gebhart/patrepeval huggingface dataset:
Low resistance barrier layer for isolating, adhering, and passivating copper metal in semiconductor fabrication (2023)

Cubic or metastable cubic refractory metal carbides act as barrier layers to isolate, adhere, and passivate copper in semiconductor fabrication. One or more barrier layers of the metal carbide are deposited in conjunction with copper metallizations to form a multilayer characterized by a cubic crystal structure with a strong (100) texture. Suitable barrier layer materials include refractory transition metal carbides such as vanadium carbide (VC), niobium carbide (NbC), tantalum carbide (TaC), chromium carbide (Cr.sub.3 C.sub.2), tungsten carbide (WC), and molybdenum carbide (MoC).
Scenario Analysis: Risk and Return of Aluminium Tolerant Lucerne (2019)

Lucerne (Medicago sativa) yield is limited by aluminium stress associated with acid soils (Campbell et al. 1988; Scott et al. 2008). With the aid of transgenic technologies, the development of aluminium tolerant (Al Tol) lucerne is proposed. Modelled scenario analysis was conducted to explore the potential net benefits of Al Tol lucerne as part of a grazing system for a sheep production system in the high rainfall zone of south west Victoria.
SAW Microsensor Brain Implant for Prediction and Monitoring of Seizures (2007)

An implantable surface acoustic wave (SAW) microsensor has been developed for early detection and monitoring of seizures based on local temperature changes in the brain's epileptogenic zones that occur prior to and during an epileptic event. Three SAW sensors were designed and fabricated: a 172 MHz filter, a 434 MHz filter, and a 434 MHz delay line. Their temperature sensitivities were tested by measuring the phase change between the input and output waveforms as a function of temperature. We achieved a phase sensitivity of 144 phase degrees per degC and a minimum detectable temperature of 5 mK for the 434-MHz, 10.2-mus delay line. Based on the sensitivity tests, a prototype 434 MHz SAW sensor was fabricated to a size of 11times1times1.1 mm, which is commensurate with existing brain implantable probes. Because of possible damping of the surface waves by the surrounding tissue or fluid, a glass housing with dry air was built on the top of the SAW substrate. Test and reference sensors were used in the prototype system to minimize the effect of source instabilities and to amplify the temperature effect. The phase change between the output waveforms of the sensors was measured with phase detector electronics after they were converted to lower (10.7 MHz) frequencies by standard mixers. The complete prototype sensor was tested in a saline water bath and found to detect as low as 3 mK changes of temperature caused by the addition of hot water.
Family‐based and case‐control studies reveal no association oflipocalin‐type prostaglandin D2 synthasewith schizophrenia (2007)

Several observations point to the involvement of disturbed lipid biology in schizophrenia. Reduced response to niacin flushing test, which involves vasodilatation induced by prostaglandin D2 (PGD2), is among the evidences, together with decreased CSF levels of lipocalin-type prostaglandin D2 synthase (PTGDS), the enzyme responsible for the synthesis of PGD2 in the brain. Since PTGDS is also a carrier for lipophilic molecules such as retinoids and thyroid hormones, altered PTGDS levels might influence both PGD2-mediated signaling, and vitamin A and thyroid hormone availability. To test whether genetic variants of PTGDS are involved in the etiology of schizophrenia, we searched for variants in the coding and regulatory regions of the gene. We identified four previously described polymorphisms. Using two case-control samples from Portugal and Brazil, none of the polymorphisms tested was associated with the disease. In addition, no transmission distortion was observed in an independent parents-offspring sample from the Azorean Islands. Our data do not support the involvement of the PTGDS gene in the etiology of schizophrenia.
Abstract 3528: Novel enzymatic DNA fragmentation integrated into library construction (2019)

Abstract Next Generation Sequencing (NGS) is rapidly becoming a powerful tool, by providing a high resolution and global view of the cancer genome mainly through whole genome, whole exome and transcriptome sequencing. This knowledge is important to support drug development targeted towards precision medicine. Obtaining high quality sequencing data begins with optimal sample preparation. DNA fragmentation is one of the critical first steps in the construction of high quality libraries for NGS, but current fragmentation methods create a bottleneck on library preparation throughput. We have developed an efficient, one tube fragmentation system that integrates enzyme-based DNA fragmentation with end-repair and dA-tailing in a single step, followed by adaptor ligation in the same tube. This streamlined method is compatible with a wide range of DNA samples and input amounts, resulting in reproducible and reliable fragment sizes. Genomic DNA (100pg to 500ng) with various GC content, was used in the construction of libraries, that were sequenced on an Illumina platform. For low input samples, PCR amplification was performed prior to sequencing. Libraries constructed using intact genomic DNA and this novel library preparation method produced substantially higher yields than standard methods and mechanically-fragmented DNA. Enzyme-based shearing increases library yield by reducing DNA damage and sample loss. High library yields also enable PCR-free workflows from as little as 50ng starting material. This method can be used for DNA extraction and library preparation from whole blood and dried blood samples.Sequencing quality of libraries generated with inputs ranging from 100pg to 500ng DNA show similar coverage uniformity and fragment size distribution, with minimal GC bias. We have developed an enzymatic DNA fragmentation kit that enables the construction of high quality libraries from a range of sample types and inputs with minimal sequence bias, high yields and low duplication rates. This method eliminates the need for expensive equipment to fragment DNA as well as numerous cleanup and liquid transfer steps thereby reducing the time, cost and errors associated with library construction. These advances in NGS technologies, supported by powerful bioinformatics tools, promises to revolutionize cancer research, diagnosis and therapy. Citation Format: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis. Novel enzymatic DNA fragmentation integrated into library construction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3528.
Machine Learning for Acoustic Emission Signatures in Composite Laminates (2017)

Development of new composite material systems and structures require detailed understanding of failure mechanisms and failure progression. The identification of damage initiation on a damage-mode basis is essential for validation of progressive damage analysis techniques. Damage progression is the industry pathway towards expanding the composite design space to limit weight and increase confidence in structural performance. The challenge in validating these techniques is that the initial damage events predicted by analysis occur at a scale that are smaller than the defects measured by standard laboratory level inspection techniques (x-ray, ultrasound, digital image correlation). Of the techniques, acoustic emission has been found to be one of the most sensitive methods for identifying the onset of damage. However, characterizing the nature of the damage event from the acoustic emission signal has been challenge for many years. This paper describes a method for classifying acoustic emission signals that applies machine learning to a feature called the frequency distribution function. The method is demonstrated on composite laminates specimens and compared to observations from in-situ testing inspection techniques.
GPR17 gene disruption does not alter food intake or glucose homeostasis in mice (2015)

Significance Hypothalamic agouti-related peptide (AGRP) neurons control food intake and body weight. G protein-coupled receptor 17 (GPR17) was recently shown to be expressed in these neurons and controls their activity, thereby reducing body weight and food intake in mice. In the current study, we demonstrate that Gpr17 -deficient mice have normal hypothalamic and circulating AGRP levels. Body weight, food intake, and glucose homeostasis appear normal in the GPR17-deficient mice. The current data do not validate GPR17 as a therapeutic target for obesity or type 2 diabetes.
Population Analysis of Streptococcus suis Isolates from Slaughtered Swine by Use of Minimum Core Genome Sequence Typing (2014)

Streptococcus suis, an important zoonotic pathogen, is a highly diverse species with only a subset of strains that cause disease in humans. Our previous study proposed a minimum core genome (MCG) sequence typing method and defined seven MCG groups, with MCG group 1 as the prevalent group causing human infections. In this study, we identified a set of 10 single nucleotide polymorphisms (SNPs) distributed in six genes that were used to identify the seven MCG groups. The 10 SNPs were typed for 179 S. suis isolates collected from slaughtered pigs. The most prevalent groups among the tested isolates were MCG groups 6 and 7. Most of the isolates (147/179) were genotyped as mrp negative, epf negative, sly negative, and CDS2157 positive. The 179 isolates were also typed by multilocus sequence typing (MLST) and divided into 115 sequence types (STs), 111 of which were new. The 6 serotypes (29, 11, 5, 12, 30, and 2) represented 72.3% of the serotyped isolates. Our data show that the typing assay facilitates the application of genome data to the surveillance of S. suis.
Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi (2018)

Asexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In <i>Aspergillus</i>, the production of asexual spores is primarily governed by the BrlA→AbaA→WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and governs not only the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genus <i>Aspergillus</i>, the structure and degree of conservation of the <i>wetA</i> gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses of comparisons between <i>wetA</i> null mutant and wild-type asexual spores in three representative species spanning the diversity of the genus <i>Aspergillus</i>: <i>A. nidulans</i>, <i>A. flavus</i>, and <i>A. fumigatus</i> We discovered that WetA regulates asexual sporulation in all three species via a negative-feedback loop that represses BrlA, the cascade's first step. Furthermore, data from chromatin immunoprecipitation sequencing (ChIP-seq) experiments in <i>A. nidulans</i> asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA→AbaA→WetA cascade's regulatory role in cellular and chemical asexual spore development is functionally conserved but that the <i>wetA</i>-associated GRN has diverged during <i>Aspergillus</i> evolution.<b>IMPORTANCE</b> The formation of resilient spores is a key factor contributing to the survival and fitness of many microorganisms, including fungi. In the fungal genus <i>Aspergillus</i>, spore formation is controlled by a complex gene regulatory network that also impacts a variety of other processes, including secondary metabolism. To gain mechanistic insights into how fungal spore formation is controlled across <i>Aspergillus</i>, we dissected the gene regulatory network downstream of a major regulator of spore maturation (WetA) in three species that span the diversity of the genus: the genetic model <i>A. nidulans</i>, the human pathogen <i>A. fumigatus</i>, and the aflatoxin producer <i>A. flavus</i> Our data show that WetA regulates asexual sporulation in all three species via a negative-feedback loop and likely binds a novel regulatory element that we term the WetA response element (WRE). These results shed light on how gene regulatory networks in microorganisms control important biological processes and evolve across diverse species.
Formation mechanism of a smooth, defect-free surface of fused silica optics using rapid CO2 laser polishing (2019)

Abstract Surface defects introduced by conventional mechanical processing methods can induce irreversible damage and reduce the service life of optics applied in high-power lasers. Compared to mechanical processing, laser polishing with moving beam spot is a noncontact processing method, which is able to form a defect-free surface. This work aims to explore the mechanism of forming a smooth, defect-free fused silica surface by high-power density laser polishing with coupled multiple beams. The underlying mechanisms of laser polishing was revealed by numerical simulations and the theoretical results were verified by experiments. The simulated polishing depth and machined surface morphology were in close agreement with the experimental results. To obtain the optimized polishing quality, the effects of laser polishing parameters (e.g. overlap rate, pulse width and polishing times) on the polishing quality were experimentally investigated. It was found that the processing efficiency of fused silica materials by carbon dioxide (CO 2 ) laser polishing could reach 8.68 mm 2 s −1 , and the surface roughness ( Ra ) was better than 25 nm. Besides, the cracks on pristine fused silica surfaces introduced by initial grinding process were completely removed by laser polishing to achieve a defect-free surface. The maximum laser polishing rate can reach 3.88 μ m s −1 , much higher than that of the traditional mechanical polishing methods. The rapid CO 2 laser polishing can effectively achieve smooth, defect-free surface, which is of great significance to improve the surface quality of fused silica optics applied in high-power laser facilities.
Nanobiosensors: Constraint of DNA on Functionalized Graphene Improves its Biostability and Specificity Small 11/2010 (2010)

The cover picture shows how single-stranded DNA can be effectively and promptly adsorbed onto functionalized graphene via hydrophobic and π-stacking interactions. Interestingly, the absorbed single-stranded DNA can be effectively protected from enzymatic cleavage, which is encouraging for potential graphene-based biomedical applications involving complex cellular and biofluids samples. Anisotropy, fluorescence, NMR, and CD studies suggest that single-stranded DNA adsorbed onto functionalized graphene forms strong molecular interactions that prevent DNase I from approaching the constrained DNA. Furthermore, constraining a single-stranded DNA probe on graphene improves the specificity of its response to a target sequence. The unique features of DNA–graphene interactions are promising traits that may be exploited to construct DNA–graphene nanobiosensors with facile design, excellent sensitivity, selectivity, and biostability. For more information, please read the Communication “Constraint of DNA on Functionalized Graphene Improves its Biostability and Specificity” by Y. Lin et al., beginning on page 1205.
Supplementary Figure S1 from Targeting DNA Damage Repair Functions of Two Histone Deacetylases, HDAC8 and SIRT6, Sensitizes Acute Myeloid Leukemia to NAMPT Inhibition (2023)

&lt;p&gt;Knockdown of selected genes has modest effects on MOLM13 responses to KPT-9274 treatment.&lt;/p&gt;
Triple-Negative Breast Cancer: Current Understanding and Future Therapeutic Breakthrough Targeting Cancer Stemness (2019)

Triple-negative breast cancer (TNBC) is cancer that tested as negative for estrogen receptors (ER), progesterone receptors (PR), and excess human epidermal growth factor receptor 2 (HER2) protein which accounts for 15%-20% of all breast cancer cases. TNBC is considered to be a poorer prognosis than other types of breast cancer, mainly because it involves more aggressive phenotypes that are similar to stem cell-like cancer cells (cancer stem cell, CSC). Thus, targeted treatment of TNBC remains a major challenge in clinical practice. This review article surveys the latest evidence concerning the role of genomic alteration in current TNBC treatment responses, current clinical trials and potential targeting sites, CSC and drug resistance, and potential strategies targeting CSCs in TNBC. Furthermore, the role of insulin-like growth factor 1 receptor (IGF-1R) and nicotinic acetylcholine receptors (nAChR) in stemness expression, chemoresistance, and metastasis in TNBC and their relevance to potential treatments are also discussed and highlighted.
Screening of 19 traditional Mexican medicinal plants for effects on the metabolic syndrome related targets PPARα, β/δ, and γ in an in vitro luciferase reporter gene assay (2015)

In the present study, the effect of traditionally prepared infusions of 19 traditional Mexican medicinal plants on the metabolic syndrome related peroxisome proliferator-activated receptors (PPAR) α, β/δ, and γ was investigated using a novel luciferase reporter gene assay [1]. COS-1 cells were co-transfected with the luciferase reporter plasmid p17m2G, containing a GAL4 upstream activating sequence in the promoter region, an expression vector for the human PPARβ/δ ligand-binding domain fused to the GAL4 DNA-binding domain pPPARβ/δ-GAL4, and the secreted alkaline phosphatase control vector pSEAP. The results are relative to the luciferase expression levels, which were normalized using secreted alkaline phosphatase (SEAP) activity. All extracts (all at 6.25, 25, and 100 µg/mL), and GW0742 (positive control, 0.1 nM) were dissolved in DMSO and added to the medium of the transfected cells. The same approach was used for PPARα and PPARγ in which case the COS-1 cells were transfected with pPPARα or γ-GAL4 and p17m2G, respectively (positive controls 50 µM WY14643/10 µM troglitazone). In the above described assay, significant effects could be detected for both Aloe vera (L.) Burm.f. (commercial whole leaf preparation) and Larrea tridentata (DC.) Coville while no activity above DMSO vehicle negative control levels could be detected for any of the other samples. In the case of A. vera leaf juice, significant effects as compared to the negative controls were observed at all three PPAR targets hinting to its high potential for metabolic syndrome therapy. For the dried leaves of L. tridentata, significant activity was only observed for the PPARα target, which is mainly associated with a potential for the treatment of anti-hyperlipidaemia.
A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics (2020)

Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
ACCL: FPGA-Accelerated Collectives over 100 Gbps TCP-IP (2021)

Collective operations such as scatter, gather, reduce, etc are utilized broadly to implement distributed HPC applications and are the target of extensive optimization in all MPI implementations as well as dedicated collective libraries by accelerator vendors (e.g. NCCL and RCCL by NVidia and AMD respectively). We present ACCL, an open-source FPGA-accelerated collectives library designed to serve applications running primarily in Xilinx FPGAs. Compared to previous collective communication solutions for FPGA, ACCL is flexible and extensible, easily portable, and fast. We evaluate ACCL up to 8 nodes and demonstrate that ACCL outperforms OpenMPI over 100 Gbps TCP-IP for large messages.
Site selectivity studies on the catalyzed reaction of isotopically labeled MnRe(CO)10 with tert-butyl isocyanide. Implications for metal dimer and cluster reactions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSite selectivity studies on the catalyzed reaction of isotopically labeled MnRe(CO)10 with tert-butyl isocyanide. Implications for metal dimer and cluster reactionsPeter Johnston, Graham J. Hutchings, and Neil J. CovilleCite this: J. Am. Chem. Soc. 1989, 111, 5, 1902–1903Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/ja00187a067https://doi.org/10.1021/ja00187a067research-articleACS PublicationsRequest reuse permissionsArticle Views84Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Efficient hybrid white light-emitting diodes by organic-inorganic materials at different CCT from 3000K to 9000K (2015)

The hybrid white light-emitting didoes (LED) with polyfluoren (PFO) polymer and quantum dot (QD) was investigated using dispensing method at the different correlated color temperature (CCT) for cool and warm color temperature. This result indicates that the hybrid white LED device has the higher luminous efficiency than the convention one, which could be attributed to the increased utilization rate of the UV light. Furthermore, the CIE 1931 coordinate of high quality white hybrid LED with different CCT range from 3000K to 9000K is demonstrated. Consequently, the angular-dependent CCT and the thermal issue of the hybrid white LED device were also analyzed in this study.