asthma multimorbidity represent two distinct diseases with the following differences: (i) genomic and transcriptomic background (Toll-Like Receptors and IL-17 for rhinitis alone as a local disease; IL-33 and IL-5 for allergic and non-allergic multimorbidity as a systemic disease), (ii) allergen sensitization patterns (mono- or pauci-sensitization versus polysensitization), (iii) severity of symptoms, and (iv) treatment response. In conclusion, rhinitis alone (local disease) and rhinitis with asthma multimorbidity (systemic disease) should be considered as two distinct diseases, possibly modulated by the microbiome, and may be a model for understanding the epidemics of chronic and autoimmune diseases.
Structural Characterization of the Inflammatory Moiety of a Variable Major Lipoprotein of Borrelia recurrentis (2000)

Louse-borne relapsing fever, caused by Borrelia recurrentis, provides one of the best documented examples of the causative role of tumor necrosis factor (TNF) in the pathology of severe infection in humans. We have identified the principal TNF-inducing factor of B. recurrentis as a variable major lipoprotein (Vmp). Here we report the complete gene sequence of Vmp, including its lipoprotein leader sequence. Using metabolically labeled forms of the native Vmp we confirm that the TNF inducing properties are associated with the lipid portion of the molecule. Quadrupole orthogonal time of flight mass spectrometry unequivocally locates the lipidic moiety at the NH(2)-terminal cysteine of the native polypeptide, and indicates the existence of three forms which are consistent with the structures C16:0, C16:0, C16:0 glyceryl cysteine; C18:1, C16:0, C16:0 glyceryl cysteine; and C18:0, C16:0, C16:0 glyceryl cysteine. These data provide the first direct evidence that the TNF inducing lipid modification of native Borrelia lipoproteins is a structural homologue of the murein lipoprotein of Escherichia coli.
A flip-chip MMIC design with coplanar waveguide transmission line in the W-band (1998)

This paper describes a design method for flip-chip monolithic millimeter-wave integrated circuits (MMICs) with a coplanar waveguide (CPW) transmission line for W-band applications. We proposed a test structure for obtaining accurate flip-chip CPW line models. We examined the transmission line characteristics of the CPW line using the test structure in the millimeter-wave range and modeled them. Using the CPW line models, we designed and fabricated both two- and three-stage amplifiers using 0.15-/spl mu/m InGaP/InGaAs high electron-mobility transistor technology. The maximum power gain of the two-stage amplifier is 12 dB at 79 GHz. The three-stage amplifier has a maximum power gain of 16 dB at 77 GHz. The agreement of measured S-parameters with calculated results demonstrates that the proposed test structure is suitable for characterizing flip-chip CPW lines and provides very accurate models.
Apatite phosphate doped by cobalt as hight efficient catalyst of multi-component synthesis of therapeutic spiropyrimidine compound (2022)

Spiropyrimidines vanquish a significant situation in the field of heterocyclic chemistry, they are broadly utilized as an antibacterial, an inhibitor of multidrug opposition, or an antiplatelet and antithrombotic drug. Phosphate, the principal Moroccan mineral wealth occupies a vital spot in the economic sector and its valuation is a goal continually looked for. Among the conceivable outcomes of valorization, its utilization in heterogeneous catalysis which thought about an exceptionally encouraging new way. In this context, the focus on the reaction of the synthesis of spiropyrimidine, catalyzed by natural phosphate (NP) and by fluoroapatite (Fap), are used alone or doped by cobalt. These phosphate catalysts were characterized by XRD, IR and SEM, while the synthesized spiropyrimidine was identified by IR, GC-MS and NMR. The obtained yield with fluorapatite doped by cobalt (Co/Fap), at room temperature in ethanol is very high and shows a high impact performance induced by a synergistic effect compared to that of NP alone.
In vivo characterization of the immune response towards the pathogenic Escherichia coli antigen SslE and modulation of the intestinal microbiota (2017)

Abstract Pathogenic E. coli, both intestinal (InPEC) and extraintestinal (ExPEC), account for a wide range of diseases, which can be fatal across developing and developed countries. They can acquire a vast array of virulence factors which may dramatically increase the severity of the infection. Emergence of resistant strains often renders antibiotics inefficient; in the case of Shiga toxin-producing E. coli, antibiotics therapy can even be detrimental. Hence, an E. coli vaccine with broad coverage could be a promising alternative to prevent the spread of such diseases, while offering the potential for protection against several InPEC and ExPEC at once. Using the «reverse vaccinology» approach on ExPEC strains, nine antigens were identified as protective against a murine sepsis model. With 82% protective efficacy, SslE (Secreted and Surface-associated Lipoprotein of E. coli) was the most potent candidate. Additional models showed SslE to also be cross-protective against other ExPEC strains. Functional assays have demonstrated in vitro and ex vivo that SslE is a mucinase which plays an important role in colonization and virulence of E. coli. To better understand the mechanism behind such protection, we are investigating the intestinal and systemic immune responses obtained after immunization with SslE using different routes of administration. In-depth analysis of each regimen will allow us to determine the most efficient method of immunization for SslE to be protective. Further, using this selected model of immunization, we will evaluate the potential perturbation caused by SslE immunization on the murine intestinal microbiome. These findings will be important to help us optimize the development of a potential broad spectrum E. coli vaccine.
In-Memory Versioning (IMV) (2023)

In this letter, we propose and evaluate designs for a novel hardware-assisted data versioning system (in-memory versioning or IMV) in the context of high-performance computing. Our main novelty and advantage over recent published work is that it does not require any changes to host processor logic, instead augmenting a memory controller within memory modules. It is faster and more efficient than existing high-performance computing (HPC) checkpointing schemes and works from hours to sub-second checkpoint intervals. The main premise is to perform most operations in hardware at cache-line granularity, avoiding operating system (OS) latency and page copying bandwidth overhead. Energy is saved by keeping data movement in the memory module, compared with page granularity cross channel or cross-network copying that is currently used. For a 1-second checkpoint commit interval, we demonstrate up to 20x checkpoint performance and 70x energy savings using IMV versus page copy-on-write (COW).
Investigation of Lithium Sulfur Dioxide (Li/SO2) Battery Safety Hazard (1981)

Abstract : The lithium/sulfur dioxide primary electrochemical cell has received considerable attention as a high energy power source in the last decade. However, during the same time a number of safety hazards have been associated with its use. This report is the initial part of a research-oriented investigation intended to identify and document present Li/SO2 safety hazards, then to identify the chemical reactions responsible for these hazards, and finally to investigate methods of controlling them. This report presents the results of a survey of the safety hazards associated with Li/SO2 cells. The report documents specific safety incidents experienced with Li/SO2 cells, presents some of the causes identified or postulated for the incidents, and identifies general aspects of Li/SO2 use presently believed to be potentially hazardous. The survey was carried out by reviewing safety studies and reports of safety incidents appearing in the literature and by gathering unpublished information of the experiences of users of Li/SO2 cells in both government and industry. The results of the report can serve as basis for deciding which aspects of the Li/SO2 safety hazard at present need further investigation.
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery (2009)

GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.
Resolution (in Mass Spectrometry) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.