gebhart/patrepeval huggingface dataset:
Boundary smoothing for mesh segmentation (2009)

In segmentation for reverse engineering, an input triangular mesh is usually split into segments for each of which a parametric surface is generated. The segment boundaries must be smooth for fine surfaces to be generated, but today's segmentation methods cannot necessarily generate a sufficient level of smoothness. The authors of this paper were inspired by the work reported in, and here try to extend it to efficiently segment a mesh obtained by scanning an object. Fuzzy boundary curves between two neighboring regions are globally rectified using a graph cut approach in which new energy functions are constructed. However, some curves are still not smooth since there are no straight lines around them in the original scanned mesh models, although the corresponding physical curves are smooth. To achieve further smoothing, we split some triangles by adding points and edges based on virtual triangle subdivision and the graph cut approach. As a result, significant further straightening of boundaries is achieved with simple straightest geodesics.
ChemInform Abstract: SYNTH. VON TRIARYLOXYMETHANEN (1971)

Abstract Die Reaktion der Aryldichlormethyläther (I) mit den Wasser‐ und alkoholfreien überschüssigen Phenolaten (II) in Dimethoxyäthan führt zu den Triaryloxymethanen (III) mit Ausbeuten zwischen 70 und 80%.
Rapidly Tunable Quantum Cascade Lasers (2015)

Operation principles and designs of rapidly tunable quantum cascade lasers (QCL) were analyzed theoretically and experimentally. Theoretical analysis shows that by adding a special polarization transition with controllable intensity or energy to existing QCL designs, one can achieve emission frequency modulation Δυ ≈ 30 GHz for the carrier wavelength of 10 μm, while introducing additional optical losses of not more than 10 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> in the laser waveguide. Proof-of-principle electrically tunable QCL demonstrated frequency shift of 4.5 GHz. Rapid and continuous frequency tuning of a single-mode distributed-feedback quantum cascade laser (DFB QCL) by optical generation of electron-hole pairs in the laser waveguide and active area was demonstrated. Application of optimized pumping geometry made possible to achieve continuous tuning of a room-temperature-operated DFB QCL in the range of 0.6 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> (20 GHz) using 1.3-μm telecom diode laser as a pumping source. The wavelength of the optically tunable DFB QCL was modulated at frequencies up to 300 MHz.
Physiologically based pharmacokinetic modeling in drug discovery and development: A pharmaceutical industry perspective (2015)

The application of physiologically based pharmacokinetic (PBPK) modeling has developed rapidly within the pharmaceutical industry and is becoming an integral part of drug discovery and development. In this study, we provide a cross pharmaceutical industry position on "how PBPK modeling can be applied in industry" focusing on the strategies for application of PBPK at different stages, an associated perspective on the confidence and challenges, as well as guidance on interacting with regulatory agencies and internal best practices.
‘Candidatus Phytoplasma pruni’, a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes (2012)

X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rRNA gene RFLP group 16SrIII, subgroup A. Phylogenetic analyses of 16S rRNA gene sequences revealed that the X-disease phytoplasma strains formed a distinct subclade within the phytoplasma clade, supporting the hypothesis that they represented a lineage distinct from those of previously described 'Candidatus Phytoplasma' species. Nucleotide sequence alignments revealed that all studied X-disease phytoplasma strains shared less than 97.5 % 16S rRNA gene sequence similarity with previously described 'Candidatus Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of X-disease phytoplasma strain PX11CT1(R) as representative of a novel taxon, 'Candidatus Phytoplasma pruni'. Results from nucleotide and phylogenetic analyses of secY and ribosomal protein (rp) gene sequences provided additional molecular markers of the 'Ca. Phytoplasma pruni' lineage. We propose that the term 'Ca. Phytoplasma pruni' be applied to phytoplasma strains whose 16S rRNA gene sequences contain the oligonucleotide sequences of unique regions that are designated in the formally published description of the taxon. Such strains include X-disease phytoplasma and--within the tolerance of a single base difference in one unique sequence--peach rosette, peach red suture, and little peach phytoplasmas. Although not employed for taxon delineation in this work, we further propose that secY, rp, and other genetic loci from the reference strain of a taxon, and where possible oligonucleotide sequences of unique regions of those genes that distinguish taxa within a given 16Sr group, be incorporated in emended descriptions and as part of future descriptions of 'Candidatus Phytoplasma' taxa.
ChemInform Abstract: Pheromone Synthesis. Part 118. Synthesis of the Enantiomers of (E)‐1‐Ethyl‐5‐methyl‐4‐heptenyl Acetate (Quadrilure), the Aggregation Pheromone of Cathartus quadricollis. (1990)

Abstract The (R) and (S) isomers (XIa) and (XIb) of the title compound are prepared in 8 steps and in 34‐35% overall yields starting from (R)‐ and (S)‐methyl 3‐hydroxypentanoate (Ia) and (Ib), respectively.
Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection (2022)

Abstract Rationale Severe viral respiratory infections are often characterized by extensive myeloid cell infiltration and activation and persistent lung tissue injury. However, the immunological mechanisms driving excessive inflammation in the lung remain elusive. Objectives To identify the mechanisms that drive immune cell recruitment in the lung during viral respiratory infections and identify novel drug targets to reduce inflammation and disease severity. Methods Preclinical murine models of influenza virus and SARS-CoV-2 infection. Results Oxidized cholesterols and the oxysterol-sensing receptor GPR183 were identified as drivers of monocyte-macrophage infiltration to the lung during influenza virus (IAV) and SARS-CoV-2 infections. Both IAV and SARS-CoV-2 infections upregulated the enzymes cholesterol 25-hydroxylase (CH25H) and cytochrome P450 family 7 subfamily member B1 (CYP7B1) in the lung, resulting in local production of the oxidized cholesterols 25-hydroxycholesterol and 7α,25-dihydroxycholesterol (7α,25-OHC). Loss-of-function mutation of GPR183, or treatment with a GPR183 antagonist, reduced macrophage infiltration and inflammatory cytokine production in the lungs of IAV- or SARS-CoV-2-infected mice. The GPR183 antagonist also significantly attenuated the severity of SARS-CoV-2 infection by reducing weight loss and viral loads. Conclusion This study demonstrates that oxysterols drive inflammation in the lung and provides the first preclinical evidence for therapeutic benefit of targeting GPR183 during severe viral respiratory infections. Author Summary Viral infections trigger oxysterol production in the lung, attracting macrophages via GPR183. Blocking GPR183 reduced inflammation and disease severity in SARS-CoV-2 infection, making GPR183 a putative target for therapeutic intervention.
Secretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v1-like protein, CaRRP1 that participates in stress response (2015)

Secreted proteins maintain cell structure and biogenesis besides acting in signaling events crucial for cellular homeostasis during stress adaptation. To understand the underlying mechanism of stress-responsive secretion, the dehydration-responsive secretome was developed from suspension-cultured cells of chickpea. Cell viability of the suspension culture remained unaltered until 96 h, which gradually declined at later stages of dehydration. Proteomic analysis led to the identification of 215 differentially regulated proteins, involved in a variety of cellular functions that include metabolism, cell defence, and signal transduction suggesting their concerted role in stress adaptation. One-third of the secreted proteins were devoid of N-terminal secretion signals suggesting a non-classical secretory route. Screening of the secretome identified a leaderless Bet v 1-like protein, designated CaRRP1, the export of which was inhibited by brefeldin A. We investigated the gene structure and genomic organization and demonstrated that CaRRP1 may be involved in stress response. Its expression was positively associated with abiotic and biotic stresses. CaRRP1 could complement the aberrant growth phenotype of yeast mutant, deficient in vesicular transport, indicating a partial overlap of protein secretion and stress response. Our study provides the most comprehensive analysis of dehydration-responsive secretome and the complex metabolic network operating in plant extracellular space.
UltraDuke Version 1 (2019)

DukeUltrasound is an ultrasound dataset collected at Duke University with a Verasonics c52v probe. It contains delay-and-sum (DAS) beamformed data as well as data post-processed with Siemens Dynamic TCE for speckle reduction, contrast enhancement and improvement in conspicuity of anatomical structures.
Tinnitus of futures past: Modern tinnitus clinical practice guidelines and the practice of Edmund Prince Fowler Snr (1872–1966) (2015)

Tinnitus is the perception of sound in the absence of an external sound source. Fifty years ago Edmund Prince Fowler Snr (1872–1966) was one of the world's leading tinnitus clinicians. In this review, Fowler's practice is compared to the clinical practice guidelines for tinnitus recently released by the American Academy of Otolaryngology. Despite half a century passing since Fowler's last publication, his approach to tinnitus is, in many ways, still best practice. Fowler's progressive approach to tinnitus and focus on the individual is still a benchmark for current and future practice, and an example of how we can learn from the past.
Thin composite matched impedance magneto-dielectric metamaterial absorbers (2010)

Low loss magneto-dielectric substrates when used as substrates for patch antennas are shown to miniaturize the aperture size of the patch antennas while preserving or improving the operational bandwidth. We demonstrated that the properties of a PEC backed low loss matched impedance magneto-dielectric metamaterial slab with frequency dependent permittivity and permeability could effectively be achieved using a multi-layered thin composite structure. In this paper, we demonstrate that modified equations from [2] can be used to optimize thin composite structures to design high loss matched impedance magneto-dielectric metamaterials for absorber applications above 1 GHz. The design technique is based on using a genetic algorithm (GA) to optimize thin multi-layered metallo-dielectric metamaterial slab comprised of a periodic array of electrically small metallic frequency selective surface (FSS) screen sandwiched between two different dielectric materials, one of which is backed by a perfectly conducting ground plane. Examples will be presented to demonstrate the effectiveness of the optimized absorber structures.
Generic Models for Mobility Management in Next Generation Networks (2005)

In the network community different mobility management techniques have been proposed over the years. However, many of these techniques share a surprisingly high number of similarities. In this technical report we analyze and evaluate the most relevant mobility management techniques, pointing out differences and similarities. For macro-mobility we consider Mobile IP (MIP), the Session Initiation Protocol (SIP) and mobility management techniques typical of a GSM network; for micro-mobility we describe and analyze several protocols such as: Hierarchical MIP, TeleMIP, IDMP, Cellular IP and HAWAII.
CD4+ T cells determine the ability of spleen cells from F1 hybrid mice to induce neonatal tolerance to alloantigens and autoimmunity in parental mice (1995)

Spleen cells from F1 hybrid mice injected into newborn parental mice induce a state of cytolytic unresponsiveness to the corresponding alloantigens. However, these mice develop a transient autoimmune syndrome characterized by the production of multiple autoantibodies and glomerulonephritis. Previous reports indicated that the depletion of F1 donor T cells, shortly prior the injection into parental mice, does not interfere with any of these events. Here, we have explored whether the continuous absence of T cells in F1 mice influences the ability of their spleen cells to induce neonatal tolerance to alloantigens and the associated autoimmune manifestations. Our results revealed that spleen cells from athymic (BALB/c x C57BL/6) F1 hybrid (CB6F1) nu/nu mice or from euthymic CB6F1 mice depleted from birth of CD4+ T cells, but not of CD8+ T cells, are unable to induce neonatal tolerance to alloantigens and autoimmune manifestations. By contrast, the partial reconstitution of T cells in CB6F1 nu/nu mice, after the neonatal graft of a syngeneic thymus, restored the capacity of spleen cells from these mice to induce tolerance and autoimmunity when injected into newborn BALB/c mice. These results demonstrate that the functional defect of spleen cells from athymic CB6F1 nu/nu mice to induce neonatal tolerance to alloantigens is directly related to the long-term absence of mature CD4+ T cells. Interestingly, a new increase in the titers of anti-DNA Ab was observed when spleen cells from athymic CB6F1 nu/nu mice were injected into adult BALB/c mice that had been tolerized at birth with normal CB6F1 spleen cells. This finding indicates that B cells from CB6F1 nu/nu mice recover their capacity to interact with alloreactive Th2 cells when they are placed into mice having functional CD4+ T cells. These data indicate that the continuous absence of CD4+ T cells causes a reversible functional defect in F1 spleen cells that determines their inability to induce neonatal tolerance and autoimmunity.
Quantification of Rare Cancer Cells in Patients With Gastrointestinal Cancer by Nanostructured Substrate (2014)

Detecting the cancer cells in the peripheral blood, i.e. circulating tumor cell (CTC), have been considered as the "liquid biopsy" and become a particular area of focus. A deep insight into CTC provides a potential alternative method for early diagnosis of solid tumor. Previous studies showed that CTC counts could be regarded as an indicator in tumor diagnosis, predicting clinical outcomes and monitoring treatment responses. In this report, we utilize our facile and efficient CTC detection device made of hydroxyapatite/chitosan (HA/CTS) for rare cancer cells isolation and enumeration in clinical use. A biocompatible and surface roughness controllable nanofilm was deposited onto a glass slide to achieve enhanced topographic interactions with nanoscale cellular surface components, anti-EpCAM (epithelial cell adhesion molecule, EpCAM) were then coated onto the surface of nanosubstrate for specific capture of CTCs. This device performed a considerable and stable capture yields. We evaluated the relationship performance between serial CTC changes and the changes of tumor volume/serum tumor marker in gastrointestinal cancer patients undergoing anti-cancer treatments. The present study results showed that changes in the number of CTC were associated with tumor burden and progression. Enumeration of CTCs in cancer patients may predict clinical response. Longitudinal monitoring of individual patients during the therapeutic process showed a close correlation between CTC quantity and clinical response to anti-cancer therapy. Effectively capture of this device is capable of CTCs isolation and quantification for monitoring of cancer and predicting treatment response.
E. H. Carr, Norman Angell, and Reassessing the Realist–Utopian Debate (2013)

While the realist argument presented by E. H. Carr in The Twenty Years’ Crisis has received much attention from scholars, recent scholarship has suggested that traditional interpretations of the work and the debate in which it figured have not accurately reflected the inter-war discourse. In this article, the author provides detail to support these claims through an examination of Carr's landmark work in comparison with prominent ‘utopian’ counterparts, primarily Norman Angell but also others such as Leonard Woolf and Arnold Toynbee. The conclusion of this article calls for increased emphasis on the works of internationalist writers of the inter-war period. It also echoes other scholars in calling for renewed focus on early twentieth-century internationalist thought and a critical reappraisal of Carr's landmark work through the prism of his policy recommendations and the critique he received during the original ‘great debate’.
Identifying Malnutrition in End-stage Renal Disease (ESRD) (P12-037-19) (2019)

Malnutrition and appetite disturbances, such as anorexia, are commonly reported amongst hemodialysis patients. Nutrition management is a complex issue in ESRD and greater understanding is needed into the associated clinical mediators in ESRD. However, there is currently limited data on anorexia and the pathophysiology framework involved. The aim of this study was to assess the relationship between appetite score and associated clinical biomarkers as a means to identify malnutrition. This work is part of an ongoing international multicenter effort to better define and develop treatment strategies for cachexia in patients with ESRD. A cross-sectional analysis study included 106 patients from two hemodialysis (HD) units within the United Kingdom (U.K). Appetite score was assessed using the Functional Assessment of Anorexia/Cachexia Therapy (FAACT). Clinical bio-makers included Body Mass Index (BMI), Albumin and C-reactive protein (CRP). Correlations between FAACT and clinical bio-markers were determined using Spearman’s rho for non-normally distributed scales. There was no significant relationship between FAACT and albumin levels (r = 0.14; P = 0.16) or BMI (r = 0.28; P = .19). However, there was a moderate and significant negative correlation between FAACT and CRP levels (r = 0.31; P < 0.001) indicating an inverse relationship between appetite (e.g., decreased FAACT score) and CRP levels (e.g., higher inflammation). We found a significant and incremental relationship between inflammation and anorexia which is supported by previous research. The FAACT may be a useful tool in identifying patients at higher risk of malnutrition-inflammation cachexia syndrome which has been associated with higher hospitalization and morality rates. Nutritional status and inflammation are important aspects of clinical practice in ESRD. A more focused approach to anorexia in ESRD is warranted. This study was funded by the Public Health Agency (Ref: STL/5179/15) and the Northern Ireland Kidney Research Fund. Noble et al., was funded by the National Institute for Health Research and the Health and Social Care Research and Development Division of the Public Health Agency Office Northern Ireland NIHR (CDV/4872/13).
Multishelled Metal Oxide Hollow Spheres: Easy Synthesis and Formation Mechanism (2016)

Uniform multishelled NiO, Co3 O4 , ZnO, and Au@NiO hollow spheres were synthesized (NiO and Co3 O4 hollow spheres for the first time) by a simple shell-by-shell self-assembly allowing for tuning of the the size, thickness and shell numbers by controlling the heat treatment, glucose/metal salt molar ratio, and hydrothermal reaction time. These findings further the development of synthetic methodologies for multishelled hollow structures and could open up new opportunities for deeper understanding of the mechanisms of shell-by-shell self-assembly. Moreover, the double-shelled NiO hollow sphere exhibits a higher photocatalytic activity for degradation of methyl orange than its morphological counterparts.
Power aware scheduling on real-time multi-core systems (2016)

Multi-core systems are being used in many real-time systems for fast computation and with increasing complexity of real-time systems, effective management of power is becoming a challenge. To address this challenge, scheduling strategy becomes an important factor to utilize power efficiently. This paper proposes a new priority (NP) calculation for task scheduling based on task parameters such as user priority, duration, deadline and slack. Considering multi-core system with each core assigned to different frequencies, two scheduling algorithms are proposed: Slowest Cores Available (SCA) and Fastest Cores Available (FCA). Algorithms are analyzed in terms of execution time, idle time, power consumption and processor utilization.
Isotropic Effect of Fluid Flow on Scaling of Surface Roughness during Copper Electrodeposition (2008)

The effect of fluid flow on the scaling properties of roughness during surface growth is studied by copper electrodeposition (and silver electrodeposition, for comparison) and atomic force microscopy measurements. The electrodeposited surface becomes smoother as the Reynolds number increases. Furthermore, fewer growth sites are observed at higher flow rates. Scaling analysis of the self-affine surface indicates that the saturated root-mean-square height decreases with increasing flow and the roughness depends on the fraction of the limiting current. The experimental scaling exponents can be divided into universal and local exponents, and , where the local growth exponent depends on the flow as expressed by the fraction of the limiting current and is the mass-transfer-dependent component of the roughness exponent. In order to generalize the results, similar experiments with silver electrodeposition show the same trend. The universal roughness exponent and the universal growth exponent are obtained by extrapolation to infinite flow velocity . The scaling exponents are found to be isotropic, as they are independent of the flow direction.
The Role of Juvenile Hormones in Crustacean Reproduction (1993)

Synopsis. Similar to juvenile hormone production in adult insects, the production of methyl farnesoate (MF) seems to be related to reproduction in both sexes in mature crustaceans. The mandibular organ (MO) synthesizes MF, and its activity corresponds to reproductive stages. High MF levels in the blood are found in vitellogenic females and reproduc? tively active males. Conversely, low levels are found in immature females, non-vitellogenic females, and males that are in reproductive diapause. The MO is under inhibitory control by neurosecretory factors from the sinus gland located in the eyestalks, and may be stimulated by factors from the brain and/or thoracic ganglion.
Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database (2021)

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to ‘ E. flexneri’ ) because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli . Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli , present evidence supporting this reclassification, and show that assigning E. coli / Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.