gebhart/patrepeval huggingface dataset:
The Dolastatins. 22. Synthesis Of Boc-Dolaproinyl Dolaphenine and Four Related Chiral Isomers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Dolastatins. 22. Synthesis Of Boc-Dolaproinyl Dolaphenine and Four Related Chiral IsomersGeorge R. Pettit, Jozsef Barkoczy, Jayaram K. Srirangam, Sheo Bux Singh, Delbert L. Herald, Michael D. Williams, Darko Kantoci, Fiona Hogan, and Thomas L. GroyCite this: J. Org. Chem. 1994, 59, 11, 2935–2938Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/jo00090a009https://doi.org/10.1021/jo00090a009research-articleACS PublicationsRequest reuse permissionsArticle Views178Altmetric-Citations9LEARN 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
Spurious-Free Time-to-Digital Conversion in an ADPLL Using Short Dithering Sequences (2011)

We propose an enhancement to the digital phase detection mechanism in an all-digital phase-locked loop (ADPLL) by randomization of the frequency reference using carefully chosen dither sequences. This dithering renders the digital phase detector, realized as a time-to-digital converter (TDC), free from any phase domain spurious tones generated as a consequence of an ill-conditioned sampling of the feedback variable oscillator phase. In modern nanoscale technologies, TDC has a time quantization of 5 to 30 ps. This deadband can potentially result in spurious tones, whenever a near integer-N relationship arises between the oscillator frequency and the TDC sampling process. This work proposes injection of a spectrum-friendly short sequence dither into the reference clock signal to overcome the quantization introduced limit-cycles. This results in robust phase tracking performance and spurious-free operation of the ADPLL, which was verified in a 65-nm CMOS GSM/EDGE transmitter.
Convolutional Neural Network Classification of Basal Cell Carcinoma in Harmonically Generated Microscopy Images (2022)

Basal cell carcinoma (BCC) is the most common form of skin cancer, which could cause local damage of nerves or tissues. Since the tumor growth of BCC is slow and not painful, it could lead to delayed tumor detection and hence necessary subsequent prompt intervention. This paper proposes a computer-aided diagnosis (CAD) method which uses the Gabor filter to extract characteristic scale information according to the characteristic of infected dendritic melanocytes in the third harmonic generation image. Scale information of image which is extracted from Gabor filter allows automatic adjustment of scale range and more accurate segmentation of the infected basal cells in medical images. Subsequently, normal and infected collagen fiber images are used to train convolution neural network (CNN) which are initialized with extracted features as kernels within convolution layers, resulting in high tumor detection accuracy and speed of convergence in harmonically generated microscopy (HGM) images. Experimental results show that this algorithm can accurately classify HGM images, with reduction in time and labor, and thus provides an efficient assisted tool in biomedical image analytics.
An inter-residue network model to identify mutational-constrained regions on the Ebola coat glycoprotein (2017)

Recently, progress has been made in the development of vaccines and monoclonal antibody cocktails that target the Ebola coat glycoprotein (GP). Based on the mutation rates for Ebola virus given its natural sequence evolution, these treatment strategies are likely to impose additional selection pressure to drive acquisition of mutations in GP that escape neutralization. Given the high degree of sequence conservation among GP of Ebola viruses, it would be challenging to determine the propensity of acquiring mutations in response to vaccine or treatment with one or a cocktail of monoclonal antibodies. In this study, we analyzed the mutability of each residue using an approach that captures the structural constraints on mutability based on the extent of its inter-residue interaction network within the three-dimensional structure of the trimeric GP. This analysis showed two distinct clusters of highly networked residues along the GP1-GP2 interface, part of which overlapped with epitope surfaces of known neutralizing antibodies. This network approach also permitted us to identify additional residues in the network of the known hotspot residues of different anti-Ebola antibodies that would impact antibody-epitope interactions.
Scheduling Cluster Tools in Semiconductor Manufacturing: Recent Advances and Challenges (2017)

Cluster tools are automated robotic manufacturing systems containing multiple computer-controlled process modules. They have been increasingly used for wafer fabrication. This paper reviews the modeling and scheduling methods for cluster tools with both nonrevisiting and revisiting processes. For nonrevisiting processes, we focus on the modeling and scheduling problems of cluster tools with different constraints. Then, their solution methods are reviewed and compared. For revisiting processes, this paper first discusses the scheduling problem of some general manufacturing systems with revisiting. Then, the modeling and scheduling methodologies used to solve the scheduling problems of cluster tools with revisiting processes are reviewed. Future research directions and conclusions are finally discussed. Note to Practitioners-Semiconductor manufacturing systems are among the most advanced and complicated manufacturing systems. Their key equipment is highly automated robot-based cluster tools. With wafer residency time constraints, wafer revisiting, activity time variation, chamber cleaning requirements, and failure-prone process modules (PMs), it is very challenging to schedule and control them. This paper surveys their modeling and scheduling methods. Scheduling them requires one to schedule their robot tasks and processing activities simultaneously. Owing to wafer residency time constraints and the lack of buffers among PMs, it is difficult to conduct their optimal scheduling. This paper presents a thorough review of the state-ofthe-art research results about modeling and optimal scheduling of clusters tools and indicates the future research directions.
A Universal Approach to Developing Fast Algorithm for Simplified Order-16 ICT (2007)

Simplified order-16 integer cosine transform (ICT) has been proved to be an efficient coding tool especially for high-definition (HD) video coding and is much simpler than ICT and discrete cosine transform (DCT). To further reduce the computational complexity, a universal approach to developing fast algorithm mainly for, but not restricted to, simplified order-16 ICT is proposed in this paper. The fast algorithm developed by the proposed approach involves additions and shiftings only and can save about 90% of the computational time compared with matrix multiplication.
Development and Characterization of New Inhibitors of the Human and Mouse Hematopoietic Prostaglandin D<sub>2</sub>Synthases (2010)

The hematopoietic prostaglandin D(2) synthase has a proinflammatory effect in a range of diseases, including allergic asthma, where its product prostaglandin D(2) (PGD(2)) has a role in regulating many of the hallmark disease characteristics. Here we describe the development and characterization of a novel series of hematopoietic prostaglandin D(2) synthase inhibitors with potency similar to that of known inhibitors. Compounds N-benzhydryl-5-(3-hydroxyphenyl)thiophene-2-carboxamide (compound 8) and N-(1-amino-1-oxo-3-phenylpropan-2-yl)-6-(thiophen-2-yl)nicotinamide (compound 34) demonstrated low micromolar potency in the inhibition of the purified enzyme, while only 34 reduced Toll-like receptor (TLR) inducible PGD(2) production in both mouse primary bone marrow-derived macrophages and the human megakaryocytic cell line MEG-01S. Importantly, 34 demonstrated a greater selectivity for inhibition of PGD(2) synthesis versus other eicosanoids that lie downstream of PGH(2) (PGE(2) and markers of prostacyclin (6-keto PGF(1alpha)) and thromboxane (TXB(2))) when compared to the known inhibitors HQL-79 (compound 1) and 2-phenyl-5-(1H-pyrazol-3-yl)thiazole (compound 2). Compound 34 therefore represents a selective hematopoietic prostaglandin D(2) synthase inhibitor.
DNA-DNA hybridization assay for detection of Salmonella spp. in foods (1983)

We have developed a DNA-DNA hybridization test for the presence of Salmonella spp. in foods. This test requires an initial pre-enrichment of food samples in nutrient broth but does not require selective enrichment. Samples of food cultures are collected on membrane filters and assayed by molecular hybridization to labeled probes. The probes consist of DNA sequences which are unique to the genus Salmonella and are widely distributed in the genus. A diverse panel of foods was assayed successfully by this methodology.
Hybrid Affinity Propagation (2013)

In this paper, we address a problem of managing tagged images with hybrid summarization. We formulate this problem as finding a few image exemplars to represent the image set semantically and visually, and solve it in a hybrid way by exploiting both visual and textual information associated with images. We propose a novel approach, called homogeneous and heterogeneous message propagation ($\text{H}^\text{2}\text{MP}$). Similar to the affinity propagation (AP) approach, $\text{H}^\text{2}\text{MP}$ reduce the conventional \emph{vector} message propagation to \emph{scalar} message propagation to make the algorithm more efficient. Beyond AP that can only handle homogeneous data, $\text{H}^\text{2}\text{MP}$ generalizes it to exploit extra heterogeneous relations and the generalization is non-trivial as the reduction to scalar messages from vector messages is more challenging. The main advantages of our approach lie in 1) that $\text{H}^\text{2}\text{MP}$ exploits visual similarity and in addition the useful information from the associated tags, including the associations relation between images and tags and the relations within tags, and 2) that the summary is both visually and semantically satisfactory. In addition, our approach can also present a textual summary to a tagged image collection, which can be used to automatically generate a textual description. The experimental results demonstrate the effectiveness and efficiency of the roposed approach.
Purification of serine racemase: Biosynthesis of the neuromodulator <scp>d</scp> -serine (1999)

High levels of D-serine occur in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate receptors. In glial cultures of rat cerebral cortex, D-serine is enriched in type II astrocytes and is released upon stimulation with agonists of non-N-methyl-D-aspartate glutamate receptors. The high levels of D-serine in discrete areas of rat brain imply the existence of a biosynthetic pathway. We have purified from rat brain a soluble enzyme that catalyzes the direct racemization of L-serine to D-serine. Purified serine racemase has a molecular mass of 37 kDa and requires pyridoxal 5'-phosphate for its activity. The enzyme is highly selective toward L-serine, failing to racemize any other amino acid tested. Properties such as pH optimum, Km values, and the requirement for pyridoxal phosphate resemble those of bacterial racemases, suggesting that the biosynthetic pathway for D-amino acids is conserved from bacteria to mammalian brain.
Performance analysis of a hardware accelerator of dependence management for task-based dataflow programming models (2016)

Along with the popularity of multicore and manycore, task-based dataflow programming models obtain great attention for being able to extract high parallelism from applications without exposing the complexity to programmers. One of these pioneers is the OpenMP Superscalar (OmpSs). By implementing dynamic task dependence analysis, dataflow scheduling and out-of-order execution in runtime, OmpSs achieves high performance using coarse and medium granularity tasks. In theory, for the same application, the more parallel tasks can be exposed, the higher possible speedup can be achieved. Yet this factor is limited by task granularity, up to a point where the runtime overhead outweighs the performance increase and slows down the application. To overcome this handicap, Picos was proposed to support task-based dataflow programming models like OmpSs as a fast hardware accelerator for fine-grained task and dependence management, and a simulator was developed to perform design space exploration. This paper presents the very first functional hardware prototype inspired by Picos. An embedded system based on a Zynq 7000 All-Programmable SoC is developed to study its capabilities and possible bottlenecks. Initial scalability and hardware consumption studies of different Picos designs are performed to find the one with the highest performance and lowest hardware cost. A further thorough performance study is employed on both the prototype with the most balanced configuration and the OmpSs software-only alternative. Results show that our OmpSs runtime hardware support significantly outperforms the software-only implementation currently available in the runtime system for fine-grained tasks.
Low Temperature LiMn2 O 4 Spinel Films for Secondary Lithium Batteries (1992)

Low temperature thin film spinel, with , are fabricated for use in secondary batteries. The spinel crystal structure is obtained by in situ postdeposition annealing of the films at temperatures as low as 400°C. Such temperatures are compatible with semiconductor processing, permitting future integration of the batteries with electronics. 1–3 μm thin films are tested in arrangements. They intercalate nearly one Li+ ion at an average potential of 4.1 V and show very good intercalation kinetics, so that a 10 C discharge rate produces an energy density of 500 W‐h per kilogram of active cathode material. These films show very promising cycle life, even at 55°C. Films cycled more than 220 times maintain more than 70% of their original capacity.
Murine Immune Responses to Virus-Like Particle-Associated Pre- and Postfusion Forms of the Respiratory Syncytial Virus F Protein (2015)

The development of vaccines for respiratory syncytial virus has been hampered by a lack of understanding of the requirements for eliciting high titers of neutralizing antibodies. The results of this study suggest that particle-associated RSV F protein containing mutations that stabilize the structure in a prefusion conformation may stimulate higher titers of protective antibodies than particles containing F protein in a wild-type or postfusion conformation. These findings indicate that the prefusion F protein assembled into VLPs has the potential to produce a successful RSV vaccine candidate.
RAGE (Yin) Versus LRP (Yang) Balance Regulates Alzheimer Amyloid β-Peptide Clearance Through Transport Across the Blood–Brain Barrier (2004)

Accumulation of amyloid beta-peptide (Abeta) in the central nervous system (CNS) may initiate pathogenic cascades mediating neurovascular and neuronal dysfunctions associated with the development of cerebral beta-amyloidosis and cognitive decline in patients with Alzheimer disease (AD) and with related familial cerebrovascular disorders. Whether Abeta-related pathology in the CNS is reversible or not and what key therapeutic targets are controlling Abeta/amyloid levels in the aging brain remain debatable. In this article, we summarize recent evidence why the receptor for advanced glycation end products and low-density lipoprotein receptor related protein 1 in the vascular CNS barriers are critical for regulation of Abeta homeostasis in the CNS and how altered activities in these 2 receptors at the blood-brain barrier may contribute to the CNS Abeta accumulation resulting in neuroinflammation, disconnect between the cerebral blood flow and metabolism, altered synaptic transmission, neuronal injury, and amyloid deposition into parenchymal and neurovascular lesions. We briefly discuss the potential of advanced glycation end products and low-density lipoprotein receptor related protein 1-based therapeutic strategies to control brain Abeta in animal models of AD and ultimately in patients with AD and related familial cerebrovascular beta-amyloidoses.
Sulfone Coupling and Double-Elimination Strategy for Carotenoid Synthesis (2005)

[Reaction: see text]. A highly efficient synthetic method of carotenoid compounds has been developed on the basis of the sulfone coupling and double-elimination strategy. This method highlighted the sulfone-mediated coupling with the novel C(10) dialdehyde, 2,7-dimethyl-4-octenedial, which was easily prepared and efficiently utilized in the synthesis of the conjugated polyene chains.
Cryptococcus nodaensis sp nov, a yeast isolated from soil in Japan that produces a salt-tolerant and thermostable glutaminase (1999)

An anamorphic basidiomycetous yeast, which produced a salt-tolerant and thermostable glutaminase, was isolated from soil in Japan and classified in the genus Cryptococcus. Its substrate specificity suggests that this enzyme is an L-glutaminase asparaginase (EC 3.5.1.38). The strain, G60, resembles Cryptococcus laurentii in the taxonomic criteria traditionally employed for yeasts, however it can be distinguished as a separate species based on DNA–DNA reassociation experiments and sequence analysis of the large sub-unit rDNA. Phenotypically, the isolate can be differentiated from C. laurentii by the inability to utilize arbutin as a sole source of carbon. Based on sequence analysis, the strain is related to a group of hymenomycetous yeasts including Bulleromyces albus, Bullera unica, C. laurentii and C. skinneri. The strain, which is formally described as Cryptococcus nodaensis, is industrially important for the formation of the umami taste during production of proteolytic seasonings.
Recapitulation of HIV-1 Env-Antibody Coevolution in Macaques Leading to Neutralization Breadth (2020)

ABSTRACT Neutralizing antibodies elicited by HIV-1 coevolve with viral Envs in distinctive patterns, in some cases acquiring substantial breadth. Here we show that primary HIV-1 Envs, when expressed by simian-human immunodeficiency viruses in rhesus macaques, elicited patterns of Env-antibody coevolution strikingly similar to those in humans. This included conserved immunogenetic, structural and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2-apex mode of recognition like that of human bNAbs PGT145/PCT64-35M. Another rhesus antibody bound the CD4-binding site by CD4 mimicry mirroring human bNAbs 8ANC131/CH235/VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design. One sentence summary Virus-antibody coevolution in rhesus macaques recapitulates developmental features of human antibodies.
Methodology to Create Reproducible Validation/Reference Materials for Comparison of Filter-Based Measurements of Carbonaceous Aerosols That Measure BC, BrC, EC, OC, and TC (2021)

A simple method that reproducibly creates validation/reference materials for comparison of methods that measure the carbonaceous content of atmospheric particulate matter deposited on filter media at concentrations relevant to atmospheric levels has been developed and evaluated. Commonly used methods to determine the major carbonaceous components of particles collected on filters include optical attenuation for “Black” (BC) and “Brown” (BrC) carbon, thermal-optical analysis (TOA) for “Elemental” (EC) and “Organic” (OC) carbon, and total combustion for “Total” carbon (TC). The new method uses a commercial inkjet printer to deposit ink containing both organic and inorganic components onto filter substrates at programmable print densities (print levels, as specified by the printer–software combination). A variety of filter media were evaluated. The optical attenuation (ATN) of the deposited sample was determined at 880 nm and 370 nm. Reproducibility or precision (as standard deviation or in percent as coefficient of variation) in ATN for Teflon-coated glass-fiber, Teflon, and cellulose substrates was better than 5%. Reproducibility for other substrates was better than 15%. EC and OC measured on quartz-fiber filters (QFF) compared to ATN measured at 880 nm and 370 nm on either QFF or Teflon-coated glass-fiber yielded R2 > 0.92 and >0.97, respectively. Four independent laboratories participated in a round robin study together with the reference laboratory. The propagated standard deviation among the five groups across all print levels was <2.2 ATN at 880 nm and <2.7 ATN at 370 nm with a coefficient of variation of <2% at ~100 ATN.
Spleen data: Cerium oxide nanoparticles attenuate polymicrobial sepsis induced spenic damage in male Sprague Dawley rats (2018)

Sepsis is a serious life threatening medical emergency which, if not treated properly, oftentimes results in organ failure and death. Current sepsis treatment protocols are largely centered on the use of antibiotics and supportive care. Recent studies have suggested that antibiotics fail to be effective for sepsis treatment when administered during hypo-dynamic phase of sepsis that is usually characterized by the presence of a cytokine storm. As such, there is an urgent need to develop novel therapeutic drugs that target the inflammatory cytokines that are secreted as a result of increased reactive oxygen species. Cerium oxide nanoparticles (CeO<sub>2</sub>) have been shown to act as anti-inflammatory and anti-oxidant agent. More recently, they have been shown to attenuate polymicrobial insult-induced mortality in Sprague Dawley rats. Here, we investigated whether CeO<sub>2</sub> nanoparticles can attenuate splenic damage in this animal model of sepsis. A single intravenous dose (0.5 mg/kg) of CeO<sub>2</sub> nanoparticles attenuated the sepsis-induced loss in splenic cell structural integrity. These improvements in splenic structure were accompanied by a decrease in expression of late phase pro-inflammatory cytokine high mobility group box 1 (HMGB1) along with reduced bacterial load in the blood and peritoneal fluid of septic animals. Taken together these findings suggest that CeO<sub>2</sub> nanoparticles can be used to attenuate polymicrobial insult-induced splenic damage in Sprague dawley rats.