gebhart/patrepeval huggingface dataset:
Discovery and Biosynthesis of Streptosactin, a Sactipeptide with an Alternative Topology Encoded by Commensal Bacteria in the Human Microbiome (2020)

Mammalian microbiomes encode thousands of biosynthetic gene clusters (BGCs) and represent a new frontier in natural product research. We recently found an abundance of quorum sensing-regulated BGCs in mammalian microbiome streptococci that code for ribosomally synthesized and post-translationally modified peptides (RiPPs) and contain one or more radical S-adenosylmethionine (RaS) enzymes, a versatile superfamily known to catalyze some of the most unusual reactions in biology. In the current work, we target a widespread group of streptococcal RiPP BGCs and elucidate both the reaction carried out by its encoded RaS enzyme and identify its peptide natural product, which we name streptosactin. Streptosactin is the first sactipeptide identified from <i>Streptococcus</i> spp.; it contains two sequential four amino acid sactionine macrocycles, an unusual topology for this compound family. Bioactivity assays reveal potent but narrow-spectrum activity against the producing strain and its closest relatives that carry the same BGC, suggesting streptosactin may be a long-suspected fratricidal agent of <i>Streptococcus thermophilus</i>. Our results highlight mammalian streptococci as a rich source of unusual enzymatic chemistries and bioactive natural products.
Cut‐points for Waist Circumference in Europids and South Asians (2009)

There is little strong evidence that currently recommended higher waist circumference cut-points for Europids compared with South Asians are associated with similar risk for type 2 diabetes. This study was designed to provide such evidence. Longitudinal studies over 5 years were conducted among 5,515 Europid and 2,214 ethnically South Asian participants. Age-standardized diabetes incidence at different levels of waist circumference and incidence difference relative to a reference value were calculated. The Youden Index was used to determine waist circumference cut-points. At currently recommended cut-points, estimated annual diabetes incidence for a 50-year-old Europid was <0.6% for both sexes, and for a 50-year-old South Asian, 5.8% for men and 2.1% for women. Annual diabetes incidence of 1% was observed for a 50 year old at a waist circumference 35-40 cm greater in Europid compared to South Asian men and women. Incidence difference between recommended cut-points and a reference value (80 cm in men, 70 cm in women) was 0.3 and 4.4% per year for Europid and South Asian men, and 0.2 and 0.8% per year for Europid and South Asian women, respectively. Waist circumference cut-points chosen using the Youden Index were shown to be dependent on obesity levels in the population. The much higher observed risk of diabetes in South Asians compared to Europids at the respective recommended waist circumference cut-points suggests that differences between them should be greater. Approaches that use the Youden Index to select waist circumference cut-points are inappropriate and should not be used for this purpose.
Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data (2022)

The kingdom Fungi is highly diverse in morphology and ecosystem function. Yet fungi are challenging to characterize as they can be difficult to culture and morphologically indistinct. Overall, their description and analysis lag far behind other microbes such as bacteria. Classification of species via high-throughput sequencing is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. With the rapid development of sequencing technologies, however, standardized procedures for taxonomic assignment of long sequence reads have not yet been well established. Focusing on nanopore sequencing technology, we compared classification and community composition analysis pipelines using shotgun and amplicon sequencing data generated from mock communities comprising 43 fungal species. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungal-specific database. During the assessment of classification algorithms, we found that applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. We also generated draft genome assemblies for three fungal species from nanopore data which were absent from genome databases. Our study improves sequence-based classification and estimation of relative sequence abundance using real fungal community data and provides a practical guide for the design of metagenomics analyses focusing on fungi. <b>IMPORTANCE</b> Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.
Histone Deacetylase 11 (HDAC11) Regulates Cytotoxic T-Cell Function and Memory Phenotype (2012)

Abstract Abstract 840 T-cells are an essential component of immune mediated tumor rejection. Adoptive transfer of T-cells results in a durable anti-tumor response in some patients with hematological malignancies. To further improve the efficacy of T-cell adoptive transfers, a better understanding of the regulatory checkpoints of these cells is needed. Here we show that HDAC11 is a negative regulator of CD8+ T-cell function, thus representing a potential target in adoptive immunotherapy. HDACs are a group of enzymes initially known for their role in deacetylating histones, thereby condensing chromatin structure and repressing gene expression. The known roles of HDACs as epigenetic regulators have recently expanded to include more complex regulatory functions including interactions with non-histone targets. HDAC11 is the most recently identified member of the HDAC family, and is highly expressed in brain, testis and T-cells. Recently, our group reported HDAC11 as a regulator of IL-10 production in antigen presenting cells. To determine the role of HDAC11 in T-cell biology, T-cells from HDAC11 knock out (HDAC11KO) mice were compared to wild-type T-cells in number, function and phenotype. HDAC11KO T-cells had no differences in absolute number or percentages of CD4+ or CD8+ lymphocytes. However CD8+ T-cells were hyper-proliferative upon CD3/CD28 stimulation and produced significantly higher levels of the pro-inflammatory, Tc1 cytokines IL-2, INF-γ, and TNF-α. However, no significant increases in the production of the Tc2 cytokines IL-4, IL-6 or IL-10 were seen. Further investigation of phenotypic differences also revealed that HDAC11KO mice have a larger percentage of central memory CD8+ T-cells. Additionally, HDAC11KO CD8+ T-cells express higher levels of the transcription factor Eomes, a known contributor to central memory cell formation as well as a controller of granzyme B and perforin production in CD8+ T-cells. This Tc1 and central memory-like phenotype translated to delayed tumor progression and survival in vivo in C1498 AML bearing mice treated with adoptively transferred HDAC11KO T-cells, as compared with wild type T-cells. Collectively, we have demonstrated HDAC11 as a negative regulator of CD8+ T-cell function, and a novel potential target to augment the efficacy of adoptive T-cell tumor immunotherapy. Disclosures: No relevant conflicts of interest to declare.
Synthesis of WC Nanotubes (2006)

A nonaqueous, solvent- and template-free, and straightforward route is described for the synthesis of inorganic WC nanotubes (see figure). The thermal decomposition of W(CO)6 in the presence of Mg powder is carried out at 900 °C under the autogenic pressure of the precursors in a closed Swagelok reactor to yield WC nanotubes for the first time. The reaction mechanism is supported by experimental data.
Characteristics of Copper Spiral Inductors Utilizing FePt Nanodot Films (2009)

We propose a novel Cu spiral inductor with an FePt magnetic nanodot (MND) layer of FePt magnetic nanodots dispersed in SiO2 film by self-assembled nanodot desposition (SAND). We expected an increase in inductance by adopting an MND layer. Nanodot sizes ranging from 2.5 to 3.5 nm in diameter can be well controlled. By optimizing thermal annealing conditions, we formed an FePt MND film with an electromagnetic permeability of 7.7 for passive devices used in a standard radio-frequency integrated circuit (RFIC) process. The quality factors of various spiral inductors were simulated and compared with the measured quality factors of the Cu spiral inductors we fabricated. In addition, the high-frequency characteristics of Cu spiral inductors were successfully observed.
${\rm C}^+_{60}$ IONS IN COLLISIONS WITH CRYSTALLINE SURFACES: KINEMATICS AND DYNAMICS (1996)

Collisions of [Formula: see text] ions with surfaces of highly oriented pyrolytic graphite (HOPG), diamond (111) and heteroepitaxial fullerite films on mica in the impact energy range between 100 and 1500 eV are studied by mass, energy, and angle resolved time-of-flight mass spectrometry. For the graphite and diamond surfaces, highly inelastic scattering has been observed. The analysis of the velocity dependence of the scattered ions reveals that the normal and tangential component of the ion velocity have different significance for the collision dynamics. The normal component of the velocity appears to determine the amount of energy transferred into vibrational and deformational energy of the projectile and target. The final kinetic energy is independent of the impact energy for impact angles of ≈20° and impact energies between 140 and 450 eV. This observation can be explained by the existence of an upper bound of the final kinetic energy that is defined by the amount of energy stored in the deformed molecule without being deposited or destroyed. The tangential component is partially transformed into rotational energy of the [Formula: see text] in the collision with the surface, as may be explained by a simple rolling ball model. In contrast, scattering from heteroepitaxial fullerite films is nearly elastic for impact energies up to 230 eV and impact angles of about 20°. Additionally, the velocity distributions reveal a low velocity component. Its relative intensity increases with increasing impact energy and remains the only feature in the velocity distribution for impact energies higher than 290 eV. This component is due to sputtering of surface molecules. The angular dependent intensities of the fast ions exhibit a rich structure. This can be attributed to rainbow scattering, as confirmed by classical trajectory and molecular dynamics calculations with different levels of sophistication. These calculations also show that linear collision sequences along the closed packed rows of the fullerite surface may be generated as the result of the [Formula: see text] impact. A detailed study of these collision sequences by molecular dynamics calculations reveals that rainbow effects might be possible when these sequences are defocused due to thermal motion of the surface molecules. The contribution of this process to the measured velocity and angular distributions is discussed.
Strid i bebyggelse - Vilka faktorer möjliggör framgång (2018)

Världen globaliseras och urbaniseras i en allt högre takt vilket innebär utmaningar för framtida försvarsmakter. Försvarsmakterna kommer mer frekvent att få lösa militära operationer genom strid i bebyggelse (SIB). Denna undersöknings ansats är att pröva Alice Hills teori om framgångsfaktorer som analyserats fram ur krigshistoriens militära operationer i kontexten SIB. Hills argumenterar för en mängd framgångsfaktorer. Denna undersökning prövar faktorerna utbildningsståndpunkt/stridserfarenhet, tillgång till infanteriförband, nyttjande av indirekt bekämpning och tredje parts inverkan på operationer. Dessa faktorer prövas i en jämförande fallstudie av operationerna i Fallujah 2004 Operation Vigilant Resolve (misslyckad operation) och Operation Phantom Fury (framgångsrik operation) vilka båda ingick i Operation Iraqi Freedom. De källor som har nyttjats för att genomföra teoriprövningen är Vincent L. Foulks, ”The Battle for Fallujah: Occupation, Resistance and Stalemate in the War in Iraq” och Bing Wests ”No True Glory: A Frontline Account of the Battle for Fallujah”. Resultatet av undersökningen stärker Hills teori om de fyra prövade framgångsfaktorerna. Fallstudien påvisar att ingående förband i Operation Vigilant Resolve (misslyckad operation) endast hade en grundlagd utbildningsståndpunkt i SIB samt att stora delar av förbanden saknade stridserfarenhet. Vidare påvisar undersökningen att det var låg numerär av infanteriförband och att mixen mellan infanteri och pansarförband medförde att infanteriförbanden inte kunde lösa uppgiften att skydda pansarförbanden i tillräcklig omfattning. I denna operation finns inget som bevisar att någon form att markgrupperad, indirekt bekämpning nyttjats. Tredje parts påverkan var stor givet förutsättningen att endast en mindre del av befolkning flytt staden Fallujah. Operation Phantom Fury påvisar det motsatta gentemot Operation Vigilant Resolve. Förbanden var bättre utbildade genom att de fått dra lärdom under genomförande under Operation Vigilant Resolve samt att de fått stridserfarenhet genom samma operation. Stor numerär av infanteri och en bättre mix av infanteri och pansarförband där infanteriet understöddes av pansarförbanden istället för tvärtom som var fallet vid Operation Vigilant Resolve. Operation nyttjade indirekt bekämpning i form av granatkastare och artilleri i stor omfattning. Den fjärde och sist prövande framgångsfaktorn, tredje parts inverkan på operationen påvisar att stora delar av staden Fallujah var utrymd vilket indirekt påverkar framförallt faktorn nyttjande av indirekt bekämpning. Sammanfattningsvis stärker denna teoriprövande fallstudie Hills förklaringskraft avseende de fyra utvalda framgångsfaktorerna. Detta ger en vetenskaplig grund att bygga framtidens förband kring där SIB kommer vara frekvent återkommande.
Cisplatin Tumor Biodistribution and Efficacy after Intratumoral Injection of a Biodegradable Extended Release Implant (2011)

Local delivery of chemotherapeutic drugs has long been recognized as a potential method for reaching high drug doses at the target site while minimizing systemic exposure. Cisplatin is one of the most effective chemotherapeutic agents for the treatment of various tumors; however, its systemic toxicity remains the primary dose-limiting factor. Here we report that incorporation of cisplatin into a fatty acid-based polymer carrier followed by a local injection into the solid tumor resulted in a successful tumor growth inhibition in heterotopic mouse bladder tumor model in mice. Platinum concentration in the tumor tissue surrounding the injected implant remained above the therapeutic level up to 14 days after the injection, while the plasma levels were several orders of magnitude lower comparing to systemic delivery. The reported delivery system increased the maximum tolerated dose of cisplatin 5 times compared to systemic delivery, thus potentially improving antitumor efficacy of cisplatin in solid tumor model.
Tensorial Time Scales for Turbulent Gradient Transport of Reynolds Stresses (2005)

On the notion that the Reynolds stresses are transported with different tune scale depending on the transport direction, the third order velocity correlations are represented by a new turbulent gradient transport model with tensorial Lagrangian time scale. In order to verify the proposed model, DNS data are first obtained in a turbulent channel flow at Re = 180 and tensorial Lagrangian time scales are computed. The present model predictions are compared with DNS data and those predicted by the third-order turbulent transport model of Hanjalic and Launder that uses a scalar time scale. The result demonstrates that the Reynolds stresses are indeed transported with different time scale depending on the transport direction.
Classification of Volumetric Images Using Multi-Instance Learning and Extreme Value Theorem (2019)

Volumetric imaging is an essential diagnostic tool for medical practitioners. The use of popular techniques such as convolutional neural networks (CNN) for analysis of volumetric images is constrained by the availability of detailed (with local annotations) training data and GPU memory. In this paper, the volumetric image classification problem is posed as a multi-instance classification problem and a novel method is proposed to adaptively select positive instances from positive bags during the training phase. This method uses the extreme value theory to model the feature distribution of the images without a pathology and use it to identify positive instances of an imaged pathology. The experimental results, on three separate image classification tasks (i.e. classify retinal OCT images according to the presence or absence of fluid build-ups, emphysema detection in pulmonary 3D-CT images and detection of cancerous regions in 2D histopathology images) show that the proposed method produces classifiers that have similar performance to fully supervised methods and achieves the state of the art performance in all examined test cases.
Supplementary Figures 1 - 4 from Outlier Kinase Expression by RNA Sequencing as Targets for Precision Therapy (2023)

&lt;p&gt;PDF file - 1133K, This file contains supplemental figures validating RNA-Seq method for measuring gene expression and nominating outlier kinases in individual cancer samples.&lt;/p&gt;
In vivo validation of the design rules of the coronary arteries and their application in the assessment of diffuse disease. (2002)

The conventional rationale that uses per cent diameter reduction to assess diffuse coronary artery disease is not appropriate because no normal reference segments exist. In a recent publication, we have proposed a theoretical model based on physical principles that relate the various morphological and haemodynamic parameters (cross-sectional area, length, volume and flow) of the normal coronary arterial tree. The model was validated using haemodynamic simulations based on detailed morphological data of the pig coronary arterial tree. This paper extends the model validation to in vivo swine studies. Coronary arteriography was performed in five swine (15-18 kg body weight) after power injection of contrast material into the coronary artery. Coronary arterial length was obtained using a 3D reconstruction technique. The arterial volume, cross-sectional area and blood flow were measured using videodensitometry. The proposed relationships between these quantities were validated. Furthermore, a sensitivity analysis was demonstrated based on a simulation of diffuse coronary artery disease (approximately 40% reduction in cross-sectional area). The results of a sensitivity analysis based on a simulation of diffuse coronary artery disease suggest that the relationships between arterial volume, cross-sectional area, blood flow and the distal arterial length can be utilized to quantify moderate levels of diffuse coronary artery disease.
Critical issues in post Cu CMP cleaning (2002)

Application of dilute HF with respect to post Cu CMP cleaning showed evidence of some critical issues that may seriously impact process performance. First of all it was seen that due to the heterogeneity of the surface after CMP drying problems can occur due to differences in wettability or due to topography. The cleaning of alumina slurry by under-etching with HF showed possible redeposition of these particles on the surface in case of a non-optimised rinsing and drying step. Furthermore a pattern dependent form of corrosion of the Cu was observed. Since single lines were more seriously impacted than dense meander/fork structures extrapolation of the latter to give process yield data may result in erroneous results. Finally it was shown that megasonic energy was very efficient in order to remove deposited slurry residues from the wafer surfaces.
Phase Noise Measurements of AlN Contour-Mode Resonators with Carrier Suppression Technique (2018)

International audience
Dead-Time Distortion in Generalized Selective Harmonic Control (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The selective harmonic control (SHC) method of pulsewidth modulation is meant to place switching edges to eliminate or set precisely given harmonics. This manuscript discusses the practical impact of edge placement sensitivity due to dead time that occurs in generalized SHC. It further provides experimental validation to theoretical work presented in a previous publication. </para>
Figure S6 from MFF Regulation of Mitochondrial Cell Death Is a Therapeutic Target in Cancer (2023)

&lt;p&gt;Anti-glioma activity of MFF peptidomimetic&lt;/p&gt;
The Role of Excipients in Quality by Design (QbD) (2018)

The quality of a design is measured by product performance against predictions based on the design inputs. The role of excipients in quality by design (QbD) can be divided into three stages namely: development pharmaceutics, design of experiments (DoE) and control strategy. Using only established and approved excipients from pharmaceutically aligned manufacturers and distributors is essential to finished product quality and patient safety. Excipient functionalities are qualitative classifications describing the purposes or roles of an excipient in a drug product, and are the rationale for inclusion in the formulation. Excipient risk management must address three sources of excipient-related risk namely: safety, supply chain integrity and technological risks associated with complexity and uncertainty. QbD refers to continuous improvement, but continual monitoring is also essential to better understand the limitations of the product in commercial reality, with old assumptions, models, and analyses under constant revision namely: communication with suppliers, build in compensatory flexibility, risk assessment and contingencies.
Performance Enhancements for Zero-Flow Simulation of Vapor Compression Cycles (2023)

Models that correctly describe the dynamic behavior of vapor compression cycle at low or zero refrigerant mass flow rates are valuable because they can be used to handle low load, on/off cycling and inactive component conditions. However, low- or zero-flow simulation imposes significant computational challenges because of high frequency oscillations in mass flow. We explore techniques that may be used for improving robustness and performance of low- or zero-flow simulation. Comparisons are conducted to demonstrate the efficacy of the proposed techniques. It is shown that these techniques can result in simulations that are more robustand significantly faster than real-time.